Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold82
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: 2626005
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.31
Warning! 196346 characters in sequence are not A, C, G, or T
File 9 of 17
Found at i:1111178 original size:2 final size:2
Alignment explanation
Indices: 1111171--1111237 Score: 54
Period size: 2 Copynumber: 35.0 Consensus size: 2
1111161 TCATTTTGTT
* * *
1111171 TA TA TA TA TA TA TA TA TA T- TT TA T- TA TGA TA TG TA TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA
1111212 -A T- TA TA -A TCA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA T-A TA TA TA TA TA TA TA TA
1111238 ATAATATGTA
Statistics
Matches: 53, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
1 5 0.09
2 44 0.83
3 4 0.08
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1111207 original size:19 final size:19
Alignment explanation
Indices: 1111180--1111228 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
1111170 TTATATATAT
*
1111180 ATATATATATTTTATTATG
1 ATATATATATTTAATTATG
* *
1111199 ATATGTATATTTAATTATA
1 ATATATATATTTAATTATG
1111218 ATCATATATAT
1 AT-ATATATAT
1111229 ATATATATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (19 bp):
ATATATATATTTAATTATG
Found at i:1112339 original size:22 final size:21
Alignment explanation
Indices: 1112303--1112343 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1112293 ATTAACAAAA
*
1112303 ATATTTAATAAAATATATTAC
1 ATATTAAATAAAATATATTAC
1112324 ATATTAAATTAAAATATATT
1 ATATTAAA-TAAAATATATT
1112344 TAAAAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
ATATTAAATAAAATATATTAC
Found at i:1113969 original size:32 final size:32
Alignment explanation
Indices: 1113919--1113987 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 32
1113909 TTTTTAATTA
*
1113919 TTATCAAATTTAAGAGTAATTATATCTAATAT
1 TTATCAAACTTAAGAGTAATTATATCTAATAT
* *
1113951 TTATCAAACTTATA-AGTAATTTTATCTGATAT
1 TTATCAAACTTA-AGAGTAATTATATCTAATAT
1113983 TTATC
1 TTATC
1113988 CAAGCCCATT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 32 0.97
33 1 0.03
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.46
Consensus pattern (32 bp):
TTATCAAACTTAAGAGTAATTATATCTAATAT
Found at i:1114494 original size:19 final size:20
Alignment explanation
Indices: 1114472--1114509 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1114462 TTACACAAAA
1114472 TTACTT-TATAAAAACAAGC
1 TTACTTATATAAAAACAAGC
*
1114491 TTACTTATATAAATACAAG
1 TTACTTATATAAAAACAAG
1114510 TATAACAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.47, C:0.13, G:0.05, T:0.34
Consensus pattern (20 bp):
TTACTTATATAAAAACAAGC
Found at i:1114544 original size:21 final size:21
Alignment explanation
Indices: 1114520--1114569 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
1114510 TATAACAATT
1114520 TGTACATATAATA-TAAATATA
1 TGTACATATAA-ACTAAATATA
*
1114541 TGTACAT-TAAACTTAACTATA
1 TGTACATATAAAC-TAAATATA
1114562 TGTACATA
1 TGTACATA
1114570 ATTTTTTCCT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 1 0.04
20 3 0.12
21 21 0.84
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.38
Consensus pattern (21 bp):
TGTACATATAAACTAAATATA
Found at i:1116290 original size:20 final size:20
Alignment explanation
Indices: 1116215--1116342 Score: 105
Period size: 20 Copynumber: 5.8 Consensus size: 20
1116205 TTTTACCTAG
* *
1116215 ATGTATTGATACATTTTTCA
1 ATGTATCGATACATTCTTCA
* *
1116235 ATGTATCGATACATGT-ATGA
1 ATGTATCGATACAT-TCTTCA
1116255 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
1116275 ATGTATCGATACATTCTGTTTTTTTACTTA
1 ATGTATCGATACATTC-------TT-C--A
1116305 GATGTATCGATACATTCTTCA
1 -ATGTATCGATACATTCTTCA
1116326 ATGTATCGATACATTCT
1 ATGTATCGATACATTCT
1116343 ATCTTTTTTC
Statistics
Matches: 90, Mismatches: 5, Indels: 26
0.74 0.04 0.21
Matches are distributed among these distances:
19 1 0.01
20 64 0.71
21 2 0.02
23 1 0.01
24 2 0.02
27 2 0.02
28 1 0.01
30 1 0.01
31 16 0.18
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:1116331 original size:51 final size:51
Alignment explanation
Indices: 1116255--1116390 Score: 220
Period size: 51 Copynumber: 2.7 Consensus size: 51
1116245 ACATGTATGA
* **
1116255 ATGTATCGATACATTCTTCAATGTATCGATACATTCTGT-TTTTTTACTTAG
1 ATGTATCGATACATTCTTCAATGTATCGATACATTCTATCTTTTTT-CCCAG
1116306 ATGTATCGATACATTCTTCAATGTATCGATACATTCTATCTTTTTTCCCAG
1 ATGTATCGATACATTCTTCAATGTATCGATACATTCTATCTTTTTTCCCAG
*
1116357 ATGTATCGATACATTTTTCAATGTATCGATACAT
1 ATGTATCGATACATTCTTCAATGTATCGATACAT
1116391 CTAGTTAAAA
Statistics
Matches: 80, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
51 74 0.93
52 6 0.08
ACGTcount: A:0.27, C:0.18, G:0.11, T:0.44
Consensus pattern (51 bp):
ATGTATCGATACATTCTTCAATGTATCGATACATTCTATCTTTTTTCCCAG
Found at i:1118698 original size:97 final size:97
Alignment explanation
Indices: 1118542--1118771 Score: 327
Period size: 97 Copynumber: 2.4 Consensus size: 97
1118532 TTTATTTATC
* *
1118542 GGGGATACTTCAACCCTATTCCTCCGAGGGGATACTCCAACCCTGCTTTTAAACACATCAAAGTT
1 GGGGACACTTCAACCCTATTCCTCCGAGGGGATACTCCAACCCCGCTTTTAAACACATCAAAGTT
1118607 TAAATCTTATTCTCACTTAAATTATCATCATA
66 TAAATCTTATTCTCACTTAAATTATCATCATA
* * **
1118639 GGGGACACTTTAACCCCATTCCTCCGAGGGGATAC-CCTAACCCCGCTTTTAAATGCATCAAAGT
1 GGGGACACTTCAACCCTATTCCTCCGAGGGGATACTCC-AACCCCGCTTTTAAACACATCAAAGT
* * *
1118703 TTAAATTTTATTCTCACTTAAATTGTCATCATC
65 TTAAATCTTATTCTCACTTAAATTATCATCATA
* * * *
1118736 GGGAACACTCCAACCCTATTCTTCTGAGGGGATACT
1 GGGGACACTTCAACCCTATTCCTCCGAGGGGATACT
1118772 TGAGTGCAAT
Statistics
Matches: 116, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
96 2 0.02
97 114 0.98
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.31
Consensus pattern (97 bp):
GGGGACACTTCAACCCTATTCCTCCGAGGGGATACTCCAACCCCGCTTTTAAACACATCAAAGTT
TAAATCTTATTCTCACTTAAATTATCATCATA
Found at i:1128096 original size:15 final size:17
Alignment explanation
Indices: 1128071--1128102 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1128061 TATCTATCAA
1128071 ACCTGCCAGTG-TTGGT
1 ACCTGCCAGTGCTTGGT
1128087 ACCT-CCAGTGCTTGGT
1 ACCTGCCAGTGCTTGGT
1128103 CGTCCTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.12, C:0.28, G:0.28, T:0.31
Consensus pattern (17 bp):
ACCTGCCAGTGCTTGGT
Found at i:1130350 original size:10 final size:10
Alignment explanation
Indices: 1130335--1130369 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
1130325 TCTTCGTACC
1130335 AAAAAAAACA
1 AAAAAAAACA
1130345 AAAAAAAACA
1 AAAAAAAACA
*
1130355 AAAACAAACA
1 AAAAAAAACA
1130365 AAAAA
1 AAAAA
1130370 GGGGTCCAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAAACA
Found at i:1130359 original size:16 final size:17
Alignment explanation
Indices: 1130338--1130369 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1130328 TCGTACCAAA
1130338 AAAAACAAA-AAAAAAC
1 AAAAACAAACAAAAAAC
1130354 AAAAACAAACAAAAAA
1 AAAAACAAACAAAAAA
1130370 GGGGTCCAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (17 bp):
AAAAACAAACAAAAAAC
Found at i:1131509 original size:28 final size:28
Alignment explanation
Indices: 1131478--1131800 Score: 386
Period size: 28 Copynumber: 11.5 Consensus size: 28
1131468 CGTTCATCTC
* *
1131478 TTCAAAGCCCACAGGTCAATGGCATCAT
1 TTCAAAGCCCACAAGTCAGTGGCATCAT
*
1131506 TTCAAAGCCCACAAGTTAGTGGCATCAT
1 TTCAAAGCCCACAAGTCAGTGGCATCAT
* *
1131534 TTCAAAGCCCACAAGTCAATGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCAT
*
1131562 TTCCAAGCCCACAAGTCAGTGGCA-CATT
1 TTCAAAGCCCACAAGTCAGTGGCATCA-T
*
1131590 TTCCAAGCCCACAAGTCAGTGGCA-CATT
1 TTCAAAGCCCACAAGTCAGTGGCATCA-T
*
1131618 TTCAAAGCCCACAAGTCAGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCAT
* *
1131646 TTCCAAGCCCACAAGTCAGTGGCATCTTT
1 TTCAAAGCCCACAAGTCAGTGGCATC-AT
1131675 TTC-AAGCCCACAAGTCAGTGGCATCATT
1 TTCAAAGCCCACAAGTCAGTGGCATCA-T
*
1131703 TTC-AAGCCCACAAGTTAGTGGCA-CACT
1 TTCAAAGCCCACAAGTCAGTGGCATCA-T
* * **
1131730 TTCAAAGCCCACAAGTCAGTGGTACCCC
1 TTCAAAGCCCACAAGTCAGTGGCATCAT
* * *
1131758 TTCAAAGCCCACAAGTTAATGGCATCCTCT
1 TTCAAAGCCCACAAGTCAGTGGCAT-C-AT
1131788 TTCAAAGCCCACA
1 TTCAAAGCCCACA
1131801 TAAGTCGGTG
Statistics
Matches: 263, Mismatches: 24, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
27 7 0.03
28 234 0.89
29 8 0.03
30 14 0.05
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCATCAT
Found at i:1131836 original size:25 final size:25
Alignment explanation
Indices: 1131788--1131837 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
1131778 GGCATCCTCT
*
1131788 TTCAAAGCCCACATAAGTCGGTGGC
1 TTCAAAGCCCACATAAGTCAGTGGC
* *
1131813 TTCAAAGGCCACATAAGTTAGTGGC
1 TTCAAAGCCCACATAAGTCAGTGGC
1131838 ACATTTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.22
Consensus pattern (25 bp):
TTCAAAGCCCACATAAGTCAGTGGC
Found at i:1131985 original size:25 final size:25
Alignment explanation
Indices: 1131957--1132031 Score: 68
Period size: 25 Copynumber: 3.2 Consensus size: 25
1131947 ATTAGCTCAA
*
1131957 TGTCACTGGCCTTGAATCATCACAT
1 TGTCACTGGCCTTGAATCAGCACAT
* * * * *
1131982 TGTC-C--ACCTT-TATTAGCTCAA
1 TGTCACTGGCCTTGAATCAGCACAT
1132003 TGTCACTGGCCTTGAATCAGCACAT
1 TGTCACTGGCCTTGAATCAGCACAT
1132028 TGTC
1 TGTC
1132032 CACTTTTCCC
Statistics
Matches: 35, Mismatches: 11, Indels: 8
0.65 0.20 0.15
Matches are distributed among these distances:
21 10 0.29
22 5 0.14
24 5 0.14
25 15 0.43
ACGTcount: A:0.23, C:0.28, G:0.16, T:0.33
Consensus pattern (25 bp):
TGTCACTGGCCTTGAATCAGCACAT
Found at i:1132015 original size:24 final size:24
Alignment explanation
Indices: 1131942--1132015 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 24
1131932 CATATTGGCA
1131942 CCTTTATTAGCTCAATGTCACTGG
1 CCTTTATTAGCTCAATGTCACTGG
* * * * * *
1131966 CCTTGAATCATCACATTGTC-C--A
1 CCTT-TATTAGCTCAATGTCACTGG
1131988 CCTTTATTAGCTCAATGTCACTGG
1 CCTTTATTAGCTCAATGTCACTGG
1132012 CCTT
1 CCTT
1132016 GAATCAGCAC
Statistics
Matches: 34, Mismatches: 12, Indels: 8
0.63 0.22 0.15
Matches are distributed among these distances:
21 10 0.29
22 5 0.15
24 9 0.26
25 10 0.29
ACGTcount: A:0.22, C:0.28, G:0.14, T:0.36
Consensus pattern (24 bp):
CCTTTATTAGCTCAATGTCACTGG
Found at i:1132067 original size:48 final size:48
Alignment explanation
Indices: 1131948--1132315 Score: 537
Period size: 48 Copynumber: 7.8 Consensus size: 48
1131938 GGCACCTTTA
* * * *
1131948 TTAGCTCAATGTCACTGGCCTTGAATCATCACATTGTCCACCTTT--A
1 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCCC
*
1131994 TTAGCTCAATGTCACTGGCCTTGAATCAGCACATTGTCCACTTTTCCC
1 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCCC
* * *
1132042 TTAGTTCAATGTCGTTGGCCTTGAATCAGCACATTGTCCACTTTTCAC
1 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCCC
*
1132090 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCATTTTTCCC
1 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCCC
* * *
1132138 TTAGCTCAATGTCGCTGGCCTTGAATAAGCACATTGTCCACCTTT--A
1 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCCC
* * *
1132184 TTAGCTCAATATCGCTGGCCTTGAATCAGCACATTTTCCCCTTTTCCC
1 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCCC
1132232 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCCC
1 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCCC
* * **
1132280 TTAGCTCGATGTCGTTGGCCTTGAATTGGCACATTG
1 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTG
1132316 GCAGTCCTCT
Statistics
Matches: 290, Mismatches: 28, Indels: 6
0.90 0.09 0.02
Matches are distributed among these distances:
46 83 0.29
48 207 0.71
ACGTcount: A:0.20, C:0.28, G:0.17, T:0.35
Consensus pattern (48 bp):
TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCCC
Found at i:1132193 original size:142 final size:143
Alignment explanation
Indices: 1131911--1132315 Score: 552
Period size: 142 Copynumber: 2.9 Consensus size: 143
1131901 TTAAAGTCTG
* * * * *
1131911 ATATCGTTGGCATTGAATCAGCATATTG-GCACCTTT-A-TTAGCTCAATGTCACTGGCCTTGAA
1 ATATCGTTGGCCTTGAATCAGCACATTGTCCACTTTTCACTTAGCTCAATGTCGCTGGCCTTGAA
* * * * * *
1131973 TCATCACATTGTCCACCTTT--ATTAGCTCAATGTCACTGGCCTTGAATCAGCACATTGTCCACT
66 TCAGCACATTGTCCACTTTTCCCTTAGCTCAATGTCGCTGGCCTTGAATAAGCACATTGTCCACC
* *
1132036 TTTCCCTTAGTTCA
131 TTT-CATTAGCTCA
*
1132050 ATGTCGTTGGCCTTGAATCAGCACATTGTCCACTTTTCACTTAGCTCAATGTCGCTGGCCTTGAA
1 ATATCGTTGGCCTTGAATCAGCACATTGTCCACTTTTCACTTAGCTCAATGTCGCTGGCCTTGAA
*
1132115 TCAGCACATTGTCCATTTTTCCCTTAGCTCAATGTCGCTGGCCTTGAATAAGCACATTGTCCACC
66 TCAGCACATTGTCCACTTTTCCCTTAGCTCAATGTCGCTGGCCTTGAATAAGCACATTGTCCACC
1132180 TTT-ATTAGCTCA
131 TTTCATTAGCTCA
* * * *
1132192 ATATCGCTGGCCTTGAATCAGCACATTTTCCCCTTTTCCCTTAGCTCAATGTCGCTGGCCTTGAA
1 ATATCGTTGGCCTTGAATCAGCACATTGTCCACTTTTCACTTAGCTCAATGTCGCTGGCCTTGAA
* * **
1132257 TCAGCACATTGTCCACTTTTCCCTTAGCTCGATGTCGTTGGCCTTGAATTGGCACATTG
66 TCAGCACATTGTCCACTTTTCCCTTAGCTCAATGTCGCTGGCCTTGAATAAGCACATTG
1132316 GCAGTCCTCT
Statistics
Matches: 236, Mismatches: 25, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
139 25 0.11
140 6 0.03
141 1 0.00
142 162 0.69
144 42 0.18
ACGTcount: A:0.21, C:0.27, G:0.17, T:0.35
Consensus pattern (143 bp):
ATATCGTTGGCCTTGAATCAGCACATTGTCCACTTTTCACTTAGCTCAATGTCGCTGGCCTTGAA
TCAGCACATTGTCCACTTTTCCCTTAGCTCAATGTCGCTGGCCTTGAATAAGCACATTGTCCACC
TTTCATTAGCTCA
Found at i:1132271 original size:190 final size:190
Alignment explanation
Indices: 1131948--1132315 Score: 610
Period size: 190 Copynumber: 1.9 Consensus size: 190
1131938 GGCACCTTTA
* * *
1131948 TTAGCTCAATGTCACTGGCCTTGAATCATCACATTGTCCACCTTTATTAGCTCAATGTCACTGGC
1 TTAGCTCAATGTCACTGGCCTTGAATAAGCACATTGTCCACCTTTATTAGCTCAATATCACTGGC
* *
1132013 CTTGAATCAGCACATTGTCCACTTTTCCCTTAGTTCAATGTCGTTGGCCTTGAATCAGCACATTG
66 CTTGAATCAGCACATTGTCCACTTTTCCCTTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTG
1132078 TCCACTTTTCACTTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCATTTTTCCC
131 TCCACTTTTCACTTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCATTTTTCCC
* *
1132138 TTAGCTCAATGTCGCTGGCCTTGAATAAGCACATTGTCCACCTTTATTAGCTCAATATCGCTGGC
1 TTAGCTCAATGTCACTGGCCTTGAATAAGCACATTGTCCACCTTTATTAGCTCAATATCACTGGC
* *
1132203 CTTGAATCAGCACATTTTCCCCTTTTCCCTTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTG
66 CTTGAATCAGCACATTGTCCACTTTTCCCTTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTG
* * * **
1132268 TCCACTTTTCCCTTAGCTCGATGTCGTTGGCCTTGAATTGGCACATTG
131 TCCACTTTTCACTTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTG
1132316 GCAGTCCTCT
Statistics
Matches: 164, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
190 164 1.00
ACGTcount: A:0.20, C:0.28, G:0.17, T:0.35
Consensus pattern (190 bp):
TTAGCTCAATGTCACTGGCCTTGAATAAGCACATTGTCCACCTTTATTAGCTCAATATCACTGGC
CTTGAATCAGCACATTGTCCACTTTTCCCTTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTG
TCCACTTTTCACTTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCATTTTTCCC
Found at i:1133049 original size:20 final size:20
Alignment explanation
Indices: 1133024--1133098 Score: 105
Period size: 20 Copynumber: 3.8 Consensus size: 20
1133014 TTTTACCCAG
1133024 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
** * *
1133044 ATGTATCGATACAAGTATGA
1 ATGTATCGATACATTTTTCA
*
1133064 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
1133084 ATGTATCGATACATT
1 ATGTATCGATACATT
1133099 CTGTCTTTTT
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:0.15, G:0.13, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1135456 original size:97 final size:97
Alignment explanation
Indices: 1135297--1135541 Score: 368
Period size: 97 Copynumber: 2.5 Consensus size: 97
1135287 AATTTTATTT
* * * * * *
1135297 ATCGGGGATACTCTAACCCTATTCATCCGAAGGGATACTCCAACCCCGCTTTTAAACACATCAAA
1 ATCGGAGACACTCCAACCCCATTCCTCCGAGGGGATACTCCAACCCCGCTTTTAAACACATCAAA
1135362 GTTTAAATCTTATTCTCACTTAAATTGTCATC
66 GTTTAAATCTTATTCTCACTTAAATTGTCATC
* *
1135394 ATCGGAGACACTTCAACCCCATTCCTCCGAGGGGATACTCCAACCCCGCTTTTAAACGCATCAAA
1 ATCGGAGACACTCCAACCCCATTCCTCCGAGGGGATACTCCAACCCCGCTTTTAAACACATCAAA
*
1135459 GTTTAAATTTTATTCTCACTTAAATTGTCATC
66 GTTTAAATCTTATTCTCACTTAAATTGTCATC
* * *
1135491 ATCGGGGACACTCCAA-CCCATTCCTCCGAGGGGATACTGC-ACCCCGTTTTT
1 ATCGGAGACACTCCAACCCCATTCCTCCGAGGGGATACTCCAACCCCGCTTTT
1135542 CAATCAAAAA
Statistics
Matches: 135, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
95 10 0.07
96 23 0.17
97 102 0.76
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.29
Consensus pattern (97 bp):
ATCGGAGACACTCCAACCCCATTCCTCCGAGGGGATACTCCAACCCCGCTTTTAAACACATCAAA
GTTTAAATCTTATTCTCACTTAAATTGTCATC
Found at i:1137550 original size:54 final size:57
Alignment explanation
Indices: 1137491--1137607 Score: 150
Period size: 57 Copynumber: 2.1 Consensus size: 57
1137481 ATAATTAACA
* *
1137491 ATAATTCAATTTAAAAC-TA-TA-TATATGTTACATTACTTATGATAATCTTATAAT
1 ATAATTCAATTTAAAACAAATTAGTATATGTTACATTACTTATGATAATCTAATAAT
* * * * *
1137545 ATAATTTAATTTTAAACAAATTAGTATATGTTATATTATTTTTGATAATCTAATAAT
1 ATAATTCAATTTAAAACAAATTAGTATATGTTACATTACTTATGATAATCTAATAAT
1137602 ATAATT
1 ATAATT
1137608 TAGTATAAAT
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
54 15 0.28
55 1 0.02
56 2 0.04
57 35 0.66
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (57 bp):
ATAATTCAATTTAAAACAAATTAGTATATGTTACATTACTTATGATAATCTAATAAT
Found at i:1139624 original size:27 final size:26
Alignment explanation
Indices: 1139559--1139631 Score: 65
Period size: 27 Copynumber: 2.7 Consensus size: 26
1139549 ATTCAAATTC
1139559 TTTAATAATTTAATAATAAAATAAAAAT
1 TTTAA-AATTT-ATAATAAAATAAAAAT
* ** * *
1139587 TCTAATGTTTATAATACAATTAAATAT
1 TTTAAAATTTATAATA-AAATAAAAAT
1139614 TTTAAAATTTATTAATAA
1 TTTAAAATTTA-TAATAA
1139632 TAATTATTCG
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
26 6 0.17
27 20 0.57
28 9 0.26
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (26 bp):
TTTAAAATTTATAATAAAATAAAAAT
Found at i:1143940 original size:32 final size:32
Alignment explanation
Indices: 1143893--1143971 Score: 122
Period size: 32 Copynumber: 2.5 Consensus size: 32
1143883 AAAACCACAA
* * *
1143893 ACTTATGTGGGCTTTGAAAGGGGTTGCCACCG
1 ACTTGTGTGGGCTTTGAAAAGGATTGCCACCG
*
1143925 ACTTGTGTGGACTTTGAAAAGGATTGCCACCG
1 ACTTGTGTGGGCTTTGAAAAGGATTGCCACCG
1143957 ACTTGTGTGGGCTTT
1 ACTTGTGTGGGCTTT
1143972 AGAGAATGGT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.19, C:0.18, G:0.32, T:0.32
Consensus pattern (32 bp):
ACTTGTGTGGGCTTTGAAAAGGATTGCCACCG
Found at i:1143985 original size:32 final size:31
Alignment explanation
Indices: 1143893--1144259 Score: 121
Period size: 28 Copynumber: 12.6 Consensus size: 31
1143883 AAAACCACAA
* * * *
1143893 ACTTATGTGGGCTTTGAAAGGGGTTGCCACCG
1 ACTTGTGTGGACTTTGAAA-AGGATGCCACCG
1143925 ACTTGTGTGGACTTTGAAAAGGATTGCCACCG
1 ACTTGTGTGGACTTTGAAAAGGA-TGCCACCG
* * *
1143957 ACTTGTGTGGGCTTTAGAGAATGG-TGCCACTG
1 ACTTGTGTGGACTTT-GA-AAAGGATGCCACCG
* * * **
1143989 ACTTGT-AGG-CTTTG-GAAGGGTGCCACTA
1 ACTTGTGTGGACTTTGAAAAGGATGCCACCG
* * * *
1144017 ACTTATG-GG-CTTTGAAAGGGA-GCTACGG
1 ACTTGTGTGGACTTTGAAAAGGATGCCACCG
* *
1144045 A---GTTTGGA-TTT-AAAAGGATGCCACTG
1 ACTTGTGTGGACTTTGAAAAGGATGCCACCG
* * **
1144071 AC-T-TGTGGACTTTGAAATGG-TGCTACTA
1 ACTTGTGTGGACTTTGAAAAGGATGCCACCG
* * * **
1144099 ACTTATG-GG-CTTTAAAAAAGAAAATGCCACTA
1 ACTTGTGTGGACTTT-GAAAAG--GATGCCACCG
* *
1144131 ACTTGTG-GG-CTTTTGAAAA-GACGCCACTG
1 ACTTGTGTGGAC-TTTGAAAAGGATGCCACCG
*
1144160 AC-T-TGTGGACTTTG-AAAGGATGCCACTG
1 ACTTGTGTGGACTTTGAAAAGGATGCCACCG
* **
1144188 ACTTGTG-GG-CTTTG-AAAGGGTGCCACTA
1 ACTTGTGTGGACTTTGAAAAGGATGCCACCG
* * *
1144216 ACTTATG-GG-CTTTG-AAAGGATGCTACTG
1 ACTTGTGTGGACTTTGAAAAGGATGCCACCG
1144244 ACTTGTG-GG-CTTTGAA
1 ACTTGTGTGGACTTTGAA
1144260 GGGTGCCATT
Statistics
Matches: 265, Mismatches: 44, Indels: 55
0.73 0.12 0.15
Matches are distributed among these distances:
25 7 0.03
26 11 0.04
27 13 0.05
28 111 0.42
29 30 0.11
30 8 0.03
31 4 0.02
32 72 0.27
33 5 0.02
34 4 0.02
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.29
Consensus pattern (31 bp):
ACTTGTGTGGACTTTGAAAAGGATGCCACCG
Found at i:1144012 original size:28 final size:28
Alignment explanation
Indices: 1143898--1145035 Score: 374
Period size: 27 Copynumber: 40.9 Consensus size: 28
1143888 CACAAACTTA
*
1143898 TGTGGGCTTTGAAAGGGGTTGCCACCGACT
1 TGTGGGCTTTGAAA-GGG-TGCCACTGACT
* *
1143928 TGTGTGGACTTTGAAAAGGATTGCCACCGACTT
1 TGTG-GG-CTTTG-AAAGG-GTGCCACTGAC-T
*
1143961 GTGTGGGCTTTAGAGAATGGTGCCACTGACT
1 -TGTGGGCTTT-GA-AAGGGTGCCACTGACT
* * *
1143992 TGTAGGCTTTGGAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * *
1144020 TATGGGCTTTGAAAGGGAGCTACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
1144048 T-T-GGATTTAAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
1144074 TGTGGACTTTGAAATGGTGCTACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * ** *
1144102 TATGGGCTTTAAAAAAGAAAATGCCACTAACT
1 TGTGGGCTTT--GAAAG--GGTGCCACTGACT
* **
1144134 TGTGGGCTTTTGAAAAGACGCCACTGACT
1 TGTGGGC-TTTGAAAGGGTGCCACTGACT
* *
1144163 TGTGGACTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
1144191 TGTGGGCTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
1144219 TATGGGCTTTGAAAGGATGCTACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
1144247 TGTGGGCTTTG-AAGGGTGCCATTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
1144274 TGTGAGCTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* ** * *
1144302 TGTGGGC-TTAAAAGAATGCCACGGAAT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * * *
1144329 TGTGGAC-ATGAAAGGATGTCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * * * *
1144356 TATGGAC-ATAAAAGGATGCCACAGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * *
1144383 TGTGGACTTTAAAAGGATGCCACAGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * ** *
1144411 TGTGGAC-TTAAAAGGGTGCCACAAAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
1144438 TGTGGAC-TTAAAAGGGTGCCA-TGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACT-GACT
* * * *
1144465 TGTGGACTTTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* ** * *
1144493 TATGAAC-TTAAAAGGGTGCCACGGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * ** *
1144520 TGTAGAC-TTAAAATGGTGCCACAAAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * *
1144547 TATGGAC-TTAAAAGGGTTCCA-TGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACT-GACT
* * * *
1144574 TGTGGACTTTAAAAGGTTGCCACAGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * *
1144602 TGTGGAC-TTAAAAGGATTCCACGGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
1144629 TGTGGAC-TTAAAAAGGTGCCA-TGAAGT
1 TGTGGGCTTTGAAAGGGTGCCACTG-ACT
* * * * * *
1144656 TATGGAC-TTAAAAGGATGTCACGGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * * *
1144683 TGTAGAC-TTAAAAGGGTACCACAGATT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * *
1144710 TATGGAC-TTAAAAGGGGTGCCACGGAGT
1 TGTGGGCTTTGAAA-GGGTGCCACTGACT
* * * * * *
1144738 TAT-GGATTTTAAAAGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
1144765 TGTGGACTTTAAAAGGGTGCCA-TGGAGT
1 TGTGGGCTTTGAAAGGGTGCCACT-GACT
* * * *
1144793 TGTGGAC-TTAAAAGGATGCCACGGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
1144820 TGTGGAC-TTAAAAGGGTGCCACAGAGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
1144847 TGTGGAC-TTAAAAGGGTACCA-TGGACG
1 TGTGGGCTTTGAAAGGGTGCCACT-GACT
* * * *
1144874 TGTAGACTTTAAAAGGGTGCCACAGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
1144902 TGT-GAC-TTAAAAGGATGCCACAGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * * * *
1144928 TATGGAC-TTAAAAAGATGCCACAGATT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
1144955 TATGGAC-TTGAAAGGGTGCCACGGATT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * *
1144982 TGTGGAC-TTAAAATGATGCCACAGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
1145009 TGTGGACTTTAAAAGGAATGCCACTGA
1 TGTGGGCTTTGAAAGG-GTGCCACTGA
1145036 ATCTTGGACT
Statistics
Matches: 901, Mismatches: 171, Indels: 73
0.79 0.15 0.06
Matches are distributed among these distances:
26 40 0.04
27 449 0.50
28 300 0.33
29 26 0.03
30 16 0.02
31 6 0.01
32 47 0.05
33 13 0.01
34 4 0.00
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.26
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGGTGCCACTGACT
Found at i:1144193 original size:117 final size:111
Alignment explanation
Indices: 1143898--1144306 Score: 356
Period size: 117 Copynumber: 3.5 Consensus size: 111
1143888 CACAAACTTA
* * *
1143898 TGTGGGCTTTGAAAGGGGTTGCCACCGACTTGTGTGGACTTTGAAAAGGATTGCCACCGACTTGT
1 TGTGGGCTTTGAAA--GG-AGCCACTGAC-T-TGTGGACTTTG-AAAGGA-TGCCACTGAC-T-T
* * * * * ** **
1143963 GTGGGCTTTAGAGAATGGTGCCACTGACTTGTAGGCTTTGGAAGGGTGCCACTAACT
57 GTGGACTTT-GA-AAGGGTGCCACTAACTTATGGGCTTTAAAAGAATGCCACTAACT
* * * * *
1144020 TATGGGCTTTGAAAGGGAGCTACGGAGTT-TGGA-TTTAAAAGGATGCCACTGACTTGTGGACTT
1 TGTGGGCTTTGAAA-GGAGCCACTGACTTGTGGACTTTGAAAGGATGCCACTGACTTGTGGACTT
* *
1144083 TGAAATGGTGCTACTAACTTATGGGCTTTAAAAAAGAAAATGCCACTAACT
65 TGAAAGGGTGCCACTAACTTATGGGCTTT--AAAAG--AATGCCACTAACT
* *
1144134 TGTGGGCTTTTGAAAAGACGCCACTGACTTGTGGACTTTGAAAGGATGCCACTGACTTGTGGGCT
1 TGTGGGC-TTTGAAAGGA-GCCACTGACTTGTGGACTTTGAAAGGATGCCACTGACTTGTGGACT
* * * *
1144199 TTGAAAGGGTGCCACTAACTTATGGGCTTTGAAAGGATGCTACTGACT
64 TTGAAAGGGTGCCACTAACTTATGGGCTTTAAAAGAATGCCACTAACT
* * * * *
1144247 TGTGGGCTTTGAAGGGTGCCATTGACTTGT-GAGCTTTGAAAGGGTGCCACTAACTTGTGG
1 TGTGGGCTTTGAAAGGAGCCACTGACTTGTGGA-CTTTGAAAGGATGCCACTGACTTGTGG
1144307 GCTTAAAAGA
Statistics
Matches: 243, Mismatches: 35, Indels: 29
0.79 0.11 0.09
Matches are distributed among these distances:
110 24 0.10
111 39 0.16
112 19 0.08
113 18 0.07
114 28 0.12
115 25 0.10
116 7 0.03
117 59 0.24
118 1 0.00
119 1 0.00
120 6 0.02
121 3 0.01
122 13 0.05
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.29
Consensus pattern (111 bp):
TGTGGGCTTTGAAAGGAGCCACTGACTTGTGGACTTTGAAAGGATGCCACTGACTTGTGGACTTT
GAAAGGGTGCCACTAACTTATGGGCTTTAAAAGAATGCCACTAACT
Found at i:1144322 original size:55 final size:55
Alignment explanation
Indices: 1143898--1144432 Score: 282
Period size: 55 Copynumber: 9.4 Consensus size: 55
1143888 CACAAACTTA
* * * **
1143898 TGTGGGCTTTGAAAGGGGTTGCCACCGACTTGTGTGGACTTTGAAAAGGATTGCCACCGACTT
1 TGTGGGCTTT-AAA-AGGATGCCACTGAC-T-TGTGG-CTTTG-AAAGGA-TGCCACTAAC-T
* *
1143961 GTGTGGGCTTTAGAGAATGG-TGCCACTGACTTGTAGGCTTTGGAAGGGTGCCACTAACT
1 -TGTGGGCTTTA-A-AA-GGATGCCACTGACTTGT-GGCTTTGAAAGGATGCCACTAACT
* * * * * * * *
1144020 TATGGGCTTTGAAAGGGA-GCTACGGAGTT-TGGATTTAAAAGGATGCCACTGACT
1 TGTGGGCTTT-AAAAGGATGCCACTGACTTGTGGCTTTGAAAGGATGCCACTAACT
* * * * * * *
1144074 TGTGGACTTTGAAATGG-TGCTACTAACTTATGGGCTTTAAAAAAGAAAATGCCACTAACT
1 TGTGGGCTTT-AAAAGGATGCCACTGACTTGT-GGCTTT--GAAAG--GATGCCACTAACT
* *
1144134 TGTGGGCTTTTGAAAA-GACGCCACTGACTTGTGGACTTTGAAAGGATGCCACTGACT
1 TGTGGGC-TTT-AAAAGGATGCCACTGACTTGTGG-CTTTGAAAGGATGCCACTAACT
* * * * * *
1144191 TGTGGGCTTTGAAAGGGTGCCACTAACTTATGGGCTTTGAAAGGATGCTACTGACT
1 TGTGGGCTTTAAAAGGATGCCACTGACTTGT-GGCTTTGAAAGGATGCCACTAACT
* * * *
1144247 TGTGGGCTTT-GAAGGGTGCCATTGACTTGTGAGCTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTAAAAGGATGCCACTGACTTGTG-GCTTTGAAAGGATGCCACTAACT
* * * * * ** *
1144302 TGTGGGC-TTAAAAGAATGCCACGGAATTGTGGAC-ATGAAAGGATGTCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTGACTTGTGG-CTTTGAAAGGATGCCACTAACT
* * * * * * *
1144356 TATGGAC-ATAAAAGGATGCCACAGAGTTGTGGACTTTAAAAGGATGCCAC-AGAGT
1 TGTGGGCTTTAAAAGGATGCCACTGACTTGTGG-CTTTGAAAGGATGCCACTA-ACT
* *
1144411 TGTGGAC-TTAAAAGGGTGCCAC
1 TGTGGGCTTTAAAAGGATGCCAC
1144433 AAAGTTGTGG
Statistics
Matches: 376, Mismatches: 72, Indels: 55
0.75 0.14 0.11
Matches are distributed among these distances:
54 87 0.23
55 98 0.26
56 61 0.16
57 21 0.06
58 15 0.04
59 6 0.02
60 28 0.07
61 25 0.07
62 8 0.02
63 4 0.01
64 20 0.05
65 3 0.01
ACGTcount: A:0.27, C:0.16, G:0.30, T:0.27
Consensus pattern (55 bp):
TGTGGGCTTTAAAAGGATGCCACTGACTTGTGGCTTTGAAAGGATGCCACTAACT
Found at i:1144331 original size:27 final size:27
Alignment explanation
Indices: 1144285--1145024 Score: 712
Period size: 27 Copynumber: 27.2 Consensus size: 27
1144275 GTGAGCTTTG
** * *
1144285 AAAGGGTGCCACTAACTTGTGGGCTTA
1 AAAGGGTGCCACGGAGTTGTGGACTTA
** * * *
1144312 AAAGAATGCCACGGAATTGTGGACATG
1 AAAGGGTGCCACGGAGTTGTGGACTTA
* * * *
1144339 AAAGGATGTCACGGAGTTATGGACATA
1 AAAGGGTGCCACGGAGTTGTGGACTTA
* *
1144366 AAAGGATGCCACAGAGTTGTGGACTTTA
1 AAAGGGTGCCACGGAGTTGTGGAC-TTA
* *
1144394 AAAGGATGCCACAGAGTTGTGGACTTA
1 AAAGGGTGCCACGGAGTTGTGGACTTA
**
1144421 AAAGGGTGCCACAAAGTTGTGGACTTA
1 AAAGGGTGCCACGGAGTTGTGGACTTA
*
1144448 AAAGGGTGCCATGGAGTTGTGGACTTTA
1 AAAGGGTGCCACGGAGTTGTGGAC-TTA
* *
1144476 AAAGGGTGCCACGGAGTTATGAACTTA
1 AAAGGGTGCCACGGAGTTGTGGACTTA
* *
1144503 AAAGGGTGCCACGGACTTGTAGACTTA
1 AAAGGGTGCCACGGAGTTGTGGACTTA
* ** *
1144530 AAATGGTGCCACAAAGTTATGGACTTA
1 AAAGGGTGCCACGGAGTTGTGGACTTA
* *
1144557 AAAGGGTTCCATGGAGTTGTGGACTTTA
1 AAAGGGTGCCACGGAGTTGTGGAC-TTA
* * *
1144585 AAAGGTTGCCACAGACTTGTGGACTTA
1 AAAGGGTGCCACGGAGTTGTGGACTTA
* * *
1144612 AAAGGATTCCACGGACTTGTGGACTTA
1 AAAGGGTGCCACGGAGTTGTGGACTTA
* * * *
1144639 AAAAGGTGCCATGAAGTTATGGACTTA
1 AAAGGGTGCCACGGAGTTGTGGACTTA
* * * *
1144666 AAAGGATGTCACGGACTTGTAGACTTA
1 AAAGGGTGCCACGGAGTTGTGGACTTA
* * * *
1144693 AAAGGGTACCACAGATTTATGGACTTA
1 AAAGGGTGCCACGGAGTTGTGGACTTA
* *
1144720 AAAGGGGTGCCACGGAGTTATGGATTTTA
1 AAA-GGGTGCCACGGAGTTGTGGA-CTTA
1144749 AAA-GGTGCCACGGAGTTGTGGACTTTA
1 AAAGGGTGCCACGGAGTTGTGGAC-TTA
*
1144776 AAAGGGTGCCATGGAGTTGTGGACTTA
1 AAAGGGTGCCACGGAGTTGTGGACTTA
* *
1144803 AAAGGATGCCACGGACTTGTGGACTTA
1 AAAGGGTGCCACGGAGTTGTGGACTTA
*
1144830 AAAGGGTGCCACAGAGTTGTGGACTTA
1 AAAGGGTGCCACGGAGTTGTGGACTTA
* * *
1144857 AAAGGGTACCATGGACG-TGTAGACTTTA
1 AAAGGGTGCCACGGA-GTTGTGGAC-TTA
* *
1144885 AAAGGGTGCCACAGACTTGT-GACTTA
1 AAAGGGTGCCACGGAGTTGTGGACTTA
* * * *
1144911 AAAGGATGCCACAGACTTATGGACTTA
1 AAAGGGTGCCACGGAGTTGTGGACTTA
* * * * * *
1144938 AAAAGATGCCACAGATTTATGGACTTG
1 AAAGGGTGCCACGGAGTTGTGGACTTA
*
1144965 AAAGGGTGCCACGGATTTGTGGACTTA
1 AAAGGGTGCCACGGAGTTGTGGACTTA
* * * *
1144992 AAATGATGCCACAGACTTGTGGACTTTA
1 AAAGGGTGCCACGGAGTTGTGGAC-TTA
1145020 AAAGG
1 AAAGG
1145025 AATGCCACTG
Statistics
Matches: 594, Mismatches: 107, Indels: 23
0.82 0.15 0.03
Matches are distributed among these distances:
26 21 0.04
27 433 0.73
28 134 0.23
29 6 0.01
ACGTcount: A:0.32, C:0.15, G:0.29, T:0.25
Consensus pattern (27 bp):
AAAGGGTGCCACGGAGTTGTGGACTTA
Found at i:1144403 original size:82 final size:81
Alignment explanation
Indices: 1144153--1145024 Score: 748
Period size: 82 Copynumber: 10.6 Consensus size: 81
1144143 TTGAAAAGAC
* * * * * *
1144153 GCCACTGACTTGTGGACTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTA-A
1 GCCACGGAGTTGTGGAC-TTAAAAGGATGCCACAGACTTGTGGAC-TTAAAAGGGTGCCAC-AGA
* * * * *
1144217 CTTATGGGCTTTGAAAGGAT
63 GTTGTGGAC-TTAAAAGGGT
* * * * ** * ** *
1144237 GCTACTGACTTGTGGGCTTTGAAGGGTGCCATTGACTTGT-GAGCTTTGAAAGGGTGCCACTA-A
1 GCCACGGAGTTGTGGACTTAAAAGGATGCCACAGACTTGTGGA-C-TTAAAAGGGTGCCAC-AGA
* * **
1144300 CTTGTGGGCTTAAAAGAAT
63 GTTGTGGACTTAAAAGGGT
* * * * * * * * *
1144319 GCCACGGAATTGTGGACATGAAAGGATGTCACGGAGTTATGGACATAAAAGGATGCCACAGAGTT
1 GCCACGGAGTTGTGGACTTAAAAGGATGCCACAGACTTGTGGACTTAAAAGGGTGCCACAGAGTT
*
1144384 GTGGACTTTAAAAGGAT
66 GTGGAC-TTAAAAGGGT
* * * * **
1144401 GCCACAGAGTTGTGGACTTAAAAGGGTGCCACAAAGTTGTGGACTTAAAAGGGTGCCATGGAGTT
1 GCCACGGAGTTGTGGACTTAAAAGGATGCCACAGACTTGTGGACTTAAAAGGGTGCCACAGAGTT
1144466 GTGGACTTTAAAAGGGT
66 GTGGAC-TTAAAAGGGT
* * * * * * *
1144483 GCCACGGAGTTATGAACTTAAAAGGGTGCCACGGACTTGTAGACTTAAAATGGTGCCACAAAGTT
1 GCCACGGAGTTGTGGACTTAAAAGGATGCCACAGACTTGTGGACTTAAAAGGGTGCCACAGAGTT
*
1144548 ATGGACTTAAAAGGGT
66 GTGGACTTAAAAGGGT
* * * * * * *
1144564 TCCATGGAGTTGTGGACTTTAAAAGGTTGCCACAGACTTGTGGACTTAAAAGGATTCCACGGACT
1 GCCACGGAGTTGTGGAC-TTAAAAGGATGCCACAGACTTGTGGACTTAAAAGGGTGCCACAGAGT
*
1144629 TGTGGACTTAAAAAGGT
65 TGTGGACTTAAAAGGGT
* * * * * * * *
1144646 GCCATGAAGTTATGGACTTAAAAGGATGTCACGGACTTGTAGACTTAAAAGGGTACCACAGATTT
1 GCCACGGAGTTGTGGACTTAAAAGGATGCCACAGACTTGTGGACTTAAAAGGGTGCCACAGAGTT
*
1144711 ATGGACTTAAAAGGGGT
66 GTGGACTTAAAA-GGGT
* * * * **
1144728 GCCACGGAGTTATGGATTTTAAAAGG-TGCCACGGAGTTGTGGACTTTAAAAGGGTGCCATGGAG
1 GCCACGGAGTTGTGGA-CTTAAAAGGATGCCACAGACTTGTGGAC-TTAAAAGGGTGCCACAGAG
*
1144792 TTGTGGACTTAAAAGGAT
64 TTGTGGACTTAAAAGGGT
* * * * **
1144810 GCCACGGACTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTACCATGGACG-
1 GCCACGGAGTTGTGGACTTAAAAGGATGCCACAGACTTGTGGACTTAAAAGGGTGCCACAGA-GT
*
1144874 TGTAGACTTTAAAAGGGT
65 TGTGGAC-TTAAAAGGGT
* * * * * *
1144892 GCCACAGACTTGT-GACTTAAAAGGATGCCACAGACTTATGGACTTAAAAAGATGCCACAGATTT
1 GCCACGGAGTTGTGGACTTAAAAGGATGCCACAGACTTGTGGACTTAAAAGGGTGCCACAGAGTT
* *
1144956 ATGGACTTGAAAGGGT
66 GTGGACTTAAAAGGGT
* *
1144972 GCCACGGATTTGTGGACTTAAAATGATGCCACAGACTTGTGGACTTTAAAAGG
1 GCCACGGAGTTGTGGACTTAAAAGGATGCCACAGACTTGTGGAC-TTAAAAGG
1145025 AATGCCACTG
Statistics
Matches: 654, Mismatches: 120, Indels: 30
0.81 0.15 0.04
Matches are distributed among these distances:
80 21 0.03
81 198 0.30
82 335 0.51
83 85 0.13
84 15 0.02
ACGTcount: A:0.30, C:0.15, G:0.29, T:0.26
Consensus pattern (81 bp):
GCCACGGAGTTGTGGACTTAAAAGGATGCCACAGACTTGTGGACTTAAAAGGGTGCCACAGAGTT
GTGGACTTAAAAGGGT
Found at i:1144404 original size:109 final size:107
Alignment explanation
Indices: 1144285--1145032 Score: 655
Period size: 109 Copynumber: 6.9 Consensus size: 107
1144275 GTGAGCTTTG
* * * * * *
1144285 AAAGGGTGCCACTAACTTGTGGGCTTAAAAGAATGCCACGGAA-TTGTGGACATGAAAGGATGTC
1 AAAGGGTGCCACGAACTTGTGGACTTAAAAG-GTGCCAC-GAAGTTGTGGACTTAAAAGGGTGTC
* * * *
1144349 ACGGAGTTATGGACATAAAAGGATGCCACAGAGTTGTGGACTTTA
64 ATGGAGTTGTGGACTTAAAAGGATGCCACAGACTTGTGGAC-TTA
* * * *
1144394 AAAGGATGCCAC-AGAGTTGTGGACTTAAAAGGGTGCCACAAAGTTGTGGACTTAAAAGGGTGCC
1 AAAGGGTGCCACGA-ACTTGTGGACTTAAAA-GGTGCCACGAAGTTGTGGACTTAAAAGGGTGTC
* * * * *
1144458 ATGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTATGAACTTA
64 ATGGAGTTGTGGAC-TTAAAAGGATGCCACAGACTTGTGGACTTA
* * * *
1144503 AAAGGGTGCCACGGACTTGTAGACTTAAAATGGTGCCACAAAGTTATGGACTTAAAAGGGT-TCC
1 AAAGGGTGCCACGAACTTGTGGACTTAAAA-GGTGCCACGAAGTTGTGGACTTAAAAGGGTGT-C
*
1144567 ATGGAGTTGTGGACTTTAAAAGGTTGCCACAGACTTGTGGACTTA
64 ATGGAGTTGTGGAC-TTAAAAGGATGCCACAGACTTGTGGACTTA
* * * * * *
1144612 AAAGGATTCCACGGACTTGTGGACTTAAAAAGGTGCCATGAAGTTATGGACTTAAAAGGATGTCA
1 AAAGGGTGCCACGAACTTGTGGACTT-AAAAGGTGCCACGAAGTTGTGGACTTAAAAGGGTGTCA
* * * * * * *
1144677 CGGACTTGTAGACTTAAAAGGGTACCACAGATTTATGGACTTA
65 TGGAGTTGTGGACTTAAAAGGATGCCACAGACTTGTGGACTTA
* * * * * *
1144720 AAAGGGGTGCCACGGAGTTATGGATTTTAAAAGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGC
1 AAA-GGGTGCCACGAACTTGTGGA-CTTAAAAGGTGCCACGAAGTTGTGGAC-TTAAAAGGGTGT
*
1144785 CATGGAGTTGTGGACTTAAAAGGATGCCACGGACTTGTGGACTTA
63 CATGGAGTTGTGGACTTAAAAGGATGCCACAGACTTGTGGACTTA
* * * * *
1144830 AAAGGGTGCCAC-AGAGTTGTGGACTTAAAAGGGTACCATGGACG-TGTAGACTTTAAAAGGGTG
1 AAAGGGTGCCACGA-ACTTGTGGACTTAAAA-GGTGCCA-CGAAGTTGTGGAC-TTAAAAGGGTG
* ** * *
1144893 CCACAGACTTGT-GACTTAAAAGGATGCCACAGACTTATGGACTTA
62 TCATGGAGTTGTGGACTTAAAAGGATGCCACAGACTTGTGGACTTA
* * * * * * * * * *
1144938 AAAAGATGCCAC-AGATTTATGGACTTGAAAGGGTGCCACGGATTTGTGGACTTAAAATGATGCC
1 AAAGGGTGCCACGA-ACTTGTGGACTT-AAAAGGTGCCACGAAGTTGTGGACTTAAAAGGGTGTC
** *
1145002 ACAGACTTGTGGACTTTAAAAGGAATGCCAC
64 ATGGAGTTGTGGAC-TTAAAAGG-ATGCCAC
1145033 TGAATCTTGG
Statistics
Matches: 535, Mismatches: 85, Indels: 37
0.81 0.13 0.06
Matches are distributed among these distances:
107 22 0.04
108 106 0.20
109 318 0.59
110 89 0.17
ACGTcount: A:0.32, C:0.15, G:0.29, T:0.25
Consensus pattern (107 bp):
AAAGGGTGCCACGAACTTGTGGACTTAAAAGGTGCCACGAAGTTGTGGACTTAAAAGGGTGTCAT
GGAGTTGTGGACTTAAAAGGATGCCACAGACTTGTGGACTTA
Found at i:1144487 original size:191 final size:191
Alignment explanation
Indices: 1144165--1145024 Score: 883
Period size: 191 Copynumber: 4.5 Consensus size: 191
1144155 CACTGACTTG
* * * * * * * *
1144165 TGGACTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTA-ACTTATGGGCTTT
1 TGGAC-TTAAAAGGATGCCACAGAGTTGTGGACTTTAAAAGGGTGCCAC-AGAGTTGTGGAC-TT
* * * * ** * * *
1144229 GAAAGGATGCTACTGACTTGTGGGCTTTGAAGGGTGCCATTGACTTGT-GAGCTTTGAAAGGGTG
63 AAAAGGATGCCACAGACTTGTGGACTTAAAAGGGTGCCATGGAGTTGTGGA-C-TTAAAAGGGTG
** * * ** * * * * * *
1144293 CCACTAACTTGTGGGCTTAAAAGAATGCCACGGAATTGTGGACATGAAA-GGATGTCACGGAGTT
126 CCACGGACTTGTAGACTTAAAAGGGTGCCACAGACTTGTGGACTTAAAAGGGATGCCACAGAGTT
1144357 A
191 A
* *
1144358 TGGACATAAAAGGATGCCACAGAGTTGTGGACTTTAAAAGGATGCCACAGAGTTGTGGACTTAAA
1 TGGACTTAAAAGGATGCCACAGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAA
* * *
1144423 AGGGTGCCACAAAGTTGTGGACTTAAAAGGGTGCCATGGAGTTGTGGACTTTAAAAGGGTGCCAC
66 AGGATGCCACAGACTTGTGGACTTAAAAGGGTGCCATGGAGTTGTGGAC-TTAAAAGGGTGCCAC
* * * * * *
1144488 GGAGTTAT-GAACTTAAAAGGGTGCCACGGACTTGTAGACTTAAAATGG-TGCCACAAAGTTA
130 GGACTTGTAG-ACTTAAAAGGGTGCCACAGACTTGTGGACTTAAAAGGGATGCCACAGAGTTA
* * ** * *
1144549 TGGACTTAAAAGGGTTCCATGGAGTTGTGGACTTTAAAAGGTTGCCACAGACTTGTGGACTTAAA
1 TGGACTTAAAAGGATGCCACAGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAA
* * * * * * *
1144614 AGGATTCCACGGACTTGTGGACTTAAAAAGGTGCCATGAAGTTATGGACTTAAAAGGATGTCACG
66 AGGATGCCACAGACTTGTGGACTTAAAAGGGTGCCATGGAGTTGTGGACTTAAAAGGGTGCCACG
* * * * *
1144679 GACTTGTAGACTTAAAAGGGTACCACAGATTTATGGACTTAAAAGGGGTGCCACGGAGTTA
131 GACTTGTAGACTTAAAAGGGTGCCACAGACTTGTGGACTTAAAAGGGATGCCACAGAGTTA
* * **
1144740 TGGATTTTAAAAGG-TGCCACGGAGTTGTGGACTTTAAAAGGGTGCCATGGAGTTGTGGACTTAA
1 TGGA-CTTAAAAGGATGCCACAGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAA
* ** * *
1144804 AAGGATGCCACGGACTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTACCAT
65 AAGGATGCCACAGACTTGTGGACTTAAAAGGGTGCCATGGAGTTGTGGACTTAAAAGGGTGCCAC
* *
1144869 GGACGTGTAGACTTTAAAAGGGTGCCACAGACTTGT-GACTTAAAA-GGATGCCACAGACTTA
130 GGACTTGTAGAC-TTAAAAGGGTGCCACAGACTTGTGGACTTAAAAGGGATGCCACAGAGTTA
* * * * * *
1144930 TGGACTTAAAAAGATGCCACAGATTTATGGAC-TTGAAAGGGTGCCACGGATTTGTGGACTTAAA
1 TGGACTTAAAAGGATGCCACAGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAA
*
1144994 ATGATGCCACAGACTTGTGGACTTTAAAAGG
66 AGGATGCCACAGACTTGTGGAC-TTAAAAGG
1145025 AATGCCACTG
Statistics
Matches: 560, Mismatches: 97, Indels: 23
0.82 0.14 0.03
Matches are distributed among these distances:
189 56 0.10
190 92 0.16
191 332 0.59
192 75 0.13
193 5 0.01
ACGTcount: A:0.30, C:0.15, G:0.29, T:0.26
Consensus pattern (191 bp):
TGGACTTAAAAGGATGCCACAGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAA
AGGATGCCACAGACTTGTGGACTTAAAAGGGTGCCATGGAGTTGTGGACTTAAAAGGGTGCCACG
GACTTGTAGACTTAAAAGGGTGCCACAGACTTGTGGACTTAAAAGGGATGCCACAGAGTTA
Found at i:1145488 original size:20 final size:20
Alignment explanation
Indices: 1145451--1145487 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
1145441 GTTTTTTTAG
*
1145451 TATAAGCAAGATGGTTTTGA
1 TATAACCAAGATGGTTTTGA
1145471 TATAACCAA-ATGGTTTT
1 TATAACCAAGATGGTTTT
1145488 TTCTTGGTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (20 bp):
TATAACCAAGATGGTTTTGA
Found at i:1146355 original size:22 final size:21
Alignment explanation
Indices: 1146308--1146398 Score: 62
Period size: 20 Copynumber: 4.2 Consensus size: 21
1146298 CATGTCCTTG
*
1146308 TTTTTTTATTTTTCTTATTC-C
1 TTTTTTTATTTTGCTT-TTCAC
*
1146329 -CTTTTTATTTTGCTTTTACAC
1 TTTTTTTATTTTGCTTTT-CAC
* *
1146350 TTTTTTTTGTTTTTCTTTTCA-
1 -TTTTTTTATTTTGCTTTTCAC
* *
1146371 TTTTTTATGCTTTTGCTTTTGAC
1 TTTTTT-T-ATTTTGCTTTTCAC
1146394 TTTTT
1 TTTTT
1146399 CGTCATTTTG
Statistics
Matches: 55, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
19 2 0.04
20 20 0.36
21 2 0.04
22 12 0.22
23 19 0.35
ACGTcount: A:0.09, C:0.13, G:0.05, T:0.73
Consensus pattern (21 bp):
TTTTTTTATTTTGCTTTTCAC
Found at i:1153111 original size:21 final size:22
Alignment explanation
Indices: 1153085--1153127 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1153075 ATTTCTTCTC
1153085 TCTTTT-CTTTCTCTTTTTTTT
1 TCTTTTGCTTTCTCTTTTTTTT
* *
1153106 TCTTTTGTTTTTTCTTTTTTTT
1 TCTTTTGCTTTCTCTTTTTTTT
1153128 AGTTGAACCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.84
Consensus pattern (22 bp):
TCTTTTGCTTTCTCTTTTTTTT
Found at i:1153116 original size:12 final size:11
Alignment explanation
Indices: 1153087--1153127 Score: 55
Period size: 12 Copynumber: 3.5 Consensus size: 11
1153077 TTCTTCTCTC
*
1153087 TTTTCTTTCTCT
1 TTTTTTTTCT-T
1153099 TTTTTTTTCTT
1 TTTTTTTTCTT
1153110 TTGTTTTTTCTT
1 TT-TTTTTTCTT
1153122 TTTTTT
1 TTTTTT
1153128 AGTTGAACCT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 7 0.26
12 20 0.74
ACGTcount: A:0.00, C:0.12, G:0.02, T:0.85
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:1155130 original size:128 final size:127
Alignment explanation
Indices: 1154998--1155252 Score: 336
Period size: 129 Copynumber: 2.0 Consensus size: 127
1154988 AATGAAGATT
* *
1154998 AAAAATTAGTTAATAATAA-AAAATACATATCAATATTAAGAAAAGTTTACA-TTAATAAGGACT
1 AAAAATTAGTTAATAATAATAAAAGACATATCAATA--AAGAAAAGTTTACATTTAATAAGAACT
* * *
1155061 TCAAGGTTAATAAAAATAATAAATAAAGATTAATTAGTATTTTAA-TTTAATAAAAATTCATTAA
64 TCAA-GTTAATAAAAA-AATAAATAAA-ATTAATTAATATCTTAATTTTAATAAAAAATCATTAA
1155125 TA
126 TA
* * * * *
1155127 AAAAATTAGTTAATATTAATAAAAGATATATCAATAAATAAAAGTTTACATTTAATAAGAATTTT
1 AAAAATTAGTTAATAATAATAAAAGACATATCAATAAAGAAAAGTTTACATTTAATAAGAACTTC
* *
1155192 AAGTTAATAAAGAAATAAATAAAATTACTTAATATCTTAATTTTAATAAAAAATCATTAAT
66 AAGTTAATAAAAAAATAAATAAAATTAATTAATATCTTAATTTTAATAAAAAATCATTAAT
1155253 TAGTTAAAAA
Statistics
Matches: 111, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
126 14 0.13
127 29 0.26
128 23 0.21
129 31 0.28
130 14 0.13
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.35
Consensus pattern (127 bp):
AAAAATTAGTTAATAATAATAAAAGACATATCAATAAAGAAAAGTTTACATTTAATAAGAACTTC
AAGTTAATAAAAAAATAAATAAAATTAATTAATATCTTAATTTTAATAAAAAATCATTAATA
Found at i:1155162 original size:21 final size:21
Alignment explanation
Indices: 1155120--1155170 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
1155110 ATAAAAATTC
* *
1155120 ATTAATAAAAAATTAGTTAAT
1 ATTAATAAAAGATTAGTCAAT
1155141 ATTAATAAAAGATATA-TCAAT
1 ATTAATAAAAGAT-TAGTCAAT
1155162 A--AATAAAAG
1 ATTAATAAAAG
1155171 TTTACATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 8 0.30
21 17 0.63
22 2 0.07
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.31
Consensus pattern (21 bp):
ATTAATAAAAGATTAGTCAAT
Found at i:1155314 original size:7 final size:7
Alignment explanation
Indices: 1155302--1155336 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
1155292 ATTAGTATTT
1155302 TTATATA
1 TTATATA
1155309 TTATATA
1 TTATATA
1155316 TTATATA
1 TTATATA
1155323 TTATATA
1 TTATATA
1155330 TTATATA
1 TTATATA
1155337 AATAGATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
TTATATA
Found at i:1156638 original size:34 final size:36
Alignment explanation
Indices: 1156592--1156663 Score: 103
Period size: 36 Copynumber: 2.1 Consensus size: 36
1156582 TTTTTTTTAG
* * *
1156592 TTGATTACTATATAT-T-TTATCGTTTGTAGGATAT
1 TTGATTAATATATATATATTATCATTTGTAGAATAT
1156626 TTGATTAATATATATATATTATCATTTGTAGAATAT
1 TTGATTAATATATATATATTATCATTTGTAGAATAT
1156662 TT
1 TT
1156664 TCTATATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
34 14 0.42
35 1 0.03
36 18 0.55
ACGTcount: A:0.32, C:0.04, G:0.11, T:0.53
Consensus pattern (36 bp):
TTGATTAATATATATATATTATCATTTGTAGAATAT
Found at i:1157676 original size:16 final size:17
Alignment explanation
Indices: 1157655--1157688 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1157645 AATATAGTAA
*
1157655 ATATT-AAATTAAAAAT
1 ATATTAAAAATAAAAAT
1157671 ATATTAAAAATAAAAAT
1 ATATTAAAAATAAAAAT
1157688 A
1 A
1157689 ATGTGGGCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
ATATTAAAAATAAAAAT
Found at i:1157686 original size:17 final size:16
Alignment explanation
Indices: 1157635--1157688 Score: 56
Period size: 15 Copynumber: 3.4 Consensus size: 16
1157625 ATATTTAATG
*
1157635 AAAATATATTAATATA
1 AAAATATATTAAAATA
** *
1157651 GTAA-ATATTAAATTA
1 AAAATATATTAAAATA
1157666 AAAATATATTAAAAATA
1 AAAATATATT-AAAATA
1157683 AAAATA
1 AAAATA
1157689 ATGTGGGCAG
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
15 11 0.38
16 7 0.24
17 11 0.38
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (16 bp):
AAAATATATTAAAATA
Found at i:1157688 original size:31 final size:30
Alignment explanation
Indices: 1157622--1157688 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 30
1157612 AAAAATTAAC
* * *
1157622 AAAATATTTAATGAAAATATATTAATATAG
1 AAAATATTAAATAAAAATATATTAAAATAG
*
1157652 TAAATATTAAATTAAAAATATATTAAAAATA-
1 AAAATATTAAA-TAAAAATATATT-AAAATAG
1157683 AAAATA
1 AAAATA
1157689 ATGTGGGCAG
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
30 9 0.30
31 16 0.53
32 5 0.17
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (30 bp):
AAAATATTAAATAAAAATATATTAAAATAG
Found at i:1161042 original size:20 final size:20
Alignment explanation
Indices: 1161019--1161094 Score: 98
Period size: 20 Copynumber: 3.8 Consensus size: 20
1161009 AAAGTACCCA
1161019 AATGTATCGATACATTTTTC
1 AATGTATCGATACATTTTTC
* * * *
1161039 AATGTATCGATTCATGTATG
1 AATGTATCGATACATTTTTC
* *
1161059 AATGTATTGATACATTCTTC
1 AATGTATCGATACATTTTTC
1161079 AATGTATCGATACATT
1 AATGTATCGATACATT
1161095 CTGTCTTTTT
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (20 bp):
AATGTATCGATACATTTTTC
Found at i:1162751 original size:11 final size:11
Alignment explanation
Indices: 1162726--1162755 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
1162716 CCCACTAGAT
1162726 TATTTTTCAAA
1 TATTTTTCAAA
1162737 -ATTTTTCAAA
1 TATTTTTCAAA
1162747 TATTTTTCA
1 TATTTTTCA
1162756 TAAAAACTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (11 bp):
TATTTTTCAAA
Found at i:1175030 original size:19 final size:19
Alignment explanation
Indices: 1175006--1175077 Score: 81
Period size: 19 Copynumber: 3.5 Consensus size: 19
1174996 CCTTCATACC
1175006 CAAAAAAAAACAAAAAAAA
1 CAAAAAAAAACAAAAAAAA
1175025 CAAAAAAAAACAAAAAACAA
1 CAAAAAAAAACAAAAAA-AA
* *
1175045 AAAAAATAAAAAATAAAAAAA
1 CAAAAA-AAAACA-AAAAAAA
1175066 CGAAGAAAAAAA
1 C-AA-AAAAAAA
1175078 TAACCAAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
19 17 0.38
20 7 0.16
21 7 0.16
22 11 0.24
23 3 0.07
ACGTcount: A:0.86, C:0.08, G:0.03, T:0.03
Consensus pattern (19 bp):
CAAAAAAAAACAAAAAAAA
Found at i:1175043 original size:26 final size:26
Alignment explanation
Indices: 1175010--1175093 Score: 89
Period size: 26 Copynumber: 3.0 Consensus size: 26
1175000 CATACCCAAA
1175010 AAAAAACAAAAAAAACAAAAAAAAAC
1 AAAAAACAAAAAAAACAAAAAAAAAC
*
1175036 AAAAAACAAAAAAAATAAAAAATAAA-
1 AAAAAACAAAAAAAACAAAAAA-AAAC
*
1175062 AAAACGAAGAAAAAAATAACCAAAAAAAAAC
1 AAAA--AA-CAAAAAA-AA-CAAAAAAAAAC
1175093 A
1 A
1175094 GAAAGGGGTC
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
26 25 0.52
27 3 0.06
28 2 0.04
29 6 0.12
30 5 0.10
31 7 0.15
ACGTcount: A:0.85, C:0.10, G:0.02, T:0.04
Consensus pattern (26 bp):
AAAAAACAAAAAAAACAAAAAAAAAC
Found at i:1175065 original size:9 final size:9
Alignment explanation
Indices: 1175008--1175057 Score: 75
Period size: 9 Copynumber: 5.7 Consensus size: 9
1174998 TTCATACCCA
1175008 AAAAAAAAC
1 AAAAAAAAC
1175017 AAAAAAAAC
1 AAAAAAAAC
1175026 AAAAAAAA-
1 AAAAAAAAC
*
1175034 ACAAAAAAC
1 AAAAAAAAC
*
1175043 AAAAAAAAT
1 AAAAAAAAC
1175052 AAAAAA
1 AAAAAA
1175058 TAAAAAAACG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
8 7 0.19
9 30 0.81
ACGTcount: A:0.90, C:0.08, G:0.00, T:0.02
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:1175077 original size:1 final size:1
Alignment explanation
Indices: 1175007--1175065 Score: 64
Period size: 1 Copynumber: 59.0 Consensus size: 1
1174997 CTTCATACCC
* * * * * *
1175007 AAAAAAAAACAAAAAAAACAAAAAAAAACAAAAAACAAAAAAAATAAAAAATAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1175066 CGAAGAAAAA
Statistics
Matches: 46, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.90, C:0.07, G:0.00, T:0.03
Consensus pattern (1 bp):
A
Found at i:1176344 original size:28 final size:28
Alignment explanation
Indices: 1176310--1176775 Score: 585
Period size: 28 Copynumber: 16.5 Consensus size: 28
1176300 CGTTCATCTC
* *
1176310 TTCAAAGCCCACAAATTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
1176338 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * **
1176366 TTCAAAGCCCATAAGTCGGTGGCAACTTTT
1 TTCAAAGCCCACAAGTCAGTGGC-A-TCCT
* *
1176396 TTCAAAGCCCACAAGTCAGTAGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
1176424 TTCAAAGCCCATAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
1176452 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
1176480 TTCAAAGCCCACAAGTCGGTGGCAACTCTT
1 TTCAAAGCCCACAAGTCAGTGGC-A-TCCT
* * *
1176510 TTCAAAACCCACAATTCAGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
1176538 TTCAAAGCCCACAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
1176566 TTCAAAGCCCACAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * * * *
1176594 TTCAAAGTCTACAAGTTAATGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
1176622 TTCAAAGCCCACAAGTCAGTGGCA-CCAT
1 TTCAAAGCCCACAAGTCAGTGGCATCC-T
*
1176650 TTCAAAGCCCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-TCCT
*
1176679 TTCAAAGCCCACAAGTCAGTGACATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
1176707 TTCAAAGCCCATAAGTCAGGGGCA-CTCT
1 TTCAAAGCCCACAAGTCAGTGGCATC-CT
* *
1176735 TTCAAAGCTCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
1176763 TTCAAAGCCCACA
1 TTCAAAGCCCACA
1176776 CGAGTTGGTG
Statistics
Matches: 382, Mismatches: 47, Indels: 18
0.85 0.11 0.04
Matches are distributed among these distances:
27 3 0.01
28 306 0.80
29 29 0.08
30 44 0.12
ACGTcount: A:0.30, C:0.31, G:0.17, T:0.23
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCATCCT
Found at i:1176512 original size:114 final size:113
Alignment explanation
Indices: 1176310--1176775 Score: 659
Period size: 114 Copynumber: 4.1 Consensus size: 113
1176300 CGTTCATCTC
* *
1176310 TTCAAAGCCCACAAATTAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCC
1 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCC
* * *
1176375 CATAAGTCGGTGGCAACTTTTTTCAAAGCCCACAAGTCAGTAGCACCCT
66 CACAAGTCGGTGGC-ACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCT
*
1176424 TTCAAAGCCCATAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCC
1 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCC
* * * *
1176489 CACAAGTCGGTGGCAACTCTTTTCAAAACCCACAATTCAGTGGCATCTT
66 CACAAGTCGGTGGC-ACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCT
* * *
1176538 TTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGTC
1 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCC
* *** * *
1176603 TACAAGTTAATGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACCAT
66 CACAAGTCGGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCT
* * *
1176650 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGACATCCTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGC
* *
1176715 CCATAAGTCAGG-GGCACTC-TTTCAAAGCTCACAAGTCAGTGGCACCCT
65 CCACAAGTC-GGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCT
1176763 TTCAAAGCCCACA
1 TTCAAAGCCCACA
1176776 CGAGTTGGTG
Statistics
Matches: 313, Mismatches: 36, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
112 49 0.16
113 88 0.28
114 176 0.56
ACGTcount: A:0.30, C:0.31, G:0.17, T:0.23
Consensus pattern (113 bp):
TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCC
CACAAGTCGGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCT
Found at i:1177739 original size:20 final size:20
Alignment explanation
Indices: 1177716--1177790 Score: 105
Period size: 20 Copynumber: 3.8 Consensus size: 20
1177706 AAGTACCCAG
1177716 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
1177736 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
1177756 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
*
1177776 ATGTATTGATACATT
1 ATGTATCGATACATT
1177791 CTGTCTTTTT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1182164 original size:7 final size:7
Alignment explanation
Indices: 1182152--1182181 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
1182142 ATTTCAACTA
1182152 TTTTATC
1 TTTTATC
1182159 TTTTATC
1 TTTTATC
*
1182166 TTTTAAC
1 TTTTATC
1182173 TTTTATC
1 TTTTATC
1182180 TT
1 TT
1182182 AATAATAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (7 bp):
TTTTATC
Found at i:1183985 original size:17 final size:16
Alignment explanation
Indices: 1183963--1184070 Score: 65
Period size: 17 Copynumber: 6.4 Consensus size: 16
1183953 TTTGTATTTT
1183963 TTAAAAAATAAAAAATA
1 TTAAAAAATAAAAAA-A
*
1183980 TTAAAAAATTAAAAAA
1 TTAAAAAATAAAAAAA
1183996 TTAAGAAAATGAATAAAAGA
1 TTAA-AAAAT-AA-AAAA-A
* * * *
1184016 ATATAAGA-AATAAAA
1 TTAAAAAATAAAAAAA
*
1184031 GTAAAAAATAAAAATAA
1 TTAAAAAATAAAAA-AA
**
1184048 AGAAAAAATAAAATAAA
1 TTAAAAAATAAAA-AAA
*
1184065 ATAAAA
1 TTAAAA
1184071 TAGATATAAT
Statistics
Matches: 71, Mismatches: 13, Indels: 14
0.72 0.13 0.14
Matches are distributed among these distances:
15 6 0.08
16 12 0.17
17 41 0.58
18 2 0.03
19 7 0.10
20 3 0.04
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (16 bp):
TTAAAAAATAAAAAAA
Found at i:1184060 original size:5 final size:5
Alignment explanation
Indices: 1184023--1184072 Score: 50
Period size: 5 Copynumber: 10.0 Consensus size: 5
1184013 AGAATATAAG
* *
1184023 AAATA AAAGTA AAA-A ATA-A AAATA AAGAAA AAATA AAATA AAATA AAATA
1 AAATA AAA-TA AAATA AAATA AAATA AA-ATA AAATA AAATA AAATA AAATA
1184073 GATATAATCC
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
4 6 0.16
5 23 0.61
6 9 0.24
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (5 bp):
AAATA
Found at i:1186698 original size:20 final size:20
Alignment explanation
Indices: 1186670--1186744 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
1186660 TTTTACCTAG
1186670 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * * *
1186690 ATATATCGATACGTGTATGA
1 ATGTATCGATACATTTTTCA
* * *
1186710 ATGTATCGATATATTCTGCA
1 ATGTATCGATACATTTTTCA
1186730 ATGTATCGATACATT
1 ATGTATCGATACATT
1186745 ATGTCTTTTT
Statistics
Matches: 41, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1186771 original size:24 final size:24
Alignment explanation
Indices: 1186739--1186786 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1186729 AATGTATCGA
1186739 TACATTATGTCTTTTTACCTAGAT
1 TACATTATGTCTTTTTACCTAGAT
1186763 TACATTATGTCTTTTTACCTAGAT
1 TACATTATGTCTTTTTACCTAGAT
1186787 GTATCGATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.17, G:0.08, T:0.50
Consensus pattern (24 bp):
TACATTATGTCTTTTTACCTAGAT
Found at i:1190044 original size:19 final size:19
Alignment explanation
Indices: 1190007--1190046 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1189997 GAAGGGCCAC
*
1190007 TTTTTTTTATTGATGTTCA
1 TTTTTTTTATTGATATTCA
* *
1190026 TTTTTTTTCTTGCTATTCA
1 TTTTTTTTATTGATATTCA
1190045 TT
1 TT
1190047 CCCATTATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.12, C:0.10, G:0.07, T:0.70
Consensus pattern (19 bp):
TTTTTTTTATTGATATTCA
Found at i:1190188 original size:14 final size:14
Alignment explanation
Indices: 1190169--1190195 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1190159 AAAGGGCATT
1190169 AGTCATGGAGCAGC
1 AGTCATGGAGCAGC
1190183 AGTCATGGAGCAG
1 AGTCATGGAGCAG
1190196 TAAACTGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.19, G:0.37, T:0.15
Consensus pattern (14 bp):
AGTCATGGAGCAGC
Found at i:1198479 original size:13 final size:13
Alignment explanation
Indices: 1198461--1198486 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1198451 ACATAAAATG
1198461 TTGTATCGATACA
1 TTGTATCGATACA
1198474 TTGTATCGATACA
1 TTGTATCGATACA
1198487 CTGATCTTTG
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):
TTGTATCGATACA
Found at i:1198589 original size:52 final size:52
Alignment explanation
Indices: 1198495--1198624 Score: 192
Period size: 52 Copynumber: 2.5 Consensus size: 52
1198485 CACTGATCTT
* *
1198495 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACA-TTTTAAAA
1 TGTATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACTATT-AAA
*
1198546 TGTATCGATACATGCAGGCAAATTTTCTCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACTATTAAA
* *
1198598 TGTATCGATACATGCAAGCAACTTTTC
1 TGTATCGATACATGCAGGCAAATTTTC
1198625 ATATTTCGGG
Statistics
Matches: 72, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
51 19 0.26
52 50 0.69
53 3 0.04
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACTATTAAA
Found at i:1203363 original size:9 final size:9
Alignment explanation
Indices: 1203345--1203392 Score: 60
Period size: 9 Copynumber: 5.0 Consensus size: 9
1203335 CCTTTACACC
1203345 CAAAAAAAA
1 CAAAAAAAA
*
1203354 CAAAACAAA
1 CAAAAAAAA
1203363 CAAAAAAAAA
1 C-AAAAAAAA
1203373 CAAAAAAAA
1 CAAAAAAAA
1203382 CCAAGAAAAAA
1 -CAA-AAAAAA
1203393 TAGCAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
9 17 0.50
10 11 0.32
11 6 0.18
ACGTcount: A:0.83, C:0.15, G:0.02, T:0.00
Consensus pattern (9 bp):
CAAAAAAAA
Found at i:1203370 original size:19 final size:20
Alignment explanation
Indices: 1203346--1203404 Score: 75
Period size: 19 Copynumber: 2.9 Consensus size: 20
1203336 CTTTACACCC
*
1203346 AAAAAAAACAAAACAAA-CA
1 AAAAAAAACAAAAAAAACCA
1203365 AAAAAAAACAAAAAAAACCA
1 AAAAAAAACAAAAAAAACCA
1203385 AGAAAAAATAGCAAAAAAAA
1 A-AAAAAA-A-CAAAAAAAA
1203405 GAAAAGGTCT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
19 16 0.46
20 3 0.09
21 6 0.17
22 1 0.03
23 9 0.26
ACGTcount: A:0.83, C:0.12, G:0.03, T:0.02
Consensus pattern (20 bp):
AAAAAAAACAAAAAAAACCA
Found at i:1203373 original size:10 final size:10
Alignment explanation
Indices: 1203346--1203404 Score: 66
Period size: 10 Copynumber: 5.7 Consensus size: 10
1203336 CTTTACACCC
1203346 AAAAAAAAC-
1 AAAAAAAACA
*
1203355 AAAACAAACA
1 AAAAAAAACA
1203365 AAAAAAAACA
1 AAAAAAAACA
*
1203375 AAAAAAACCA
1 AAAAAAAACA
1203385 AGAAAAAATAGCA
1 A-AAAAAA-A-CA
1203398 AAAAAAA
1 AAAAAAA
1203405 GAAAAGGTCT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
9 8 0.19
10 19 0.45
11 6 0.14
12 6 0.14
13 3 0.07
ACGTcount: A:0.83, C:0.12, G:0.03, T:0.02
Consensus pattern (10 bp):
AAAAAAAACA
Found at i:1203399 original size:23 final size:23
Alignment explanation
Indices: 1203346--1203404 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
1203336 CTTTACACCC
*
1203346 AAAAA-AAACAAAACAAACAAAA
1 AAAAACAAAAAAAACAAACAAAA
* *
1203368 AAAAACAAAAAAAACCAAGAAAA
1 AAAAACAAAAAAAACAAACAAAA
* *
1203391 AATAGCAAAAAAAA
1 AAAAACAAAAAAAA
1203405 GAAAAGGTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
22 5 0.16
23 26 0.84
ACGTcount: A:0.83, C:0.12, G:0.03, T:0.02
Consensus pattern (23 bp):
AAAAACAAAAAAAACAAACAAAA
Found at i:1204658 original size:28 final size:28
Alignment explanation
Indices: 1204618--1205513 Score: 961
Period size: 28 Copynumber: 31.5 Consensus size: 28
1204608 ATGTTCATCC
*
1204618 CTTTCAAAGCCCACGAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
*
1204646 CTTTCAAAGCCCACAAGTCAGCGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
*
1204674 CTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1204702 CTTTCAAAGCCCACAAGTCAGTAGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
*
1204730 CTTTCAGAGCCCACAAGTCAGTGGCAC-
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
1204757 CTTTTCGAAGCCCATAAGTCAGTGGCACC
1 C-TTTCAAAGCCCACAAGTCAGTGGCACT
* * *
1204786 CTTTCGAAGCCCACATGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
1204814 CTTTCGAAGCCCACAAGTCAGCGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1204842 CTTTCGAAGGCCC-CAAGTCAGTGGCACC
1 CTTTC-AAAGCCCACAAGTCAGTGGCACT
* *
1204870 CTTTCGAAGCCCACAATTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
*
1204898 CTTTTGAAA-CCCACAAGTCAGTGGCA-T
1 C-TTTCAAAGCCCACAAGTCAGTGGCACT
*
1204925 CCTTTCAAAGCCCACGAGTCAGTGGCACAT
1 -CTTTCAAAGCCCACAAGTCAGTGGCAC-T
* *
1204955 TTTTCAAAGCCCACGAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
1204983 CTTTCAAAGCCCACAAGTCAGTGGCA-T
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1205010 CCTTTCAAAGCCCACGCAAGTTAGTGGCACC
1 -CTTTCAAAGCCCA--CAAGTCAGTGGCACT
* *
1205041 CTTTTAAAGCCCACGCAAGTCAATGGCAC-
1 CTTTCAAAGCCCA--CAAGTCAGTGGCACT
*
1205070 CTTTTCAAAGCCCACGAGTCAGTGGCACT
1 C-TTTCAAAGCCCACAAGTCAGTGGCACT
*
1205099 CTTTCAAAGCCCACAAGTCAGTGGCATT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
*
1205127 CTTTCAAAGCCCACGCAAGTCAGTGGCACC
1 CTTTCAAAGCCCA--CAAGTCAGTGGCACT
* *
1205157 CTTTTAAAGCCCACGCAAGTCAGTAGCACT
1 CTTTCAAAGCCCA--CAAGTCAGTGGCACT
1205187 CTTTTCAAAGCCCACGCAAGTCAGTGGCACT
1 C-TTTCAAAGCCCA--CAAGTCAGTGGCACT
** *
1205218 CCTTTCAAAGCCCATGAGTCAGTGGCACC
1 -CTTTCAAAGCCCACAAGTCAGTGGCACT
* **
1205247 CTTTCAAAACCCATGAGTCAGTGGCAC-
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1205274 CTTTTC-TAGCCCACAAGTTAGTGGCACT
1 C-TTTCAAAGCCCACAAGTCAGTGGCACT
*
1205302 TTTTC-AAGCCCACAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
* * * *
1205329 TTTTCAAAACCCACAAGTCAATGGCATT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
*
1205357 TTTTC-AAGCCCACAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1205384 TTTTCAAAGCCCACAAGTTAGTGGCA-T
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
1205411 CCTTTCAAAGCCCACAAATCAATGGAAC-
1 -CTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
1205439 CTTTTCAAAACCCACAAGTTAGTGACACT
1 C-TTTCAAAGCCCACAAGTCAGTGGCACT
* **
1205468 CTTTTCAAAGCCCACAAGCCAGTAGTAACT
1 C-TTTCAAAGCCCACAAGTCAGT-GGCACT
*
1205498 CTTTTCAAAGCTCACA
1 C-TTTCAAAGCCCACA
1205514 CGTGTCGGTG
Statistics
Matches: 758, Mismatches: 82, Indels: 54
0.85 0.09 0.06
Matches are distributed among these distances:
27 86 0.11
28 451 0.59
29 71 0.09
30 110 0.15
31 39 0.05
32 1 0.00
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.23
Consensus pattern (28 bp):
CTTTCAAAGCCCACAAGTCAGTGGCACT
Found at i:1206193 original size:20 final size:20
Alignment explanation
Indices: 1206121--1206195 Score: 98
Period size: 20 Copynumber: 3.8 Consensus size: 20
1206111 TACTCAGATA
* * *
1206121 TATCGATACATTTTTCAATA
1 TATCGATACATTATGCAATG
1206141 TATCGATACATGTATG-AATG
1 TATCGATACAT-TATGCAATG
*
1206161 TATCGATATATTATGCAATG
1 TATCGATACATTATGCAATG
1206181 TATCGATACATTATG
1 TATCGATACATTATG
1206196 TCTTTTTACC
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 4 0.08
20 42 0.88
21 2 0.04
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (20 bp):
TATCGATACATTATGCAATG
Found at i:1210385 original size:21 final size:22
Alignment explanation
Indices: 1210360--1210400 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1210350 AAAATAAAAA
*
1210360 AAATTAGATTA-ATTAAATATT
1 AAATTAGATTAGAATAAATATT
*
1210381 AAATTATATTAGAATAAATA
1 AAATTAGATTAGAATAAATA
1210401 CACATAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (22 bp):
AAATTAGATTAGAATAAATATT
Found at i:1212688 original size:17 final size:17
Alignment explanation
Indices: 1212645--1212690 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
1212635 TATTTAAATA
*
1212645 ATAAATATTAATAATAAT
1 ATAAATATT-TTAATAAT
* *
1212663 ATTATTATTTTAATAAT
1 ATAAATATTTTAATAAT
1212680 ATAAATATTTT
1 ATAAATATTTT
1212691 TAATCATTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
17 16 0.70
18 7 0.30
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATAAATATTTTAATAAT
Found at i:1213556 original size:17 final size:18
Alignment explanation
Indices: 1213512--1213564 Score: 53
Period size: 17 Copynumber: 3.1 Consensus size: 18
1213502 TATCTAATTA
1213512 AATATTTAAATTT-TTATT
1 AATATTT-AATTTATTATT
1213530 -ATATTT--TTTATT-TT
1 AATATTTAATTTATTATT
1213544 AATATTTAATTTAATTATT
1 AATATTTAATTT-ATTATT
1213563 AA
1 AA
1213565 ATATAAGTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 11
0.73 0.00 0.28
Matches are distributed among these distances:
14 5 0.17
15 8 0.28
17 9 0.31
18 3 0.10
19 4 0.14
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
AATATTTAATTTATTATT
Found at i:1213824 original size:18 final size:22
Alignment explanation
Indices: 1213779--1213818 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1213769 TTTTTTAGTG
1213779 AATATTTTTAATAAACTTAATA
1 AATATTTTTAATAAACTTAATA
1213801 AATATTTTTAA-AAA-TTAA
1 AATATTTTTAATAAACTTAA
1213819 AATATTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 3 0.17
22 11 0.61
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (22 bp):
AATATTTTTAATAAACTTAATA
Found at i:1213894 original size:21 final size:21
Alignment explanation
Indices: 1213863--1213946 Score: 61
Period size: 21 Copynumber: 4.1 Consensus size: 21
1213853 AAATTTTTAG
1213863 AAAA-TAT-TTTTAAAAATAT
1 AAAATTATATTTTAAAAATAT
* *
1213882 AAAATTATATTTTTAAAATTT
1 AAAATTATATTTTAAAAATAT
* * *
1213903 AAAATCTGA-CTTTAAAAAAAAT
1 AAAAT-T-ATATTTTAAAAATAT
*
1213925 AAAAAT-TATTTTAAAAAT-T
1 AAAATTATATTTTAAAAATAT
1213944 AAA
1 AAA
1213947 GAAATACAAC
Statistics
Matches: 49, Mismatches: 11, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
19 8 0.16
20 11 0.22
21 16 0.33
22 13 0.27
23 1 0.02
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.39
Consensus pattern (21 bp):
AAAATTATATTTTAAAAATAT
Found at i:1213894 original size:22 final size:21
Alignment explanation
Indices: 1213866--1213907 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1213856 TTTTTAGAAA
1213866 ATATTTTTAAAAATATAAAATT
1 ATATTTTT-AAAATATAAAATT
*
1213888 ATATTTTTAAAATTTAAAAT
1 ATATTTTTAAAATATAAAAT
1213908 CTGACTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
ATATTTTTAAAATATAAAATT
Found at i:1214001 original size:17 final size:18
Alignment explanation
Indices: 1213961--1214001 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
1213951 TACAACATGG
*
1213961 AATTA-AAAATCATTTTA
1 AATTATAAAATCATTTGA
*
1213978 AAATATAAAAT-ATTTGA
1 AATTATAAAATCATTTGA
1213995 AATTATA
1 AATTATA
1214002 TTTTTGAATG
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39
Consensus pattern (18 bp):
AATTATAAAATCATTTGA
Found at i:1214216 original size:8 final size:8
Alignment explanation
Indices: 1214205--1214266 Score: 53
Period size: 7 Copynumber: 8.1 Consensus size: 8
1214195 TTTTATTAAA
1214205 AATATTTT
1 AATATTTT
1214213 AATA-TTT
1 AATATTTT
*
1214220 ATATATATT
1 A-ATATTTT
*
1214229 -A-ATTTA
1 AATATTTT
1214235 AATATTTT
1 AATATTTT
1214243 AAT-TTTT
1 AATATTTT
1214250 AAT-TTTT
1 AATATTTT
1214257 AATATATTT
1 AATAT-TTT
1214266 A
1 A
1214267 TTAAGTTTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
6 3 0.07
7 20 0.45
8 15 0.34
9 6 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
AATATTTT
Found at i:1214260 original size:22 final size:23
Alignment explanation
Indices: 1214208--1214267 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
1214198 TATTAAAAAT
1214208 ATTTTAATA-TTTATATATATTA
1 ATTTTAATATTTTATATATATTA
* *
1214230 ATTTAAATATTTTA-AT-TTTTA
1 ATTTTAATATTTTATATATATTA
1214251 ATTTTTAATATATTTAT
1 A-TTTTAATAT-TTTAT
1214268 TAAGTTTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
21 5 0.16
22 18 0.58
23 8 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
ATTTTAATATTTTATATATATTA
Found at i:1214448 original size:23 final size:22
Alignment explanation
Indices: 1214422--1214470 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1214412 TTTTGTGATG
1214422 TCATATGTCAATATTATGTAATA
1 TCATATGTCAATA-TATGTAATA
* *
1214445 TCATATGTTAATATATGTGATA
1 TCATATGTCAATATATGTAATA
1214467 TCAT
1 TCAT
1214471 GTGTTAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 12 0.50
23 12 0.50
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.45
Consensus pattern (22 bp):
TCATATGTCAATATATGTAATA
Found at i:1214467 original size:22 final size:23
Alignment explanation
Indices: 1214400--1214478 Score: 88
Period size: 23 Copynumber: 3.5 Consensus size: 23
1214390 TTTACTAAAG
* * * *
1214400 CATATGATAACATTTTGTGATGT
1 CATATGTTAATATTATGTGATAT
* *
1214423 CATATGTCAATATTATGTAATAT
1 CATATGTTAATATTATGTGATAT
1214446 CATATGTTAATA-TATGTGATAT
1 CATATGTTAATATTATGTGATAT
*
1214468 CATGTGTTAAT
1 CATATGTTAAT
1214479 TATTTATTGG
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
22 19 0.40
23 28 0.60
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.44
Consensus pattern (23 bp):
CATATGTTAATATTATGTGATAT
Found at i:1215447 original size:16 final size:18
Alignment explanation
Indices: 1215403--1215461 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 18
1215393 AAAATAATAT
1215403 TTATAT-TTTAATTATTTAA
1 TTATATATTTAA--ATTTAA
1215422 TTATATATTTAAATTTAA
1 TTATATATTTAAATTTAA
*
1215440 -TA-ATATTT-AATATAA
1 TTATATATTTAAATTTAA
1215455 TTATATA
1 TTATATA
1215462 AATATAATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
15 6 0.17
16 8 0.22
17 5 0.14
18 6 0.17
19 6 0.17
20 5 0.14
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTATATATTTAAATTTAA
Found at i:1215453 original size:27 final size:26
Alignment explanation
Indices: 1215395--1215453 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 26
1215385 AAGTACAGAA
*
1215395 AATA-ATATTTATATTTTAATTATTT
1 AATATATATTTAAATTTTAATTATTT
1215420 AATTATATATTTAAA-TTTAATAATATTT
1 AA-TATATATTTAAATTTTAAT--TATTT
1215448 AATATA
1 AATATA
1215454 ATTATATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
25 2 0.07
26 8 0.28
27 12 0.41
28 7 0.24
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
AATATATATTTAAATTTTAATTATTT
Found at i:1215460 original size:15 final size:15
Alignment explanation
Indices: 1215425--1215475 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
1215415 TATTTAATTA
*
1215425 TATATTTAAATTTAAT
1 TATATTT-AATATAAT
*
1215441 AATATTTAATATAAT
1 TATATTTAATATAAT
*
1215456 TATA-TAAATATAAT
1 TATATTTAATATAAT
1215470 ATATAT
1 -TATAT
1215476 AAAATTATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 9 0.31
15 14 0.48
16 6 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TATATTTAATATAAT
Found at i:1215470 original size:5 final size:5
Alignment explanation
Indices: 1215447--1215513 Score: 59
Period size: 5 Copynumber: 13.4 Consensus size: 5
1215437 TAATAATATT
* * *
1215447 TAATA TAAT- T-ATA TAAATA TAATA T-ATA TAAAA TTATTA AAATA TAATA
1 TAATA TAATA TAATA T-AATA TAATA TAATA TAATA -TAATA TAATA TAATA
1215496 TAATA TAATA TAAATA TA
1 TAATA TAATA T-AATA TA
1215514 TTTTTAAATT
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
3 2 0.04
4 6 0.12
5 30 0.60
6 12 0.24
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAATA
Found at i:1215491 original size:16 final size:16
Alignment explanation
Indices: 1215472--1215584 Score: 55
Period size: 15 Copynumber: 7.4 Consensus size: 16
1215462 AATATAATAT
1215472 ATATAAAATTATTAAA
1 ATATAAAATTATTAAA
* * *
1215488 ATATAATA-TAATATA
1 ATATAAAATTATTAAA
1215503 ATAT-AAATATATT---
1 ATATAAAAT-TATTAAA
* *
1215516 -TTTA-AATTATTATA
1 ATATAAAATTATTAAA
*
1215530 ATAT-AAATTATTAAT
1 ATATAAAATTATTAAA
*
1215545 ATATAAAAATTAATATAA
1 ATAT-AAAATTATTA-AA
*
1215563 ATATAAAA-TATTTTAA
1 ATATAAAATTA-TTAAA
1215579 ATATAA
1 ATATAA
1215585 TATATCTACC
Statistics
Matches: 72, Mismatches: 13, Indels: 24
0.66 0.12 0.22
Matches are distributed among these distances:
11 4 0.06
12 5 0.07
14 2 0.03
15 23 0.32
16 20 0.28
17 13 0.18
18 5 0.07
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATATAAAATTATTAAA
Found at i:1215505 original size:54 final size:51
Alignment explanation
Indices: 1215446--1215573 Score: 127
Period size: 57 Copynumber: 2.4 Consensus size: 51
1215436 TTAATAATAT
1215446 TTAATATAATTATATAAATATAATAT-ATATAAAATTATTAAAATATAATATAA
1 TTAATATAATTATATAAATATAATATAATAT-AAATTATTAAAATATAA-A-AA
* * *
1215499 TATAATATAAATATATTTTTAAAT-TATTATAATATAAATTATTAATATATAAAAA
1 T-TAATAT-AAT-TA--TATAAATATAATATAATATAAATTATTAAAATATAAAAA
*
1215554 TTAATATAAATATA-AAATAT
1 TTAATATAATTATATAAATAT
1215574 TTTAAATATA
Statistics
Matches: 63, Mismatches: 5, Indels: 17
0.74 0.06 0.20
Matches are distributed among these distances:
49 4 0.06
50 2 0.03
52 2 0.03
53 3 0.05
54 12 0.19
55 6 0.10
56 3 0.05
57 21 0.33
58 10 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (51 bp):
TTAATATAATTATATAAATATAATATAATATAAATTATTAAAATATAAAAA
Found at i:1215514 original size:23 final size:22
Alignment explanation
Indices: 1215441--1215589 Score: 79
Period size: 21 Copynumber: 6.9 Consensus size: 22
1215431 TAAATTTAAT
*
1215441 AATATTTAATATAAT-TATATA
1 AATATATAATATAATATATATA
*
1215462 AATATAATATATATAAAAT-TATTA
1 AATAT-ATA-ATATAATATATA-TA
1215486 AA-ATATAATATAATATAATATA
1 AATATATAATATAATAT-ATATA
* *
1215508 AATATAT-TTTTAA-AT-TATTA
1 AATATATAATATAATATATA-TA
1215528 TAATATA-AATTATTAATATATA-A
1 -AATATATAA-TA-TAATATATATA
1215551 AA-AT-TAATATAA-ATATA-A
1 AATATATAATATAATATATATA
*
1215569 AATATTTTAAATATAATATAT
1 AATA-TAT-AATATAATATAT
1215590 CTACCTAAAT
Statistics
Matches: 101, Mismatches: 7, Indels: 38
0.69 0.05 0.26
Matches are distributed among these distances:
18 8 0.08
19 6 0.06
20 5 0.05
21 26 0.26
22 23 0.23
23 24 0.24
24 7 0.07
25 2 0.02
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
AATATATAATATAATATATATA
Found at i:1215549 original size:42 final size:40
Alignment explanation
Indices: 1215443--1215551 Score: 109
Period size: 42 Copynumber: 2.7 Consensus size: 40
1215433 AATTTAATAA
1215443 TATT-TAATATAATTATATAA-ATAT-AATATATATAAAAT
1 TATTATAATATAATTAT-TAATATATAAATATATATAAAAT
* * * *
1215481 TATTAAAATATAA-TATAATATAATATAAATATATTTTTAAAT
1 TATTATAATATAATTATTA-AT-ATATAAATATA-TATAAAAT
1215523 TATTATAATATAAATTATTAATATATAAA
1 TATTATAATAT-AATTATTAATATATAAA
1215552 AATTAATATA
Statistics
Matches: 57, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
37 1 0.02
38 8 0.14
39 7 0.12
40 4 0.07
41 6 0.11
42 23 0.40
43 4 0.07
44 4 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (40 bp):
TATTATAATATAATTATTAATATATAAATATATATAAAAT
Found at i:1215585 original size:27 final size:27
Alignment explanation
Indices: 1215492--1215588 Score: 90
Period size: 27 Copynumber: 3.4 Consensus size: 27
1215482 ATTAAAATAT
1215492 AATATAATATAATATAAATATATTTTTA
1 AATATAATATAATATAAATATA-TTTTA
* *
1215520 AAT-TATTATAATATAAATTATTAATATATA
1 AATATAATATAATATAAA-TA-T-AT-TTTA
*
1215550 AAAATTAATATAAATATAAA-ATATTTTA
1 AATA-TAATAT-AATATAAATATATTTTA
1215578 AATATAATATA
1 AATATAATATA
1215589 TCTACCTAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 16
0.72 0.08 0.21
Matches are distributed among these distances:
26 1 0.02
27 19 0.34
28 11 0.20
29 4 0.07
30 7 0.12
31 1 0.02
32 5 0.09
33 8 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (27 bp):
AATATAATATAATATAAATATATTTTA
Found at i:1215587 original size:75 final size:71
Alignment explanation
Indices: 1215424--1215589 Score: 176
Period size: 75 Copynumber: 2.3 Consensus size: 71
1215414 TTATTTAATT
* * *
1215424 ATATATTTAAATTTAATA-ATATTTAATATAATTATATAAATATAATATATATAAAATTATTAAA
1 ATAT-TTTAAATATAATATATATTTAATATAATAATATAAATATAATATATATAAAATTAATAAA
*
1215488 ATATAAT
65 ATATAAA
* * * *
1215495 ATAATAT-AATATAAATATATTTTTAAATTATTATAATATAAATTATTAATATATA-AAAATTAA
1 ATATTTTAAATAT-AATATATATTT-AA-TATAATAATATAAA-TA-TAATATATATAAAATTAA
1215558 TATAAATATAAA
61 TA-AAATATAAA
1215570 ATATTTTAAATATAATATAT
1 ATATTTTAAATATAATATAT
1215590 CTACCTAAAT
Statistics
Matches: 77, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
69 4 0.05
70 6 0.08
71 8 0.10
72 2 0.03
73 12 0.16
74 11 0.14
75 29 0.38
76 5 0.06
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (71 bp):
ATATTTTAAATATAATATATATTTAATATAATAATATAAATATAATATATATAAAATTAATAAAA
TATAAA
Found at i:1221022 original size:17 final size:17
Alignment explanation
Indices: 1221000--1221050 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
1220990 ATATTAAGCA
1221000 GAAAAAATAAGTCAAGT
1 GAAAAAATAAGTCAAGT
*
1221017 GAAAAAATGAGGTTCAA-T
1 GAAAAAAT-AAG-TCAAGT
*
1221035 TAAAAAATAAGTCAAG
1 GAAAAAATAAGTCAAG
1221051 CCTTGATTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 4 0.14
17 10 0.36
18 10 0.36
19 4 0.14
ACGTcount: A:0.57, C:0.06, G:0.18, T:0.20
Consensus pattern (17 bp):
GAAAAAATAAGTCAAGT
Found at i:1221415 original size:23 final size:22
Alignment explanation
Indices: 1221389--1221436 Score: 53
Period size: 23 Copynumber: 2.1 Consensus size: 22
1221379 ATTTGGCATA
1221389 TTAATATT-TTTATTAAAATTATT
1 TTAA-ATTATTTATT-AAATTATT
*
1221412 TTAAATTAATTTATTCAATTATT
1 TTAAATT-ATTTATTAAATTATT
1221435 TT
1 TT
1221437 TATTTTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
22 3 0.14
23 13 0.59
24 6 0.27
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
TTAAATTATTTATTAAATTATT
Found at i:1221963 original size:17 final size:17
Alignment explanation
Indices: 1221941--1221988 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
1221931 AAATAAGATT
1221941 ATTTTTATTA-ATTTAAA
1 ATTTTTATTATATTT-AA
*
1221958 ATTTTT-TTATATTTAT
1 ATTTTTATTATATTTAA
1221974 ATTTTTATATATATT
1 ATTTTTAT-TATATT
1221989 ACCGATTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 10 0.37
17 11 0.41
18 6 0.22
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
ATTTTTATTATATTTAA
Found at i:1221977 original size:16 final size:17
Alignment explanation
Indices: 1221940--1221985 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
1221930 TAAATAAGAT
1221940 TATTTTTATTA-ATTTAA
1 TATTTTT-TTATATTTAA
*
1221957 AATTTTTTTATATTT-A
1 TATTTTTTTATATTTAA
*
1221973 TATTTTTATATAT
1 TATTTTTTTATAT
1221986 ATTACCGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 15 0.60
17 10 0.40
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TATTTTTTTATATTTAA
Found at i:1222259 original size:2 final size:2
Alignment explanation
Indices: 1222252--1222285 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1222242 TCTACTAAAG
1222252 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1222286 TAAAATTATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1223183 original size:17 final size:18
Alignment explanation
Indices: 1223153--1223186 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1223143 TTTTATATAA
*
1223153 TTTTTATTCTTTTTTTCC
1 TTTTTATTCATTTTTTCC
1223171 TTTTT-TTCATTTTTTC
1 TTTTTATTCATTTTTTC
1223187 TTTAACAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTTATTCATTTTTTCC
Found at i:1224884 original size:13 final size:13
Alignment explanation
Indices: 1224866--1224891 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1224856 TACAGCAAGT
1224866 ATGTATCGATACA
1 ATGTATCGATACA
1224879 ATGTATCGATACA
1 ATGTATCGATACA
1224892 CAAAAAATTG
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:1227140 original size:21 final size:21
Alignment explanation
Indices: 1227107--1227151 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1227097 TTGCAAGTTG
*
1227107 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1227129 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
1227149 AAA
1 AAA
1227152 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1228975 original size:15 final size:15
Alignment explanation
Indices: 1228955--1228985 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1228945 TAAAAATGTC
*
1228955 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1228970 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1228985 C
1 C
1228986 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1231085 original size:13 final size:13
Alignment explanation
Indices: 1231064--1231102 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
1231054 ACATTTTTCT
1231064 TTGTATCGATACA
1 TTGTATCGATACA
*
1231077 TTGTCTCGATACA
1 TTGTATCGATACA
*
1231090 TTATATCGATACA
1 TTGTATCGATACA
1231103 GGGTGATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1231265 original size:20 final size:20
Alignment explanation
Indices: 1231222--1231267 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1231212 AAATCTTTTG
1231222 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
1231243 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
1231263 CAAAA
1 CAAAA
1231268 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:1233674 original size:13 final size:13
Alignment explanation
Indices: 1233656--1233681 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1233646 TACAGCAAGT
1233656 ATGTATCGATACA
1 ATGTATCGATACA
1233669 ATGTATCGATACA
1 ATGTATCGATACA
1233682 CAAAAAATTG
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:1235931 original size:21 final size:21
Alignment explanation
Indices: 1235898--1235942 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1235888 TTGCAAGTTG
*
1235898 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1235920 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
1235940 AAA
1 AAA
1235943 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1238360 original size:33 final size:33
Alignment explanation
Indices: 1238318--1238531 Score: 94
Period size: 33 Copynumber: 6.0 Consensus size: 33
1238308 TTTGAAGTAA
1238318 TGTATCGATACAATTCATCATGTATCGATACAT
1 TGTATCGATACAATTCATCATGTATCGATACAT
*
1238351 TGTATCGATATAATGTGC--CATGTATCGATACAAAT
1 TGTATCGATACAAT-T-CATCATGTATCGATAC--AT
* *
1238386 AGTGGTA-GGATAGCTACTGTCAGTTTCATGTATCGATACAATTGTCT
1 --T-GTATCGATA-C-AAT-TCA---TCATGTATCGATAC-A-----T
* * *
1238433 ATGTATCGATACAA-TGAACATGTATCGATATAT
1 -TGTATCGATACAATTCATCATGTATCGATACAT
* ** * *
1238466 TGTATTGATACAAAGCATAATATATCGATACAT
1 TGTATCGATACAATTCATCATGTATCGATACAT
** *
1238499 TGTATCGATACAAAGCATAATGTATCGATACAT
1 TGTATCGATACAATTCATCATGTATCGATACAT
1238532 CTTGGTGTGT
Statistics
Matches: 141, Mismatches: 19, Indels: 42
0.70 0.09 0.21
Matches are distributed among these distances:
32 12 0.09
33 71 0.50
34 1 0.01
35 3 0.02
37 5 0.04
38 5 0.04
39 16 0.11
42 4 0.03
43 13 0.09
44 1 0.01
45 4 0.03
46 5 0.04
47 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.34
Consensus pattern (33 bp):
TGTATCGATACAATTCATCATGTATCGATACAT
Found at i:1238457 original size:19 final size:19
Alignment explanation
Indices: 1238412--1238462 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
1238402 CTGTCAGTTT
*
1238412 CATGTATCGATACAATTGT
1 CATGTATCGATACAATTGA
1238431 CTATGTATCGATACAA-TGAA
1 C-ATGTATCGATACAATTG-A
1238451 CATGTATCGATA
1 CATGTATCGATA
1238463 TATTGTATTG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (19 bp):
CATGTATCGATACAATTGA
Found at i:1240866 original size:22 final size:21
Alignment explanation
Indices: 1240838--1240881 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1240828 GATGATTTTG
* *
1240838 ATGAAAAATGAAATATTTTGAA
1 ATGAAAAAT-AAAAAATTTGAA
1240860 ATGAAAAATAAAAAATTTGAA
1 ATGAAAAATAAAAAATTTGAA
1240881 A
1 A
1240882 GAAGATTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.27
Consensus pattern (21 bp):
ATGAAAAATAAAAAATTTGAA
Found at i:1240902 original size:10 final size:10
Alignment explanation
Indices: 1240887--1240911 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1240877 TGAAAGAAGA
1240887 TTTGATGAAT
1 TTTGATGAAT
1240897 TTTGATGAAT
1 TTTGATGAAT
1240907 TTTGA
1 TTTGA
1240912 AGAAAGGATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.20, T:0.52
Consensus pattern (10 bp):
TTTGATGAAT
Found at i:1241019 original size:13 final size:13
Alignment explanation
Indices: 1241001--1241059 Score: 58
Period size: 13 Copynumber: 5.0 Consensus size: 13
1240991 TAGTAACCTT
1241001 TGTATCGATACAA
1 TGTATCGATACAA
1241014 TGTATCGATACAA
1 TGTATCGATACAA
* *
1241027 ---A--GA-ATAT
1 TGTATCGATACAA
1241034 TGTATCGATACAA
1 TGTATCGATACAA
1241047 TGTATCGATACAA
1 TGTATCGATACAA
1241060 AGAATATTGT
Statistics
Matches: 36, Mismatches: 4, Indels: 12
0.69 0.08 0.23
Matches are distributed among these distances:
7 2 0.06
8 2 0.06
10 2 0.06
12 2 0.06
13 28 0.78
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1241039 original size:20 final size:20
Alignment explanation
Indices: 1241014--1241078 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
1241004 ATCGATACAA
1241014 TGTATCGATACAAAGAATAT
1 TGTATCGATACAAAGAATAT
1241034 TGTATCGATAC-----A-A-
1 TGTATCGATACAAAGAATAT
1241047 TGTATCGATACAAAGAATAT
1 TGTATCGATACAAAGAATAT
1241067 TGTATCGATACA
1 TGTATCGATACA
1241079 TCTGGATTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
15 1 0.03
18 1 0.03
19 1 0.03
20 23 0.61
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (20 bp):
TGTATCGATACAAAGAATAT
Found at i:1241042 original size:33 final size:33
Alignment explanation
Indices: 1241000--1241078 Score: 158
Period size: 33 Copynumber: 2.4 Consensus size: 33
1240990 ATAGTAACCT
1241000 TTGTATCGATACAATGTATCGATACAAAGAATA
1 TTGTATCGATACAATGTATCGATACAAAGAATA
1241033 TTGTATCGATACAATGTATCGATACAAAGAATA
1 TTGTATCGATACAATGTATCGATACAAAGAATA
1241066 TTGTATCGATACA
1 TTGTATCGATACA
1241079 TCTGGATTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.32
Consensus pattern (33 bp):
TTGTATCGATACAATGTATCGATACAAAGAATA
Found at i:1247298 original size:18 final size:20
Alignment explanation
Indices: 1247247--1247298 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
1247237 CTGCGAGTTT
**
1247247 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGAA
*
1247267 CATATATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
1247286 CATGTAT-GATACA
1 CATGTATCGATACA
1247299 TTGTATCGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 6 0.21
19 8 0.29
20 14 0.50
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:1247935 original size:19 final size:18
Alignment explanation
Indices: 1247911--1247951 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
1247901 TTATTTAAAA
*
1247911 ATTTATATTTTTTTATTAT
1 ATTTATA-TATTTTATTAT
*
1247930 ATTTATATATTTTATTTT
1 ATTTATATATTTTATTAT
1247948 ATTT
1 ATTT
1247952 TAATTAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (18 bp):
ATTTATATATTTTATTAT
Found at i:1247992 original size:18 final size:18
Alignment explanation
Indices: 1247964--1248021 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 18
1247954 ATTAAATTTA
1247964 AAATATTTTATATTTATAT
1 AAAT-TTTTATATTTATAT
1247983 AAATTTTTATATATTA-AT
1 AAATTTTTATAT-TTATAT
1248001 -AA-TTTT-TA-TTATAT
1 AAATTTTTATATTTATAT
1248015 AAATTTT
1 AAATTTT
1248022 AAAAAAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
13 3 0.09
14 2 0.06
15 4 0.11
16 7 0.20
17 2 0.06
18 10 0.29
19 7 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
AAATTTTTATATTTATAT
Found at i:1247995 original size:20 final size:19
Alignment explanation
Indices: 1247971--1248014 Score: 56
Period size: 17 Copynumber: 2.3 Consensus size: 19
1247961 TTAAAATATT
1247971 TTATATTTATATAAATTTTTA
1 TTATATTTA-AT-AATTTTTA
1247992 -TATA-TTAATAATTTTTA
1 TTATATTTAATAATTTTTA
1248009 TTATAT
1 TTATAT
1248015 AAATTTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
17 8 0.38
18 6 0.29
19 3 0.14
20 4 0.19
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTATATTTAATAATTTTTA
Found at i:1248143 original size:2 final size:2
Alignment explanation
Indices: 1248136--1248182 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1248126 GGCTTCATGC
1248136 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1248178 TA TA T
1 TA TA T
1248183 TATCACATAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1249684 original size:14 final size:14
Alignment explanation
Indices: 1249609--1249683 Score: 62
Period size: 14 Copynumber: 5.2 Consensus size: 14
1249599 GATTTATATA
**
1249609 AAAATAATAATTTT
1 AAAATAATAATAAT
* *
1249623 AATATAATTATAAT
1 AAAATAATAATAAT
* *
1249637 ATAATCAA-ATATAAA
1 AAAAT-AATA-ATAAT
1249652 AAAATAATAATAAT
1 AAAATAATAATAAT
1249666 AAAATAATAATATAT
1 AAAATAATAATA-AT
1249681 AAA
1 AAA
1249684 TTATTGTATT
Statistics
Matches: 47, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
14 31 0.66
15 16 0.34
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.33
Consensus pattern (14 bp):
AAAATAATAATAAT
Found at i:1251234 original size:16 final size:17
Alignment explanation
Indices: 1251213--1251247 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
1251203 GAAATAAAAT
*
1251213 AAAATTAAATAAG-TAA
1 AAAATTAAAAAAGATAA
1251229 AAAATTAAAAAAGATAA
1 AAAATTAAAAAAGATAA
1251246 AA
1 AA
1251248 GTGAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.20
Consensus pattern (17 bp):
AAAATTAAAAAAGATAA
Found at i:1253065 original size:44 final size:44
Alignment explanation
Indices: 1253007--1253091 Score: 111
Period size: 44 Copynumber: 1.9 Consensus size: 44
1252997 AAATGAAAGG
*
1253007 TGTACAGTGTATACAAGAA-GATCAAATTT-AGACCATATCAATAT
1 TGTACAGTATATACAA-AAGGATCAAATTTGA-ACCATATCAATAT
* *
1253051 TGTATAGTATATACAAAAGGATTAAATTTGAACCATATCAA
1 TGTACAGTATATACAAAAGGATCAAATTTGAACCATATCAA
1253092 CAGCAAAGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
43 2 0.06
44 33 0.92
45 1 0.03
ACGTcount: A:0.45, C:0.12, G:0.13, T:0.31
Consensus pattern (44 bp):
TGTACAGTATATACAAAAGGATCAAATTTGAACCATATCAATAT
Found at i:1254861 original size:19 final size:18
Alignment explanation
Indices: 1254839--1254874 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1254829 AAAAATGTGG
1254839 AAATAAAGAAAAAATAAAT
1 AAATAAA-AAAAAATAAAT
*
1254858 AAATAAATAAAAATAAA
1 AAATAAAAAAAAATAAA
1254875 CAACGTACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATAAAAAAAAATAAAT
Found at i:1255182 original size:216 final size:205
Alignment explanation
Indices: 1254923--1255533 Score: 563
Period size: 216 Copynumber: 3.0 Consensus size: 205
1254913 GGATGCTAAC
* * * *
1254923 GCATCTATTTAATGA-GAAATATTATTAGTTTAATTGGTATATAATTATAATACTTATTAATTAA
1 GCATCTATTTTATAATGAAA-ATTCTTAATTTAATTGGTATATAA-TATAATACTTATTAATT-A
* * * *
1254987 TAATTAATCTAAAATTAAAAATATTTGCTCATTAAGCAGTTTGAATAATTTAAATTATTGTAAAA
63 TAATTAATCTAAAATTAAAAGTATTTGCTCATTGAGTAGTTTAAATAATTTAAATTA-TGTAAAA
* * *
1255052 AAGTATAATTCAATATAAATATAAAGTATATCTAAATTAAAATCAA-ATAATATAATCTCGTAAC
127 AAGTATAATTCAATATAAATACAAAGTATACCTAAATTAAAAT-AAGATAATATAATCTCATAA-
* *
1255116 TCTTATTATATAAATTATAAAA
190 -ATT-TTAT-T--ATAAT-AAA
* **
1255138 TGCATCTATTTTATAATGAAAATTCTTAATTTAATTGGTATATAACTGTAATACAAATTAACTTA
1 -GCATCTATTTTATAATGAAAATTCTTAATTTAATTGGTATATAA-TATAATACTTATTAA-TTA
* * * * * * * *
1255203 TAATTAATCTAAAATGAAAAGTTTTTGCTTATTGATTAATTTAAATAATTTAAGTTA-CTATAAA
63 TAATTAATCTAAAATTAAAAGTATTTGCTCATTGAGTAGTTTAAATAATTTAAATTATGTAAAAA
* *
1255267 AGTGTAATTCAATATGAATACAAAGTATACCTAAATTAAAATAAGATAATATAATCTCATAAATT
128 AGTATAATTCAATATAAATACAAAGTATACCTAAATTAAAATAAGATAATATAATCTCATAAATT
1255332 TTATTATAATAAA
193 TTATTATAATAAA
* *
1255345 --A--TA--TTATAATAAAAATTCTTAATTTAATTGGTATATAATAGTAATA-TTAATCAATTGA
1 GCATCTATTTTATAATGAAAATTCTTAATTTAATTGGTATATAATA-TAATACTT-ATTAATT-A
* * ** *
1255403 GAATTAATCTAAAAATAAAAGTCCTAGCTCATTTGAGTAGTTTAAATAATTTAAATTACTGT-AA
63 TAATTAATCTAAAATTAAAAGTATTTGCTCA-TTGAGTAGTTTAAATAATTTAAATTA-TGTAAA
* * * * * * *
1255467 AAA-TGTAATTC-AGAT--GT--AAAGTATATCTAAATTAAAATTAGATGATATAATCTTATAAA
126 AAAGTATAATTCAATATAAATACAAAGTATACCTAAATTAAAATAAGATAATATAATCTCATAAA
1255526 TTTTATTA
191 TTTTATTA
1255534 CGTAATTAAT
Statistics
Matches: 336, Mismatches: 50, Indels: 38
0.79 0.12 0.09
Matches are distributed among these distances:
196 46 0.14
198 1 0.00
199 3 0.01
200 71 0.21
201 31 0.09
202 6 0.02
203 1 0.00
204 1 0.00
207 3 0.01
208 4 0.01
210 1 0.00
211 4 0.01
212 2 0.01
213 2 0.01
214 59 0.18
216 95 0.28
217 6 0.02
ACGTcount: A:0.46, C:0.07, G:0.08, T:0.40
Consensus pattern (205 bp):
GCATCTATTTTATAATGAAAATTCTTAATTTAATTGGTATATAATATAATACTTATTAATTATAA
TTAATCTAAAATTAAAAGTATTTGCTCATTGAGTAGTTTAAATAATTTAAATTATGTAAAAAAGT
ATAATTCAATATAAATACAAAGTATACCTAAATTAAAATAAGATAATATAATCTCATAAATTTTA
TTATAATAAA
Found at i:1255367 original size:13 final size:13
Alignment explanation
Indices: 1255333--1255358 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1255323 TCATAAATTT
1255333 TATTATAATAAAA
1 TATTATAATAAAA
1255346 TATTATAATAAAA
1 TATTATAATAAAA
1255359 ATTCTTAATT
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:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TATTATAATAAAA
Found at i:1255569 original size:196 final size:197
Alignment explanation
Indices: 1255148--1255533 Score: 496
Period size: 200 Copynumber: 2.0 Consensus size: 197
1255138 TGCATCTATT
* * *
1255148 TTATAATGAAAATTCTTAATTTAATTGGTATATAACTGTAATACAAATTAACTTATAATTAATCT
1 TTATAATAAAAATTCTTAATTTAATTGGTATATAACTGTAATACAAATCAACTTAGAATTAATCT
** * * * * *
1255213 AAAATGAAAAGTTTTTGCTTATTGATTAATTTAAATAATTTAAGTTACTATAAAAGTGTAATTCA
66 AAAATGAAAAGTCCTAGCTCATTGAGTAATTTAAATAATTTAAATTACTATAAAAATGTAATTCA
*
1255278 ATATGAATACAAAGTATACCTAAATTAAAATAAGATAATATAATCTCATAAATTTTATTATAATA
131 AGATG-ATA-AAAGTATACCTAAATTAAAATAAGATAATATAATCTCATAAATTTTATTATAAT-
1255343 AAATA
193 AAATA
**
1255348 TTATAATAAAAATTCTTAATTTAATTGGTATATAA-TAGTAATATTAATCAA-TTGAGAATTAAT
1 TTATAATAAAAATTCTTAATTTAATTGGTATATAACT-GTAATACAAATCAACTT-AGAATTAAT
* *
1255411 CTAAAAAT-AAAAGTCCTAGCTCATTTGAGTAGTTTAAATAATTTAAATTACTGTAAAAATGTAA
64 CT-AAAATGAAAAGTCCTAGCTCA-TTGAGTAATTTAAATAATTTAAATTACTATAAAAATGTAA
* * * *
1255475 TTC-AGATG-T-AAAGTATATCTAAATTAAAATTAGATGATATAATCTTATAAATTTTATTA
127 TTCAAGATGATAAAAGTATACCTAAATTAAAATAAGATAATATAATCTCATAAATTTTATTA
1255534 CGTAATTAAT
Statistics
Matches: 163, Mismatches: 19, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
196 46 0.28
198 1 0.01
199 3 0.02
200 70 0.43
201 43 0.26
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.40
Consensus pattern (197 bp):
TTATAATAAAAATTCTTAATTTAATTGGTATATAACTGTAATACAAATCAACTTAGAATTAATCT
AAAATGAAAAGTCCTAGCTCATTGAGTAATTTAAATAATTTAAATTACTATAAAAATGTAATTCA
AGATGATAAAAGTATACCTAAATTAAAATAAGATAATATAATCTCATAAATTTTATTATAATAAA
TA
Done.