Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold23
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3125668
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.28
Warning! 362582 characters in sequence are not A, C, G, or T
File 8 of 18
Found at i:1100747 original size:28 final size:27
Alignment explanation
Indices: 1100707--1100778 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 27
1100697 GAAATAAAGC
* *
1100707 CGGGGTTGAAGTATCCCC-TCGAAGGTAA
1 CGGGGTTGGAGTATCCCCAT-GAA-ATAA
1100735 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCC-ATGAAATAA
*
1100763 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
1100779 TCGATTATGA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
28 35 0.90
29 3 0.08
30 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.22
Consensus pattern (27 bp):
CGGGGTTGGAGTATCCCCATGAAATAA
Found at i:1100829 original size:107 final size:106
Alignment explanation
Indices: 1100628--1100831 Score: 234
Period size: 107 Copynumber: 1.9 Consensus size: 106
1100618 GAAATAAAAT
* *
1100628 CGGGATTGGAGTATCCCTTCGGAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATAAATAT
1 CGGGATTGGAGTATCCC-TCGGAAATAACGAGGTTGGAGTATCCCCAATTATGAAAAATAAATAT
* * *
1100693 TTTGGAAATAAAGCCGGGGTTGAAGTATCCCCTCGAAGGTAA
65 TTTGGAAATAAAACCAGAGTTGAAGTATCCCCTCGAAGGTAA
* * * *
1100735 CGGGGTTGGAGTATCCC-CGATGAAATAACGAGGTTGGAGTATCCTCGATTATGAAAAACT-AGT
1 CGGGATTGGAGTATCCCTCG--GAAATAACGAGGTTGGAGTATCCCCAATTATGAAAAA-TAAAT
* * *
1100798 GTTTTGGAATTAAAATCAGAGTTGGAA-TATCCCC
63 ATTTTGGAAATAAAACCAGAGTT-GAAGTATCCCC
1100832 GATTGTGGAG
Statistics
Matches: 81, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
105 2 0.02
107 75 0.93
108 4 0.05
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.26
Consensus pattern (106 bp):
CGGGATTGGAGTATCCCTCGGAAATAACGAGGTTGGAGTATCCCCAATTATGAAAAATAAATATT
TTGGAAATAAAACCAGAGTTGAAGTATCCCCTCGAAGGTAA
Found at i:1100906 original size:130 final size:132
Alignment explanation
Indices: 1100735--1101014 Score: 363
Period size: 130 Copynumber: 2.1 Consensus size: 132
1100725 TCGAAGGTAA
* * *
1100735 CGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTATGAAAAACTAG-TG
1 CGGGGTTGGAGTATCCCCCAAGAAATAACGAGGTTGGAGTATCCCCGATTATGAAAAA-TAGATG
* * *
1100799 TTTTGGAATTAAAATCA-GAGTTGGAATATCCCCGATTGTGGAGAA-TTGGTG-TTTTAGAAATA
65 TTTTAGAAATAAAATCAGGAGTTGGAATATCCCCGATTGT-GAAAAGTTGGTGTTTTTAGAAATA
1100861 AAAC
129 AAAC
* * * *
1100865 CGGGGTTCGAGTATCCCCTCAAG-AATAATGGGGTTGGAGTATCCCCGATTATGAAAAATTGATG
1 CGGGGTTGGAGTATCCCC-CAAGAAATAACGAGGTTGGAGTATCCCCGATTATGAAAAATAGATG
* * *
1100929 TTTTAGAAATAAAATCAGGGGTTGGAGTATCCCCGATTGTGAAAAGTTGGTGTTTTTGGAAATAA
65 TTTTAGAAATAAAATCAGGAGTTGGAATATCCCCGATTGTGAAAAGTTGGTGTTTTTAGAAATAA
*
1100994 AAT
130 AAC
*
1100997 CGGAGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
1101015 GATTAAAGGA
Statistics
Matches: 129, Mismatches: 16, Indels: 8
0.84 0.10 0.05
Matches are distributed among these distances:
129 2 0.02
130 70 0.54
131 28 0.22
132 29 0.22
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (132 bp):
CGGGGTTGGAGTATCCCCCAAGAAATAACGAGGTTGGAGTATCCCCGATTATGAAAAATAGATGT
TTTAGAAATAAAATCAGGAGTTGGAATATCCCCGATTGTGAAAAGTTGGTGTTTTTAGAAATAAA
AC
Found at i:1101097 original size:51 final size:51
Alignment explanation
Indices: 1100894--1101130 Score: 273
Period size: 52 Copynumber: 4.6 Consensus size: 51
1100884 CAAGAATAAT
* * *
1100894 GGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAATCA
1 GGGGTTGGAGTATCCCCGATTATGGAAAATTGGTGTTTTAGAAATAAAA-CC
* * *
1100946 GGGGTTGGAGTATCCCCGATTGT-GAAAAGTTGGTGTTTTTGGAAATAAAATC
1 GGGGTTGGAGTATCCCCGATTATGGAAAA-TTGGTG-TTTTAGAAATAAAACC
* *
1100998 GGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTT-GAAAATAAAACC
1 GGGGTTGGAGTATCCCCGATT-ATGGAAAATTGGTGTTTTAG-AAATAAAACC
* * *
1101050 GGGGTTAGAGTATCCCCGATTGTGGAAAATTAGTGTTTTAGAAATAAAACC
1 GGGGTTGGAGTATCCCCGATTATGGAAAATTGGTGTTTTAGAAATAAAACC
* * * *
1101101 GGGGTTGAAATATTCCTGATTAT-GAAAATT
1 GGGGTTGGAGTATCCCCGATTATGGAAAATT
1101131 TGAGAAACTT
Statistics
Matches: 158, Mismatches: 21, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
50 7 0.04
51 47 0.30
52 80 0.51
53 19 0.12
54 5 0.03
ACGTcount: A:0.33, C:0.10, G:0.26, T:0.31
Consensus pattern (51 bp):
GGGGTTGGAGTATCCCCGATTATGGAAAATTGGTGTTTTAGAAATAAAACC
Found at i:1103480 original size:51 final size:51
Alignment explanation
Indices: 1103424--1103538 Score: 196
Period size: 51 Copynumber: 2.3 Consensus size: 51
1103414 AAAATGCCTG
*
1103424 AATGTATCGATACATTGCAAAATGTATCGATACATTTGGGTAAACTTCCTA
1 AATGTATCGATACATTGCAAAATGTATCGATACATCTGGGTAAACTTCCTA
* *
1103475 GATGTATCGATACATTGTAAAATGTATCGATACATCTGGGTAAACTTCCTA
1 AATGTATCGATACATTGCAAAATGTATCGATACATCTGGGTAAACTTCCTA
1103526 AATGTATC-ATACA
1 AATGTATCGATACA
1103539 AAGATCGATG
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
50 5 0.08
51 55 0.92
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Consensus pattern (51 bp):
AATGTATCGATACATTGCAAAATGTATCGATACATCTGGGTAAACTTCCTA
Found at i:1103581 original size:21 final size:21
Alignment explanation
Indices: 1103557--1103599 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1103547 TGTATCGATA
1103557 TAATGTATCGATACACTTCCT
1 TAATGTATCGATACACTTCCT
*
1103578 TAATGTATCGATACATTTCCT
1 TAATGTATCGATACACTTCCT
1103599 T
1 T
1103600 GGCAGTAGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.21, G:0.09, T:0.42
Consensus pattern (21 bp):
TAATGTATCGATACACTTCCT
Found at i:1107234 original size:20 final size:20
Alignment explanation
Indices: 1107209--1107246 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1107199 GAAACTTTCC
1107209 AGAATGTATCAATACATTAA
1 AGAATGTATCAATACATTAA
*
1107229 AGAATGTATCGATACATT
1 AGAATGTATCAATACATT
1107247 GTATCGATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.32
Consensus pattern (20 bp):
AGAATGTATCAATACATTAA
Found at i:1107251 original size:13 final size:13
Alignment explanation
Indices: 1107233--1107258 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1107223 CATTAAAGAA
1107233 TGTATCGATACAT
1 TGTATCGATACAT
1107246 TGTATCGATACAT
1 TGTATCGATACAT
1107259 GGGTTACTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1109759 original size:20 final size:20
Alignment explanation
Indices: 1109736--1109835 Score: 109
Period size: 20 Copynumber: 5.0 Consensus size: 20
1109726 TGCTTTGTAT
*
1109736 TGATACATTATATCGATACA
1 TGATACATTGTATCGATACA
1109756 TGAT-CATTGTATCGATACA
1 TGATACATTGTATCGATACA
*
1109775 T-AGACAATTGTATCGATACA
1 TGATAC-ATTGTATCGATACA
* *
1109795 T-AGGACATTGTATTGATACA
1 TGA-TACATTGTATCGATACA
1109815 TGATTA-ATTGTATCGATACA
1 TGA-TACATTGTATCGATACA
1109835 T
1 T
1109836 TGCTTGTAAC
Statistics
Matches: 70, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
18 1 0.01
19 16 0.23
20 48 0.69
21 5 0.07
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (20 bp):
TGATACATTGTATCGATACA
Found at i:1109813 original size:40 final size:39
Alignment explanation
Indices: 1109746--1109835 Score: 121
Period size: 40 Copynumber: 2.3 Consensus size: 39
1109736 TGATACATTA
1109746 TATCGATACATGATCATTGTATCGATACATAGA-CAATTG
1 TATCGATACATGATCATTGTATCGATACAT-GATCAATTG
* *
1109785 TATCGATACATAGGA-CATTGTATTGATACATGATTAATTG
1 TATCGATACAT--GATCATTGTATCGATACATGATCAATTG
1109825 TATCGATACAT
1 TATCGATACAT
1109836 TGCTTGTAAC
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
39 13 0.28
40 31 0.67
41 2 0.04
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.36
Consensus pattern (39 bp):
TATCGATACATGATCATTGTATCGATACATGATCAATTG
Found at i:1112982 original size:34 final size:34
Alignment explanation
Indices: 1112938--1113005 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
1112928 CTTGACTTAG
* *
1112938 ATTTGTTTCAAAGGTCTTGGAGGC-TGATCTTGAA
1 ATTTGCTTC-AAGGTCTTGGAGACTTGATCTTGAA
*
1112972 ATTTGCTTCAAGGTCTTTGAGACTTGATCTTGAA
1 ATTTGCTTCAAGGTCTTGGAGACTTGATCTTGAA
1113006 TTAATAAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 12 0.40
34 18 0.60
ACGTcount: A:0.24, C:0.13, G:0.24, T:0.40
Consensus pattern (34 bp):
ATTTGCTTCAAGGTCTTGGAGACTTGATCTTGAA
Found at i:1113467 original size:41 final size:41
Alignment explanation
Indices: 1113367--1113474 Score: 159
Period size: 39 Copynumber: 2.7 Consensus size: 41
1113357 ACTTATCTTC
1113367 TTTATTTATCTCTTAATTAATTTAA-TTAGAGATAAAATTA
1 TTTATTTATCTCTTAATTAATTTAATTTAGAGATAAAATTA
* * *
1113407 TTT-TTTATCTTTTAATTAATTTAATTTA-AGATAAATTTT
1 TTTATTTATCTCTTAATTAATTTAATTTAGAGATAAAATTA
1113446 TTTCATTTATCTCTTAATTAATTTAATTT
1 TTT-ATTTATCTCTTAATTAATTTAATTT
1113475 TATATAATTG
Statistics
Matches: 61, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
39 32 0.52
40 6 0.10
41 23 0.38
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.57
Consensus pattern (41 bp):
TTTATTTATCTCTTAATTAATTTAATTTAGAGATAAAATTA
Found at i:1114032 original size:3 final size:3
Alignment explanation
Indices: 1114024--1114062 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
1114014 CCCTTAACTG
* * *
1114024 TTA TTA TTA TTT TTA TTA TTA TCA TTA ATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1114063 GCTACGAGAG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1114363 original size:2 final size:2
Alignment explanation
Indices: 1114356--1114384 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1114346 TAAACAAATG
1114356 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1114385 ATTAGAAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1115090 original size:26 final size:27
Alignment explanation
Indices: 1115036--1115109 Score: 79
Period size: 26 Copynumber: 2.9 Consensus size: 27
1115026 TTGTATTTAT
1115036 TATTAA-TATAAT-AAATATT-ATCGTA
1 TATTAATTATAATAAAATATTAATC-TA
1115061 -ATTAATTATAATAAAATATTAAT-TA
1 TATTAATTATAATAAAATATTAATCTA
1115086 TATT-ATTCATAATAAAAATATTAA
1 TATTAATT-ATAAT-AAAATATTAA
1115110 AATTATTAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
24 5 0.12
25 11 0.26
26 15 0.35
27 12 0.28
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (27 bp):
TATTAATTATAATAAAATATTAATCTA
Found at i:1125036 original size:2 final size:2
Alignment explanation
Indices: 1124987--1125027 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1124977 TTTGCCTTTG
1124987 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1125028 GTGTCTCTCC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1125699 original size:12 final size:12
Alignment explanation
Indices: 1125659--1125731 Score: 77
Period size: 11 Copynumber: 6.4 Consensus size: 12
1125649 TAAAATTAAG
1125659 TAATAT-AAATA
1 TAATATAAAATA
1125670 TAATA-AAAAT-
1 TAATATAAAATA
1125680 T-AT-TAAAATA
1 TAATATAAAATA
*
1125690 TAATTTAAAATA
1 TAATATAAAATA
1125702 TAATATAAAAT-
1 TAATATAAAATA
1125713 TAATATAAATATA
1 TAATATAAA-ATA
1125726 TTAATA
1 -TAATA
1125732 GATTAAAATT
Statistics
Matches: 53, Mismatches: 1, Indels: 13
0.79 0.01 0.19
Matches are distributed among these distances:
9 7 0.13
10 2 0.04
11 20 0.38
12 19 0.36
14 5 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
TAATATAAAATA
Found at i:1126168 original size:13 final size:12
Alignment explanation
Indices: 1126134--1126187 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 12
1126124 CTTTTCTAAT
*
1126134 TTTTTAA-TTAT
1 TTTTTAATTTAA
1126145 TTTTTAA--TAA
1 TTTTTAATTTAA
1126155 TTTTTATATTTAA
1 TTTTTA-ATTTAA
1126168 TTTATTAATTT-A
1 TTT-TTAATTTAA
1126180 TTTTTAAT
1 TTTTTAAT
1126188 ATAAATACTA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
10 8 0.21
11 13 0.34
12 4 0.11
13 10 0.26
14 3 0.08
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTTAATTTAA
Found at i:1126254 original size:36 final size:36
Alignment explanation
Indices: 1126211--1126318 Score: 126
Period size: 36 Copynumber: 3.2 Consensus size: 36
1126201 AACATAATCA
1126211 AATTTTAATATATATTTTATTATTTAATATAAATAT
1 AATTTTAATATATATTTTATTATTTAATATAAATAT
1126247 AATTTT-A-ATA-A---T-TTATTTAA-ATAAATAT
1 AATTTTAATATATATTTTATTATTTAATATAAATAT
* *
1126275 AA-TTTATTTTTATATTTTATTATTTAATATAAATAT
1 AATTTTA-ATATATATTTTATTATTTAATATAAATAT
1126311 AATTTTAA
1 AATTTTAA
1126319 GTTATTTATT
Statistics
Matches: 59, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
27 3 0.05
28 10 0.17
29 8 0.14
30 3 0.05
31 1 0.02
33 1 0.02
34 4 0.07
35 9 0.15
36 16 0.27
37 4 0.07
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (36 bp):
AATTTTAATATATATTTTATTATTTAATATAAATAT
Found at i:1126316 original size:32 final size:32
Alignment explanation
Indices: 1126221--1126316 Score: 115
Period size: 32 Copynumber: 3.0 Consensus size: 32
1126211 AATTTTAATA
1126221 TATATTTTATTATTTAATATAAATATAATTTT
1 TATATTTTATTATTTAATATAAATATAATTTT
* * ** *
1126253 AATAATTTATTTAAATAA-ATATAAT-TTATTTT
1 TATATTTTA-TTATTTAATATA-AATATAATTTT
1126285 TATATTTTATTATTTAATATAAATATAATTTT
1 TATATTTTATTATTTAATATAAATATAATTTT
1126317 AAGTTATTTA
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
31 9 0.18
32 32 0.64
33 9 0.18
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (32 bp):
TATATTTTATTATTTAATATAAATATAATTTT
Found at i:1126458 original size:21 final size:21
Alignment explanation
Indices: 1126434--1126488 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
1126424 AATTACTTAT
1126434 TTTAATATCACTGTTACAATA
1 TTTAATATCACTGTTACAATA
* *
1126455 TTTAATCTCA-TCGTTACAGTA
1 TTTAATATCACT-GTTACAATA
* *
1126476 ATTAATTTCACTG
1 TTTAATATCACTG
1126489 CTATCATTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 1 0.04
21 26 0.93
22 1 0.04
ACGTcount: A:0.33, C:0.16, G:0.07, T:0.44
Consensus pattern (21 bp):
TTTAATATCACTGTTACAATA
Found at i:1127548 original size:14 final size:14
Alignment explanation
Indices: 1127506--1127565 Score: 66
Period size: 14 Copynumber: 4.0 Consensus size: 14
1127496 TTTATACATA
1127506 TGGATGAATGCATT
1 TGGATGAATGCATT
*
1127520 TAGATAAACGAATGCATT
1 TGGAT----GAATGCATT
1127538 TGGATGAATGCATT
1 TGGATGAATGCATT
*
1127552 TGAATGAATGCATT
1 TGGATGAATGCATT
1127566 AATGCATGAG
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
14 26 0.67
18 13 0.33
ACGTcount: A:0.35, C:0.08, G:0.23, T:0.33
Consensus pattern (14 bp):
TGGATGAATGCATT
Found at i:1127652 original size:14 final size:15
Alignment explanation
Indices: 1127628--1127656 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1127618 ACTTATCAAA
1127628 TAATATATGTCTTTT
1 TAATATATGTCTTTT
1127643 TAAT-TATGTCTTTT
1 TAATATATGTCTTTT
1127657 AGTGACTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.62
Consensus pattern (15 bp):
TAATATATGTCTTTT
Found at i:1130899 original size:219 final size:219
Alignment explanation
Indices: 1130534--1130945 Score: 583
Period size: 219 Copynumber: 1.9 Consensus size: 219
1130524 AAAAAGGTCT
1130534 TAGATTATTTTGATACCTATGCACCAGTGGCTAGGATGACTTCAATTCAAGTTCTTTTAGCATTA
1 TAGATTATTTTGATACCTATGCACCAGTGGCTAGGATGACTTCAATTCAAGTTCTTTTAGCATTA
* * *
1130599 GCATATATTTATAAGTTACATGTGCATCAATAGATGTTAAGGCAGCCTTTTCTAAATGATGAACT
66 GCATATATTGATAAGTTACATGTGCATCAATAGATGTTAAGACAACCTTTTCTAAATGATGAACT
*
1130664 CAATAAAGAAGTATATATAAAACAATCAGAAAGTTATGTGTTGCCCTAAAATGAAAAGAAAGTCA
131 CAATAAAGAAGTATATATAAAACAATCAGAAAGTTATGTATTGCCCTAAAATGAAAAGAAAGTCA
1130729 AGGGATTTAGATAAAAAGAAAATC
196 AGGGATTTAGATAAAAAGAAAATC
* * * *** *
1130753 TAGATTATTTTGATACTTATGCACTAGTGGCTAGGATGATTTCAATTTGGGTTCTTTTGGCATTA
1 TAGATTATTTTGATACCTATGCACCAGTGGCTAGGATGACTTCAATTCAAGTTCTTTTAGCATTA
* * * * *
1130818 GCATCTATTGATAAGTTGCATGTGTATCAAATTGATGTTAAGACAACCTTTTC-AAATGGTGAAC
66 GCATATATTGATAAGTTACATGTGCATC-AATAGATGTTAAGACAACCTTTTCTAAATGATGAAC
* * ** ** * * *
1130882 TTAATGAAGAAGTATATATGGAACAATTGGAAGGTTATGTATTGCCTTGAAATGAAAAGAAAGT
130 TCAATAAAGAAGTATATATAAAACAATCAGAAAGTTATGTATTGCCCTAAAATGAAAAGAAAGT
1130946 TTGCAAATTA
Statistics
Matches: 167, Mismatches: 25, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
219 146 0.87
220 21 0.13
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.33
Consensus pattern (219 bp):
TAGATTATTTTGATACCTATGCACCAGTGGCTAGGATGACTTCAATTCAAGTTCTTTTAGCATTA
GCATATATTGATAAGTTACATGTGCATCAATAGATGTTAAGACAACCTTTTCTAAATGATGAACT
CAATAAAGAAGTATATATAAAACAATCAGAAAGTTATGTATTGCCCTAAAATGAAAAGAAAGTCA
AGGGATTTAGATAAAAAGAAAATC
Found at i:1134158 original size:16 final size:16
Alignment explanation
Indices: 1134134--1134168 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1134124 TCCCTGAGAC
*
1134134 TAATTTAAAAATAAAA
1 TAATCTAAAAATAAAA
*
1134150 TAATCTAAAATTAAAA
1 TAATCTAAAAATAAAA
1134166 TAA
1 TAA
1134169 AATTAACAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (16 bp):
TAATCTAAAAATAAAA
Found at i:1134181 original size:12 final size:11
Alignment explanation
Indices: 1134141--1134186 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
1134131 GACTAATTTA
1134141 AAAATAAAA-T
1 AAAATAAAATT
**
1134151 AATCTAAAATT
1 AAAATAAAATT
1134162 AAAATAAAATT
1 AAAATAAAATT
1134173 AACAATAAAATT
1 AA-AATAAAATT
1134185 AA
1 AA
1134187 TAATCATAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
10 7 0.23
11 12 0.40
12 11 0.37
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (11 bp):
AAAATAAAATT
Found at i:1136780 original size:24 final size:24
Alignment explanation
Indices: 1136728--1136780 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1136718 TATCACAGTC
* *
1136728 AAATTTTTTTTAGGAAATTTTCAA
1 AAATTTTTTTTAGAAAATTTTAAA
*
1136752 GAATTTTTTTT-GTAAAATTTTAAA
1 AAATTTTTTTTAG-AAAATTTTAAA
1136776 AAATT
1 AAATT
1136781 AGCTGTCATA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.40, C:0.02, G:0.08, T:0.51
Consensus pattern (24 bp):
AAATTTTTTTTAGAAAATTTTAAA
Found at i:1137194 original size:22 final size:20
Alignment explanation
Indices: 1137147--1137186 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
1137137 TTTTAAATTT
1137147 AAAATTTTTAAAATTTATCA
1 AAAATTTTTAAAATTTATCA
1137167 AAAATTTTTATTAAATTTAT
1 AAAATTTTTA--AAATTTAT
1137187 ATTAAATTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.56
22 8 0.44
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (20 bp):
AAAATTTTTAAAATTTATCA
Found at i:1138099 original size:24 final size:23
Alignment explanation
Indices: 1138065--1138116 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 23
1138055 ACCTTAGCAC
1138065 AAAAAAAATAC-AAACAA-AAAGA
1 AAAAAAAATACGAAA-AAGAAAGA
1138087 AAAAAAAGGATACGAAAAAGAAAGA
1 AAAAAAA--ATACGAAAAAGAAAGA
1138112 AAAAA
1 AAAAA
1138117 TAAAGCTTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
22 7 0.27
24 6 0.23
25 13 0.50
ACGTcount: A:0.79, C:0.06, G:0.12, T:0.04
Consensus pattern (23 bp):
AAAAAAAATACGAAAAAGAAAGA
Found at i:1139447 original size:27 final size:28
Alignment explanation
Indices: 1139416--1139468 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
1139406 GCCATTAGGG
1139416 GGTTAAAGTGAAATTCTG-AAAGTTTGA
1 GGTTAAAGTGAAATTCTGAAAAGTTTGA
* *
1139443 GGTTAAAGTGCAATTTTGAAAAGTTT
1 GGTTAAAGTGAAATTCTGAAAAGTTT
1139469 AAGGACTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 16 0.70
28 7 0.30
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.36
Consensus pattern (28 bp):
GGTTAAAGTGAAATTCTGAAAAGTTTGA
Found at i:1145181 original size:112 final size:111
Alignment explanation
Indices: 1144981--1145310 Score: 378
Period size: 112 Copynumber: 3.0 Consensus size: 111
1144971 GACATAGAAG
* * * * *
1144981 AACATCAAATTTGTATGGTTGTCAAAGAAATTCATATTTCATACAA-TTGATCCAATT-GTGTTT
1 AACATCAAATTTGTTTGATTTTCAAAGAAATTTATATTT-ATACAATTTGATCC-ATTCGTGTCT
* *
1145044 AGGAAAAAGGGGCATGCATCCTATCAGTTTTGAAAATTTTGAGCTAAT
64 AGGAAAAAGGGGCATGTATCCTATCAGTTTTGAAAATTTTGAGCCAAT
*
1145092 AACATCAAATTTGTTTGATTTTCAAAGAAATTTGTACTTTATACAATTTGATCCATTCGTGTCTA
1 AACATCAAATTTGTTTGATTTTCAAAGAAATTTATA-TTTATACAATTTGATCCATTCGTGTCTA
* *
1145157 GGAAAATGGGGCATGTATCCTATCAGTTTT-AAAACTTTTAAGCCAAT
65 GGAAAAAGGGGCATGTATCCTATCAGTTTTGAAAA-TTTTGAGCCAAT
* * * ** * * * * **
1145204 AACATTAAAGTTCTTTGATTTTTGAAGGAATTTATATTTTATGCGATCTGATCCATTCGTACCTA
1 AACATCAAATTTGTTTGATTTTCAAAGAAATTTATA-TTTATACAATTTGATCCATTCGTGTCTA
* **
1145269 GGAAAAAGAGGCATGTATCCTATCAGTTTTGAATTTTTTGAG
65 GGAAAAAGGGGCATGTATCCTATCAGTTTTGAAAATTTTGAG
1145311 GCAACTAAAG
Statistics
Matches: 186, Mismatches: 28, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
111 44 0.24
112 140 0.75
113 2 0.01
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (111 bp):
AACATCAAATTTGTTTGATTTTCAAAGAAATTTATATTTATACAATTTGATCCATTCGTGTCTAG
GAAAAAGGGGCATGTATCCTATCAGTTTTGAAAATTTTGAGCCAAT
Found at i:1146304 original size:98 final size:100
Alignment explanation
Indices: 1146140--1146329 Score: 233
Period size: 98 Copynumber: 1.9 Consensus size: 100
1146130 TAGGTTTTTG
* *
1146140 GTTTCATCTAGGTCATTTAATTGAGTCTTGATTTTACCTAAATCATTGTTCAAGTTTTTGGATTT
1 GTTTCATCTAGGTCATTTAATTGAGTCTTGATTTTACCTAAATCATTATTCAAGTTTTGGGATTT
1146205 ATCCAAGCCA-TTTCATTGAGACTTAGGTTTGTAT
66 ATCCAAGCCATTTTCATTGAGACTTAGGTTTGTAT
* * * * * * *
1146239 GTTT-ATCTAGG-CTATTTCATTGAGTCTTGGTTTTGCCTAAGTCATTATTTAGGTTTTGGGTTT
1 GTTTCATCTAGGTC-ATTTAATTGAGTCTTGATTTTACCTAAATCATTATTCAAGTTTTGGGATT
* * * *
1146302 TATCTAGGCTATTTTCATTGAGTCTTAG
65 TATCCAAGCCATTTTCATTGAGACTTAG
1146330 TTTAACCCAA
Statistics
Matches: 76, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
97 1 0.01
98 56 0.74
99 19 0.25
ACGTcount: A:0.21, C:0.13, G:0.18, T:0.47
Consensus pattern (100 bp):
GTTTCATCTAGGTCATTTAATTGAGTCTTGATTTTACCTAAATCATTATTCAAGTTTTGGGATTT
ATCCAAGCCATTTTCATTGAGACTTAGGTTTGTAT
Found at i:1146384 original size:61 final size:59
Alignment explanation
Indices: 1146239--1146385 Score: 195
Period size: 61 Copynumber: 2.4 Consensus size: 59
1146229 AGGTTTGTAT
* ** *
1146239 GTTTATCTAGGCTATTTCATTGAGTCTTGGTTTTGCCTAAGTCATTATTTAGGTTTTGG
1 GTTTATCTAGGCTATTTCATTGAGTCTTAGTTTAACCCAAGTCATTATTTAGGTTTTGG
*
1146298 GTTTTATCTAGGCTATTTTCATTGAGTCTTAGTTTAACCCAAGTCATTTATTTAGGTTTTTG
1 G-TTTATCTAGGCTA-TTTCATTGAGTCTTAGTTTAACCCAAGTCA-TTATTTAGGTTTTGG
* *
1146360 GTTTCATCTAGGCCATTTCGTTGAGT
1 GTTT-ATCTAGGCTATTTCATTGAGT
1146386 TTGTCATTTT
Statistics
Matches: 77, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
59 1 0.01
60 13 0.17
61 39 0.51
62 24 0.31
ACGTcount: A:0.18, C:0.14, G:0.20, T:0.48
Consensus pattern (59 bp):
GTTTATCTAGGCTATTTCATTGAGTCTTAGTTTAACCCAAGTCATTATTTAGGTTTTGG
Found at i:1147595 original size:104 final size:104
Alignment explanation
Indices: 1147441--1147812 Score: 577
Period size: 104 Copynumber: 3.6 Consensus size: 104
1147431 ATCGGTTTCA
* * *
1147441 CCCTAATCAACCCTTT-TGACTTAGGTTTTATCCTAGTCACTCTTTGTTGACATGTTGCTTTCAT
1 CCCTAGTCAACCCTTTCTGACTTAGGTTTTATCCTAGTCACTCTTTATTGACATGTTGGTTTCAT
1147505 CCTGATCAACCTCTTAAACTTGTTGACTTATTAATTTTG
66 CCTGATCAACCTCTTAAACTTGTTGACTTATTAATTTTG
*
1147544 CCCTAGTCAACCCTTTCTGATTTAGGTTTTATCCTAGTCACTCTTTATTGACATGTTGGTTTCAT
1 CCCTAGTCAACCCTTTCTGACTTAGGTTTTATCCTAGTCACTCTTTATTGACATGTTGGTTTCAT
*
1147609 CATGATCAACCTCTTAAACTTGTTGACTTATTAATTTTG
66 CCTGATCAACCTCTTAAACTTGTTGACTTATTAATTTTG
* * * *
1147648 CCCTGGTCAACCCTTTCTGATTTAGGTTTTATCCTAGTCACTCTTTATTGACATATCGGTTTCAT
1 CCCTAGTCAACCCTTTCTGACTTAGGTTTTATCCTAGTCACTCTTTATTGACATGTTGGTTTCAT
* *
1147713 CCTGATCAACCTCTTAAACTTGTTGACTTATCATTTTTG
66 CCTGATCAACCTCTTAAACTTGTTGACTTATTAATTTTG
* * * * * *
1147752 CCCTGGTCAGCCCTTTCTAACTTAGGTTTTAT-CTTGTCACTCTTTGTTGACATGTTAGTTT
1 CCCTAGTCAACCCTTTCTGACTTAGGTTTTATCCTAGTCACTCTTTATTGACATGTTGGTTT
1147813 TCTCCCAGCC
Statistics
Matches: 249, Mismatches: 19, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
103 39 0.16
104 210 0.84
ACGTcount: A:0.20, C:0.23, G:0.13, T:0.44
Consensus pattern (104 bp):
CCCTAGTCAACCCTTTCTGACTTAGGTTTTATCCTAGTCACTCTTTATTGACATGTTGGTTTCAT
CCTGATCAACCTCTTAAACTTGTTGACTTATTAATTTTG
Found at i:1148053 original size:67 final size:66
Alignment explanation
Indices: 1147838--1148055 Score: 235
Period size: 67 Copynumber: 3.3 Consensus size: 66
1147828 TTTAAACTTA
* * * * *
1147838 TTGAC-TTATCGATTTTGCCGTAATAAACA-CTTTTCTAACTTTGGTTCTGCCTTAGTCTCTTTT
1 TTGACTTTATCGATTTTGCCCTGATCAACACCTTTTC-AACTTAGGTTCTGCCTTTGTCTCTTTT
1147901 AG
65 AG
** * * * * *
1147903 TTGACTTTATCGATTTCACCCTGGTCGACACTCTTTCCACCGTAGGTTCTG-CTTTAGTCTCTTT
1 TTGACTTTATCGATTTTGCCCTGATCAACAC-CTTTTCAACTTAGGTTCTGCCTTT-GTCTCTTT
1147967 TAG
64 TAG
* * * *
1147970 TTAACTTTATCAATTTTGCCTTGATCAACATCCTTTTCAACTTAGGTTCAGCCTTTGTCTCTTTT
1 TTGACTTTATCGATTTTGCCCTGATCAACA-CCTTTTCAACTTAGGTTCTGCCTTTGTCTCTTTT
1148035 AG
65 AG
1148037 TTGACTTTATCGATTTTGC
1 TTGACTTTATCGATTTTGC
1148056 TTTGGTTAGC
Statistics
Matches: 122, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
65 5 0.04
66 20 0.16
67 87 0.71
68 10 0.08
ACGTcount: A:0.18, C:0.22, G:0.14, T:0.45
Consensus pattern (66 bp):
TTGACTTTATCGATTTTGCCCTGATCAACACCTTTTCAACTTAGGTTCTGCCTTTGTCTCTTTTA
G
Found at i:1148080 original size:67 final size:66
Alignment explanation
Indices: 1147875--1148084 Score: 210
Period size: 67 Copynumber: 3.1 Consensus size: 66
1147865 CACTTTTCTA
* * ** * *
1147875 ACTTTGGTTCTGCCTTAGTCTCTTTTAGTTGACTTTATCGATTTCACCCTGG-TCG-ACACTCTT
1 ACTTAGGTTCTGCCTTTGTCTCTTTTAGTTGACTTTATCGATTTTGCCTTGGTTAGCAC-CT-TT
1147938 TCC
64 TCC
* * * * * *
1147941 ACCGTAGGTTCTG-CTTTAGTCTCTTTTAGTTAACTTTATCAATTTTGCCTTGATCAACATCCTT
1 A-CTTAGGTTCTGCCTTT-GTCTCTTTTAGTTGACTTTATCGATTTTGCCTTGGTTAGCA-CCTT
*
1148005 TTCA
63 TTCC
* *
1148009 ACTTAGGTTCAGCCTTTGTCTCTTTTAGTTGACTTTATCGATTTTGCTTTGGTTAGCACCTTTTC
1 ACTTAGGTTCTGCCTTTGTCTCTTTTAGTTGACTTTATCGATTTTGCCTTGGTTAGCACCTTTTC
1148074 C
66 C
1148075 GACTTAGGTT
1 -ACTTAGGTT
1148085 TCACCCTAGT
Statistics
Matches: 115, Mismatches: 22, Indels: 13
0.77 0.15 0.09
Matches are distributed among these distances:
66 11 0.10
67 91 0.79
68 9 0.08
69 3 0.03
70 1 0.01
ACGTcount: A:0.16, C:0.23, G:0.15, T:0.46
Consensus pattern (66 bp):
ACTTAGGTTCTGCCTTTGTCTCTTTTAGTTGACTTTATCGATTTTGCCTTGGTTAGCACCTTTTC
C
Found at i:1148097 original size:67 final size:67
Alignment explanation
Indices: 1147867--1148110 Score: 188
Period size: 67 Copynumber: 3.6 Consensus size: 67
1147857 GTAATAAACA
* * * * * ** * * *
1147867 CTTTTCTAACTTTGGTTCTGCCTTAGTCTCTTTTAGTTGACTTTATCGATTTCACCCTGGTCGAC
1 CTTTTC-AACTTAGGTTCAGCCCTAGTCTCTTTTAGTTAACTTTATCAATTTTGCCTTGATCAAC
1147932 A-C
65 ATC
* * * * **
1147934 TCTTTCCACCGTAGGTTCTGCTTTAGTCTCTTTTAGTTAACTTTATCAATTTTGCCTTGATCAAC
1 -CTTTTCAACTTAGGTTCAGCCCTAGTCTCTTTTAGTTAACTTTATCAATTTTGCCTTGATCAAC
1147999 ATC
65 ATC
* * * * * * * *
1148002 CTTTTCAACTTAGGTTCAGCCTTTGTCTCTTTTAGTTGACTTTATCGATTTTGCTTTGGTTAGCA
1 CTTTTCAACTTAGGTTCAGCCCTAGTCTCTTTTAGTTAACTTTATCAATTTTGCCTTGATCAACA
1148067 -C
66 TC
* * *
1148068 CTTTTCCGACTTAGGTTTCA-CCCTAGTCTCTTCTACTTAACTT
1 CTTTT-CAACTTAGG-TTCAGCCCTAGTCTCTTTTAGTTAACTT
1148111 ATTTCACCCT
Statistics
Matches: 143, Mismatches: 30, Indels: 7
0.79 0.17 0.04
Matches are distributed among these distances:
66 6 0.04
67 127 0.89
68 10 0.07
ACGTcount: A:0.16, C:0.24, G:0.14, T:0.46
Consensus pattern (67 bp):
CTTTTCAACTTAGGTTCAGCCCTAGTCTCTTTTAGTTAACTTTATCAATTTTGCCTTGATCAACA
TC
Found at i:1149732 original size:24 final size:24
Alignment explanation
Indices: 1149667--1149721 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
1149657 GCTTAGCCCA
* * *
1149667 AAAAAAAAAATA-CAAACAGAAAG
1 AAAAAAAACATATGAAAAAGAAAG
1149690 AAAAAAAACATATGAAAAAGAAAG
1 AAAAAAAACATATGAAAAAGAAAG
1149714 AAAAAAAA
1 AAAAAAAA
1149722 AGCTTGGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 11 0.39
24 17 0.61
ACGTcount: A:0.80, C:0.05, G:0.09, T:0.05
Consensus pattern (24 bp):
AAAAAAAACATATGAAAAAGAAAG
Found at i:1150651 original size:335 final size:335
Alignment explanation
Indices: 1150041--1150652 Score: 920
Period size: 335 Copynumber: 1.8 Consensus size: 335
1150031 TCATGCATCG
** * * *
1150041 TGTTAGGATCAAGTGCTTACCACTAGGCCAAAAGCTATAGCTGTTAGTCAGGGCGCAACTTTAAT
1 TGTTAGGATCAAGCACTTACCACTAAGCCAAAAGCTATAGCTATTAGTCAAGGCGCAACTTTAAT
* * * * * *
1150106 TCCTTAAACCCAAGGTAAATTCTTGAAGGGCACCCCCCACAATTCACAATGGCAATGCAGAGCCC
66 TCCTTAAACCCAAGGTAAATTCCTGAAGGGCAACACCCACAATTCACAATGACAACGCAAAGCCC
* * * *
1150171 CGTATCTATTACGTGCTGCGGGTGGGCTTGAGGGGCTTCGCAAAGCACACGTGGGCCTCGACAGG
131 CGCATCTATTACGTGCTGCGGGTAGGCCTGAGGGGCTTCGCAAAGCACACATGGGCCTCGACAGG
* * * *
1150236 CTGGGCTTGTTAAGCACTAATACCGCGCCCATACGTGATAGTGAATCCCTAAGGGTGAGCGCTGG
196 CCGGGCTTGTCAAGCACTAATACCACGCCCATACGCGATAGTGAATCCCTAAGGGTGAGCGCTGG
*
1150301 TCCCCATAAGCCAACAATCTCCCCCCCTAGCGACACCTGGGGGATTCAAACCTGCAACCTCGCTC
261 CCCCCATAAGCCAACAATCTCCCCCCCTAGCGACACCTGGGGGATTCAAACCTGCAACCTCGCTC
1150366 TGATACCAGT
326 TGATACCAGT
1150376 TGTTAGGATCAAGCACTTACCACTAAGCCAAAAGCTATAGCTATTAGTCAAGGCGCAACTTTAAT
1 TGTTAGGATCAAGCACTTACCACTAAGCCAAAAGCTATAGCTATTAGTCAAGGCGCAACTTTAAT
** *
1150441 TCCTTAAACCCAAGGTGGATTCCTGAAGGGCAACACCCACAATTCATC-ATGACAGCGCAAAGCC
66 TCCTTAAACCCAAGGTAAATTCCTGAAGGGCAACACCCACAATTCA-CAATGACAACGCAAAGCC
** * * **
1150505 TTGCATCTATTACGTGCTGTGGGTAGGCCTGAGGGGCTTCGCAAGGCACACATGGGCCTCGGTAG
130 CCGCATCTATTACGTGCTGCGGGTAGGCCTGAGGGGCTTCGCAAAGCACACATGGGCCTCGACAG
* * *
1150570 GCCGGGCTTGTCAAGCACTAATACCATGCCCATATGCGATAGTGAATCCCTAAGGGTGATCGCTG
195 GCCGGGCTTGTCAAGCACTAATACCACGCCCATACGCGATAGTGAATCCCTAAGGGTGAGCGCTG
1150635 GCCCCCATAAGCCAACAA
260 GCCCCCATAAGCCAACAA
1150653 ATTCCAATCT
Statistics
Matches: 244, Mismatches: 32, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
335 243 1.00
336 1 0.00
ACGTcount: A:0.27, C:0.28, G:0.24, T:0.22
Consensus pattern (335 bp):
TGTTAGGATCAAGCACTTACCACTAAGCCAAAAGCTATAGCTATTAGTCAAGGCGCAACTTTAAT
TCCTTAAACCCAAGGTAAATTCCTGAAGGGCAACACCCACAATTCACAATGACAACGCAAAGCCC
CGCATCTATTACGTGCTGCGGGTAGGCCTGAGGGGCTTCGCAAAGCACACATGGGCCTCGACAGG
CCGGGCTTGTCAAGCACTAATACCACGCCCATACGCGATAGTGAATCCCTAAGGGTGAGCGCTGG
CCCCCATAAGCCAACAATCTCCCCCCCTAGCGACACCTGGGGGATTCAAACCTGCAACCTCGCTC
TGATACCAGT
Found at i:1153601 original size:20 final size:20
Alignment explanation
Indices: 1153557--1153601 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1153547 GTTAACAGCC
1153557 CATG-TTCATGCATTTTGAG
1 CATGTTTCATGCATTTTGAG
1153576 CTATGTTTCATGCATTTAT-AG
1 C-ATGTTTCATGCATTT-TGAG
1153597 CATGT
1 CATGT
1153602 CCAGCAACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
19 1 0.04
20 7 0.30
21 14 0.61
22 1 0.04
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.44
Consensus pattern (20 bp):
CATGTTTCATGCATTTTGAG
Found at i:1154260 original size:20 final size:20
Alignment explanation
Indices: 1154235--1154309 Score: 105
Period size: 20 Copynumber: 3.8 Consensus size: 20
1154225 TGTTACCCAG
1154235 ATGTATCGATACATTTTTTA
1 ATGTATCGATACATTTTTTA
* * *
1154255 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTTA
* *
1154275 ATGTATCAATACATTCTTTA
1 ATGTATCGATACATTTTTTA
1154295 ATGTATCGATACATT
1 ATGTATCGATACATT
1154310 ATGTTTTTTT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (20 bp):
ATGTATCGATACATTTTTTA
Found at i:1154295 original size:40 final size:39
Alignment explanation
Indices: 1154235--1154312 Score: 129
Period size: 40 Copynumber: 2.0 Consensus size: 39
1154225 TGTTACCCAG
* *
1154235 ATGTATCGATACATTTTTTAATGTATCGATACATGTATGA
1 ATGTATCAATACATTCTTTAATGTATCGATACAT-TATGA
1154275 ATGTATCAATACATTCTTTAATGTATCGATACATTATG
1 ATGTATCAATACATTCTTTAATGTATCGATACATTATG
1154313 TTTTTTTACC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 4 0.11
40 32 0.89
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.42
Consensus pattern (39 bp):
ATGTATCAATACATTCTTTAATGTATCGATACATTATGA
Found at i:1154330 original size:71 final size:71
Alignment explanation
Indices: 1154255--1154403 Score: 228
Period size: 71 Copynumber: 2.1 Consensus size: 71
1154245 ACATTTTTTA
* *
1154255 ATGTATCGATACATGTATGAATGTATCAATACATTCTTTAATGTATCGATACATTATGT-TTTTT
1 ATGTATCGATACATGTATGAATGTATCAATACATTCTTCAATGTATCGATACATTATATCTTTTT
1154319 TACCCAG
66 T-CCCAG
** * *
1154326 ATGTATCGATACATGTATGAATGTATTGATACATTCTTCAATGTATCGTTACATTCTATCTTTTT
1 ATGTATCGATACATGTATGAATGTATCAATACATTCTTCAATGTATCGATACATTATATCTTTTT
1154391 TCCCAG
66 TCCCAG
1154397 ATGTATC
1 ATGTATC
1154404 TATAAATTTT
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
71 65 0.92
72 6 0.08
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (71 bp):
ATGTATCGATACATGTATGAATGTATCAATACATTCTTCAATGTATCGATACATTATATCTTTTT
TCCCAG
Found at i:1154368 original size:20 final size:20
Alignment explanation
Indices: 1154326--1154382 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
1154316 TTTTACCCAG
* *
1154326 ATGTATCGATACATGT-ATGA
1 ATGTATCGATACAT-TCTTCA
*
1154346 ATGTATTGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
*
1154366 ATGTATCGTTACATTCT
1 ATGTATCGATACATTCT
1154383 ATCTTTTTTC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:1154369 original size:91 final size:91
Alignment explanation
Indices: 1154207--1154382 Score: 237
Period size: 91 Copynumber: 1.9 Consensus size: 91
1154197 TACCTAGATA
* * * *
1154207 TATCGATACATTCTGTCTTGTTACCCAGATGTATCGATACATTTTTTAATGTATCGATACATGTA
1 TATCGATACATTATGTCTTGTTACCCAGATGTATCGATACATGTATGAATGTATCGATACATGTA
*
1154272 TGAATGTATCAATACATTCTTTAATG
66 TCAATGTATCAATACATTCTTTAATG
* * *
1154298 TATCGATACATTATGTTTTTTTACCCAGATGTATCGATACATGTATGAATGTATTGATACAT-TC
1 TATCGATACATTATGTCTTGTTACCCAGATGTATCGATACATGTATGAATGTATCGATACATGT-
* **
1154362 TTCAATGTATCGTTACATTCT
65 ATCAATGTATCAATACATTCT
1154383 ATCTTTTTTC
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
90 1 0.01
91 72 0.99
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (91 bp):
TATCGATACATTATGTCTTGTTACCCAGATGTATCGATACATGTATGAATGTATCGATACATGTA
TCAATGTATCAATACATTCTTTAATG
Found at i:1154428 original size:71 final size:71
Alignment explanation
Indices: 1154255--1154430 Score: 210
Period size: 71 Copynumber: 2.5 Consensus size: 71
1154245 ACATTTTTTA
* * * * *
1154255 ATGTATCGATACATGTATGAATGTATCAATACATTCTTTAATGTATCGATACATTATGTTTTTTT
1 ATGTATCGATAAATGTATCAATGTATCGATACATTCTTCAATGTATCGATACATTATATTTTTTT
1154320 ACCCAG
66 ACCCAG
* * * * *
1154326 ATGTATCGATACATGTATGAATGTATTGATACATTCTTCAATGTATCGTTACATTCTATCTTTTT
1 ATGTATCGATAAATGTATCAATGTATCGATACATTCTTCAATGTATCGATACATTATAT-TTTTT
1154391 T-CCCAG
65 TACCCAG
* * * *
1154397 ATGTATCTATAAATTTTTCAATGCATCGATACAT
1 ATGTATCGATAAATGTATCAATGTATCGATACAT
1154431 CTAGTTAAAA
Statistics
Matches: 91, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
71 85 0.93
72 6 0.07
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.43
Consensus pattern (71 bp):
ATGTATCGATAAATGTATCAATGTATCGATACATTCTTCAATGTATCGATACATTATATTTTTTT
ACCCAG
Found at i:1168237 original size:1 final size:1
Alignment explanation
Indices: 1168231--1168291 Score: 50
Period size: 1 Copynumber: 61.0 Consensus size: 1
1168221 TCCTTCGTAC
* ** * ** **
1168231 AAAAAAAAACAAAAAAATGAAAAAAACAAAAAAAACCAAAAAAACCAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1168292 CAAACAAACA
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.87, C:0.10, G:0.02, T:0.02
Consensus pattern (1 bp):
A
Found at i:1168246 original size:8 final size:8
Alignment explanation
Indices: 1168233--1168303 Score: 79
Period size: 9 Copynumber: 8.4 Consensus size: 8
1168223 CTTCGTACAA
1168233 AAAAAAAC
1 AAAAAAAC
*
1168241 AAAAAAATG
1 AAAAAAA-C
1168250 AAAAAAAC
1 AAAAAAAC
1168258 AAAAAAAACC
1 -AAAAAAA-C
1168268 AAAAAAACC
1 AAAAAAA-C
*
1168277 AAAAAAAA
1 AAAAAAAC
1168285 AAAAAAAC
1 AAAAAAAC
*
1168293 AAACAAAC
1 AAAAAAAC
1168301 AAA
1 AAA
1168304 TAAAGGGTCT
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
8 24 0.44
9 30 0.55
10 1 0.02
ACGTcount: A:0.85, C:0.13, G:0.01, T:0.01
Consensus pattern (8 bp):
AAAAAAAC
Found at i:1168255 original size:17 final size:16
Alignment explanation
Indices: 1168231--1168295 Score: 85
Period size: 17 Copynumber: 3.8 Consensus size: 16
1168221 TCCTTCGTAC
1168231 AAAAAAAAACAAAAAA
1 AAAAAAAAACAAAAAA
*
1168247 ATGAAAAAAACAAAAAA
1 A-AAAAAAAACAAAAAA
1168264 AACCAAAAAAACCAAAAAA
1 AA--AAAAAAA-CAAAAAA
1168283 AAAAAAAAACAAA
1 AAAAAAAAACAAA
1168296 CAAACAAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
16 5 0.12
17 22 0.51
18 7 0.16
19 9 0.21
ACGTcount: A:0.86, C:0.11, G:0.02, T:0.02
Consensus pattern (16 bp):
AAAAAAAAACAAAAAA
Found at i:1168259 original size:27 final size:26
Alignment explanation
Indices: 1168229--1168303 Score: 98
Period size: 25 Copynumber: 2.9 Consensus size: 26
1168219 CATCCTTCGT
*
1168229 ACAAAAAAAAACAAAAAAATGAAAAAA
1 ACAAAAAAAAACAAAAAAA-CAAAAAA
* *
1168256 ACAAAAAAAACCAAAAAAACCAAAAA
1 ACAAAAAAAAACAAAAAAACAAAAAA
*
1168282 A-AAAAAAAAACAAACAAACAAA
1 ACAAAAAAAAACAAAAAAACAAA
1168304 TAAAGGGTCT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
25 18 0.43
26 6 0.14
27 18 0.43
ACGTcount: A:0.84, C:0.13, G:0.01, T:0.01
Consensus pattern (26 bp):
ACAAAAAAAAACAAAAAAACAAAAAA
Found at i:1169996 original size:13 final size:13
Alignment explanation
Indices: 1169978--1170003 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1169968 CAATTTTTTG
1169978 TGTATCGATACAT
1 TGTATCGATACAT
1169991 TGTATCGATACAT
1 TGTATCGATACAT
1170004 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1170750 original size:28 final size:28
Alignment explanation
Indices: 1170733--1171160 Score: 554
Period size: 28 Copynumber: 15.0 Consensus size: 28
1170723 AATCCAGTAG
*
1170733 GTCAGTGGCATCCTTTCAAAGCCCATAA
1 GTCAGTGGCATCCTTTCAAAGCCCACAA
1170761 GTCAGTGGCATCCTTTCAAAGCCCACAA
1 GTCAGTGGCATCCTTTCAAAGCCCACAA
* *
1170789 ATCAGTGGTATCCTTTCAAAGCCCACAA
1 GTCAGTGGCATCCTTTCAAAGCCCACAA
1170817 GTCAGTGGCATCCTTTCAAAGCCCACAA
1 GTCAGTGGCATCCTTTCAAAGCCCACAA
* *
1170845 GTCAGTGGTACCCCTTT-AAAGCCCACAA
1 GTCAGTGGCA-TCCTTTCAAAGCCCACAA
* *
1170873 GTCGGTGGCACCCTTTCAAAGCCCACAA
1 GTCAGTGGCATCCTTTCAAAGCCCACAA
* *
1170901 GTCGGTGGCAACTCTTTTCAAAGCCCACAA
1 GTCAGTGGC-A-TCCTTTCAAAGCCCACAA
*
1170931 GTCAGTGGCAT-CTCTTCAAAAGACCACAA
1 GTCAGTGGCATCCT-TTC-AAAGCCCACAA
*
1170960 GTTAGTGGCATCCTTTCAAAGCCCACAA
1 GTCAGTGGCATCCTTTCAAAGCCCACAA
*
1170988 GTCAGTGGCACCCTTTCAAAGCCCACAA
1 GTCAGTGGCATCCTTTCAAAGCCCACAA
1171016 GTCAGTGGCATACCCTTTCAAAGCCCACACAA
1 GTCAGTGGCAT--CCTTTCAAAG-CC-CACAA
* * * *
1171048 ATTAGTGGCACCCTTCCAAAGCCCACAA
1 GTCAGTGGCATCCTTTCAAAGCCCACAA
* *
1171076 GTCAATGGCACCCTTTCAAAGCCCACAA
1 GTCAGTGGCATCCTTTCAAAGCCCACAA
* * *
1171104 GTCAGTGGTACCCCTTCAAAGCCCACAA
1 GTCAGTGGCATCCTTTCAAAGCCCACAA
1171132 GTCAGTGGCATCCCCTTTCAAAGCCCACA
1 GTCAGTGGCAT--CCTTTCAAAGCCCACA
1171161 CAAGTTGGTG
Statistics
Matches: 354, Mismatches: 33, Indels: 24
0.86 0.08 0.06
Matches are distributed among these distances:
27 7 0.02
28 240 0.68
29 32 0.09
30 60 0.17
31 2 0.01
32 13 0.04
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (28 bp):
GTCAGTGGCATCCTTTCAAAGCCCACAA
Found at i:1171126 original size:116 final size:114
Alignment explanation
Indices: 1170733--1171160 Score: 585
Period size: 116 Copynumber: 3.7 Consensus size: 114
1170723 AATCCAGTAG
* * * *
1170733 GTCAGTGGCATCCTTTCAAAGCCCATAAGTCAGTGGCATCCTTTCAAAGCCCACAAATCAGTGG-
1 GTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGC
* * *
1170797 -TATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAA
66 ATACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTCCAAAGCCCACAA
* * *
1170845 GTCAGTGGTACCCCTTT-AAAGCCCACAAGTCGGTGGCACCCTTTCAAAGCCCACAAGTCGGTGG
1 GTCAGTGGCA-CCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGG
* * * *
1170909 CA-ACTCTTTTCAAAGCCCACAAGTCAGTGGCATCTCTTCAAAAGACCACAA
65 CATAC-CCTTTCAAAGCCCACAAGTCAGTGGCA-CCCTTCCAAAGCCCACAA
* *
1170960 GTTAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGC
1 GTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGC
* *
1171025 ATACCCTTTCAAAGCCCACACAAATTAGTGGCACCCTTCCAAAGCCCACAA
66 ATACCCTTTCAAAG-CC-CACAAGTCAGTGGCACCCTTCCAAAGCCCACAA
* * *
1171076 GTCAATGGCACCCTTTCAAAGCCCACAAGTCAGTGGTACCCCTTCAAAGCCCACAAGTCAGTGGC
1 GTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGC
*
1171141 ATCCCCTTTCAAAGCCCACA
66 ATACCCTTTCAAAGCCCACA
1171161 CAAGTTGGTG
Statistics
Matches: 276, Mismatches: 31, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
112 51 0.18
113 6 0.02
114 35 0.13
115 79 0.29
116 92 0.33
117 13 0.05
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (114 bp):
GTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGC
ATACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTCCAAAGCCCACAA
Found at i:1171181 original size:25 final size:26
Alignment explanation
Indices: 1171146--1171197 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
1171136 GTGGCATCCC
*
1171146 CTTTCAAAGCCCACACAAGTTGGTGG
1 CTTTCAAAGCCCACACAAGTTAGTGG
*
1171172 CTTT-AAAGCCCACATAAGTTAGTGG
1 CTTTCAAAGCCCACACAAGTTAGTGG
1171197 C
1 C
1171198 ACATTTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 20 0.83
26 4 0.17
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (26 bp):
CTTTCAAAGCCCACACAAGTTAGTGG
Found at i:1171353 original size:46 final size:46
Alignment explanation
Indices: 1171278--1171536 Score: 331
Period size: 46 Copynumber: 5.6 Consensus size: 46
1171268 CCGATATCAT
* * * * *
1171278 TGGCATTGAATCAACATATTG-GCACCTTTATTAGCTCAATGTTGC
1 TGGCCTTGAATCAGCACATTGTCCACCTTTATTAGCTCAATGTCGC
1171323 TGGCCTTGAATCAGCACATTGTCCACCTTTATTAGCTCAATGTCGC
1 TGGCCTTGAATCAGCACATTGTCCACCTTTATTAGCTCAATGTCGC
* * * *
1171369 TAGTCTTGAATCAACACATTGTCCACCTTTATTAGCTTAATGTCGC
1 TGGCCTTGAATCAGCACATTGTCCACCTTTATTAGCTCAATGTCGC
* * * *
1171415 TGGCCTTGAATCAGCACATTGTTCACTTTTCCCTTAGCTCAATGTTGC
1 TGGCCTTGAATCAGCACATTGTCCACCTTT--ATTAGCTCAATGTCGC
* *
1171463 TGGCCTTGAATCAGCACATTGTCCACTTTTCCCTTAGCTCAATGTCGC
1 TGGCCTTGAATCAGCACATTGTCCACCTTT--ATTAGCTCAATGTCGC
*
1171511 TGGCCTTGAATCAGCACATTTTCCAC
1 TGGCCTTGAATCAGCACATTGTCCAC
1171537 TTTTCCTTTA
Statistics
Matches: 191, Mismatches: 20, Indels: 3
0.89 0.09 0.01
Matches are distributed among these distances:
45 18 0.09
46 89 0.47
48 84 0.44
ACGTcount: A:0.22, C:0.27, G:0.16, T:0.35
Consensus pattern (46 bp):
TGGCCTTGAATCAGCACATTGTCCACCTTTATTAGCTCAATGTCGC
Found at i:1171466 original size:48 final size:48
Alignment explanation
Indices: 1171307--1171579 Score: 338
Period size: 48 Copynumber: 5.8 Consensus size: 48
1171297 TGGCACCTTT
* *
1171307 ATTAGCTCAATGTTGCTGGCCTTGAATCAGCACATTGTCCACCTTT--
1 ATTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCC
* * * *
1171353 ATTAGCTCAATGTCGCTAGTCTTGAATCAACACATTGTCCACCTTT--
1 ATTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCC
* *
1171399 ATTAGCTTAATGTCGCTGGCCTTGAATCAGCACATTGTTCACTTTTCC
1 ATTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCC
* *
1171447 CTTAGCTCAATGTTGCTGGCCTTGAATCAGCACATTGTCCACTTTTCC
1 ATTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCC
* *
1171495 CTTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTTTCCACTTTTCC
1 ATTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCC
* * * ** * **
1171543 TTTACCTCGATGTCATTGGACTTGAATTGGCACATTG
1 ATTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTG
1171580 GCACTCCTCT
Statistics
Matches: 200, Mismatches: 25, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
46 82 0.41
48 118 0.59
ACGTcount: A:0.21, C:0.26, G:0.16, T:0.36
Consensus pattern (48 bp):
ATTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCC
Found at i:1172290 original size:20 final size:20
Alignment explanation
Indices: 1172265--1172337 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1172255 TTACCCAGAT
1172265 GTATCGATACATTTTTCAAC
1 GTATCGATACATTTTTCAAC
* * * *
1172285 GTATCGATACATGTATGAAT
1 GTATCGATACATTTTTCAAC
*
1172305 GTATCGATACATTTTTTAAC
1 GTATCGATACATTTTTCAAC
1172325 GTATCGATACATT
1 GTATCGATACATT
1172338 CTGTCTTTTT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.40
Consensus pattern (20 bp):
GTATCGATACATTTTTCAAC
Found at i:1178433 original size:32 final size:33
Alignment explanation
Indices: 1178370--1178434 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 33
1178360 CACACCCAGA
*
1178370 TGTATCGATACATATTGCTTGGTATCAATACAT
1 TGTATCGATACATATTGCTTGATATCAATACAT
*
1178403 TGTATCGATACATGTT-CTTGATATCAATACAT
1 TGTATCGATACATATTGCTTGATATCAATACAT
1178435 AGTGAATTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATATTGCTTGATATCAATACAT
Found at i:1178519 original size:13 final size:13
Alignment explanation
Indices: 1178483--1178519 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1178473 ACTTACATAA
* *
1178483 TATCGATATAGTG
1 TATCGATACATTG
1178496 TATCGATACATTG
1 TATCGATACATTG
1178509 TATCGATACAT
1 TATCGATACAT
1178520 GGTCAAATGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (13 bp):
TATCGATACATTG
Found at i:1186607 original size:100 final size:101
Alignment explanation
Indices: 1186491--1186693 Score: 338
Period size: 101 Copynumber: 2.0 Consensus size: 101
1186481 ATTTCGAAAA
*
1186491 TAAATTTGTTTTGTAAAATTTGGGAGATAAC-AAAAAGGGGAAGAAATTTGTTTTAGAAAAAGAA
1 TAAATTTGTTTTGTAAAATTTGGGAGATAACAAAAAAGGGGAAGAAATTTATTTTAGAAAAAGAA
* *
1186555 TGCTTTAAATATTTTATTAAAGGG-GAGAAAAAATTT
66 TCCTTTAAAAATTTTATT-AAGGGAGAGAAAAAATTT
*
1186591 TAAATTTGTTTTGTAAAATTTGGGAGATAACAAAAAAGGGGGAGAAATTTATTTTAGAAAAAGAA
1 TAAATTTGTTTTGTAAAATTTGGGAGATAACAAAAAAGGGGAAGAAATTTATTTTAGAAAAAGAA
*
1186656 TCCTTTAAAAATTTTATTAAGGGAGAGAAAATATTT
66 TCCTTTAAAAATTTTATTAAGGGAGAGAAAAAATTT
1186692 TA
1 TA
1186694 TTAAGGGGGA
Statistics
Matches: 96, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
100 36 0.38
101 60 0.62
ACGTcount: A:0.44, C:0.02, G:0.19, T:0.34
Consensus pattern (101 bp):
TAAATTTGTTTTGTAAAATTTGGGAGATAACAAAAAAGGGGAAGAAATTTATTTTAGAAAAAGAA
TCCTTTAAAAATTTTATTAAGGGAGAGAAAAAATTT
Found at i:1195443 original size:20 final size:20
Alignment explanation
Indices: 1195368--1195445 Score: 59
Period size: 20 Copynumber: 3.8 Consensus size: 20
1195358 TAAAACCCAG
* *
1195368 AATGTATCGATACAATGAGA
1 AATGTATCGATACATTGAAA
* *
1195388 AATGTATCGATATAATTGTAAG
1 AATGTATCGATA-CATTG-AAA
* **
1195410 CATGTATC-AGTACATTGACT
1 AATGTATCGA-TACATTGAAA
1195430 AATGTATCGATACATT
1 AATGTATCGATACATT
1195446 TCCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
20 26 0.58
21 9 0.20
22 10 0.22
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTGAAA
Found at i:1206408 original size:19 final size:20
Alignment explanation
Indices: 1206371--1206408 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1206361 TCCCGTAGCT
1206371 ATGTATCGATACAATTCATA
1 ATGTATCGATACAATTCATA
1206391 ATGTATCGATAC-ATTCAT
1 ATGTATCGATACAATTCAT
1206409 TTGAAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACAATTCATA
Found at i:1206550 original size:20 final size:20
Alignment explanation
Indices: 1206525--1206579 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
1206515 CTACCAATTT
**
1206525 CATGTATTGATACAATTGTG
1 CATGTATTGATACAATTGAA
*
1206545 CATGTATCGATACAA-TGAA
1 CATGTATTGATACAATTGAA
1206564 CATGTATTGATACAAT
1 CATGTATTGATACAAT
1206580 ATACCGATAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (20 bp):
CATGTATTGATACAATTGAA
Found at i:1207623 original size:27 final size:27
Alignment explanation
Indices: 1207593--1207775 Score: 179
Period size: 27 Copynumber: 6.1 Consensus size: 27
1207583 ACACGGAATG
1207593 ATGGGCATGGAATAAAAAAATGAAGGC
1 ATGGGCATGGAATAAAAAAATGAAGGC
*
1207620 ATGGGCATGGAATAAAAAATTGAAGGC
1 ATGGGCATGGAATAAAAAAATGAAGGC
1207647 ATGGAGTGATGGGCATGGAATAAAAAAATGAAGGC
1 --------ATGGGCATGGAATAAAAAAATGAAGGC
1207682 ATGGGCATGGAATAAAAAAATTGAAGGC
1 ATGGGCATGGAATAAAAAAA-TGAAGGC
1207710 ATGGGATGATGGGCATGGAATAAAAAAAATGAAGGC
1 --------ATGGGCATGGAAT-AAAAAAATGAAGGC
*
1207746 ATGGGCATGGAAT-AAGAAATGAAGGC
1 ATGGGCATGGAATAAAAAAATGAAGGC
1207772 ATGG
1 ATGG
1207776 AATGATGGAA
Statistics
Matches: 135, Mismatches: 3, Indels: 37
0.77 0.02 0.21
Matches are distributed among these distances:
26 16 0.12
27 46 0.34
28 20 0.15
35 26 0.19
36 20 0.15
37 7 0.05
ACGTcount: A:0.44, C:0.07, G:0.32, T:0.17
Consensus pattern (27 bp):
ATGGGCATGGAATAAAAAAATGAAGGC
Found at i:1207666 original size:35 final size:35
Alignment explanation
Indices: 1207620--1207750 Score: 163
Period size: 36 Copynumber: 3.9 Consensus size: 35
1207610 AAATGAAGGC
*
1207620 ATGGGCATGGAAT-AAAAAATTGAAGGCATGGAGTG
1 ATGGGCATGGAATAAAAAAAATGAAGGCATGG-GTG
1207655 ATGGGCATGGAAT-AAAAAAATGAAGGC-------
1 ATGGGCATGGAATAAAAAAAATGAAGGCATGGGTG
*
1207682 ATGGGCATGGAATAAAAAAATTGAAGGCATGGGATG
1 ATGGGCATGGAATAAAAAAAATGAAGGCATGGG-TG
1207718 ATGGGCATGGAATAAAAAAAATGAAGGCATGGG
1 ATGGGCATGGAATAAAAAAAATGAAGGCATGGG
1207751 CATGGAATAA
Statistics
Matches: 84, Mismatches: 3, Indels: 17
0.81 0.03 0.16
Matches are distributed among these distances:
27 13 0.15
28 13 0.15
35 26 0.31
36 32 0.38
ACGTcount: A:0.44, C:0.06, G:0.33, T:0.18
Consensus pattern (35 bp):
ATGGGCATGGAATAAAAAAAATGAAGGCATGGGTG
Found at i:1207710 original size:63 final size:62
Alignment explanation
Indices: 1207591--1207783 Score: 327
Period size: 62 Copynumber: 3.1 Consensus size: 62
1207581 AAACACGGAA
1207591 TGATGGGCATGGAATAAAAAAATGAAGGCATGGGCATGGAATAAAAAATTGAAGGCATGGAG
1 TGATGGGCATGGAATAAAAAAATGAAGGCATGGGCATGGAATAAAAAATTGAAGGCATGGAG
1207653 TGATGGGCATGGAATAAAAAAATGAAGGCATGGGCATGGAATAAAAAAATTGAAGGCATGG-G
1 TGATGGGCATGGAATAAAAAAATGAAGGCATGGGCATGGAAT-AAAAAATTGAAGGCATGGAG
* *
1207715 ATGATGGGCATGGAATAAAAAAAATGAAGGCATGGGCATGGAATAAGAAA-TGAAGGCATGGAA
1 -TGATGGGCATGGAAT-AAAAAAATGAAGGCATGGGCATGGAATAAAAAATTGAAGGCATGGAG
1207778 TGATGG
1 TGATGG
1207784 AAAAATGAAA
Statistics
Matches: 125, Mismatches: 2, Indels: 8
0.93 0.01 0.06
Matches are distributed among these distances:
62 60 0.48
63 38 0.30
64 27 0.22
ACGTcount: A:0.44, C:0.06, G:0.33, T:0.18
Consensus pattern (62 bp):
TGATGGGCATGGAATAAAAAAATGAAGGCATGGGCATGGAATAAAAAATTGAAGGCATGGAG
Found at i:1207772 original size:26 final size:27
Alignment explanation
Indices: 1207718--1207775 Score: 91
Period size: 26 Copynumber: 2.1 Consensus size: 27
1207708 GCATGGGATG
1207718 ATGGGCATGGAATAAAAAAAATGAAGGC
1 ATGGGCATGGAAT-AAAAAAATGAAGGC
*
1207746 ATGGGCATGGAAT-AAGAAATGAAGGC
1 ATGGGCATGGAATAAAAAAATGAAGGC
1207772 ATGG
1 ATGG
1207776 AATGATGGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 16 0.55
28 13 0.45
ACGTcount: A:0.45, C:0.07, G:0.33, T:0.16
Consensus pattern (27 bp):
ATGGGCATGGAATAAAAAAATGAAGGC
Found at i:1209084 original size:79 final size:79
Alignment explanation
Indices: 1208988--1209652 Score: 1048
Period size: 79 Copynumber: 8.4 Consensus size: 79
1208978 GTTAAGTTTC
* *
1208988 TCAATTTTTCACAATCGGGGATACTCCAATCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
*
1209053 TTATCTCTAAAACA
66 TTATTTCTAAAACA
* *
1209067 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
*
1209132 TTATTTCTAAAATA
66 TTATTTCTAAAACA
* * * * *
1209146 TTAATTTTTCACAATCGGGGATACTCCAACCCCTTTATTTTCGAGGGGATACTCCAACCCCGGCT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
1209211 TTATTTCTAAAACA
66 TTATTTCTAAAACA
* *
1209225 TCAATTTTTCATAATCGGGGATACTCCAACCCTGTTATTTCCGAGGGGATACTTCAACCCCGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
1209290 TTATTTCTAAAACA
66 TTATTTCTAAAACA
* * * *
1209304 CCAATTTTTCATAATCGGGGATACTCCAACCCTGTTATTTCTGAGGGGATACTCCAACCTCGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
1209369 TTATCTT-TAAAACA
66 TTAT-TTCTAAAACA
* *
1209383 TCAATTTTTC-TAAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGAT
1 TCAATTTTTCAT-AATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGT
*
1209447 TTTATTTCTAAAATA
65 TTTATTTCTAAAACA
* * *
1209462 TTAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTCCGAAGGGATACTCCAACCCCGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
1209527 TTATTTCTAAAACA
66 TTATTTCTAAAACA
* * *
1209541 CCAATTTTTCATAATC-GGGATACTCCAACCCCGTTATTTCCAAGGGGATACTTCAACCCCGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
1209605 TTATTTCTAAAACA
66 TTATTTCTAAAACA
*
1209619 TCAATTTTTCATAATCGGGGATACTCTAACCCCG
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCG
1209653 ATTTTATTCT
Statistics
Matches: 537, Mismatches: 44, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
78 77 0.14
79 458 0.85
80 2 0.00
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (79 bp):
TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
TTATTTCTAAAACA
Found at i:1209660 original size:51 final size:52
Alignment explanation
Indices: 1209584--1209730 Score: 151
Period size: 51 Copynumber: 2.8 Consensus size: 52
1209574 TTATTTCCAA
*
1209584 GGGGATACT-TCAACCCCGGTTTTATT-TCTAAAACATCAATTTTT-CATAATC
1 GGGGATACTCT-AACCCCGATTTTATTCTCTAAAACA-CAATTTTTCCATAATC
* * **
1209635 GGGGATACTCTAACCCCGATTTTATTCTTTAGAACACCGTTTTTCCATAATC
1 GGGGATACTCTAACCCCGATTTTATTCTCTAAAACACAATTTTTCCATAATC
* * *
1209687 GGGGATACTCTAGCCCCG-TTGTTA-TCTATAAAATACTAATTTTT
1 GGGGATACTCTAACCCCGATT-TTATTCTCTAAAACAC-AATTTTT
1209731 TTTTCTCGTC
Statistics
Matches: 80, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
51 40 0.50
52 40 0.50
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (52 bp):
GGGGATACTCTAACCCCGATTTTATTCTCTAAAACACAATTTTTCCATAATC
Found at i:1215884 original size:61 final size:59
Alignment explanation
Indices: 1215788--1216779 Score: 1396
Period size: 61 Copynumber: 16.4 Consensus size: 59
1215778 TAGCCATTCC
* * *
1215788 AGTCCTCAAAGAGCAGGACACCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCCTTT
1 AGTCCTCAAAGAGCAGGAC-GCTTTTTCTTTCAAAGCCCACACAAGTTGGTGGCA-CCTTT
1215849 AGTCCTCAAAGAGCAGGACGCTTTTTCCTTAT-AAAGCCCACACAAGTTGGTGGCACCTTT
1 AGTCCTCAAAGAGCAGGACGCTTTTT-CTT-TCAAAGCCCACACAAGTTGGTGGCACCTTT
* * *
1215909 AGTCCTAAAAGAGCAGGATGCCTTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACCCTCT
1 AGTCCTCAAAGAGCAGGACG-CTTTTTCTTTCAAAGCCCACACAAGTTGGTGGCA-CCTTT
1215970 AGTCCTCAAAGAGCAGGACGCCTTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT
1 AGTCCTCAAAGAGCAGGACG-CTTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT
* *
1216030 AGTCCTCAAAGAGCATGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
1 AGTCCTCAAAGAGCAGGACGCTTTTT-CTTTCAAAGCCCACACAAGTTGGTGGCACCTTT
* *
1216090 AGTCCTCAAAGAGCAGGACGCTTTTTTCTTTCAAAGCCCACACAAGTTAGTGGCACCCTCT
1 AGTCCTCAAAGAGCAGGACGC-TTTTTCTTTCAAAGCCCACACAAGTTGGTGGCA-CCTTT
* *
1216151 AGTCCTCAAAGAGCAGGACACCTTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACCTCT
1 AGTCCTCAAAGAGCAGGAC-GCTTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT
* * * *
1216211 AGTCCTCAAAGAGCAGGACACCTTTTCCTTCCAAAGCCCACACAAGTTGGTGGCACCCTCT
1 AGTCCTCAAAGAGCAGGAC-GCTTTTTCTTTCAAAGCCCACACAAGTTGGTGGCA-CCTTT
* *
1216272 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
1 AGTCCTCAAAGAGCAGGACG-CTTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT
*
1216332 AGTCCTCAAAGAGCAGGACGCCTTTTTCTTTCGAAGCCCACACAAGTTGGTGGCACCCTTT
1 AGTCCTCAAAGAGCAGGACG-CTTTTTCTTTCAAAGCCCACACAAGTTGGTGGCA-CCTTT
*
1216393 TGTCCTCAAAGAGCAGGACGCCTTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACCCTTT
1 AGTCCTCAAAGAGCAGGACG-CTTTTTCTTTCAAAGCCCACACAAGTTGGTGGCA-CCTTT
* * *
1216454 TGTCCTCAAAGAGCAGGACACCTTTTTCTTTCAAAGCCCACACAAGTTGGTGGCATCTTT
1 AGTCCTCAAAGAGCAGGAC-GCTTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT
* *
1216514 AGTCCTCAAAGAGCAAGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
1 AGTCCTCAAAGAGCAGGACGCTTTTT-CTTTCAAAGCCCACACAAGTTGGTGGCACCTTT
*
1216574 AGTCCTCAAAGAGCAGGACGCCTTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACCCTCT
1 AGTCCTCAAAGAGCAGGACG-CTTTTTCTTTCAAAGCCCACACAAGTTGGTGGCA-CCTTT
* * * *
1216635 AGTCCTCAAAGAGCAAGACGCCTTTTCCTTTTAAAGCCCACACAATTTGGTGGCACCCTTT
1 AGTCCTCAAAGAGCAGGACG-CTTTTTCTTTCAAAGCCCACACAAGTTGGTGGCA-CCTTT
* * *
1216696 CAGTCCTCAAAGAGCAGGATGCTTTCTT-TTTGCAAATCCCACACTAGTTGGTGGCA-CTTGT
1 -AGTCCTCAAAGAGCAGGACGCTTT-TTCTTT-CAAAGCCCACACAAGTTGGTGGCACCTT-T
*
1216757 CAGTCCTCAAAGAGCATGACGCT
1 -AGTCCTCAAAGAGCAGGACGCT
1216780 CTCTCCTTTC
Statistics
Matches: 860, Mismatches: 51, Indels: 40
0.90 0.05 0.04
Matches are distributed among these distances:
59 13 0.02
60 370 0.43
61 436 0.51
62 41 0.05
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (59 bp):
AGTCCTCAAAGAGCAGGACGCTTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT
Found at i:1216006 original size:121 final size:121
Alignment explanation
Indices: 1215788--1216778 Score: 1491
Period size: 121 Copynumber: 8.2 Consensus size: 121
1215778 TAGCCATTCC
* *
1215788 AGTCCTCAAAGAGCAGGACACCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCCTTTAGTC
1 AGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA-CCTTTAGTC
1215853 CTCAAAGAGCAGGACG-CTTTTTCCTTAT-AAAGCCCACACAAGTTGGTGGCA-CCTTT
65 CTCAAAGAGCAGGACGCCTTTTT-CTT-TCAAAGCCCACACAAGTTGGTGGCACCCTTT
* * * *
1215909 AGTCCTAAAAGAGCAGGATGCCTTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACCCTCTAGTC
1 AGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA-CCTTTAGTC
1215974 CTCAAAGAGCAGGACGCCTTTTTCTTTCAAAGCCCACACAAGTTGGTGGCA-CCTTT
65 CTCAAAGAGCAGGACGCCTTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACCCTTT
*
1216030 AGTCCTCAAAGAGCATGACG-CTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTAGTC
1 AGTCCTCAAAGAGCAGGACGCCTTTTT-CTTTTAAAGCCCACACAAGTTGGTGGCACCTTTAGTC
* * *
1216094 CTCAAAGAGCAGGACGCTTTTTTCTTTCAAAGCCCACACAAGTTAGTGGCACCCTCT
65 CTCAAAGAGCAGGACGCCTTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACCCTTT
* * *
1216151 AGTCCTCAAAGAGCAGGACACCTTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACCTCTAGTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTAGTCC
* * * *
1216216 TCAAAGAGCAGGACACCTTTTCCTTCCAAAGCCCACACAAGTTGGTGGCACCCTCT
66 TCAAAGAGCAGGACGCCTTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACCCTTT
*
1216272 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTAGTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTAGTCC
*
1216337 TCAAAGAGCAGGACGCCTTTTTCTTTCGAAGCCCACACAAGTTGGTGGCACCCTTT
66 TCAAAGAGCAGGACGCCTTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACCCTTT
* * *
1216393 TGTCCTCAAAGAGCAGGACGCCTTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACCCTTTTGTC
1 AGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA-CCTTTAGTC
* *
1216458 CTCAAAGAGCAGGACACCTTTTTCTTTCAAAGCCCACACAAGTTGGTGGCA-TCTTT
65 CTCAAAGAGCAGGACGCCTTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACCCTTT
*
1216514 AGTCCTCAAAGAGCAAGACG-CTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTAGTC
1 AGTCCTCAAAGAGCAGGACGCCTTTTT-CTTTTAAAGCCCACACAAGTTGGTGGCACCTTTAGTC
*
1216578 CTCAAAGAGCAGGACGCCTTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACCCTCT
65 CTCAAAGAGCAGGACGCCTTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACCCTTT
* * *
1216635 AGTCCTCAAAGAGCAAGACGCCTTTTCCTTTTAAAGCCCACACAATTTGGTGGCACCCTTTCAGT
1 AGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA-CCTTT-AGT
* * *
1216700 CCTCAAAGAGCAGGATG-CTTTCTT-TTTGCAAATCCCACACTAGTTGGTGGCA--CTTGT
64 CCTCAAAGAGCAGGACGCCTTT-TTCTTT-CAAAGCCCACACAAGTTGGTGGCACCCTT-T
*
1216757 CAGTCCTCAAAGAGCATGACGC
1 -AGTCCTCAAAGAGCAGGACGC
1216779 TCTCTCCTTT
Statistics
Matches: 802, Mismatches: 53, Indels: 28
0.91 0.06 0.03
Matches are distributed among these distances:
120 128 0.16
121 524 0.65
122 87 0.11
123 63 0.08
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (121 bp):
AGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTAGTCC
TCAAAGAGCAGGACGCCTTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACCCTTT
Found at i:1216953 original size:40 final size:40
Alignment explanation
Indices: 1216908--1217023 Score: 126
Period size: 45 Copynumber: 2.8 Consensus size: 40
1216898 GTTAGAGGCA
* *
1216908 CTTTTCAGTCCTCAAAGAACAGGGCACACTTCTTTCCCTT
1 CTTTTCTGTCCTCAAAGAACAGGACACACTTCTTTCCCTT
*
1216948 CTTTTCTCTTTTGTCCTCAAAGAGCAGGACACACTTCTTTCCCTT
1 C-TTT-TC---TGTCCTCAAAGAACAGGACACACTTCTTTCCCTT
* *
1216993 CTCTTT-TGTCCTTAAAGAACAGGACGCACTT
1 CT-TTTCTGTCCTCAAAGAACAGGACACACTT
1217024 TATTTTCCTT
Statistics
Matches: 64, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
40 23 0.36
41 3 0.05
42 2 0.03
44 2 0.03
45 34 0.53
ACGTcount: A:0.22, C:0.30, G:0.13, T:0.35
Consensus pattern (40 bp):
CTTTTCTGTCCTCAAAGAACAGGACACACTTCTTTCCCTT
Found at i:1217044 original size:42 final size:40
Alignment explanation
Indices: 1216915--1217058 Score: 135
Period size: 42 Copynumber: 3.4 Consensus size: 40
1216905 GCACTTTTCA
* * *
1216915 GTCCTCAAAGAACAGGGCACACTTCTTTCCCTTCTTTTCTCTTTT
1 GTCCTTAAAGAGCAGGACACACTTCTTT--C--CTTTT-TCTTTT
* * *
1216960 GTCCTCAAAGAGCAGGACACACTTCTTTCCCTTCTCTTTT
1 GTCCTTAAAGAGCAGGACACACTTCTTTCCTTTTTCTTTT
* * *
1217000 GTCCTTAAAGAACAGGACGCACTTTATTTTCCTTTTTCTTTT
1 GTCCTTAAAGAGCAGGACACAC-TT-CTTTCCTTTTTCTTTT
*
1217042 GTCCTTAGAGAGCAGGA
1 GTCCTTAAAGAGCAGGA
1217059 AGTATTTCGT
Statistics
Matches: 85, Mismatches: 12, Indels: 7
0.82 0.12 0.07
Matches are distributed among these distances:
40 25 0.29
41 5 0.06
42 28 0.33
43 1 0.01
45 26 0.31
ACGTcount: A:0.21, C:0.27, G:0.15, T:0.38
Consensus pattern (40 bp):
GTCCTTAAAGAGCAGGACACACTTCTTTCCTTTTTCTTTT
Found at i:1217076 original size:42 final size:41
Alignment explanation
Indices: 1216948--1217089 Score: 135
Period size: 42 Copynumber: 3.4 Consensus size: 41
1216938 TCTTTCCCTT
* *
1216948 CTTTTCTCTTTTGTCCTCAAAGAGCAGGACA-CACTTCTTTCC
1 CTTTT-TCTTTTGTCCTTAAAGAGCAGGA-AGCATTTCTTTCC
* * * * *
1216990 C-TTCTCTTTTGTCCTTAAAGAACAGGACGCACTTTATTTTC
1 CTTTTTCTTTTGTCCTTAAAGAGCAGGAAGCA-TTTCTTTCC
* *
1217031 CTTTTTCTTTTGTCCTTAGAGAGCAGGAAGTATTTCGTTTCC
1 CTTTTTCTTTTGTCCTTAAAGAGCAGGAAGCATTTC-TTTCC
*
1217073 CTTTTTTTCTTTGTCCT
1 CTTTTTCT-TTTGTCCT
1217090 CGAAAAACGA
Statistics
Matches: 80, Mismatches: 15, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
40 23 0.29
41 12 0.15
42 37 0.46
43 8 0.10
ACGTcount: A:0.17, C:0.25, G:0.13, T:0.45
Consensus pattern (41 bp):
CTTTTTCTTTTGTCCTTAAAGAGCAGGAAGCATTTCTTTCC
Found at i:1217872 original size:27 final size:27
Alignment explanation
Indices: 1217842--1217988 Score: 172
Period size: 27 Copynumber: 5.1 Consensus size: 27
1217832 ATACGGAATG
1217842 ATGGGCATGGAATAAAAAAATGAAGGC
1 ATGGGCATGGAATAAAAAAATGAAGGC
*
1217869 ATGGGCATGGAATAAAAAATTGAAGGC
1 ATGGGCATGGAATAAAAAAATGAAGGC
1217896 ATGGAGTGATGGGCATGGAATAAAAAAATGAAGGC
1 --------ATGGGCATGGAATAAAAAAATGAAGGC
1217931 ATGGGCATGGAATAAAAAAAATGAAGGC
1 ATGGGCATGGAAT-AAAAAAATGAAGGC
*
1217959 ATGGGCAAT-GAAT-AAGAAATGAAGGC
1 ATGGGC-ATGGAATAAAAAAATGAAGGC
1217985 ATGG
1 ATGG
1217989 AATGATGGAA
Statistics
Matches: 107, Mismatches: 3, Indels: 21
0.82 0.02 0.16
Matches are distributed among these distances:
26 16 0.15
27 39 0.36
28 24 0.22
29 2 0.02
35 26 0.24
ACGTcount: A:0.46, C:0.07, G:0.31, T:0.16
Consensus pattern (27 bp):
ATGGGCATGGAATAAAAAAATGAAGGC
Found at i:1217914 original size:62 final size:63
Alignment explanation
Indices: 1217840--1217962 Score: 230
Period size: 62 Copynumber: 2.0 Consensus size: 63
1217830 AAATACGGAA
*
1217840 TGATGGGCATGGAATAAAAAAATGAAGGCATGGGCATGGAAT-AAAAAATTGAAGGCATGGAG
1 TGATGGGCATGGAATAAAAAAATGAAGGCATGGGCATGGAATAAAAAAAATGAAGGCATGGAG
1217902 TGATGGGCATGGAATAAAAAAATGAAGGCATGGGCATGGAATAAAAAAAATGAAGGCATGG
1 TGATGGGCATGGAATAAAAAAATGAAGGCATGGGCATGGAATAAAAAAAATGAAGGCATGG
1217963 GCAATGAATA
Statistics
Matches: 59, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
62 42 0.71
63 17 0.29
ACGTcount: A:0.45, C:0.07, G:0.32, T:0.17
Consensus pattern (63 bp):
TGATGGGCATGGAATAAAAAAATGAAGGCATGGGCATGGAATAAAAAAAATGAAGGCATGGAG
Found at i:1217985 original size:26 final size:27
Alignment explanation
Indices: 1217904--1217988 Score: 129
Period size: 28 Copynumber: 3.1 Consensus size: 27
1217894 GCATGGAGTG
1217904 ATGGGCATGGAATAAAAAAATGAAGGC
1 ATGGGCATGGAATAAAAAAATGAAGGC
1217931 ATGGGCATGGAATAAAAAAAATGAAGGC
1 ATGGGCATGGAAT-AAAAAAATGAAGGC
*
1217959 ATGGGCAAT-GAAT-AAGAAATGAAGGC
1 ATGGGC-ATGGAATAAAAAAATGAAGGC
1217985 ATGG
1 ATGG
1217989 AATGATGGAA
Statistics
Matches: 55, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
26 16 0.29
27 13 0.24
28 24 0.44
29 2 0.04
ACGTcount: A:0.47, C:0.07, G:0.31, T:0.15
Consensus pattern (27 bp):
ATGGGCATGGAATAAAAAAATGAAGGC
Found at i:1219333 original size:79 final size:79
Alignment explanation
Indices: 1219202--1219867 Score: 1068
Period size: 79 Copynumber: 8.4 Consensus size: 79
1219192 GTTAAGTTTC
* * *
1219202 TCAATTTTTCACAATCGGGGATACTCCAATCTCGTTATTTTCGAGGGGATACTCCAACCCCGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTT
*
1219267 TTATCTCTAAAACA
66 TTATTTCTAAAACA
* *
1219281 TCAATTTTTCATAATCAGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTT
*
1219346 TTATTTCTAAAAGA
66 TTATTTCTAAAACA
* * * * **
1219360 TTAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCGACCCCGACT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTT
*
1219425 TCATTTCTAAAACA
66 TTATTTCTAAAACA
*
1219439 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTT
1219504 TTATTTCTAAAACA
66 TTATTTCTAAAACA
* * *
1219518 CCATTTTTTCATAATCGGGGATACTCCAACCCCGTTA-TTTCAGAGGGGATACTCCAACCTCGGT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTC-GAGGGGATACTCCAACCCCGGT
1219582 TTTATCTT-TAAAACA
65 TTTAT-TTCTAAAACA
1219597 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTT
*
1219662 TTATTTCTAAAATA
66 TTATTTCTAAAACA
* *
1219676 TTAATTTTTCACAATCGGGGATACTCCAACCCCGTTA-TTTCTGAGGGGATACTCCAACCCCGGT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTC-GAGGGGATACTCCAACCCCGGT
1219740 TTTATTTCTAAAACA
65 TTTATTTCTAAAACA
* *
1219755 CCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACGCCAACCCCGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTT
1219820 TTATTTCTAAAACA
66 TTATTTCTAAAACA
*
1219834 TCAATTTTTCATAATCGGGGATACTCTAACCCCG
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCG
1219868 ATTTTATTCT
Statistics
Matches: 543, Mismatches: 38, Indels: 12
0.92 0.06 0.02
Matches are distributed among these distances:
78 9 0.02
79 524 0.97
80 10 0.02
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (79 bp):
TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTT
TTATTTCTAAAACA
Found at i:1219865 original size:51 final size:51
Alignment explanation
Indices: 1219799--1219945 Score: 154
Period size: 52 Copynumber: 2.8 Consensus size: 51
1219789 TTATTTTCGA
* *
1219799 GGGGATACGCCAACCCCGGTTTTATTTCTAAAACATCAATTTTT-CATAATC
1 GGGGATACTCTAACCCCGGTTTTATTTCTAAAACA-CAATTTTTCCATAATC
* * * **
1219850 GGGGATACTCTAACCCCGATTTTATTCTTTAGAACACCGTTTTTCCATAATC
1 GGGGATACTCTAACCCCGGTTTTATT-TCTAAAACACAATTTTTCCATAATC
* * *
1219902 GGGGATACTCTAGCCCC-GTTGTTATCTCTAAAATACTAATTTTT
1 GGGGATACTCTAACCCCGGTT-TTATTTCTAAAACAC-AATTTTT
1219946 TTTTCTCGTC
Statistics
Matches: 77, Mismatches: 15, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
51 38 0.49
52 39 0.51
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (51 bp):
GGGGATACTCTAACCCCGGTTTTATTTCTAAAACACAATTTTTCCATAATC
Found at i:1219945 original size:52 final size:51
Alignment explanation
Indices: 1219799--1219945 Score: 156
Period size: 51 Copynumber: 2.9 Consensus size: 51
1219789 TTATTTTCGA
* * *
1219799 GGGGATACGCCAACCCCGGTTTTATT-TCTAAAACATCAATTTTTCATAATC
1 GGGGATACTCTAACCCCGATTTTATTCTCTAAAACA-CAATTTTTCATAATC
* * **
1219850 GGGGATACTCTAACCCCGATTTTATTCTTTAGAACACCGTTTTTCCATAATC
1 GGGGATACTCTAACCCCGATTTTATTCTCTAAAACACAATTTTT-CATAATC
* *
1219902 GGGGATACTCTAGCCCCG-TTGTTA-TCTCTAAAATACTAATTTTT
1 GGGGATACTCTAACCCCGATT-TTATTCTCTAAAACAC-AATTTTT
1219946 TTTTCTCGTC
Statistics
Matches: 79, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
51 40 0.51
52 39 0.49
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (51 bp):
GGGGATACTCTAACCCCGATTTTATTCTCTAAAACACAATTTTTCATAATC
Found at i:1222728 original size:7 final size:7
Alignment explanation
Indices: 1222716--1222747 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
1222706 GTCGGGCGCC
1222716 AAACCCT
1 AAACCCT
1222723 AAACCCT
1 AAACCCT
1222730 AAACCCT
1 AAACCCT
*
1222737 AAAACCT
1 AAACCCT
1222744 AAAC
1 AAAC
1222748 TTGAGGTCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.50, C:0.38, G:0.00, T:0.12
Consensus pattern (7 bp):
AAACCCT
Found at i:1222969 original size:13 final size:13
Alignment explanation
Indices: 1222951--1223039 Score: 52
Period size: 13 Copynumber: 5.9 Consensus size: 13
1222941 TTCAACAATT
1222951 TGTATCGATACAA
1 TGTATCGATACAA
1222964 TGTATCGATACATAA
1 TGTATCGATAC--AA
*
1222979 GTGTTGTATCGATAAAA
1 ----TGTATCGATACAA
*
1222996 TGTATCGATATATAA
1 TGTATCG--ATACAA
1223011 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
1223028 TGTATCGATACA
1 TGTATCGATACA
1223040 TAAGTTTTGT
Statistics
Matches: 61, Mismatches: 3, Indels: 24
0.69 0.03 0.27
Matches are distributed among these distances:
13 30 0.49
15 7 0.11
17 7 0.11
19 17 0.28
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1222988 original size:19 final size:18
Alignment explanation
Indices: 1222964--1223058 Score: 84
Period size: 19 Copynumber: 5.7 Consensus size: 18
1222954 ATCGATACAA
1222964 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
1222983 TGTATCGATA-A-AA---
1 TGTATCGATACATAAGTT
*
1222996 TGTATCGATATATAAGTGT
1 TGTATCGATACATAAGT-T
1223015 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
1223028 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
1223047 TGTATCGATACA
1 TGTATCGATACA
1223059 ATGTATCACC
Statistics
Matches: 63, Mismatches: 1, Indels: 24
0.72 0.01 0.27
Matches are distributed among these distances:
13 21 0.33
14 1 0.02
15 4 0.06
17 4 0.06
18 1 0.02
19 32 0.51
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.37
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:1222991 original size:32 final size:32
Alignment explanation
Indices: 1222950--1223065 Score: 205
Period size: 32 Copynumber: 3.6 Consensus size: 32
1222940 TTTCAACAAT
1222950 TTGTATCGATACAATGTATCGATACATAAGTG
1 TTGTATCGATACAATGTATCGATACATAAGTG
* *
1222982 TTGTATCGATAAAATGTATCGATATATAAGTG
1 TTGTATCGATACAATGTATCGATACATAAGTG
*
1223014 TTGTATCGATACAATGTATCGATACATAAGTT
1 TTGTATCGATACAATGTATCGATACATAAGTG
1223046 TTGTATCGATACAATGTATC
1 TTGTATCGATACAATGTATC
1223066 ACCACGGTCT
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 79 1.00
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.37
Consensus pattern (32 bp):
TTGTATCGATACAATGTATCGATACATAAGTG
Found at i:1225289 original size:15 final size:16
Alignment explanation
Indices: 1225271--1225313 Score: 63
Period size: 14 Copynumber: 2.8 Consensus size: 16
1225261 AGTCAAAAGT
1225271 AAACACAAAAAAACA-
1 AAACACAAAAAAACAC
1225286 AAACA-AAAAAAACAC
1 AAACACAAAAAAACAC
*
1225301 ACACACAAAAAAA
1 AAACACAAAAAAA
1225314 GTGCAAAGGC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 9 0.36
15 9 0.36
16 7 0.28
ACGTcount: A:0.79, C:0.21, G:0.00, T:0.00
Consensus pattern (16 bp):
AAACACAAAAAAACAC
Found at i:1226658 original size:34 final size:32
Alignment explanation
Indices: 1226544--1226973 Score: 256
Period size: 34 Copynumber: 13.3 Consensus size: 32
1226534 TCTTGTCTCA
* * * * *
1226544 AAGTCCACAATTCAGTGGCATCTCTTTC--TA
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTT
* * * **
1226574 AAGTCCACAACTCAGTGACATC-TTTTCTTCA
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTT
** *
1226605 AAGTCCACGGCTCCATGGCACCTTTTTCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTT
* * *
1226637 CAAAGTCCACAACTCTGTGGCA-C-TCTT-TTTA
1 --AAGTCCACAACTCCGTGGCACCTTTTTCTTTT
* * *
1226668 AAGCCCATAACTCCGTGCCACC-----CTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTT
*
1226695 AAGTCCACGACTCCGTGGCACCCTTTTTCCCTTTT
1 AAGTCCACAACTCCGTGGCA-CCTTTTT--CTTTT
* * *
1226730 AAGCCCACACCTCTGTGGCA-CTTTGTTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTTT-TT-CTTTT
* * *
1226763 AAGTCCACAACTCTGTGGCATCATTTTCCTTTT
1 AAGTCCACAACTCCGTGGCA-CCTTTTTCTTTT
** * *
1226796 AAAGTCCACAACTTTGTGACACCTTTTCCTTTT
1 -AAGTCCACAACTCCGTGGCACCTTTTTCTTTT
**
1226829 AAGTCCATGACTCCGTGGCACCCTTTTTCCTTTT
1 AAGTCCACAACTCCGTGGCA-CCTTTTT-CTTTT
* *
1226863 AAGCCCACACCTCCGTGGCACCCTTTTTCCCTTTT
1 AAGTCCACAACTCCGTGGCA-CCTTTTT--CTTTT
* * *
1226898 AAAGCCCACAACTCCATGGCACCTTGTTCCTTTT
1 -AAGTCCACAACTCCGTGGCACCTT-TTTCTTTT
* *
1226932 AAGTCCACAACTCCGTGG-ATCTTTCTTTTTTT
1 AAGTCCACAACTCCGTGGCACCTTT-TTCTTTT
*
1226964 AAGCCCACAA
1 AAGTCCACAA
1226974 GTTAGTGGCA
Statistics
Matches: 318, Mismatches: 57, Indels: 48
0.75 0.13 0.11
Matches are distributed among these distances:
27 19 0.06
28 2 0.01
29 20 0.06
30 21 0.07
31 21 0.07
32 43 0.14
33 67 0.21
34 71 0.22
35 34 0.11
36 20 0.06
ACGTcount: A:0.21, C:0.32, G:0.13, T:0.34
Consensus pattern (32 bp):
AAGTCCACAACTCCGTGGCACCTTTTTCTTTT
Found at i:1226670 original size:29 final size:29
Alignment explanation
Indices: 1226505--1226722 Score: 120
Period size: 30 Copynumber: 7.3 Consensus size: 29
1226495 CTTCAAATCT
* * **
1226505 CTCTTTTTTAAGTCCACGACTTAGTGGCA
1 CTCTTTTTAAAGTCCACAACTCCGTGGCA
* * *
1226534 -TCTTGTCTCAAAGTCCACAATTCAGTGGCA
1 CTCTT-T-TTAAAGTCCACAACTCCGTGGCA
* * *
1226564 TCTCTTTCTAAAGTCCACAACTCAGTGACA
1 -CTCTTTTTAAAGTCCACAACTCCGTGGCA
** *
1226594 -TCTTTTCTTCAAAGTCCACGGCTCCATGGCA
1 CTC-TTT-TT-AAAGTCCACAACTCCGTGGCA
* *
1226625 CCTTTTTCTTTTCAAAGTCCACAACTCTGTGGCA
1 -C----TCTTTTTAAAGTCCACAACTCCGTGGCA
* * *
1226659 CTCTTTTTAAAGCCCATAACTCCGTGCCA
1 CTCTTTTTAAAGTCCACAACTCCGTGGCA
* *
1226688 C-CCTTTT-AAGTCCACGACTCCGTGGCA
1 CTCTTTTTAAAGTCCACAACTCCGTGGCA
*
1226715 CCCTTTTT
1 CTCTTTTT
1226723 CCCTTTTAAG
Statistics
Matches: 144, Mismatches: 31, Indels: 29
0.71 0.15 0.14
Matches are distributed among these distances:
27 17 0.12
28 16 0.11
29 28 0.19
30 38 0.26
31 17 0.12
32 4 0.03
33 1 0.01
34 17 0.12
35 1 0.01
36 3 0.02
37 2 0.01
ACGTcount: A:0.22, C:0.31, G:0.14, T:0.33
Consensus pattern (29 bp):
CTCTTTTTAAAGTCCACAACTCCGTGGCA
Found at i:1226694 original size:95 final size:91
Alignment explanation
Indices: 1226541--1226751 Score: 214
Period size: 91 Copynumber: 2.3 Consensus size: 91
1226531 GCATCTTGTC
* * * *
1226541 TCAAAGTCCACAATTCAGTGGCATCTCTTTCTAAAGTCCACAACTCAGTGACATCTTTTCTTCAA
1 TCAAAGTCCACAACTCTGTGGCA-CTCTTTCTAAAGCCCACAACTCAGTGACA-C-CTT-TT--A
*
1226606 AGTCCACGGCTCCATGGCA-CCTTTTT-CTTT
60 AGTCCACGACTCCATGGCACCCTTTTTCCTTT
* * * *
1226636 TCAAAGTCCACAACTCTGTGGCACTCTTTTTAAAGCCCATAACTCCGTGCCACCCTTTTAAGTCC
1 TCAAAGTCCACAACTCTGTGGCACTCTTTCTAAAGCCCACAACTCAGTGACA-CCTTTTAAGTCC
*
1226701 ACGACTCCGTGGCACCCTTTTTCCCTTT
65 ACGACTCCATGGCACCCTTTTT-CCTTT
* *
1226729 T--AAGCCCACACCTCTGTGGCACT
1 TCAAAGTCCACAACTCTGTGGCACT
1226752 TTGTTCCTTT
Statistics
Matches: 100, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
90 18 0.18
91 27 0.27
92 2 0.02
93 7 0.07
94 25 0.25
95 21 0.21
ACGTcount: A:0.22, C:0.33, G:0.13, T:0.31
Consensus pattern (91 bp):
TCAAAGTCCACAACTCTGTGGCACTCTTTCTAAAGCCCACAACTCAGTGACACCTTTTAAGTCCA
CGACTCCATGGCACCCTTTTTCCTTT
Found at i:1226771 original size:33 final size:33
Alignment explanation
Indices: 1226689--1226949 Score: 283
Period size: 33 Copynumber: 7.7 Consensus size: 33
1226679 TCCGTGCCAC
*
1226689 CCTTTTAAGTCCACGACTCCGTGGCACCCTTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCA-CCTTTTT
* * *
1226723 CCCTTTTAAGCCCACACCTCTGTGGCA-CTTTGTT
1 -CCTTTTAAGTCCACAACTCCGTGGCACCTTT-TT
* * *
1226757 CCTTTTAAGTCCACAACTCTGTGGCATCATTTT
1 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTT
** *
1226790 CCTTTTAAAGTCCACAACTTTGTGACACC-TTTT
1 CCTTTT-AAGTCCACAACTCCGTGGCACCTTTTT
**
1226823 CCTTTTAAGTCCATGACTCCGTGGCACCCTTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCA-CCTTTTT
* *
1226857 CCTTTTAAGCCCACACCTCCGTGGCACCCTTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCA-CCTTTTT
* * *
1226891 CCCTTTTAAAGCCCACAACTCCATGGCACCTTGTT
1 -CCTTTT-AAGTCCACAACTCCGTGGCACCTTTTT
1226926 CCTTTTAAGTCCACAACTCCGTGG
1 CCTTTTAAGTCCACAACTCCGTGG
1226950 ATCTTTCTTT
Statistics
Matches: 195, Mismatches: 24, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
32 15 0.08
33 64 0.33
34 64 0.33
35 34 0.17
36 18 0.09
ACGTcount: A:0.18, C:0.34, G:0.13, T:0.35
Consensus pattern (33 bp):
CCTTTTAAGTCCACAACTCCGTGGCACCTTTTT
Found at i:1227004 original size:28 final size:30
Alignment explanation
Indices: 1226964--1227041 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 30
1226954 TTCTTTTTTT
* *
1226964 AAGCCCACAAGTTAGTGGCAA-CC-TTCAA
1 AAGCACACAAGTTGGTGGCAACCCTTTCAA
*
1226992 AAGCACACAAGTTGGT-ACAACCCTTTCAA
1 AAGCACACAAGTTGGTGGCAACCCTTTCAA
1227021 AAGTCCACACAAGTTGGTGGC
1 AAG--CACACAAGTTGGTGGC
1227042 GTCTTCTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
27 3 0.07
28 16 0.39
29 8 0.20
31 13 0.32
32 1 0.02
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (30 bp):
AAGCACACAAGTTGGTGGCAACCCTTTCAA
Found at i:1227253 original size:39 final size:39
Alignment explanation
Indices: 1227194--1227271 Score: 129
Period size: 39 Copynumber: 2.0 Consensus size: 39
1227184 ACCTTGTCTT
*
1227194 TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA
1 TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA
* *
1227233 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCA
1 TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA
1227272 CCTTTGTCAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (39 bp):
TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA
Found at i:1227321 original size:52 final size:49
Alignment explanation
Indices: 1227233--1228615 Score: 1266
Period size: 52 Copynumber: 27.8 Consensus size: 49
1227223 CACATTGGCA
* *
1227233 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA--TTT-TCATCTT
* *
1227285 TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATTTTCATCTT
* * *
1227328 TAAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCATCTTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATTTTCATCTT
** * * *
1227377 TAAGTCCGGTATCGCTGTCCTTGAATCAGCATATTGGCACCTTCGTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA--TT-TTCATCTT
* *
1227429 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATTTTCATCTT
* * *
1227478 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATT-G-GCATT-TTCATCTT
* * ** *
1227530 TAAGCCCAATGTCATTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATTTTCATCTT
* * *
1227579 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATT-G-GCATTT-TCATCTT
* * * * *
1227631 TAA-TACTAATGTTGCTAGCCTTGAATTAGCACATTGGCA----C--CTT
1 TAAGT-CCAATATCGCTGGCCTTGAATCAGCACATTGGCATTTTCATCTT
** ** * * *
1227674 TAAGTCCGGTATCGCTATCCTTGAATCAGCATATTGGCACCTTCGTCATATT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA--TT-TTCATCTT
* *
1227726 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATTTTCATCTT
* *
1227775 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCGTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA--TT-TTCATCTT
* * * *
1227827 TAAGCCCAATGTCGTTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATTTTCATCTT
* * *
1227876 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATT-G-GCATTT-TCATCTT
* * * * *
1227928 TAA-TACTAATGTTGCTAGCCTTGAATTAGCACATTGGCA----C--CTT
1 TAAGT-CCAATATCGCTGGCCTTGAATCAGCACATTGGCATTTTCATCTT
** *
1227971 TAAGTCCAATATCGCTGGCCTTGAATCAGCATGTTGGCATCTTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATTTTCATCTT
** * * *
1228020 TAAGTCCGGTATCGCTAGCCTTGAATCAGCATATTGGCACCTTCATCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA--TT-TTCATCTT
* ** *
1228072 TAAGTCCAATGTCGCTGGTTTTGAATCAGCACATTGGCATCTTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATTTTCATCTT
* * *
1228121 TAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCGTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA--TT-TTCATCTT
* * * *
1228173 TAAGTCTAATGTCGCTGGCCTTGAATCAGCACATTGGAATCTTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATTTTCATCTT
* * *
1228222 TAAGCCCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTT
1 TAAG-TCCAATATCGCTGGCCTTGAATCAGCACATTGGCA--TTT-TCATCTT
* * * *
1228275 TAAGTCCAATGTCGTTGGCCTTGAATCATCACATTGGCATCTTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATTTTCATCTT
* *
1228324 TAAGTCCAATATCTCTGGCCTTGAATCAGCATATTGGCACTTTCGTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA-TTT--TCATCTT
* *
1228376 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATTTTCATCTT
* * * * * *
1228425 TATGTCCAATATCACTAGTCCTTCAATCAGCACATTGGCACCTTT-ATCCT
1 TAAGTCCAATATCGCT-GGCCTTGAATCAGCACATTGGCA-TTTTCATCTT
* ** *
1228475 TAAGTCCAATATCGTTGGCCTTGAATCAGCGTATTGGCATCTTTAACAT-TCC
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCAT-TTT--CATCT-T
* * * * **
1228527 TAAGCCCAATGTCGTTGTCCTTGCCTCAGCACATTGGCATTTT--TCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATTTTCATCTT
* * * * * *
1228574 CAAGTCTAAATGTCGCTGGCCATGAATTAGCACATTGTCATT
1 TAAGTC-CAATATCGCTGGCCTTGAATCAGCACATTGGCATT
1228616 CTTCGCATCT
Statistics
Matches: 1089, Mismatches: 180, Indels: 128
0.78 0.13 0.09
Matches are distributed among these distances:
43 103 0.09
44 2 0.00
45 3 0.00
47 7 0.01
48 28 0.03
49 371 0.34
50 87 0.08
51 25 0.02
52 452 0.42
53 11 0.01
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (49 bp):
TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATTTTCATCTT
Found at i:1227455 original size:101 final size:101
Alignment explanation
Indices: 1227325--1228513 Score: 1311
Period size: 101 Copynumber: 11.9 Consensus size: 101
1227315 ACATTGGCAC
* * **
1227325 CTTTAAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCATCTTCATCTTTAAGTCCGGTATC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATATC
*
1227390 GCTGTCCTTGAATCAGCATATTGGCACCTTCGTCAT
66 GCTGGCCTTGAATCAGCATATTGGCACCTTCGTCAT
*
1227426 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATATC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATATC
*
1227491 GCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCAT
66 GCTGGCCTTGAATCAGCATATTGGCACCTTCGTCAT
* * ** *
1227527 CTTTAAGCCCAATGTCATTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGCCCAATATC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATATC
* *
1227592 GCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCAT
66 GCTGGCCTTGAATCAGCATATTGGCACCTTCGTCAT
* * * * * **
1227628 CTTTAA-TACTAATGTTGCTAGCCTTGAATTAGCACATTGGCA----C--CTTTAAGTCCGGTAT
1 CTTTAAGT-CCAATATCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATAT
**
1227686 CGCTATCCTTGAATCAGCATATTGGCACCTTCGTCAT
65 CGCTGGCCTTGAATCAGCATATTGGCACCTTCGTCAT
* *
1227723 ATTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATATC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATATC
1227788 GCTGGCCTTGAATCAGCATATTGGCACCTTCGTCAT
66 GCTGGCCTTGAATCAGCATATTGGCACCTTCGTCAT
* * * *
1227824 CTTTAAGCCCAATGTCGTTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGCCCAATATC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATATC
* *
1227889 GCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCAT
66 GCTGGCCTTGAATCAGCATATTGGCACCTTCGTCAT
* * * * *
1227925 CTTTAA-TACTAATGTTGCTAGCCTTGAATTAGCACATTGGCA----C--CTTTAAGTCCAATAT
1 CTTTAAGT-CCAATATCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATAT
* *
1227983 CGCTGGCCTTGAATCAGCATGTTGGCA---TCTTCAT
65 CGCTGGCCTTGAATCAGCATATTGGCACCTTCGTCAT
** * * *
1228017 CTTTAAGTCCGGTATCGCTAGCCTTGAATCAGCATATTGGCACCTTCATCATCTTTAAGTCCAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA---TCTTCATCTTTAAGTCCAAT
* ** * *
1228082 GTCGCTGGTTTTGAATCAGCACATTGGCA---TCTTCAT
63 ATCGCTGGCCTTGAATCAGCATATTGGCACCTTCGTCAT
* * * *
1228118 CTTTAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCGTCATCTTTAAGTCTAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA---TCTTCATCTTTAAGTCCAAT
* * * *
1228183 GTCGCTGGCCTTGAATCAGCACATTGG-A--ATCTTCAT
63 ATCGCTGGCCTTGAATCAGCATATTGGCACCTTCGTCAT
* * * *
1228219 CTTTAAGCCCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAA
1 CTTTAAG-TCCAATATCGCTGGCCTTGAATCAGCACATTGGCA--TCT-TCATCTTTAAGTCCAA
* * * * *
1228284 TGTCGTTGGCCTTGAATCATCACATTGGCA---TCTTCAT
62 TATCGCTGGCCTTGAATCAGCATATTGGCACCTTCGTCAT
* * *
1228321 CTTTAAGTCCAATATCTCTGGCCTTGAATCAGCATATTGGCACTTTCGTCATCTTTAAGTCCAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA---TCTTCATCTTTAAGTCCAAT
* * *
1228386 GTCGCTGGCCTTGAATCAGCACATTGGCA---TCTTCAT
63 ATCGCTGGCCTTGAATCAGCATATTGGCACCTTCGTCAT
* * * * * * *
1228422 CTTTATGTCCAATATCACTAGTCCTTCAATCAGCACATTGGCACCTTTATCCTTAAGTCCAATAT
1 CTTTAAGTCCAATATCGCT-GGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATAT
* *
1228487 CGTTGGCCTTGAATCAGCGTATTGGCA
65 CGCTGGCCTTGAATCAGCATATTGGCA
1228514 TCTTTAACAT
Statistics
Matches: 960, Mismatches: 103, Indels: 52
0.86 0.09 0.05
Matches are distributed among these distances:
92 38 0.04
93 1 0.00
95 119 0.12
96 1 0.00
97 2 0.00
99 43 0.04
100 1 0.00
101 646 0.67
102 108 0.11
103 1 0.00
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.34
Consensus pattern (101 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATATC
GCTGGCCTTGAATCAGCATATTGGCACCTTCGTCAT
Found at i:1227767 original size:297 final size:292
Alignment explanation
Indices: 1227100--1228512 Score: 1423
Period size: 297 Copynumber: 4.8 Consensus size: 292
1227090 CCTTTGTCAT
* *
1227100 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCA-C--CA---TTAAGTCCAATATC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCGTCATCTTTAAGTCCAATATC
* * * *
1227159 GCTGGCCTTGAATCAGCATATTGGCAC-CTT-GTCTTTAAGACCAATGTCGCTGGCCTTGAATCA
66 GCTGGCCTTGAATCAGCACATTGGCACTCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCA
** * *
1227222 GCACATT-G----G-CA----TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTT
131 GCACATTGGCATCGTCATCTTTAAGCCCAATATCATTGGCCTTGAATCAGCACATTGGCA--TCT
* * * * *
1227277 GTCATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC-TT-T-A-----AGT-
194 -TCATCTTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAATA
* * * * * * *
1227333 CCAATATCGCTGGCCTTGAATCAACATATTGGCATCTTC
258 CTAATGTTGCTAGCCTTGAATTAGCACATTGGCA----C
** *
1227372 ATCTTTAAGTCCGGTATCGCTGTCCTTGAATCAGCATATTGGCACCTTCGTCATCTTTAAGTCCA
1 --CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA---TCGTCATCTTTAAGTCCA
*
1227437 ATGTCGCTGGCCTTGAATCAGCACATTGGCA-TCTTCATCTTTAAGTCCAATATCGCTGGCCTTG
61 ATATCGCTGGCCTTGAATCAGCACATTGGCACTCTTCATCTTTAAGTCCAATATCGCTGGCCTTG
* * *
1227501 AATCAGCATATTGGCGCCTTCGTCATCTTTAAGCCCAATGTCATTGGCCTTGAATCAGCACATTG
126 AATCAGCACATT-G-G-CATCGTCATCTTTAAGCCCAATATCATTGGCCTTGAATCAGCACATTG
1227566 GCATCTTCATCTTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTT
188 GCATCTTCATCTTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTT
1227631 TAATACTAATGTTGCTAGCCTTGAATTAGCACATTGGCAC
253 TAATACTAATGTTGCTAGCCTTGAATTAGCACATTGGCAC
** ** *
1227671 CTTTAAGTCCGGTATCGCTATCCTTGAATCAGCATATTGGCACCTTCGTCATATTTAAGTCCAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA---TCGTCATCTTTAAGTCCAAT
*
1227736 GTCGCTGGCCTTGAATCAGCACATTGGCA-TCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAA
63 ATCGCTGGCCTTGAATCAGCACATTGGCACTCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAA
* * *
1227800 TCAGCATATTGGCACCTTCGTCATCTTTAAGCCCAATGTCGTTGGCCTTGAATCAGCACATTGGC
128 TCAGCACATTGGCA---TCGTCATCTTTAAGCCCAATATCATTGGCCTTGAATCAGCACATTGGC
1227865 ATCTTCATCTTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTA
190 ATCTTCATCTTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTA
1227930 ATACTAATGTTGCTAGCCTTGAATTAGCACATTGGCAC
255 ATACTAATGTTGCTAGCCTTGAATTAGCACATTGGCAC
* * **
1227968 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATGTTGGCATCTTCATCTTTAAGTCCGGTATC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCGTCATCTTTAAGTCCAATATC
* * * * **
1228033 GCTAGCCTTGAATCAGCATATTGGCACCTTCATCATCTTTAAGTCCAATGTCGCTGGTTTTGAAT
66 GCTGGCCTTGAATCAGCACATTGGCA-C-TCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAAT
* * * ** *
1228098 CAGCACATTGGCATCTTCATCTTTAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCT
129 CAGCACATTGGCATCGTCATCTTTAAGCCCAATATCATTGGCCTTGAATCAGCACATTGGCA---
* * * * * ** *
1228163 TCGTCATCTTTAAGTCTAATGTCGCTGGCCTTGAATCAGCACATT-G-GAATCT-TCATCTTTAA
191 TCTTCATCTTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAA
** * * * * * * *
1228225 GCCCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTTGTC
256 -TACTAATGTTGCTAGCCTTGAATTAGCACATTGGCA-------C
* * * * *
1228270 ATCTTTAAGTCCAATGTCGTTGGCCTTGAATCATCACATTGGCATCTTCATCTTTAAGTCCAATA
1 --CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCGTCATCTTTAAGTCCAATA
* * * *
1228335 TCTCTGGCCTTGAATCAGCATATTGGCACTTTCGTCATCTTTAAGTCCAATGTCGCTGGCCTTGA
64 TCGCTGGCCTTGAATCAGCACATTGGCAC--TCTTCATCTTTAAGTCCAATATCGCTGGCCTTGA
* * * * * *
1228400 ATCAGCACATTGGCATCTTCATCTTTATGTCCAATATCACTAGTCCTTCAATCAGCACATTGGCA
127 ATCAGCACATTGGCATCGTCATCTTTAAGCCCAATATCA-TTGGCCTTGAATCAGCACATTGGCA
* * * * * *
1228465 CCTTTATCCTTAAGTCCAATATCGTTGGCCTTGAATCAGCGTATTGGC
191 TCTTCATCTTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGC
1228513 ATCTTTAACA
Statistics
Matches: 982, Mismatches: 101, Indels: 82
0.84 0.09 0.07
Matches are distributed among these distances:
274 37 0.04
278 1 0.00
280 2 0.00
283 41 0.04
284 36 0.04
287 1 0.00
292 1 0.00
293 2 0.00
294 140 0.14
295 35 0.04
296 3 0.00
297 444 0.45
299 1 0.00
302 39 0.04
303 29 0.03
304 150 0.15
305 20 0.02
ACGTcount: A:0.23, C:0.26, G:0.18, T:0.33
Consensus pattern (292 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCGTCATCTTTAAGTCCAATATC
GCTGGCCTTGAATCAGCACATTGGCACTCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCA
GCACATTGGCATCGTCATCTTTAAGCCCAATATCATTGGCCTTGAATCAGCACATTGGCATCTTC
ATCTTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAATACTA
ATGTTGCTAGCCTTGAATTAGCACATTGGCAC
Found at i:1229134 original size:15 final size:15
Alignment explanation
Indices: 1229114--1229142 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1229104 CAATTTTTGA
1229114 CAACTTGAGGTCTAG
1 CAACTTGAGGTCTAG
1229129 CAACTTGAGGTCTA
1 CAACTTGAGGTCTA
1229143 AAAAAATGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.28
Consensus pattern (15 bp):
CAACTTGAGGTCTAG
Found at i:1229370 original size:32 final size:32
Alignment explanation
Indices: 1229334--1229419 Score: 154
Period size: 32 Copynumber: 2.7 Consensus size: 32
1229324 ATTTAAACAA
*
1229334 TTTGTATCGATACAATTTATCGATACATAAGT
1 TTTGTATCGATACAATATATCGATACATAAGT
*
1229366 TTTGTATCGATACAATGTATCGATACATAAGT
1 TTTGTATCGATACAATATATCGATACATAAGT
1229398 TTTGTATCGATACAATATATCG
1 TTTGTATCGATACAATATATCG
1229420 CTACGAAGCT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.40
Consensus pattern (32 bp):
TTTGTATCGATACAATATATCGATACATAAGT
Found at i:1229375 original size:19 final size:19
Alignment explanation
Indices: 1229351--1229411 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
1229341 CGATACAATT
1229351 TATCGATACATAAGTTTTG
1 TATCGATACATAAGTTTTG
1229370 TATCGATAC--AA----TG
1 TATCGATACATAAGTTTTG
1229383 TATCGATACATAAGTTTTG
1 TATCGATACATAAGTTTTG
1229402 TATCGATACA
1 TATCGATACA
1229412 ATATATCGCT
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
13 11 0.31
15 2 0.06
17 2 0.06
19 21 0.58
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (19 bp):
TATCGATACATAAGTTTTG
Found at i:1229481 original size:13 final size:13
Alignment explanation
Indices: 1229463--1229489 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1229453 CATTACTCAA
1229463 TGTATCGATACAT
1 TGTATCGATACAT
1229476 TGTATCGATACAT
1 TGTATCGATACAT
1229489 T
1 T
1229490 TGATCTTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1236826 original size:21 final size:21
Alignment explanation
Indices: 1236800--1236918 Score: 186
Period size: 21 Copynumber: 5.7 Consensus size: 21
1236790 AAAAAATGCA
1236800 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
1236821 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
1236842 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
1236863 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
* *
1236884 AATGTATCGATACA-TTCTACA
1 AATGTATCGATACATTTGTA-G
1236905 AATGTATCGATACA
1 AATGTATCGATACA
1236919 GGGTCCCAAC
Statistics
Matches: 91, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
20 3 0.03
21 88 0.97
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:1236978 original size:19 final size:19
Alignment explanation
Indices: 1236954--1237021 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
1236944 AATTCAACAA
1236954 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
1236973 TTTGTATCGAT--ATAA--
1 TTTGTATCGATACATAAGT
1236988 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
1237005 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
1237022 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 9 0.21
15 4 0.09
17 4 0.09
19 26 0.60
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:1236992 original size:32 final size:32
Alignment explanation
Indices: 1236956--1237016 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
1236946 TTCAACAATT
*
1236956 TGTATCGATACATAAGTTTTGTATCGATATAA
1 TGTATCGATACATAAGTATTGTATCGATATAA
1236988 TGTATCGATACATAAGTATTGTATCGATA
1 TGTATCGATACATAAGTATTGTATCGATA
1237017 CATAATTAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.39
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATATAA
Found at i:1237079 original size:13 final size:13
Alignment explanation
Indices: 1237061--1237086 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1237051 CATTTTTCTG
1237061 TGTATCGATACAT
1 TGTATCGATACAT
1237074 TGTATCGATACAT
1 TGTATCGATACAT
1237087 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1237083 original size:33 final size:33
Alignment explanation
Indices: 1237041--1237107 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1237031 GCCAAGGAAA
***
1237041 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
1237074 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
1237107 T
1 T
1237108 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:1239633 original size:28 final size:28
Alignment explanation
Indices: 1239564--1239636 Score: 89
Period size: 27 Copynumber: 2.6 Consensus size: 28
1239554 CTTCACAATC
*
1239564 GGGGACACTCCAACCCCGTTAATCATCGA
1 GGGGATACTCCAACCCCGTTAATCA-CGA
*
1239593 --GGATACTCCAACCCCGTTATTTC-CGA
1 GGGGATACTCCAACCCCGTTA-ATCACGA
1239619 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
1239637 ACTTTATTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
26 3 0.08
27 18 0.46
28 18 0.46
ACGTcount: A:0.25, C:0.36, G:0.21, T:0.19
Consensus pattern (28 bp):
GGGGATACTCCAACCCCGTTAATCACGA
Found at i:1239735 original size:52 final size:51
Alignment explanation
Indices: 1239455--1239788 Score: 221
Period size: 51 Copynumber: 6.4 Consensus size: 51
1239445 AATTCTCCAC
* * * * * **
1239455 AATCGGAGATATTCCAACTCCGATTTTATTTTCAAAACATTAA-TTTTCTAT
1 AATCGGGGATACTCCAACCCCGATTTTATTTCCAAAATACCAATTTTTC-AT
* * *
1239506 AATCGGGGATACTCCAACTCTGATTTTATTTCCAAAAAATACCAATTTCTTCAC
1 AATCGGGGATACTCCAACCCCGATTTTATTTCC--AAAATACCAATTT-TTCAT
* * * * ** *
1239560 AATCGGGGACACTCCAACCCCG--TTAATCATCGAGGATACTCCAACCCCGTTATTTC-C
1 AATCGGGGATACTCCAACCCCGATTTTAT-TTCCAAAATA--CCAA-----TT-TTTCAT
* * ***
1239617 GA--GGGGATACTCCAACCCCGACTTTATTTCCAAAATATTGATTTTTCAT
1 AATCGGGGATACTCCAACCCCGATTTTATTTCCAAAATACCAATTTTTCAT
* * * * *
1239666 AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTT
1 AATCGGGGATACTCCAACCCCGATTTTATTTCCAAAATACCAATTTTTC-AT
* *
1239718 AATCGGGGATACTCCAACACCGATTTTATTTCCAAAAATACCAATTTTTCAC
1 AATCGGGGATACTCCAACCCCGATTTTATTTCC-AAAATACCAATTTTTCAT
*
1239770 AATCGAGGATACTCCAACC
1 AATCGGGGATACTCCAACC
1239789 TCGTTCTTTC
Statistics
Matches: 217, Mismatches: 46, Indels: 39
0.72 0.15 0.13
Matches are distributed among these distances:
48 4 0.02
49 3 0.01
51 70 0.32
52 52 0.24
53 27 0.12
54 23 0.11
55 20 0.09
56 6 0.03
57 6 0.03
58 5 0.02
59 1 0.00
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.32
Consensus pattern (51 bp):
AATCGGGGATACTCCAACCCCGATTTTATTTCCAAAATACCAATTTTTCAT
Found at i:1239842 original size:211 final size:211
Alignment explanation
Indices: 1239455--1239847 Score: 592
Period size: 211 Copynumber: 1.9 Consensus size: 211
1239445 AATTCTCCAC
* * **
1239455 AATCGGAGATATTCCAACTCCGATTTTATTTTCAAAACATTAATTTTCTATAATCGGGGATACTC
1 AATCGGAGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACTC
* * *
1239520 CAACTCTGATTTTATTTCCAAAAAATACCAATTTCTTCACAATCGGGGACACTCCAACCCCGTTA
66 CAACACCGATTTTATTTCCAAAAAATACCAATTTCTTCACAATCGAGGACACTCCAACCCCGTTA
* * *
1239585 ATCATCGAGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATTTCCAA
131 ATCATCGAGGATACTCCAACCCCGTTACTTCCGAGGGAACACTCCAACCCCGACTTTATTTCCAA
1239650 AATATTGATTTTTCAT
196 AATATTGATTTTTCAT
* * *
1239666 AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGATACT
1 AATCGGAGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTT-CTATAATCGGGGATACT
* *
1239731 CCAACACCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATACTCCAACCTCGTT
65 CCAACACCGATTTTATTTCCAAAAAATACCAATTTCTTCACAATCGAGGACACTCCAACCCCGTT
** *
1239794 CTTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGAACACTCCAACCCCG
130 -AATCATCGAGGATACTCCAACCCCGTTACTTCCGAGGGAACACTCCAACCCCG
1239848 TTATTATCTC
Statistics
Matches: 162, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
210 26 0.16
211 102 0.63
212 34 0.21
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (211 bp):
AATCGGAGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACTC
CAACACCGATTTTATTTCCAAAAAATACCAATTTCTTCACAATCGAGGACACTCCAACCCCGTTA
ATCATCGAGGATACTCCAACCCCGTTACTTCCGAGGGAACACTCCAACCCCGACTTTATTTCCAA
AATATTGATTTTTCAT
Found at i:1243183 original size:165 final size:165
Alignment explanation
Indices: 1242738--1243183 Score: 671
Period size: 166 Copynumber: 2.7 Consensus size: 165
1242728 TCCTTTCTTG
* * * * * *
1242738 AAAATATCATTTCGTACCTTAATGGAAACTCAAAAAGATATGAAAAGTTTTTTAATTCTTTTATA
1 AAAATACCATTTCGTACCTTAATAGAAGCTCGAAAAGATATGAAAAGTTTTTAAAATCTTTTATA
* *
1242803 CCCCTACGGATGCCTATAGGAATATAAAAGATTAGAAAAAATGATTAAAATTTATCTCGATTACG
66 CCCCTATGGATGCCCATAGGAATATAAAAGATTAGAAAAAATGATTAAAATTTATCTCGATTACG
* *
1242868 AAAGTGTTAATTTAATTTTATTTTATTTATTTTCA
131 AAACTGTTAATTTAATTTAATTTTATTTATTTTCA
* * **
1242903 AAAATACCATGTCGTACCTTAATAGAAAGCTCGAAAAGATACGAAATTTTTTTAAAATCTTTTAT
1 AAAATACCATTTCGTACCTTAATAG-AAGCTCGAAAAGATATGAAAAGTTTTTAAAATCTTTTAT
*
1242968 ACCCCTACT-GATGCCCATAGGAATATAAAAGATTAGAAAAAAAT-ATTAAAATTTATCTCGTTT
65 ACCCCTA-TGGATGCCCATAGGAATATAAAAGATTAG-AAAAAATGATTAAAATTTATCTCGATT
*
1243031 ATGAAACTGTTAATTTAATTTAATTTTATTTATTTTCA
128 ACGAAACTGTTAATTTAATTTAATTTTATTTATTTTCA
* * *
1243069 AAAATACCATTTCGCACCTGAATAGAAGCTCGAAAATATATGAAAAGTTTTTAAAATCTTTTATA
1 AAAATACCATTTCGTACCTTAATAGAAGCTCGAAAAGATATGAAAAGTTTTTAAAATCTTTTATA
*
1243134 CCCCTATGGATGCCCATAAGAATATAAAAGATTAGAAAAAATGATTAAAA
66 CCCCTATGGATGCCCATAGGAATATAAAAGATTAGAAAAAATGATTAAAA
1243184 GTTAATTTTT
Statistics
Matches: 252, Mismatches: 24, Indels: 10
0.88 0.08 0.03
Matches are distributed among these distances:
164 8 0.03
165 97 0.38
166 140 0.56
167 7 0.03
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.35
Consensus pattern (165 bp):
AAAATACCATTTCGTACCTTAATAGAAGCTCGAAAAGATATGAAAAGTTTTTAAAATCTTTTATA
CCCCTATGGATGCCCATAGGAATATAAAAGATTAGAAAAAATGATTAAAATTTATCTCGATTACG
AAACTGTTAATTTAATTTAATTTTATTTATTTTCA
Found at i:1243949 original size:22 final size:20
Alignment explanation
Indices: 1243896--1243956 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
1243886 AAATAACATG
*
1243896 AAAAACACATACTTTCACAC
1 AAAAACACATACTTCCACAC
* *
1243916 ATAAAC-TA-ACTTCCAAGCAC
1 AAAAACACATACTTCC-A-CAC
*
1243936 AAAAACACATACTTTCACAC
1 AAAAACACATACTTCCACAC
1243956 A
1 A
1243957 TATATCATCA
Statistics
Matches: 31, Mismatches: 6, Indels: 8
0.69 0.13 0.18
Matches are distributed among these distances:
18 5 0.16
19 2 0.06
20 17 0.55
21 2 0.06
22 5 0.16
ACGTcount: A:0.49, C:0.30, G:0.02, T:0.20
Consensus pattern (20 bp):
AAAAACACATACTTCCACAC
Found at i:1244144 original size:24 final size:22
Alignment explanation
Indices: 1244103--1244153 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 22
1244093 TTTTCCTAGT
*
1244103 TTTTTTTTTCTCTGTTTCTTTC
1 TTTTTTTTTCTCTGTTTCTCTC
*
1244125 TTTTTTTTTCTCAATTTTTCTCTC
1 TTTTTTTTTCTC--TGTTTCTCTC
1244149 TTTTT
1 TTTTT
1244154 CTAGTTGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 12 0.48
24 13 0.52
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.76
Consensus pattern (22 bp):
TTTTTTTTTCTCTGTTTCTCTC
Found at i:1244152 original size:22 final size:22
Alignment explanation
Indices: 1244105--1244153 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
1244095 TTCCTAGTTT
** *
1244105 TTTTTTTCTCTGTTTCTTTCTT
1 TTTTTTTCTCAATTTCTTTCTC
1244127 TTTTTTTCTCAATTT-TTCTCTC
1 TTTTTTTCTCAATTTCTT-TCTC
1244149 TTTTT
1 TTTTT
1244154 CTAGTTGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.76
Consensus pattern (22 bp):
TTTTTTTCTCAATTTCTTTCTC
Found at i:1244947 original size:167 final size:164
Alignment explanation
Indices: 1244658--1245140 Score: 474
Period size: 167 Copynumber: 2.9 Consensus size: 164
1244648 AAAAGTTCAC
* * * * * * * * * *
1244658 AACTCAT-AAAATAAATTAAATTTCTCAAAACTAATTTACTAAGAGTTCAATGACAATATTAGAT
1 AACTCATAAAAATAAA-TAAATTT-TTAAAAATAATTTAATATGAATTAAATAATAACATTTGAT
* ** * * * * *
1244722 GAATTTAAAAAATTTTAGACCAAAGAAAATCCTCCCGAGAATATTTATGGAATAGAAAATTCGAT
64 GAATTTTAAAAATTAAAAACCAAA-AAAATCCCCCCGA-AAAATTTATGGAGTAGAAAATTCCAT
* *
1244787 TTTTCGAGAAAAAAAGGGAATTTCAA-GAAAAAA-TAAAA
127 ATTTC-A-AAAAAAAGAGAATTTCAAGGAAAAAATTAAAA
* * *
1244825 AACTCTTAAAAATGAATGAAATTTTGT-AAAATTATTTAATATGAATTAAATAATAACATTTGAT
1 AACTCATAAAAATAAAT-AAATTTT-TAAAAATAATTTAATATGAATTAAATAATAACATTTGAT
* * *
1244889 GAATTTTAAAAGTTAAAAACCAAGAAAAATCCCCCTCGAAAAATTTAAGGAGTAGAAAACTCCAT
64 GAATTTTAAAAATTAAAAACCAA-AAAAATCCCCC-CGAAAAATTTATGGAGTAGAAAATTCCAT
* *
1244954 ATTTCAAAAACAAGAGAATTTCAAGGAAAAAATTTAAA
127 ATTTCAAAAAAAAGAGAATTTCAAGGAAAAAATTAAAA
* * *
1244992 AACTCATGAAAATAAATAAATTTTTAAAAAATAATTTAATTTGAATTAAATAATAATATTTGATG
1 AACTCATAAAAATAAATAAATTTTT-AAAAATAATTTAATATGAATTAAATAATAACATTTGATG
** *
1245057 AATTTTAAAAATTAAAAACCAAAAAAATCCTCCCAAAAAAATTTATGGAGAAGAAAA-TCCTATA
65 AATTTTAAAAATTAAAAACCAAAAAAATCC-CCCCGAAAAATTTATGGAGTAGAAAATTCC-AT-
*
1245121 ATTT-AAAAACAAGAGGAATT
127 ATTTCAAAAAAAAGA-GAATT
1245141 CTAAAAGAAA
Statistics
Matches: 264, Mismatches: 39, Indels: 26
0.80 0.12 0.08
Matches are distributed among these distances:
165 20 0.08
166 54 0.20
167 173 0.66
168 17 0.06
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.29
Consensus pattern (164 bp):
AACTCATAAAAATAAATAAATTTTTAAAAATAATTTAATATGAATTAAATAATAACATTTGATGA
ATTTTAAAAATTAAAAACCAAAAAAATCCCCCCGAAAAATTTATGGAGTAGAAAATTCCATATTT
CAAAAAAAAGAGAATTTCAAGGAAAAAATTAAAA
Found at i:1247272 original size:52 final size:52
Alignment explanation
Indices: 1247187--1247294 Score: 128
Period size: 52 Copynumber: 2.1 Consensus size: 52
1247177 ATGCATTTGA
* * *
1247187 AATTCTAGCCATTGGACTCAATGTATCAGTACAATTCATAATGTATCGATAT
1 AATTATAGCCATTGGACTCAATGTATCAGTACAATTCACAATGTATCGATAC
* * * * *
1247239 AATTATAGCCGTTGGGCTTAATGTATC-GATACAATTTACCATGTATCGATAC
1 AATTATAGCCATTGGACTCAATGTATCAG-TACAATTCACAATGTATCGATAC
1247291 AATT
1 AATT
1247295 CACTTAGGGT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
51 1 0.02
52 46 0.98
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (52 bp):
AATTATAGCCATTGGACTCAATGTATCAGTACAATTCACAATGTATCGATAC
Found at i:1249758 original size:33 final size:32
Alignment explanation
Indices: 1249721--1249794 Score: 78
Period size: 33 Copynumber: 2.2 Consensus size: 32
1249711 TTTTTGGGTG
* *
1249721 GTTTTGAAAGTATG-ATTTGATGAAAAAGAAAGT
1 GTTTTGAAA--ATGAATTTGATGAAAAACAAAGA
*
1249754 GTTTTTGATAATGAATTTGATGAAAAACAAAGA
1 G-TTTTGAAAATGAATTTGATGAAAAACAAAGA
*
1249787 GATTTGAA
1 GTTTTGAA
1249795 GCAAAAAAGA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
32 8 0.24
33 19 0.56
34 7 0.21
ACGTcount: A:0.43, C:0.01, G:0.22, T:0.34
Consensus pattern (32 bp):
GTTTTGAAAATGAATTTGATGAAAAACAAAGA
Found at i:1249760 original size:34 final size:33
Alignment explanation
Indices: 1249722--1249785 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
1249712 TTTTGGGTGG
*
1249722 TTTTGAAAGTATG-ATTTGATGAAAAAGAAAGTGT
1 TTTTGAAA--ATGAATTTGATGAAAAACAAAGTGT
*
1249756 TTTTGATAATGAATTTGATGAAAAACAAAG
1 TTTTGAAAATGAATTTGATGAAAAACAAAG
1249786 AGATTTGAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 3 0.11
33 17 0.63
34 7 0.26
ACGTcount: A:0.44, C:0.02, G:0.20, T:0.34
Consensus pattern (33 bp):
TTTTGAAAATGAATTTGATGAAAAACAAAGTGT
Found at i:1249963 original size:13 final size:13
Alignment explanation
Indices: 1249945--1249969 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1249935 ATAATTTTAA
1249945 TGTATTGATACAT
1 TGTATTGATACAT
1249958 TGTATTGATACA
1 TGTATTGATACA
1249970 AAGAACTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (13 bp):
TGTATTGATACAT
Found at i:1252170 original size:169 final size:169
Alignment explanation
Indices: 1251882--1252221 Score: 626
Period size: 169 Copynumber: 2.0 Consensus size: 169
1251872 ATGGCCTCGT
*
1251882 CTATATTTTTTGGTTCAATTTGAGAGAGAAATGCAACGTAATCACAAGTATTTCTTAGAGATGAT
1 CTATAATTTTTGGTTCAATTTGAGAGAGAAATGCAACGTAATCACAAGTATTTCTTAGAGATGAT
* * *
1251947 CTAGTTCTTACCCTATGACTTGGATTACTAATTATCTTACCTTCCTTGACATAAGTTAACTCTCT
66 CTAGTTCTTACCCTATGACTTGGATTACCAATTATCTTACCTTCCTTAACATAAGTCAACTCTCT
*
1252012 AAAATGTTTTCTTTTGGTTTGAGTTGGCTCATGTTCTTC
131 AAAATGTTTTCTTTTGGTTTGAGTTGGCTAATGTTCTTC
1252051 CTATAATTTTTGGTTCAATTTGAGAGAGAAATGCAACGTAATCACAAGTATTTCTTAGAGATGAT
1 CTATAATTTTTGGTTCAATTTGAGAGAGAAATGCAACGTAATCACAAGTATTTCTTAGAGATGAT
1252116 CTAGTTCTTACCCTATGACTTGGATTACCAATTATCTTACCTTCCTTAACATAAGTCAACTCTCT
66 CTAGTTCTTACCCTATGACTTGGATTACCAATTATCTTACCTTCCTTAACATAAGTCAACTCTCT
*
1252181 AGAATGTTTTCTTTTGGTTTGAGTTGGCTAATGTTCTTC
131 AAAATGTTTTCTTTTGGTTTGAGTTGGCTAATGTTCTTC
1252220 CT
1 CT
1252222 CTTTTTTAGG
Statistics
Matches: 165, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
169 165 1.00
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.41
Consensus pattern (169 bp):
CTATAATTTTTGGTTCAATTTGAGAGAGAAATGCAACGTAATCACAAGTATTTCTTAGAGATGAT
CTAGTTCTTACCCTATGACTTGGATTACCAATTATCTTACCTTCCTTAACATAAGTCAACTCTCT
AAAATGTTTTCTTTTGGTTTGAGTTGGCTAATGTTCTTC
Found at i:1255355 original size:13 final size:13
Alignment explanation
Indices: 1255337--1255362 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1255327 ACAAAGATTG
1255337 ATGTATCGATACA
1 ATGTATCGATACA
1255350 ATGTATCGATACA
1 ATGTATCGATACA
1255363 TTGAGTAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1255422 original size:13 final size:13
Alignment explanation
Indices: 1255400--1255489 Score: 54
Period size: 13 Copynumber: 6.0 Consensus size: 13
1255390 GGCAGTAGCT
*
1255400 TTGTAGCGATACA
1 TTGTATCGATACA
1255413 TTGTATCGATACAAAA
1 TTGTATCGATAC---A
1255429 CTTATGTATCGATACA
1 --T-TGTATCGATACA
*
1255445 TTGTATCTATACAACA
1 TTGTATCGAT---ACA
1255461 CTTATGTATCGATACA
1 --T-TGTATCGATACA
1255477 TTGTATCGATACA
1 TTGTATCGATACA
1255490 ACACTTACGT
Statistics
Matches: 62, Mismatches: 3, Indels: 24
0.70 0.03 0.27
Matches are distributed among these distances:
13 31 0.50
14 2 0.03
16 8 0.13
18 2 0.03
19 19 0.31
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1255438 original size:19 final size:18
Alignment explanation
Indices: 1255414--1255507 Score: 73
Period size: 19 Copynumber: 5.6 Consensus size: 18
1255404 AGCGATACAT
1255414 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
1255433 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
*
1255446 TGTATCTATACAACACTTA
1 TGTATCGATACAA-ACTTA
1255465 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
1255478 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
*
1255497 CGTATCGATAC
1 TGTATCGATAC
1255508 CGTTACTGTT
Statistics
Matches: 60, Mismatches: 3, Indels: 24
0.69 0.03 0.28
Matches are distributed among these distances:
13 21 0.35
14 2 0.03
16 4 0.07
18 2 0.03
19 31 0.52
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.34
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:1255447 original size:32 final size:32
Alignment explanation
Indices: 1255401--1255507 Score: 178
Period size: 32 Copynumber: 3.3 Consensus size: 32
1255391 GCAGTAGCTT
* *
1255401 TGTAGCGATACATTGTATCGATACAAAACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
*
1255433 TGTATCGATACATTGTATCTATACAACACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
1255465 TGTATCGATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
*
1255497 CGTATCGATAC
1 TGTATCGATAC
1255508 CGTTACTGTT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 70 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.34
Consensus pattern (32 bp):
TGTATCGATACATTGTATCGATACAACACTTA
Done.