Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 174 of 208
Found at i:55419559 original size:36 final size:35
Alignment explanation
Indices: 55419488--55419785 Score: 220
Period size: 34 Copynumber: 8.5 Consensus size: 35
55419478 AAAAAATCAG
* *
55419488 AAAATTTTTCGTGTTTTCAAAAATTTCCGTG-TTTC
1 AAAAATTTTC-TGTTTTCAAAAATTTTCGTGTTTTC
*
55419523 AAAAATTTTCATGTTTTCAAAAATTCTCGTGTTTTC
1 AAAAATTTTC-TGTTTTCAAAAATTTTCGTGTTTTC
* * ** *
55419559 AAAAAAATTCCAATTTTCAAAATTTTTCGTGTTTTC
1 -AAAAATTTTCTGTTTTCAAAAATTTTCGTGTTTTC
* *
55419595 TAAAAA-CTTCTGTGTTTCAAAAATTTTCGTATTTT-
1 -AAAAATTTTCTGT-TTTCAAAAATTTTCGTGTTTTC
* *
55419630 AAAAATTTT-TGTGTTTCTAAAATTTTCGT-ATTTC
1 AAAAATTTTCTGT-TTTCAAAAATTTTCGTGTTTTC
* *
55419664 AAAAATTTTCTTGTTTTC-AAATTTTTCGT-ATTTC
1 AAAAATTTTC-TGTTTTCAAAAATTTTCGTGTTTTC
* ** *
55419698 AAATATCCTCGTGTTTTCAAAAAATTTCGGTGTTTT-
1 AAAAATTTTC-TGTTTTCAAAAATTTTC-GTGTTTTC
* * *
55419734 GAAAATTTTCTTGTTTTTCAAACAAATCTCGTG-TTTC
1 AAAAATTTTC-TG-TTTTCAAA-AATTTTCGTGTTTTC
*
55419771 ATAAATTTT-TGTTTT
1 AAAAATTTTCTGTTTT
55419786 TTTTTTAAAT
Statistics
Matches: 214, Mismatches: 36, Indels: 27
0.77 0.13 0.10
Matches are distributed among these distances:
33 3 0.01
34 66 0.31
35 45 0.21
36 65 0.30
37 29 0.14
38 6 0.03
ACGTcount: A:0.29, C:0.12, G:0.09, T:0.49
Consensus pattern (35 bp):
AAAAATTTTCTGTTTTCAAAAATTTTCGTGTTTTC
Found at i:55419697 original size:16 final size:16
Alignment explanation
Indices: 55419618--55419701 Score: 64
Period size: 16 Copynumber: 5.0 Consensus size: 16
55419608 GTTTCAAAAA
*
55419618 TTTTCGTATTTTAAAAAT
1 TTTTCGTA-TTT-CAAAT
* *
55419636 TTTT-GTGTTTCTAAAA
1 TTTTCGTATTTC-AAAT
55419652 TTTTCGTATTTCAAAAAT
1 TTTTCGTATTTC--AAAT
*
55419670 TTTCTTGT-TTTCAAAT
1 TTT-TCGTATTTCAAAT
55419686 TTTTCGTATTTCAAAT
1 TTTTCGTATTTCAAAT
55419702 ATCCTCGTGT
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
15 3 0.06
16 25 0.47
17 8 0.15
18 14 0.26
19 3 0.06
ACGTcount: A:0.27, C:0.10, G:0.07, T:0.56
Consensus pattern (16 bp):
TTTTCGTATTTCAAAT
Found at i:55419777 original size:37 final size:35
Alignment explanation
Indices: 55419711--55419786 Score: 84
Period size: 37 Copynumber: 2.1 Consensus size: 35
55419701 TATCCTCGTG
* *
55419711 TTTTCAAAAAATTTCGGTGTTTTGAAAATTTTCTTGT
1 TTTTCAAAAAATCTCGGTGTTTTCAAAA-TTT-TTGT
55419748 TTTTCAAACAAATCTC-GTG-TTTCATAAATTTTTGT
1 TTTTCAAA-AAATCTCGGTGTTTTCA-AAATTTTTGT
55419783 TTTT
1 TTTT
55419787 TTTTTAAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
35 8 0.23
36 7 0.20
37 14 0.40
38 6 0.17
ACGTcount: A:0.26, C:0.11, G:0.11, T:0.53
Consensus pattern (35 bp):
TTTTCAAAAAATCTCGGTGTTTTCAAAATTTTTGT
Found at i:55422610 original size:45 final size:46
Alignment explanation
Indices: 55422545--55422642 Score: 162
Period size: 45 Copynumber: 2.2 Consensus size: 46
55422535 ATAAGTGCCA
* *
55422545 CACTGATATGTAGCCGAAGCTACCACTGATATGTAACCGAAGTTAC
1 CACTGATATGTAGCCGAAGCTACCACTGAGATGTAACCGAAGCTAC
*
55422591 CACTGA-ATGTAGCCGAAGCTACCACTGGGATGTAACCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTACCACTGAGATGTAACCGAAGCTAC
55422636 CACTGAT
1 CACTGAT
55422643 CAATAACACT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
45 42 0.88
46 6 0.12
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (46 bp):
CACTGATATGTAGCCGAAGCTACCACTGAGATGTAACCGAAGCTAC
Found at i:55422649 original size:23 final size:23
Alignment explanation
Indices: 55422545--55422642 Score: 144
Period size: 23 Copynumber: 4.3 Consensus size: 23
55422535 ATAAGTGCCA
*
55422545 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAACCGAAGCTAC
*
55422568 CACTGATATGTAACCGAAGTTAC
1 CACTGATATGTAACCGAAGCTAC
*
55422591 CACTGA-ATGTAGCCGAAGCTAC
1 CACTGATATGTAACCGAAGCTAC
**
55422613 CACTGGGATGTAACCGAAGCTAC
1 CACTGATATGTAACCGAAGCTAC
55422636 CACTGAT
1 CACTGAT
55422643 CAATAACACT
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
22 19 0.29
23 47 0.71
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAACCGAAGCTAC
Found at i:55424216 original size:13 final size:13
Alignment explanation
Indices: 55424200--55424226 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
55424190 AATGAACAGA
55424200 GGCCCAAAACAAT
1 GGCCCAAAACAAT
55424213 GGCCCAAAACAAT
1 GGCCCAAAACAAT
55424226 G
1 G
55424227 TCAGAAACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.30, G:0.19, T:0.07
Consensus pattern (13 bp):
GGCCCAAAACAAT
Found at i:55425168 original size:8 final size:7
Alignment explanation
Indices: 55425150--55425203 Score: 60
Period size: 8 Copynumber: 7.7 Consensus size: 7
55425140 ATTTTTTAGC
55425150 TATTTCAT
1 TATTT-AT
55425158 TATTTAGT
1 TATTTA-T
55425166 TATTTATT
1 TATTTA-T
55425174 TATTTAT
1 TATTTAT
55425181 TA-TTAT
1 TATTTAT
55425187 TA-TTAT
1 TATTTAT
55425193 TA-TTAT
1 TATTTAT
55425199 TATTT
1 TATTT
55425204 CTAAATTTAT
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
6 18 0.42
7 6 0.14
8 19 0.44
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (7 bp):
TATTTAT
Found at i:55425185 original size:3 final size:3
Alignment explanation
Indices: 55425177--55425202 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
55425167 ATTTATTTAT
55425177 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
55425203 TCTAAATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:55431449 original size:87 final size:88
Alignment explanation
Indices: 55431218--55431710 Score: 737
Period size: 88 Copynumber: 5.7 Consensus size: 88
55431208 AGCAGATCAG
* * * * *
55431218 TAAAAATAGCAGATCTTGCCTTCCTACACCGACAGTGAAACAGATCAAAGACACCAGCCATGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
*
55431283 CCCTGGGTTGCAGTGGAGTAGGT
66 CCCTGGGTTGCAGTGGAGCAGGT
* *
55431306 TAAAAATAGCAGATCTTGCCTTCATGCACCGACAGCGAAGCAGATCGAAGAGACCAGCCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
*
55431371 CCCTGGGTTGCAGCGGAGCAGGT
66 CCCTGGGTTGCAGTGGAGCAGGT
* * * *
55431394 T-AAAATAGCAGATCTTGCCTTCCTGCACTGACAGCGAAGTAGATTGAAAACACCAGCCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
*
55431458 CCTTGGGTTGCAGTGGAGCAGGT
66 CCCTGGGTTGCAGTGGAGCAGGT
*
55431481 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCC-
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
*
55431545 CCCTAGGTTGCAGTGGAGCAGGT
66 CCCTGGGTTGCAGTGGAGCAGGT
55431568 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCG-A--A-ATCGAAGACACCAGCCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* *
55431629 CCCTGGGTTGCAGCGTAGCAGGT
66 CCCTGGGTTGCAGTGGAGCAGGT
* * * * *
55431652 TAAAAATAGCATATCTTACCTTCTTGCACCGACAGCGAAGCAGATCGATGACCCCAGCC
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCC
55431711 CTATTTCCCT
Statistics
Matches: 366, Mismatches: 33, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
83 20 0.05
84 55 0.15
85 1 0.00
86 1 0.00
87 138 0.38
88 151 0.41
ACGTcount: A:0.28, C:0.28, G:0.24, T:0.20
Consensus pattern (88 bp):
TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
CCCTGGGTTGCAGTGGAGCAGGT
Found at i:55431455 original size:44 final size:44
Alignment explanation
Indices: 55431320--55431544 Score: 134
Period size: 44 Copynumber: 5.1 Consensus size: 44
55431310 AATAGCAGAT
* * * * *
55431320 CTTGCCTTCATGCACCGACAGCGAAGCAGATCGAAGAGACCAGC
1 CTTGCCTTCCTGCACTGACAGCGAAGCAGATTGAAAACACCAGC
* *** * * * * *
55431364 CTTGCCTCCCTGGGTTG-CAGCGGAGCAGGTT-AAAATAGCAGAT
1 CTTGCCTTCCTGCACTGACAGCGAAGCAGATTGAAAACACCAG-C
*
55431407 CTTGCCTTCCTGCACTGACAGCGAAGTAGATTGAAAACACCAGC
1 CTTGCCTTCCTGCACTGACAGCGAAGCAGATTGAAAACACCAGC
*** * * * * * * *
55431451 CTTGCC-TCCTTGGGTTG-CAGTGGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTTCC-TGCACTGACAGCGAAGCAGATTGAAAACACCAG-C
* * * *
55431495 CTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAAC
1 CTTGCCTTCCTGCACTGACAGCGAAGCAGATTGAAAACACCAGC
55431539 CTTGCC
1 CTTGCC
55431545 CCCTAGGTTG
Statistics
Matches: 126, Mismatches: 48, Indels: 14
0.67 0.26 0.07
Matches are distributed among these distances:
42 7 0.06
43 45 0.36
44 47 0.37
45 27 0.21
ACGTcount: A:0.27, C:0.28, G:0.25, T:0.20
Consensus pattern (44 bp):
CTTGCCTTCCTGCACTGACAGCGAAGCAGATTGAAAACACCAGC
Found at i:55431511 original size:175 final size:173
Alignment explanation
Indices: 55431218--55431699 Score: 711
Period size: 175 Copynumber: 2.8 Consensus size: 173
55431208 AGCAGATCAG
* * * *
55431218 TAAAAATAGCAGATCTTGCCTTCCTACACCGACAGTGAAACAGA-TCAAAGACACCAGCCATGCC
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCG-AA-AGATTGAAA-ACACCAGCCTTGCC
*
55431282 TCCCTGGGTTGCAGTGGAGTAGGTTAAAAATAGCAGATCTTGCCTTCATGCACCGACAGCGAAGC
63 TCCCTGGGTTGCAGTGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCATGCACCGACAGCGAAGC
* * *
55431347 AGATCGAAGAGACCAGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGGT
128 AGATCGAAGACACCAACCTTGCC-CCCTAGGTTGCAGCGGAGCAGGT
*
55431394 T-AAAATAGCAGATCTTGCCTTCCTGCACTGACAGCGAAGTAGATTGAAAACACCAGCCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAA--AGATTGAAAACACCAGCCTTGCCT
* *
55431458 CCTTGGGTTGCAGTGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCA
64 CCCTGGGTTGCAGTGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCATGCACCGACAGCGAAGCA
*
55431523 GATCGAAGACACCAACCTTGCCCCCTAGGTTGCAGTGGAGCAGGT
129 GATCGAAGACACCAACCTTGCCCCCTAGGTTGCAGCGGAGCAGGT
* *
55431568 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCG-AA-ATCGAAGACACCAGCCTTGCCTCC
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAAGATTGAAAACACCAGCCTTGCCTCC
* * * * *
55431631 CTGGGTTGCAGCGTAGCAGGTTAAAAATAGCATATCTTACCTTCTTGCACCGACAGCGAAGCAGA
66 CTGGGTTGCAGTGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCATGCACCGACAGCGAAGCAGA
55431696 TCGA
131 TCGA
55431700 TGACCCCAGC
Statistics
Matches: 281, Mismatches: 22, Indels: 11
0.89 0.07 0.04
Matches are distributed among these distances:
171 85 0.30
172 1 0.00
174 25 0.09
175 165 0.59
176 5 0.02
ACGTcount: A:0.29, C:0.27, G:0.24, T:0.21
Consensus pattern (173 bp):
TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAAGATTGAAAACACCAGCCTTGCCTCC
CTGGGTTGCAGTGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCATGCACCGACAGCGAAGCAGA
TCGAAGACACCAACCTTGCCCCCTAGGTTGCAGCGGAGCAGGT
Found at i:55431973 original size:44 final size:44
Alignment explanation
Indices: 55431880--55431995 Score: 128
Period size: 44 Copynumber: 2.6 Consensus size: 44
55431870 ATCGCATCTG
* * * * *
55431880 GTCTTATCTCCCAAAAGTTGCAGTGGAGCAGACTGAGTAAGAAA
1 GTCTTATCCCCCTAAAGTTGCAGTGGAGCAGACTAAATAACAAA
*
55431924 GTCTTATCCCCCTGAAA-TTGCAGTGGGGCAGACTAAATGAACAAA
1 GTCTTATCCCCCT-AAAGTTGCAGTGGAGCAGACTAAAT-AACAAA
* *
55431969 -TCTTATCTCCCTAAAGTTGTAGTGGAG
1 GTCTTATCCCCCTAAAGTTGCAGTGGAG
55431996 TGGATTAGAA
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
43 3 0.05
44 49 0.82
45 8 0.13
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (44 bp):
GTCTTATCCCCCTAAAGTTGCAGTGGAGCAGACTAAATAACAAA
Found at i:55433383 original size:15 final size:15
Alignment explanation
Indices: 55433365--55433398 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
55433355 ATTGTTATTA
55433365 TTATTATTTCTATAC
1 TTATTATTTCTATAC
*
55433380 TTATTATTTCTATAT
1 TTATTATTTCTATAC
55433395 TTAT
1 TTAT
55433399 ACACGCATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (15 bp):
TTATTATTTCTATAC
Found at i:55433439 original size:24 final size:20
Alignment explanation
Indices: 55433407--55433457 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 20
55433397 ATACACGCAT
55433407 TTTTTTATAGTATATATATATGCA
1 TTTTTTATA-TATA-ATATAT--A
55433431 TTTTTTATATATAATATATA
1 TTTTTTATATATAATATATA
55433451 TTTTTTA
1 TTTTTTA
55433458 ACTTTTATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 8 0.30
22 6 0.22
23 4 0.15
24 9 0.33
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (20 bp):
TTTTTTATATATAATATATA
Found at i:55433441 original size:19 final size:20
Alignment explanation
Indices: 55433417--55433457 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
55433407 TTTTTTATAG
*
55433417 TATATAT-ATATGCATTTTT
1 TATATATAATATACATTTTT
*
55433436 TATATATAATATATATTTTT
1 TATATATAATATACATTTTT
55433456 TA
1 TA
55433458 ACTTTTATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (20 bp):
TATATATAATATACATTTTT
Found at i:55433447 original size:26 final size:25
Alignment explanation
Indices: 55433403--55433451 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
55433393 ATTTATACAC
55433403 GCATTTTTTTATAGTATATATATAT
1 GCATTTTTTTATAGTATATATATAT
55433428 GCA-TTTTTTATA-TATAATATATAT
1 GCATTTTTTTATAGTAT-ATATATAT
55433452 TTTTTAACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 3 0.13
24 17 0.74
25 3 0.13
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.55
Consensus pattern (25 bp):
GCATTTTTTTATAGTATATATATAT
Found at i:55437094 original size:13 final size:14
Alignment explanation
Indices: 55437078--55437107 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
55437068 TTTTTCATTA
55437078 TATTTT-ATTTTTT
1 TATTTTCATTTTTT
55437091 TATTTTCATTTTTT
1 TATTTTCATTTTTT
55437105 TAT
1 TAT
55437108 ATCAAACAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (14 bp):
TATTTTCATTTTTT
Found at i:55437927 original size:3 final size:3
Alignment explanation
Indices: 55437912--55438067 Score: 106
Period size: 3 Copynumber: 52.3 Consensus size: 3
55437902 ATTTTGATAA
* ** *
55437912 TAT TAT CAT TAT TAT TAT TAT TAT TAT TAT TAT TGC TAT TAT TA- TCT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
** * *
55437959 TCG TAT TAT TAT TAT TGT T-T GCT-T TAT TAT TAG TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT --TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * *
55438004 T-T TCAT TAT TAC TAA TAT TAT TAT TTT TAT T-T TAC TAC TCT TAT
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
55438048 TAT TAT ATAT TGT TAT TAT T
1 TAT TAT -TAT TAT TAT TAT T
55438068 TTTAAATTGT
Statistics
Matches: 121, Mismatches: 24, Indels: 16
0.75 0.15 0.10
Matches are distributed among these distances:
2 7 0.06
3 107 0.88
4 7 0.06
ACGTcount: A:0.28, C:0.06, G:0.04, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:55438196 original size:21 final size:20
Alignment explanation
Indices: 55438172--55438233 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 20
55438162 TCAGTTTGTT
55438172 TTATTTTTTATTTTCATTTTA
1 TTATTTTTTATTTT-ATTTTA
* *
55438193 TTATTTCATTATTTTATTGTTT
1 TTATTT-TTTATTTTATT-TTA
* *
55438215 TTATTATTTATATTATTTT
1 TTATTTTTTATTTTATTTT
55438234 TGTTTTTACT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
20 2 0.06
21 18 0.53
22 14 0.41
ACGTcount: A:0.21, C:0.03, G:0.02, T:0.74
Consensus pattern (20 bp):
TTATTTTTTATTTTATTTTA
Found at i:55438208 original size:16 final size:16
Alignment explanation
Indices: 55438187--55438232 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
55438177 TTTTATTTTC
55438187 ATTTTATTATTTCATT
1 ATTTTATTATTTCATT
* *
55438203 ATTTTATTGTTTTTATT
1 ATTTTATT-ATTTCATT
55438220 ATTTATATTATTT
1 ATTT-TATTATTT
55438233 TTGTTTTTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 8 0.32
17 13 0.52
18 4 0.16
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (16 bp):
ATTTTATTATTTCATT
Found at i:55438215 original size:8 final size:8
Alignment explanation
Indices: 55438187--55438233 Score: 58
Period size: 8 Copynumber: 5.6 Consensus size: 8
55438177 TTTTATTTTC
55438187 ATTTTATT
1 ATTTTATT
*
55438195 ATTTCATT
1 ATTTTATT
55438203 ATTTTATT
1 ATTTTATT
*
55438211 GTTTTTATT
1 -ATTTTATT
55438220 ATTTATATT
1 ATTT-TATT
55438229 ATTTT
1 ATTTT
55438234 TGTTTTTACT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
8 18 0.55
9 15 0.45
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (8 bp):
ATTTTATT
Found at i:55438218 original size:9 final size:9
Alignment explanation
Indices: 55438188--55438234 Score: 53
Period size: 9 Copynumber: 5.4 Consensus size: 9
55438178 TTTATTTTCA
55438188 TTTTATTA-
1 TTTTATTAT
*
55438196 TTTCATTA-
1 TTTTATTAT
*
55438204 TTTTATTGT
1 TTTTATTAT
55438213 TTTTATTAT
1 TTTTATTAT
*
55438222 TTATATTAT
1 TTTTATTAT
55438231 TTTT
1 TTTT
55438235 GTTTTTACTC
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
8 13 0.41
9 19 0.59
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74
Consensus pattern (9 bp):
TTTTATTAT
Found at i:55438222 original size:25 final size:24
Alignment explanation
Indices: 55438188--55438241 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
55438178 TTTATTTTCA
55438188 TTTTATTATTTCATTATT-TTATTGT
1 TTTTATTATTT-A-TATTATTATTGT
*
55438213 TTTTATTATTTATATTATTTTTGT
1 TTTTATTATTTATATTATTATTGT
55438237 TTTTA
1 TTTTA
55438242 CTCTTATTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 4 0.15
24 12 0.44
25 11 0.41
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.74
Consensus pattern (24 bp):
TTTTATTATTTATATTATTATTGT
Found at i:55438252 original size:24 final size:23
Alignment explanation
Indices: 55438200--55438252 Score: 54
Period size: 24 Copynumber: 2.3 Consensus size: 23
55438190 TTATTATTTC
*
55438200 ATTATTTTATTGTTTTTATTATT
1 ATTATTTTATTGTTTTTACTATT
* *
55438223 -TATATTATTTTTGTTTTTACTCTT
1 AT-TATT-TTATTGTTTTTACTATT
55438247 ATTATT
1 ATTATT
55438253 CCTTTTTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
22 1 0.04
23 4 0.17
24 18 0.75
25 1 0.04
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.72
Consensus pattern (23 bp):
ATTATTTTATTGTTTTTACTATT
Found at i:55439502 original size:13 final size:13
Alignment explanation
Indices: 55439484--55439509 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
55439474 AAAGTCAACA
55439484 CTTGAGCAGCAAG
1 CTTGAGCAGCAAG
55439497 CTTGAGCAGCAAG
1 CTTGAGCAGCAAG
55439510 TAATGACCTT
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:0.23, G:0.31, T:0.15
Consensus pattern (13 bp):
CTTGAGCAGCAAG
Found at i:55452501 original size:7 final size:7
Alignment explanation
Indices: 55452489--55452540 Score: 72
Period size: 7 Copynumber: 7.4 Consensus size: 7
55452479 AAAGGAAACC
55452489 AAACAAA
1 AAACAAA
55452496 AAACAAA
1 AAACAAA
55452503 ACAA-AAA
1 A-AACAAA
55452510 AAACAAA
1 AAACAAA
55452517 AAACAAA
1 AAACAAA
55452524 AATA-AAA
1 AA-ACAAA
55452531 AAACAAA
1 AAACAAA
55452538 AAA
1 AAA
55452541 ATAAAAAACC
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
6 3 0.07
7 35 0.85
8 3 0.07
ACGTcount: A:0.87, C:0.12, G:0.00, T:0.02
Consensus pattern (7 bp):
AAACAAA
Found at i:55452507 original size:16 final size:14
Alignment explanation
Indices: 55452473--55452549 Score: 73
Period size: 16 Copynumber: 5.1 Consensus size: 14
55452463 TCAGTGGAGG
* *
55452473 CAAAAAAAAGGAAAC
1 CAAAAAAAA-AAAAA
55452488 CAAACAAAAAACAAAA
1 CAAA-AAAAAA-AAAA
55452504 CAAAAAAAACAAAAAA
1 C-AAAAAAA-AAAAAA
*
55452520 CAAAAATAAAAAAA
1 CAAAAAAAAAAAAA
55452534 CAAAAAAATAAAAAA
1 CAAAAAAA-AAAAAA
55452549 C
1 C
55452550 CTCTACCGGG
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
14 13 0.25
15 17 0.32
16 18 0.34
17 5 0.09
ACGTcount: A:0.82, C:0.13, G:0.03, T:0.03
Consensus pattern (14 bp):
CAAAAAAAAAAAAA
Found at i:55452513 original size:21 final size:21
Alignment explanation
Indices: 55452489--55452540 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
55452479 AAAGGAAACC
55452489 AAACAAAAAACAAAACA-AAAA
1 AAACAAAAAACAAAA-ATAAAA
55452510 AAACAAAAAACAAAAATAAAA
1 AAACAAAAAACAAAAATAAAA
55452531 AAACAAAAAA
1 AAACAAAAAA
55452541 ATAAAAAACC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 1 0.03
21 29 0.97
ACGTcount: A:0.87, C:0.12, G:0.00, T:0.02
Consensus pattern (21 bp):
AAACAAAAAACAAAAATAAAA
Found at i:55453000 original size:17 final size:18
Alignment explanation
Indices: 55452978--55453015 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
55452968 TACTTCACTT
*
55452978 GAAAAAAGAAACGAA-AA
1 GAAAAAAGAAAAGAAGAA
55452995 GAAAAAAGAAAAGAAGAA
1 GAAAAAAGAAAAGAAGAA
55453013 GAA
1 GAA
55453016 TGAAAAAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (18 bp):
GAAAAAAGAAAAGAAGAA
Found at i:55453001 original size:7 final size:7
Alignment explanation
Indices: 55452991--55453034 Score: 52
Period size: 7 Copynumber: 6.1 Consensus size: 7
55452981 AAAAGAAACG
55452991 AAAAGAA
1 AAAAGAA
55452998 AAAAGAA
1 AAAAGAA
55453005 AAGAAGAA
1 AA-AAGAA
* *
55453013 GAATGAA
1 AAAAGAA
55453020 AAAAGAA
1 AAAAGAA
*
55453027 AAAGGAA
1 AAAAGAA
55453034 A
1 A
55453035 GGCCAAGGTG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
7 25 0.81
8 6 0.19
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.02
Consensus pattern (7 bp):
AAAAGAA
Found at i:55454413 original size:179 final size:179
Alignment explanation
Indices: 55454083--55454966 Score: 1118
Period size: 179 Copynumber: 4.9 Consensus size: 179
55454073 AGAAAGCAAG
*** * *
55454083 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGA-CTGAAGATAGCAGATCTTGTCTTATTGTATTGG
1 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC-GAAGATAGCAGATCTTGTCTCCCTG-AGTAG
* * * * * * *
55454147 CAGCGAAGTAGA-CTGAAGATAGC-AGATCTTATCTTCCTGTATTAGCAGCAAAATGGA-TCAAA
64 CAGTGAAGTAGATC-GAAGATAGCAAG-TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACT-GAA
* * * *
55454209 GATAGCAGATCTTGTCTTTCTGTATTGGCAGTAAAGTGGA-TCAAAGATAGTAGA
126 GATAGCAGATCTTGTCTTCCTGTATTGGCAGCAAAGTAGACT-GAAGATAGTAGA
* * *
55454263 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGCAGATATTGTCTCCTTGAGCAGCA
1 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGCAGATCTTGTCTCCCTGAGTAGCA
* *
55454328 GTGGAGTAGATCGAAGATAGCAAGTCTTGTCTTCCTATATTGGCAGCGAAGTAGACTGAAGATAG
66 GTGAAGTAGATCGAAGATAGCAAGTCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAG
*
55454393 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAGTAGA
131 CAGATCTTGTCTTCCTGTATTGGCAGCAAAGTAGACTGAAGATAGTAGA
* * * *
55454442 TCTTGTCTTCCTGTATTGGTAGCGAAGTAGATCGAAAAAAGTAGATCTTGTCTCCCTGAGTAGCA
1 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGCAGATCTTGTCTCCCTGAGTAGCA
* * * * *
55454507 GTGGAGTAGATCGAGGATAGCAAGTCTTGTCTTCCTGTATTGGCAGCAAAGTAGATTGAGGATAG
66 GTGAAGTAGATCGAAGATAGCAAGTCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAG
55454572 CAGATCTTGTCTTCCTGTATTGGCAGCAAAGTAGACTGAAGATAGTAGA
131 CAGATCTTGTCTTCCTGTATTGGCAGCAAAGTAGACTGAAGATAGTAGA
* * *
55454621 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAGCAGATCTTGTCTCCCTAAGCAGCA
1 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGCAGATCTTGTCTCCCTGAGTAGCA
* * *
55454686 GTGAAGTAGATCGAAGATAGCAAGTCTTGTCTTCCTATATTGACAACGAAGTAGACTGAAGATAG
66 GTGAAGTAGATCGAAGATAGCAAGTCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAG
* * *
55454751 CA-AGTCTTGTCTTCCTGTAGTGGCAGTAAAGTAGACTGAAGATAGGA-A
131 CAGA-TCTTGTCTTCCTGTATTGGCAGCAAAGTAGACTGAAGATAGTAGA
* * * *
55454799 GTCTTGTCTTCCTGTATTGGCAGCGAAGTAGA-CTAAGGATAGCAGATCTTATCTTCCTGTATTT
1 -TCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAA-GATAGCAGATCTTGTCTCCCTG-A-GT
* ** * * * * *
55454863 GGCAGCAAAGTAGATCGAAGATAGCAAGTCTTATCTTCCTGTATTGACAGTGAAATAGACTGAGG
62 AGCAGTGAAGTAGATCGAAGATAGCAAGTCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAG
* * *
55454928 ATAGTAGATCTTATCTTCCTGTATTGGCAGCGAAGTAGA
127 ATAGCAGATCTTGTCTTCCTGTATTGGCAGCAAAGTAGA
55454967 TCGGAGATAG
Statistics
Matches: 622, Mismatches: 71, Indels: 21
0.87 0.10 0.03
Matches are distributed among these distances:
178 5 0.01
179 468 0.75
180 59 0.09
181 89 0.14
182 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (179 bp):
TCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGCAGATCTTGTCTCCCTGAGTAGCA
GTGAAGTAGATCGAAGATAGCAAGTCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAG
CAGATCTTGTCTTCCTGTATTGGCAGCAAAGTAGACTGAAGATAGTAGA
Found at i:55454562 original size:224 final size:224
Alignment explanation
Indices: 55454071--55454984 Score: 1014
Period size: 224 Copynumber: 4.1 Consensus size: 224
55454061 GGAGAAGGTT
* * *
55454071 GAAGAAAGCAAGTCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAGCAGATCTTGTCT
1 GAAGATAGCAAGTCTTGTCTTCCTGTAGTGGCAGCAAAGTAGACTGAAGATAGCAGATCTTGTCT
** * *
55454136 TATTGTATTGGCAGCGAAGTAGACTGAAGATAGCAGATCTTATCTTCCTGTATTAGCAGCAAAAT
66 TCCTGTATTGGCAGCGAAGTAGACTGAAGATAGCAGATCTTATCTTCCTGTATTGGCAGCAAAGT
* * * *
55454201 GGATCAAAGATAGCAGATCTTGTCTTTCTGTATTGGCAGTAAAGTGGATC-AAAGATAGTAGATC
131 AGATCAAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGTGAAGTAGATCGAAA-ATAGTAGATC
* * *
55454265 TTGTCTTCCTGTATTGGCAGCGAAGTAGATC
195 TTGTCTCCCTG-AGTAGCAGCGAAGTAGATC
* ** ***
55454296 GAAGATAGC-AGATATTGTC-TCCT-TGAGCAGCAGTGGAGTAGA-TCGAAGATAGCA-AGTCTT
1 GAAGATAGCAAG-TCTTGTCTTCCTGT-AGTGGCAGCAAAGTAGACT-GAAGATAGCAGA-TCTT
* * *
55454356 GTCTTCCTATATTGGCAGCGAAGTAGACTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCG
62 GTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAGCAGATCTTATCTTCCTGTATTGGCAGCA
* * * * *
55454421 AAGTAGA-CTGAAGATAGTAGATCTTGTCTTCCTGTATTGGTAGCGAAGTAGATCGAAAAAAGTA
127 AAGTAGATC-AAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGTGAAGTAGATCGAAAATAGTA
* *
55454485 GATCTTGTCTCCCTGAGTAGCAGTGGAGTAGATC
191 GATCTTGTCTCCCTGAGTAGCAGCGAAGTAGATC
* * * *
55454519 GAGGATAGCAAGTCTTGTCTTCCTGTATTGGCAGCAAAGTAGATTGAGGATAGCAGATCTTGTCT
1 GAAGATAGCAAGTCTTGTCTTCCTGTAGTGGCAGCAAAGTAGACTGAAGATAGCAGATCTTGTCT
* * * *
55454584 TCCTGTATTGGCAGCAAAGTAGACTGAAGATAGTAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
66 TCCTGTATTGGCAGCGAAGTAGACTGAAGATAGCAGATCTTATCTTCCTGTATTGGCAGCAAAGT
* * *** * *
55454649 AGATCAAAGATAGCAGATCTTGTCTCCCT-AAGCAGCAGTGAAGTAGATCGAAGATAGCA-AGTC
131 AGATCAAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGTGAAGTAGATCGAAAATAGTAGA-TC
* *
55454712 TTGTCTTCCT-A-TATTGACAACGAAGTAGA-C
195 TTGTCTCCCTGAGTA--G-CAGCGAAGTAGATC
* *
55454742 TGAAGATAGCAAGTCTTGTCTTCCTGTAGTGGCAGTAAAGTAGACTGAAGATAGGA-AGTCTTGT
1 -GAAGATAGCAAGTCTTGTCTTCCTGTAGTGGCAGCAAAGTAGACTGAAGATAGCAGA-TCTTGT
55454806 CTTCCTGTATTGGCAGCGAAGTAGACT-AAGGATAGCAGATCTTATCTTCCTGTATTTGGCAGCA
64 CTTCCTGTATTGGCAGCGAAGTAGACTGAA-GATAGCAGATCTTATCTTCCTGTA-TTGGCAGCA
* * * * **
55454870 AAGTAGATCGAAGATAGCA-AGTCTTATCTTCCTGTATTGACAGTGAAATAGA-CTGAGGATAGT
127 AAGTAGATCAAAGATAGCAGA-TCTTGTCTTCCTGTATTGGCAGTGAAGTAGATC-GAAAATAGT
* * * *
55454933 AGATCTTATCTTCCTGTATTGGCAGCGAAGTAGATC
190 AGATCTTGTCTCCCTG-AGTAGCAGCGAAGTAGATC
*
55454969 GGAGATAGCAAGTCTT
1 GAAGATAGCAAGTCTT
55454985 ATCTCCCTAA
Statistics
Matches: 580, Mismatches: 81, Indels: 55
0.81 0.11 0.08
Matches are distributed among these distances:
221 2 0.00
222 2 0.00
223 70 0.12
224 386 0.67
225 58 0.10
226 57 0.10
227 3 0.01
228 1 0.00
229 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.29
Consensus pattern (224 bp):
GAAGATAGCAAGTCTTGTCTTCCTGTAGTGGCAGCAAAGTAGACTGAAGATAGCAGATCTTGTCT
TCCTGTATTGGCAGCGAAGTAGACTGAAGATAGCAGATCTTATCTTCCTGTATTGGCAGCAAAGT
AGATCAAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGTGAAGTAGATCGAAAATAGTAGATCT
TGTCTCCCTGAGTAGCAGCGAAGTAGATC
Found at i:55454988 original size:45 final size:45
Alignment explanation
Indices: 55454083--55454978 Score: 948
Period size: 45 Copynumber: 20.0 Consensus size: 45
55454073 AGAAAGCAAG
55454083 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGA-CTGAAGATAGCAGA
1 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC-GAAGATAGCAGA
**
55454128 TCTTGTCTTATTGTATTGGCAGCGAAGTAGA-CTGAAGATAGCAGA
1 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC-GAAGATAGCAGA
* * * * * *
55454173 TCTTATCTTCCTGTATTAGCAGCAAAATGGATCAAAGATAGCAGA
1 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGCAGA
* ** * * *
55454218 TCTTGTCTTTCTGTATTGGCAGTAAAGTGGATCAAAGATAGTAGA
1 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGCAGA
55454263 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGCAGA
1 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGCAGA
* *** * *
55454308 TATTGTC-TCCT-TGAGCAGCAGTGGAGTAGATCGAAGATAGCA-A
1 TCTTGTCTTCCTGT-ATTGGCAGCGAAGTAGATCGAAGATAGCAGA
*
55454351 GTCTTGTCTTCCTATATTGGCAGCGAAGTAGA-CTGAAGATAGCAGA
1 -TCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC-GAAGATAGCAGA
*
55454397 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGA-CTGAAGATAGTAGA
1 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC-GAAGATAGCAGA
* * * *
55454442 TCTTGTCTTCCTGTATTGGTAGCGAAGTAGATCGAAAAAAGTAGA
1 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGCAGA
* * * * * *
55454487 TCTTGTCTCCCTG-AGTAGCAGTGGAGTAGATCGAGGATAGCA-A
1 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGCAGA
* * *
55454530 GTCTTGTCTTCCTGTATTGGCAGCAAAGTAGATTGAGGATAGCAGA
1 -TCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGCAGA
* *
55454576 TCTTGTCTTCCTGTATTGGCAGCAAAGTAGA-CTGAAGATAGTAGA
1 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC-GAAGATAGCAGA
*
55454621 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAGCAGA
1 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGCAGA
* * *** *
55454666 TCTTGTCTCCCT-AAGCAGCAGTGAAGTAGATCGAAGATAGCA-A
1 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGCAGA
* * *
55454709 GTCTTGTCTTCCTATATTGACAACGAAGTAGA-CTGAAGATAGCA-A
1 -TCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC-GAAGATAGCAGA
* ** *
55454754 GTCTTGTCTTCCTGTAGTGGCAGTAAAGTAGA-CTGAAGATAGGA-A
1 -TCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC-GAAGATAGCAGA
*
55454799 GTCTTGTCTTCCTGTATTGGCAGCGAAGTAGA-CTAAGGATAGCAGA
1 -TCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAA-GATAGCAGA
* *
55454845 TCTTATCTTCCTGTATTTGGCAGCAAAGTAGATCGAAGATAGCA-A
1 TCTTGTCTTCCTGTA-TTGGCAGCGAAGTAGATCGAAGATAGCAGA
* * * * * *
55454890 GTCTTATCTTCCTGTATTGACAGTGAAATAGA-CTGAGGATAGTAGA
1 -TCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC-GAAGATAGCAGA
* *
55454936 TCTTATCTTCCTGTATTGGCAGCGAAGTAGATCGGAGATAGCA
1 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGCA
55454979 AGTCTTATCT
Statistics
Matches: 723, Mismatches: 104, Indels: 48
0.83 0.12 0.05
Matches are distributed among these distances:
43 4 0.01
44 106 0.15
45 564 0.78
46 46 0.06
47 3 0.00
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.29
Consensus pattern (45 bp):
TCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGCAGA
Found at i:55458334 original size:44 final size:44
Alignment explanation
Indices: 55458266--55458643 Score: 307
Period size: 44 Copynumber: 8.1 Consensus size: 44
55458256 TAGATCGCAT
* * *
55458266 CAGATTGAAGCCAGAAATCTTATCTCCCTAAGATTACAGCGGAG
1 CAGATTGAAGCTAGAAATCTTATCTCCCTGAGATTACAGTGGAG
55458310 CAGATTGAAGCTAGAAAT-TCTATCTCCCTGAGATTACAGTGGAG
1 CAGATTGAAGCTAGAAATCT-TATCTCCCTGAGATTACAGTGGAG
* ** * * *
55458354 CGGATT-AAAATA-AAGGATCTTATCTCTCTGAAGTTATAGTAGAGTAGATCGCAT
1 CAGATTGAAGCTAGAA--ATCTTATCTCCCTG-AG--AT--TACAGT-G---G-AG
*
55458408 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGTGGAG
1 CAGATTGAAGCTAGAAATCTTATCTCCCTGAGATTACAGTGGAG
*
55458452 CAGATTGAAGCTAGAAATCCTATCTCCCTGAGATTACAGTGGAG
1 CAGATTGAAGCTAGAAATCTTATCTCCCTGAGATTACAGTGGAG
** * * *
55458496 CAGATT-AAAATA-AAGGATCTTATCTCTCTGAAGTTATAGTAGAGTAGATCG
1 CAGATTGAAGCTAGAA--ATCTTATCTCCCTG-AG--AT--TACAGTGGA--G
*
55458547 CATTAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGTGGAG
1 C---AGATTGAAGCTAGAAATCTTATCTCCCTGAGATTACAGTGGAG
* * *
55458594 CAGATTGAAGCTAGTAATCCTATCTCCATGAGATTACAGTGGAG
1 CAGATTGAAGCTAGAAATCTTATCTCCCTGAGATTACAGTGGAG
*
55458638 CGGATT
1 CAGATT
55458644 AAAACAAAGG
Statistics
Matches: 269, Mismatches: 35, Indels: 60
0.74 0.10 0.16
Matches are distributed among these distances:
42 4 0.01
43 9 0.03
44 160 0.59
45 6 0.02
47 6 0.02
48 1 0.00
49 24 0.09
50 1 0.00
51 6 0.02
53 5 0.02
54 37 0.14
55 6 0.02
56 4 0.01
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.28
Consensus pattern (44 bp):
CAGATTGAAGCTAGAAATCTTATCTCCCTGAGATTACAGTGGAG
Found at i:55458460 original size:142 final size:142
Alignment explanation
Indices: 55458204--55458702 Score: 872
Period size: 142 Copynumber: 3.5 Consensus size: 142
55458194 CCATCGGTTG
55458204 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
1 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
* * *
55458269 ATTGAAGCCAGAAATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAGCTAGAAATTCTATC
66 ATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGAAATCCTATC
55458334 TCCCTGAGATTA
131 TCCCTGAGATTA
*
55458346 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTATAGTAGAGTAGATCGCATCAG
1 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
55458411 ATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGAAATCCTATC
66 ATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGAAATCCTATC
55458476 TCCCTGAGATTA
131 TCCCTGAGATTA
* * *
55458488 CAGTGGAGCAGATTAAAATAAAGGATCTTATCTCTCTGAAGTTATAGTAGAGTAGATCGCATTAG
1 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
*
55458553 ATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGTAATCCTATC
66 ATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGAAATCCTATC
*
55458618 TCCATGAGATTA
131 TCCCTGAGATTA
* * **
55458630 CAGTGGAGCGGATTAAAACAAAGGATCTTATCTCTTTGAAGTTACAGCGGAGTAGATCGCATCAG
1 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
*
55458695 AATGAAGC
66 ATTGAAGC
55458703 TACAACAGCA
Statistics
Matches: 341, Mismatches: 16, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
142 341 1.00
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (142 bp):
CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
ATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGAAATCCTATC
TCCCTGAGATTA
Found at i:55458662 original size:44 final size:44
Alignment explanation
Indices: 55458565--55458663 Score: 119
Period size: 44 Copynumber: 2.2 Consensus size: 44
55458555 TGAAGCCAGA
* * * *
55458565 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGT
1 AATCTTATCTCCATGAGATTACAGTGGAGCAGATTAAAACAAGT
* *
55458609 AATCCTATCTCCATGAGATTACAGTGGAGCGGATTAAAACAAAG-
1 AATCTTATCTCCATGAGATTACAGTGGAGCAGATTAAAAC-AAGT
*
55458653 GATCTTATCTC
1 AATCTTATCTC
55458664 TTTGAAGTTA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
44 44 0.96
45 2 0.04
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.28
Consensus pattern (44 bp):
AATCTTATCTCCATGAGATTACAGTGGAGCAGATTAAAACAAGT
Found at i:55459093 original size:28 final size:27
Alignment explanation
Indices: 55459054--55459124 Score: 97
Period size: 28 Copynumber: 2.6 Consensus size: 27
55459044 TTACAATAGG
55459054 CCTAATAGCCCAAATCCACTACCCAAA
1 CCTAATAGCCCAAATCCACTACCCAAA
**
55459081 CCTAATTAGCCCAAATCCACTACTTAAA
1 CCTAA-TAGCCCAAATCCACTACCCAAA
*
55459109 CCCAACTAGCCCAAAT
1 CCTAA-TAGCCCAAAT
55459125 GCCCATGACC
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 5 0.13
28 34 0.87
ACGTcount: A:0.39, C:0.38, G:0.04, T:0.18
Consensus pattern (27 bp):
CCTAATAGCCCAAATCCACTACCCAAA
Found at i:55460457 original size:19 final size:20
Alignment explanation
Indices: 55460418--55460460 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
55460408 TAATAATAAT
* *
55460418 ATATTTTTTAATTGTTATCA
1 ATATGTTTTAAATGTTATCA
55460438 ATATGTTTTAAATG-TATCA
1 ATATGTTTTAAATGTTATCA
55460457 ATAT
1 ATAT
55460461 TATTTAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.35, C:0.05, G:0.07, T:0.53
Consensus pattern (20 bp):
ATATGTTTTAAATGTTATCA
Found at i:55460466 original size:19 final size:19
Alignment explanation
Indices: 55460422--55460468 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
55460412 AATAATATAT
*
55460422 TTTTTAATTGTTATCAATA
1 TTTTTAAATGTTATCAATA
55460441 TGTTTTAAATG-TATCAATA
1 T-TTTTAAATGTTATCAATA
55460460 TTATTTAAA
1 TT-TTTAAA
55460469 AATACATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 1 0.04
19 16 0.64
20 8 0.32
ACGTcount: A:0.36, C:0.04, G:0.06, T:0.53
Consensus pattern (19 bp):
TTTTTAAATGTTATCAATA
Found at i:55460562 original size:16 final size:16
Alignment explanation
Indices: 55460541--55460578 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 16
55460531 CAAATTAACC
55460541 TTTTATTCACATAATT-
1 TTTTATT-ACATAATTG
55460557 TTTTA-TACATAATTG
1 TTTTATTACATAATTG
55460572 TTTTATT
1 TTTTATT
55460579 TCTTAAACCT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 8 0.40
15 6 0.30
16 6 0.30
ACGTcount: A:0.29, C:0.08, G:0.03, T:0.61
Consensus pattern (16 bp):
TTTTATTACATAATTG
Found at i:55462236 original size:9 final size:9
Alignment explanation
Indices: 55462218--55462251 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
55462208 ATATAAGCCA
55462218 TTTAAAATT
1 TTTAAAATT
*
55462227 TTTAAGATT
1 TTTAAAATT
55462236 TTTAAAA-T
1 TTTAAAATT
55462244 TTTAAAAT
1 TTTAAAAT
55462252 GATAAAGGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (9 bp):
TTTAAAATT
Found at i:55466844 original size:27 final size:26
Alignment explanation
Indices: 55466813--55466873 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 26
55466803 TAAAAATTTA
55466813 AAATTTATATT-GAATTACTTTATACTT
1 AAATTTATATTAGAA--ACTTTATACTT
*
55466840 AAA-TTATTATTAGAAATTTTATACTT
1 AAATTTA-TATTAGAAACTTTATACTT
55466866 AAATTTAT
1 AAATTTAT
55466874 GAGAACCACA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
26 17 0.57
27 10 0.33
28 3 0.10
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (26 bp):
AAATTTATATTAGAAACTTTATACTT
Found at i:55466878 original size:24 final size:26
Alignment explanation
Indices: 55466831--55466878 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
55466821 ATTGAATTAC
*
55466831 TTTATACTTAAATTATTATTAGAAAT
1 TTTATACTTAAATTATTATGAGAAAT
55466857 TTTATACTTAAA-T-TTATGAGAA
1 TTTATACTTAAATTATTATGAGAA
55466879 CCACAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 8 0.38
25 1 0.05
26 12 0.57
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (26 bp):
TTTATACTTAAATTATTATGAGAAAT
Found at i:55467423 original size:15 final size:17
Alignment explanation
Indices: 55467395--55467444 Score: 52
Period size: 15 Copynumber: 3.1 Consensus size: 17
55467385 AATTTATAAT
* *
55467395 TGACGAATAAATTTATA
1 TGACTAATATATTTATA
55467412 -GA-TAATATATTTATA
1 TGACTAATATATTTATA
55467427 TGATCTAATATA-TTATA
1 TGA-CTAATATATTTATA
55467444 T
1 T
55467445 TTATATTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
15 11 0.39
16 4 0.14
17 6 0.21
18 7 0.25
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (17 bp):
TGACTAATATATTTATA
Found at i:55467607 original size:13 final size:13
Alignment explanation
Indices: 55467563--55467618 Score: 60
Period size: 13 Copynumber: 4.3 Consensus size: 13
55467553 AAAATTAGTG
*
55467563 ATATATTTTAATT
1 ATATTTTTTAATT
* *
55467576 ATATTTATTATTT
1 ATATTTTTTAATT
*
55467589 AT-TTTTTTAATA
1 ATATTTTTTAATT
55467601 ATATTTTTTTAATT
1 ATA-TTTTTTAATT
55467615 ATAT
1 ATAT
55467619 GAAGTAAAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
12 9 0.26
13 13 0.38
14 12 0.35
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
ATATTTTTTAATT
Found at i:55467607 original size:14 final size:14
Alignment explanation
Indices: 55467588--55467618 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
55467578 ATTTATTATT
55467588 TATTTTTTTAATAA
1 TATTTTTTTAATAA
*
55467602 TATTTTTTTAATTA
1 TATTTTTTTAATAA
55467616 TAT
1 TAT
55467619 GAAGTAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TATTTTTTTAATAA
Found at i:55470094 original size:30 final size:30
Alignment explanation
Indices: 55470058--55470119 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
55470048 TTTTATTTTC
55470058 AGAATAATAAATTGTTTAAAATATGCTACT
1 AGAATAATAAATTGTTTAAAATATGCTACT
55470088 AGAATAATAAATTGTTTAAAATATGCTACT
1 AGAATAATAAATTGTTTAAAATATGCTACT
55470118 AG
1 AG
55470120 TCCCTATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.47, C:0.06, G:0.11, T:0.35
Consensus pattern (30 bp):
AGAATAATAAATTGTTTAAAATATGCTACT
Found at i:55472927 original size:20 final size:20
Alignment explanation
Indices: 55472902--55472964 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
55472892 ATCTAAAAAA
55472902 AAATTAGAAGAATTAGAATT
1 AAATTAGAAGAATTAGAATT
* **
55472922 AAATT---ATAATCTA-AAAA
1 AAATTAGAAGAAT-TAGAATT
55472939 AAATTAGAAGAATTAGAATT
1 AAATTAGAAGAATTAGAATT
55472959 AAATTA
1 AAATTA
55472965 TAAAACTTTG
Statistics
Matches: 32, Mismatches: 6, Indels: 10
0.67 0.12 0.21
Matches are distributed among these distances:
17 11 0.34
18 2 0.06
19 2 0.06
20 17 0.53
ACGTcount: A:0.59, C:0.02, G:0.10, T:0.30
Consensus pattern (20 bp):
AAATTAGAAGAATTAGAATT
Found at i:55472938 original size:37 final size:38
Alignment explanation
Indices: 55472891--55472967 Score: 147
Period size: 37 Copynumber: 2.1 Consensus size: 38
55472881 AATAGGGGTG
55472891 AATCTAAAAAAAAATTAGAAGAATTAGAATTAAATTAT
1 AATCTAAAAAAAAATTAGAAGAATTAGAATTAAATTAT
55472929 AATCT-AAAAAAAATTAGAAGAATTAGAATTAAATTAT
1 AATCTAAAAAAAAATTAGAAGAATTAGAATTAAATTAT
55472966 AA
1 AA
55472968 AACTTTGAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
37 34 0.87
38 5 0.13
ACGTcount: A:0.61, C:0.03, G:0.08, T:0.29
Consensus pattern (38 bp):
AATCTAAAAAAAAATTAGAAGAATTAGAATTAAATTAT
Found at i:55474536 original size:68 final size:68
Alignment explanation
Indices: 55474427--55474562 Score: 227
Period size: 68 Copynumber: 2.0 Consensus size: 68
55474417 TTTCAATCAC
* * * *
55474427 AATCTATTGTATTCAAGAGTACCACATCTTTTTGGATGAAACAAACCTCTCAATCTTAAGATAAA
1 AATCTATTGCATTCAAGAGCACCACATCTTTTTGGATGAAACAAACCACTCAATATTAAGATAAA
55474492 CGG
66 CGG
*
55474495 AATCTATTGCATTCAAGAGCACCACATCTTTTTGGATGAAACAAAGCACTCAATATTAAGATAAA
1 AATCTATTGCATTCAAGAGCACCACATCTTTTTGGATGAAACAAACCACTCAATATTAAGATAAA
55474560 CGG
66 CGG
55474563 GTCTTTAGGG
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 63 1.00
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (68 bp):
AATCTATTGCATTCAAGAGCACCACATCTTTTTGGATGAAACAAACCACTCAATATTAAGATAAA
CGG
Found at i:55475020 original size:17 final size:18
Alignment explanation
Indices: 55474993--55475026 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
55474983 GAAATTGGGA
*
55474993 GAAATTTTTAAATTTTAT
1 GAAATTTTTAAAATTTAT
55475011 GAAA-TTTTAAAATTTA
1 GAAATTTTTAAAATTTA
55475027 ACTGTCAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (18 bp):
GAAATTTTTAAAATTTAT
Found at i:55475595 original size:26 final size:26
Alignment explanation
Indices: 55475565--55475617 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
55475555 TTGGACAAGT
55475565 AGAATTTTCTAACCTATTTTCCATCA
1 AGAATTTTCTAACCTATTTTCCATCA
55475591 AGAATTTTCTAACCTATTTTCCATCA
1 AGAATTTTCTAACCTATTTTCCATCA
55475617 A
1 A
55475618 CTTCACTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.32, C:0.23, G:0.04, T:0.42
Consensus pattern (26 bp):
AGAATTTTCTAACCTATTTTCCATCA
Found at i:55475903 original size:23 final size:22
Alignment explanation
Indices: 55475872--55475917 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
55475862 ATATTAAACT
*
55475872 ATTTTTATT-TTATATATTATTG
1 ATTTTTATTATTATA-ACTATTG
55475894 ATTTTGTATTATTATAACTATTG
1 ATTTT-TATTATTATAACTATTG
55475917 A
1 A
55475918 CCTTATGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 5 0.24
23 11 0.52
24 5 0.24
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.61
Consensus pattern (22 bp):
ATTTTTATTATTATAACTATTG
Found at i:55477443 original size:25 final size:25
Alignment explanation
Indices: 55477415--55477466 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
55477405 AAAAATCAAA
* *
55477415 ATATGTAATATACA-AAATAATATAT
1 ATAT-TAATATAAATAAATAATAAAT
*
55477440 ATATTAATCTAAATAAATAATAAAT
1 ATATTAATATAAATAAATAATAAAT
55477465 AT
1 AT
55477467 GGAATGAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 7 0.30
25 16 0.70
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.37
Consensus pattern (25 bp):
ATATTAATATAAATAAATAATAAAT
Found at i:55477910 original size:24 final size:23
Alignment explanation
Indices: 55477878--55478046 Score: 137
Period size: 24 Copynumber: 7.3 Consensus size: 23
55477868 AAAAAAAAAG
* * *
55477878 TAATTATACATGAAAAACTTAGAA
1 TAATAATACATGATAAATTTA-AA
* * *
55477902 TAATAATACATAAAAAACTTAAAA
1 TAATAATACATGATAAA-TTTAAA
*
55477926 TAATAATACATGATGAATTTAAA
1 TAATAATACATGATAAATTTAAA
*
55477949 TAACAAATACATGATAAATTTAAA
1 TAA-TAATACATGATAAATTTAAA
**
55477973 TAATGTTA-ATGATAAATTTAAAA
1 TAATAATACATGATAAATTT-AAA
* * * *
55477996 TAATAATATATTACAAATTGAAA
1 TAATAATACATGATAAATTTAAA
**
55478019 TAAT-ATTGATGATAAATTTAAA
1 TAATAATACATGATAAATTTAAA
55478041 -AATAAT
1 TAATAAT
55478047 GTTAAGCTTA
Statistics
Matches: 117, Mismatches: 23, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
21 3 0.03
22 26 0.22
23 26 0.22
24 60 0.51
25 2 0.02
ACGTcount: A:0.56, C:0.05, G:0.06, T:0.33
Consensus pattern (23 bp):
TAATAATACATGATAAATTTAAA
Found at i:55477993 original size:46 final size:45
Alignment explanation
Indices: 55477900--55478040 Score: 129
Period size: 46 Copynumber: 3.0 Consensus size: 45
55477890 AAAAACTTAG
* * * * * *
55477900 AATAATAATACATAAAAAACTTAAAATAATAATACATGATGAATTTA
1 AATAAAAATACATGACAAA-TTGAAATAATATTA-ATGATAAATTTA
* * *
55477947 AATAACAAATACATGATAAATTTAAATAATGTTAATGATAAATTTAA
1 AATAA-AAATACATGACAAATTGAAATAATATTAATGATAAATTT-A
* * * *
55477994 AATAATAATATATTACAAATTGAAATAATATTGATGATAAATTTA
1 AATAAAAATACATGACAAATTGAAATAATATTAATGATAAATTTA
55478039 AA
1 AA
55478041 AATAATGTTA
Statistics
Matches: 78, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
45 3 0.04
46 42 0.54
47 22 0.28
48 11 0.14
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.33
Consensus pattern (45 bp):
AATAAAAATACATGACAAATTGAAATAATATTAATGATAAATTTA
Found at i:55478020 original size:70 final size:69
Alignment explanation
Indices: 55477920--55478051 Score: 158
Period size: 70 Copynumber: 1.9 Consensus size: 69
55477910 CATAAAAAAC
** *
55477920 TTAAAATAATAATACATGATGAATTTAAATAACAAATACATGATAAATTT-AAATAATGTTAATG
1 TTAAAATAATAATACATGACAAATTGAAAT-A-AAATACATGATAAATTTAAAATAATGTTAATG
55477984 ATAAAT
64 ATAAAT
* * * **
55477990 TTAAAATAATAATATATTACAAATTGAAATAATATTGATGATAAATTTAAAAATAATGTTAA
1 TTAAAATAATAATACATGACAAATTGAAATAAAATACATGATAAATTT-AAAATAATGTTAA
55478052 GCTTAAACAT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
68 14 0.27
69 1 0.02
70 37 0.71
ACGTcount: A:0.55, C:0.03, G:0.07, T:0.36
Consensus pattern (69 bp):
TTAAAATAATAATACATGACAAATTGAAATAAAATACATGATAAATTTAAAATAATGTTAATGAT
AAAT
Found at i:55478088 original size:24 final size:24
Alignment explanation
Indices: 55477986--55478088 Score: 63
Period size: 24 Copynumber: 4.3 Consensus size: 24
55477976 TGTTAATGAT
* * *
55477986 AAATTTAAAATAATAATATA-TTA
1 AAATTAAAAATAATATTAGATTTA
* *
55478009 CAAATT-GAAATAATATT-GATGATA
1 -AAATTAAAAATAATATTAGAT-TTA
* * *
55478033 AATTTAAAAATAATGTTA-AGCTTA
1 AAATTAAAAATAATATTAGA-TTTA
55478057 AACA-TAAAAATAATATTAGATTTA
1 AA-ATTAAAAATAATATTAGATTTA
55478081 AAATTAAA
1 AAATTAAA
55478089 TATATTTTTT
Statistics
Matches: 59, Mismatches: 12, Indels: 16
0.68 0.14 0.18
Matches are distributed among these distances:
22 1 0.02
23 14 0.24
24 43 0.73
25 1 0.02
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.35
Consensus pattern (24 bp):
AAATTAAAAATAATATTAGATTTA
Found at i:55481808 original size:15 final size:15
Alignment explanation
Indices: 55481785--55481815 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
55481775 CTAATATTTA
*
55481785 AAACTTATTAAAAAT
1 AAACATATTAAAAAT
55481800 AAACATATTAAAAAT
1 AAACATATTAAAAAT
55481815 A
1 A
55481816 CTAAGCTAAC
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:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (15 bp):
AAACATATTAAAAAT
Found at i:55482836 original size:22 final size:19
Alignment explanation
Indices: 55482811--55482859 Score: 53
Period size: 22 Copynumber: 2.4 Consensus size: 19
55482801 TATGGAGGCA
*
55482811 GAGGCTGGCGTGGAGCGGCTCG
1 GAGGCTGGC-TGCAGC-GCT-G
55482833 GAGGCGTGGCTGCAGCGCTG
1 GAGGC-TGGCTGCAGCGCTG
55482853 GAGGCTG
1 GAGGCTG
55482860 AATGCTGCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 2 0.08
20 6 0.24
21 3 0.12
22 10 0.40
23 4 0.16
ACGTcount: A:0.10, C:0.22, G:0.53, T:0.14
Consensus pattern (19 bp):
GAGGCTGGCTGCAGCGCTG
Found at i:55483860 original size:16 final size:16
Alignment explanation
Indices: 55483831--55483900 Score: 104
Period size: 16 Copynumber: 4.4 Consensus size: 16
55483821 TTTGGTTCGT
* *
55483831 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
*
55483847 CGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
*
55483863 TGTAATGGATTAGAGG
1 TGTAATGGAATAGAGG
55483879 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
55483895 TGTAAT
1 TGTAAT
55483901 AGCAAATCAA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.33, C:0.01, G:0.36, T:0.30
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:55483872 original size:32 final size:32
Alignment explanation
Indices: 55483831--55483900 Score: 122
Period size: 32 Copynumber: 2.2 Consensus size: 32
55483821 TTTGGTTCGT
*
55483831 TGTATTGGATTAGAGGCGTAATGGAATAGAGG
1 TGTAATGGATTAGAGGCGTAATGGAATAGAGG
*
55483863 TGTAATGGATTAGAGGTGTAATGGAATAGAGG
1 TGTAATGGATTAGAGGCGTAATGGAATAGAGG
55483895 TGTAAT
1 TGTAAT
55483901 AGCAAATCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.33, C:0.01, G:0.36, T:0.30
Consensus pattern (32 bp):
TGTAATGGATTAGAGGCGTAATGGAATAGAGG
Found at i:55484145 original size:16 final size:16
Alignment explanation
Indices: 55484108--55484149 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
55484098 TTAATCATAT
*
55484108 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
55484124 TT-AAATATATTATAA
1 TTAAAATATATTATAA
55484139 TTAAAATATAT
1 TTAAAATATAT
55484150 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:55484156 original size:14 final size:15
Alignment explanation
Indices: 55484117--55484158 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
55484107 TTTAAACATA
*
55484117 ATTATTATTAAATAT
1 ATTATAATTAAATAT
55484132 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
55484146 A-TATAATTTAATA
1 ATTATAATTAAATA
55484159 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:55484245 original size:120 final size:120
Alignment explanation
Indices: 55484111--55484582 Score: 831
Period size: 120 Copynumber: 3.9 Consensus size: 120
55484101 ATCATATTTA
55484111 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
55484176 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATTTAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATTTAAATT
55484231 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
* *
55484296 TATTCTTATATGAATTTACTCAAATAATAATATATGCTACTATAAAATTTAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATTTAAATT
*
55484351 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
* *
55484416 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATTTAAATT
* * * *
55484471 AAAATAATAATTATTACATATAATT-TAA-TAATAATATATAATTTAATAAAATTCTTAATAATT
1 AACATAATTATTATTAAATAT-ATTATAATTAA-AATATATAATTTAATAAAATTCTTAATAATC
55484534 AATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAA
64 AATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAA
55484583 GATAATTTGA
Statistics
Matches: 339, Mismatches: 11, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
119 3 0.01
120 333 0.98
121 3 0.01
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATTTAAATT
Found at i:55484276 original size:14 final size:15
Alignment explanation
Indices: 55484227--55484278 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
55484217 ATAAAATTTA
55484227 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
55484242 TATTAAATATATTAT
1 AATTAAATATATTAT
55484257 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
55484270 AATTTAATA
1 AATTAAATA
55484279 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:55484281 original size:59 final size:59
Alignment explanation
Indices: 55484111--55484411 Score: 260
Period size: 59 Copynumber: 5.0 Consensus size: 59
55484101 ATCATATTTA
*
55484111 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAAT
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTAAAT
* * * * * * * *
55484170 AATCA-ATATTCTTATATGAATTTACTCA-AATCATAATATATGATACT-ATAAAATT-TAAATT
1 AA-CATA-ATTATTAT-TAAATATA-TTATAATTAAAATATATAAT-TTAATAAAATTCTAAA-T
*
55484231 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAAT
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTAAAT
* * * * ** *
55484290 AATCA-ATATTCTTATATGAATTTACTCA-AA-TAATAATATATGCTACT-ATAAAATT-TAAAT
1 AA-CATA-ATTATTAT-TAAATATA-TTATAATTAA-AATATATAAT-TTAATAAAATTCTAAA-
55484350 T
59 T
*
55484351 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAAT
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTAAAT
55484410 AA
1 AA
55484412 TTAATATTCT
Statistics
Matches: 186, Mismatches: 34, Indels: 44
0.70 0.13 0.17
Matches are distributed among these distances:
58 6 0.03
59 61 0.33
60 54 0.29
61 59 0.32
62 6 0.03
ACGTcount: A:0.50, C:0.06, G:0.01, T:0.43
Consensus pattern (59 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTAAAT
Found at i:55484396 original size:14 final size:15
Alignment explanation
Indices: 55484347--55484398 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
55484337 ATAAAATTTA
55484347 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
55484362 TATTAAATATATTAT
1 AATTAAATATATTAT
55484377 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
55484390 AATTTAATA
1 AATTAAATA
55484399 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:55484679 original size:91 final size:91
Alignment explanation
Indices: 55484596--55484812 Score: 269
Period size: 91 Copynumber: 2.4 Consensus size: 91
55484586 AATTTGAAAT
* * * *
55484596 AATT-ATAACTAATAAATTATATTTTATGAATTTGTATAATTTAAAATAA-TAATTATTACATAT
1 AATTCATAA-TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAA-TATTAAATAT
55484659 AATTTAATAATAATATATAATTTCATAA
64 AATTTAATAATAATATATAATTTCATAA
* * * *
55484687 AATTCTTGATAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAA
1 AATTCATAATAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAA
* *
55484752 TTTAATAGTGATATATAATTTCATAA
66 TTTAATAATAATATATAATTTCATAA
* *
55484778 AATTCTTAATAATAAAATGT-TCTTATATGAATTTA
1 AATTCATAATAAT-AAAT-TATATTATATGAATTTA
55484813 CTAAAATCAA
Statistics
Matches: 111, Mismatches: 11, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
91 86 0.77
92 24 0.22
93 1 0.01
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (91 bp):
AATTCATAATAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAA
TTTAATAATAATATATAATTTCATAA
Found at i:55486243 original size:11 final size:11
Alignment explanation
Indices: 55486229--55486255 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
55486219 AAAAATCAAT
55486229 ACAAAAGTTTC
1 ACAAAAGTTTC
55486240 ACAAAAGTTTC
1 ACAAAAGTTTC
55486251 ACAAA
1 ACAAA
55486256 CTAATTTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.52, C:0.19, G:0.07, T:0.22
Consensus pattern (11 bp):
ACAAAAGTTTC
Found at i:55487971 original size:19 final size:19
Alignment explanation
Indices: 55487947--55487986 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
55487937 TAAAATGAAG
55487947 AATGAAGATTTGGTTTAAT
1 AATGAAGATTTGGTTTAAT
55487966 AATGAAGATTTGGTTTAAT
1 AATGAAGATTTGGTTTAAT
55487985 AA
1 AA
55487987 ATAAAATGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (19 bp):
AATGAAGATTTGGTTTAAT
Found at i:55488007 original size:32 final size:32
Alignment explanation
Indices: 55487966--55488029 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
55487956 TTGGTTTAAT
55487966 AATGAAGATTTGGTTTAATAAAT-AAAATGAAG
1 AATGAAGATTTGGTTTAAT-AATGAAAATGAAG
55487998 AATGAAGATTTGGTTTAATAATGAAAATGAAG
1 AATGAAGATTTGGTTTAATAATGAAAATGAAG
55488030 TTTTAAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 3 0.10
32 28 0.90
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.31
Consensus pattern (32 bp):
AATGAAGATTTGGTTTAATAATGAAAATGAAG
Found at i:55488341 original size:13 final size:13
Alignment explanation
Indices: 55488323--55488347 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55488313 ATCAAATTTG
55488323 TATGTACTCTTTA
1 TATGTACTCTTTA
55488336 TATGTACTCTTT
1 TATGTACTCTTT
55488348 CACTAATAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.16, G:0.08, T:0.56
Consensus pattern (13 bp):
TATGTACTCTTTA
Found at i:55490027 original size:6 final size:7
Alignment explanation
Indices: 55490006--55490036 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
55489996 GCCGGCCACC
55490006 AACCAAA
1 AACCAAA
55490013 AACCAAA
1 AACCAAA
55490020 AACCAAA
1 AACCAAA
55490027 AACCATAA
1 AACCA-AA
55490035 AA
1 AA
55490037 TGAAAAGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 19 0.83
8 4 0.17
ACGTcount: A:0.71, C:0.26, G:0.00, T:0.03
Consensus pattern (7 bp):
AACCAAA
Found at i:55496543 original size:9 final size:9
Alignment explanation
Indices: 55496531--55496564 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
55496521 ATTTAAGCCA
55496531 TTTAAAATT
1 TTTAAAATT
*
55496540 TTTAAGATT
1 TTTAAAATT
55496549 TTTAAAA-T
1 TTTAAAATT
55496557 TTTAAAAT
1 TTTAAAAT
55496565 GATAAAAGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (9 bp):
TTTAAAATT
Found at i:55499702 original size:47 final size:47
Alignment explanation
Indices: 55499646--55499740 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
55499636 AAAAAATAAA
55499646 AGTTTGGCACGAGAATGTAGCATCTAATCATTCTTAAAAATAAGACT
1 AGTTTGGCACGAGAATGTAGCATCTAATCATTCTTAAAAATAAGACT
55499693 AGTTTGGCACGAGAATGTAGCATCTAATCATTCTTAAAAATAAGACT
1 AGTTTGGCACGAGAATGTAGCATCTAATCATTCTTAAAAATAAGACT
55499740 A
1 A
55499741 TCATTGAATA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (47 bp):
AGTTTGGCACGAGAATGTAGCATCTAATCATTCTTAAAAATAAGACT
Found at i:55500396 original size:19 final size:19
Alignment explanation
Indices: 55500372--55500412 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
55500362 TTTTTACTAG
* *
55500372 TTTTTAACTTCTTTTTTAA
1 TTTTTAACGTCTTTTATAA
*
55500391 TTTTTATCGTCTTTTATAA
1 TTTTTAACGTCTTTTATAA
55500410 TTT
1 TTT
55500413 CTAATAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.20, C:0.10, G:0.02, T:0.68
Consensus pattern (19 bp):
TTTTTAACGTCTTTTATAA
Found at i:55500419 original size:10 final size:10
Alignment explanation
Indices: 55500402--55500472 Score: 56
Period size: 10 Copynumber: 7.3 Consensus size: 10
55500392 TTTTATCGTC
55500402 TTTT-ATAAT
1 TTTTAATAAT
*
55500411 TTCTAATAAT
1 TTTTAATAAT
*
55500421 TTTTTATAAT
1 TTTTAATAAT
* *
55500431 TTTTTACAAT
1 TTTTAATAAT
* *
55500441 ATTT-ACAAT
1 TTTTAATAAT
* *
55500450 TTCTAACAAT
1 TTTTAATAAT
55500460 TTTTAATAAT
1 TTTTAATAAT
55500470 TTT
1 TTT
55500473 ATTATTTAAT
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
9 10 0.20
10 41 0.80
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.58
Consensus pattern (10 bp):
TTTTAATAAT
Found at i:55500427 original size:20 final size:20
Alignment explanation
Indices: 55500402--55500471 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
55500392 TTTTATCGTC
*
55500402 TTTTATAATTTCTAATAATT
1 TTTTATAATTTCTAACAATT
* *
55500422 TTTTATAATTTTTTACAA-T
1 TTTTATAATTTCTAACAATT
* *
55500441 ATTTACAATTTCTAACAATT
1 TTTTATAATTTCTAACAATT
*
55500461 TTTAATAATTT
1 TTTTATAATTT
55500472 TATTATTTAA
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
19 15 0.38
20 24 0.62
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTTATAATTTCTAACAATT
Found at i:55507594 original size:12 final size:12
Alignment explanation
Indices: 55507577--55507603 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
55507567 TGCCCATCAC
55507577 TTTAAATATAAA
1 TTTAAATATAAA
55507589 TTTAAATATAAA
1 TTTAAATATAAA
55507601 TTT
1 TTT
55507604 TCTTTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
TTTAAATATAAA
Found at i:55510705 original size:3 final size:3
Alignment explanation
Indices: 55510697--55510756 Score: 88
Period size: 3 Copynumber: 20.3 Consensus size: 3
55510687 TATTTGTTCG
55510697 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TCTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
*
55510742 TGA TTA TTA -TA TTA T
1 TTA TTA TTA TTA TTA T
55510757 ACTTATCGGA
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
2 3 0.06
3 48 0.92
4 1 0.02
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:55511986 original size:20 final size:19
Alignment explanation
Indices: 55511959--55512013 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 19
55511949 CTAAAATGAG
55511959 AAAT-TTAAGAATAAATAA
1 AAATATTAAGAATAAATAA
*
55511977 TAAATATTAAAAATAAATAA
1 -AAATATTAAGAATAAATAA
55511997 AGAA-ATTATAGAATAAA
1 A-AATATTA-AGAATAAA
55512014 AAGTGGCAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 9 0.29
20 22 0.71
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.27
Consensus pattern (19 bp):
AAATATTAAGAATAAATAA
Found at i:55523017 original size:34 final size:34
Alignment explanation
Indices: 55522979--55523043 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
55522969 CAAAATGATG
* * * *
55522979 ATGCTCCTAAGCATGAGCTTAAACTGTTCATCTA
1 ATGCTCCTAAGAAGGAGCCTAAACTATTCATCTA
55523013 ATGCTCCTAAGAAGGAGCCTAAACTATTCAT
1 ATGCTCCTAAGAAGGAGCCTAAACTATTCAT
55523044 AAAAAATAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.29
Consensus pattern (34 bp):
ATGCTCCTAAGAAGGAGCCTAAACTATTCATCTA
Found at i:55523172 original size:46 final size:45
Alignment explanation
Indices: 55523067--55523173 Score: 121
Period size: 45 Copynumber: 2.4 Consensus size: 45
55523057 TGATCCAGTG
* *
55523067 AAGCAAGAGATTAAACTATTCATACGAAATAAATGATTACCTCCT
1 AAGCATGAGATTAAATTATTCATACGAAATAAATGATTACCTCCT
*
55523112 AAGCATGA-ATTTAAATTGTTCATAC-ATAATAAATGATGATA-CTCCT
1 AAGCATGAGA-TTAAATTATTCATACGA-AATAAATGAT--TACCTCCT
*
55523158 AAGCATGAGCTTAAAT
1 AAGCATGAGATTAAAT
55523174 AGCAGTCCAA
Statistics
Matches: 53, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
44 2 0.04
45 30 0.57
46 19 0.36
47 2 0.04
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.30
Consensus pattern (45 bp):
AAGCATGAGATTAAATTATTCATACGAAATAAATGATTACCTCCT
Found at i:55532176 original size:25 final size:25
Alignment explanation
Indices: 55532144--55532196 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
55532134 TATGATTATA
55532144 ATATTATACTTATCGGACTATAATC
1 ATATTATACTTATCGGACTATAATC
55532169 ATATTATACTTATCGGACTATAATC
1 ATATTATACTTATCGGACTATAATC
55532194 ATA
1 ATA
55532197 ACCATGTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.40
Consensus pattern (25 bp):
ATATTATACTTATCGGACTATAATC
Found at i:55535324 original size:598 final size:597
Alignment explanation
Indices: 55533925--55535839 Score: 3271
Period size: 597 Copynumber: 3.2 Consensus size: 597
55533915 AACCCAGGTT
* * * * *
55533925 AAGCCCTTCAAGCTTGGGAAGATGCTGACACATATCATTAGGCAAACTACCAGATAGACTATTGC
1 AAGCACTTCAAGCTTGGGAAGATGTTGACACATATCATTAGGCAAACTACCTGATAGGCTATTGT
* * * *
55533990 TAGAGAGATCAATGGCCTTCAGAGAAGAAACGTTGAAGATCGAAGTTGGAATCTGACTTGTAAGG
66 TGGAGAGATCAATGGTCTTCAGAGAAGAAATGTTGAAGATCGAAGTTGGAATCTGACCTGTAAGG
* *
55534055 CCTTTAATTGCTGTAATACTAAGCATTTCCAAACCAAAAAGATTACCGATTTCCTTAGGAATTTG
131 CCTTTAATTGCTGTAATACTAAGCAGTTCCAAACCAAAAAGATTACCGATTTCCTCAGGAATTTG
55534120 ACCTGCACACA-GAGTCAAAAAATCAAGGTGTCAAACTACCTATTTTGTTAGCATAAGTCAAAGA
196 ACCTGCACACATG-GTCAAAAAATCAAGGTGTCAAACTACCTATTTTGTTAGCATAAGTCAAAGA
* * *
55534184 GGTTTTCTTTTCTGTTCTACAGTAATTTGGAAACGCTAGATTTTCATATATTTCAGCATATGTTT
260 GGTTTTCTTTTCTGTTCTACAGTAATTTGGAGATGTTAGATTTTCATATATTTCAGCATATGTTT
* * *
55534249 TTCATCAAATGAAATAAAAAGTTTTTCCTTTTGTTATCTATTACAAATCAAACTTTTTTATAAAC
325 TTCATCAAATGAAATAAAAACTTTTTCCTTTTGTTATCTATTACAAATCAAACTCTTTTATAAAA
* * * *
55534314 AAATTACTTAAAATTTAAGAAATCAAGGAAATTGATTACCTTCTAGATTATTAAACCCCAAATAT
390 AAAATACTTAAAATTCAAGAAATCAAGGAAATTGATTACCTTCTAGATTATTCAATCCCAAATAT
*
55534379 AATTCTCTGAGTTGTGTCAGATTTCCAATACTTCTTGGAATGATCCCCGTCAATTGATTCAAGGA
455 AATTCTCTGAGTTGTGTCAGATTCCCAATACTTCTTGGAATGATCCCCGTCAATTGATTCAAGGA
*
55534444 CAAGGACAAATTTTTAAGGTTGCTGCATTTACCCATACTTGACGGAATGTTACCAGATAACTCAT
520 CAAGGACAAATTTTTAAGGTTGCTGCATTTGCCCATACTTGACGGAATGTTACCAGATAACTCAT
*
55534509 TGCTATACAAGTA
585 TGCTATGCAAGTA
55534522 AAGCACTTCAAGCTTGGGAAGATGTTGACACATATCATTAGGCAAACTACCTGATAGGCTATTGT
1 AAGCACTTCAAGCTTGGGAAGATGTTGACACATATCATTAGGCAAACTACCTGATAGGCTATTGT
* *
55534587 TGGAGAGATCAATGGTCTTCAGAGAAGAAATGTTGAAGATCAAAGTTGGAATCTAACCTGTAAGG
66 TGGAGAGATCAATGGTCTTCAGAGAAGAAATGTTGAAGATCGAAGTTGGAATCTGACCTGTAAGG
* * *
55534652 CCTTTAATTGCAGTAATACTAAGCAGTTCTAAACCAAGAAGATTACCGATTTCCTCAGGAATTTG
131 CCTTTAATTGCTGTAATACTAAGCAGTTCCAAACCAAAAAGATTACCGATTTCCTCAGGAATTTG
55534717 ACCTGCACACATGGTCAAAAAATCAAGGTGTCAAACTACCTATTTTGTTAGCATAAGTCAAAGAG
196 ACCTGCACACATGGTCAAAAAATCAAGGTGTCAAACTACCTATTTTGTTAGCATAAGTCAAAGAG
*
55534782 GTTTTCTTTTCTGTTCTACAGTAATTTGGAGATGTTAGATTTTCATATATTTCGGCATATGTTTT
261 GTTTTCTTTTCTGTTCTACAGTAATTTGGAGATGTTAGATTTTCATATATTTCAGCATATGTTTT
55534847 TCATCAAATGAAATAAAAACTTTTTCCTTTTGTTATCTATTACAAATCAAACTCTTTTATAAAAA
326 TCATCAAATGAAATAAAAACTTTTTCCTTTTGTTATCTATTACAAATCAAACTCTTTTATAAAAA
55534912 AAATACTTAAAATTCAAGAAATCAAGGAAATTGATTACCTTCTAGATTATTCAATCCCAAATATA
391 AAATACTTAAAATTCAAGAAATCAAGGAAATTGATTACCTTCTAGATTATTCAATCCCAAATATA
* *
55534977 ATTCTCTGAGTTGTGTCAGATTCCCAATACTTCTTGGAAGGATCCCCCGTCAGTTGATTCAAGGA
456 ATTCTCTGAGTTGTGTCAGATTCCCAATACTTCTTGGAATGAT-CCCCGTCAATTGATTCAAGGA
*
55535042 AAAGGACAAATTTTTAAGGTTGCTGCATTTGCCCATACTTGACGGAATGTTACCAGATAACTCAT
520 CAAGGACAAATTTTTAAGGTTGCTGCATTTGCCCATACTTGACGGAATGTTACCAGATAACTCAT
55535107 TGCTATGCAAGTA
585 TGCTATGCAAGTA
*
55535120 AAGCACTTCAAGCTTGGGAAGATGTTGACAAATATCATTAGGCAAACTACCTGATAGGCTATTGT
1 AAGCACTTCAAGCTTGGGAAGATGTTGACACATATCATTAGGCAAACTACCTGATAGGCTATTGT
* *
55535185 TGGAGAGA-CTAATGGTCTTCAGAGAAGAAATGTTGAAGATGGAACTTGGAATCTGACCTGTAAG
66 TGGAGAGATC-AATGGTCTTCAGAGAAGAAATGTTGAAGATCGAAGTTGGAATCTGACCTGTAAG
* *
55535249 GCCTTTAATTGCTCG-AATATTAAGCAGTTCCAAACCAATAAGATTACCGATTTCCTCAGGAATT
130 GCCTTTAATTGCT-GTAATACTAAGCAGTTCCAAACCAAAAAGATTACCGATTTCCTCAGGAATT
* *
55535313 TGACCTGCACACATAGTCGAAAAATCAAGGTGTCAAACTACCTATTTTGTTAGCATAAGTCAAAG
194 TGACCTGCACACATGGTCAAAAAATCAAGGTGTCAAACTACCTATTTTGTTAGCATAAGTCAAAG
**
55535378 AGGTTTTCTTTTCTGTTCTATGGTAATTTGGAGATGTTAGATTTTCATATATTTCAGCATATGTT
259 AGGTTTTCTTTTCTGTTCTACAGTAATTTGGAGATGTTAGATTTTCATATATTTCAGCATATGTT
* * * *
55535443 TTTCATCAAATGAAATAAAAACTTTTTCCATTTGTTATCTCTTACAAATCAAACCCTTTTATGAA
324 TTTCATCAAATGAAATAAAAACTTTTTCCTTTTGTTATCTATTACAAATCAAACTCTTTTATAAA
*
55535508 AAAAATCCTTAAAATTCAAGAAATCAAGGAAATTGATTACCTTCTAGATTATTCAATCCCAAATA
389 AAAAATACTTAAAATTCAAGAAATCAAGGAAATTGATTACCTTCTAGATTATTCAATCCCAAATA
55535573 TAATTCTCTGAGTTGTGTCAGATTCCCAATACTTCTTGGAATGATCCCCGTCAATTGATTCAAGG
454 TAATTCTCTGAGTTGTGTCAGATTCCCAATACTTCTTGGAATGATCCCCGTCAATTGATTCAAGG
55535638 ACAAGGACAAATTTTTAAGGTTGCTGCATTTGCCCATACTTGACGGAATGTTACCAGATAACTCA
519 ACAAGGACAAATTTTTAAGGTTGCTGCATTTGCCCATACTTGACGGAATGTTACCAGATAACTCA
55535703 TTGCTATGCAAGTA
584 TTGCTATGCAAGTA
55535717 AAGCACTTCAAGCTTGGGAAGATGTTGACACATATCATTAGGCAAACTACCTGATAGGCTATTGT
1 AAGCACTTCAAGCTTGGGAAGATGTTGACACATATCATTAGGCAAACTACCTGATAGGCTATTGT
** * * * * *
55535782 TGGAGAGAAT-AATAATCTTCAGAGAAGATATTTTGAAGATGGAAGATGGAACCTGACC
66 TGGAGAG-ATCAATGGTCTTCAGAGAAGAAATGTTGAAGATCGAAGTTGGAATCTGACC
55535840 AGATAATTGA
Statistics
Matches: 1249, Mismatches: 63, Indels: 12
0.94 0.05 0.01
Matches are distributed among these distances:
597 677 0.54
598 571 0.46
599 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (597 bp):
AAGCACTTCAAGCTTGGGAAGATGTTGACACATATCATTAGGCAAACTACCTGATAGGCTATTGT
TGGAGAGATCAATGGTCTTCAGAGAAGAAATGTTGAAGATCGAAGTTGGAATCTGACCTGTAAGG
CCTTTAATTGCTGTAATACTAAGCAGTTCCAAACCAAAAAGATTACCGATTTCCTCAGGAATTTG
ACCTGCACACATGGTCAAAAAATCAAGGTGTCAAACTACCTATTTTGTTAGCATAAGTCAAAGAG
GTTTTCTTTTCTGTTCTACAGTAATTTGGAGATGTTAGATTTTCATATATTTCAGCATATGTTTT
TCATCAAATGAAATAAAAACTTTTTCCTTTTGTTATCTATTACAAATCAAACTCTTTTATAAAAA
AAATACTTAAAATTCAAGAAATCAAGGAAATTGATTACCTTCTAGATTATTCAATCCCAAATATA
ATTCTCTGAGTTGTGTCAGATTCCCAATACTTCTTGGAATGATCCCCGTCAATTGATTCAAGGAC
AAGGACAAATTTTTAAGGTTGCTGCATTTGCCCATACTTGACGGAATGTTACCAGATAACTCATT
GCTATGCAAGTA
Found at i:55541423 original size:13 final size:14
Alignment explanation
Indices: 55541406--55541442 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
55541396 ATACACCTTT
55541406 TTTATATTTACTAA
1 TTTATATTTACTAA
55541420 TTATATATTTACTAA
1 TT-TATATTTACTAA
55541435 -TTATATTT
1 TTTATATTT
55541443 GAGTATTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 7 0.32
14 3 0.14
15 12 0.55
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTATATTTACTAA
Found at i:55541428 original size:15 final size:15
Alignment explanation
Indices: 55541408--55541440 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
55541398 ACACCTTTTT
55541408 TATATTTACTAATTA
1 TATATTTACTAATTA
55541423 TATATTTACTAATTA
1 TATATTTACTAATTA
55541438 TAT
1 TAT
55541441 TTGAGTATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (15 bp):
TATATTTACTAATTA
Found at i:55542205 original size:26 final size:27
Alignment explanation
Indices: 55542161--55542216 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
55542151 TAATGGAGTT
55542161 AACATTTAGTGTTTAAAAAATATCTTA
1 AACATTTAGTGTTTAAAAAATATCTTA
55542188 AACATTTAGTGTTTAAAAAATATCTTA
1 AACATTTAGTGTTTAAAAAATATCTTA
55542215 AA
1 AA
55542217 AATTATTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (27 bp):
AACATTTAGTGTTTAAAAAATATCTTA
Found at i:55543757 original size:13 final size:13
Alignment explanation
Indices: 55543725--55543757 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
55543715 AATTATACGC
*
55543725 CAAATTTTCAAGT
1 CAAATTTTCAACT
55543738 C-AATTTTCAACT
1 CAAATTTTCAACT
55543750 CAAATTTT
1 CAAATTTT
55543758 GTATGTACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.36, C:0.18, G:0.03, T:0.42
Consensus pattern (13 bp):
CAAATTTTCAACT
Found at i:55546551 original size:28 final size:28
Alignment explanation
Indices: 55546514--55546567 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
55546504 TTGTAAGCCT
*
55546514 TAAAACAATCAACAAAATATATTTTTGTC
1 TAAAACAATCAACAAAA-ATATGTTTGTC
*
55546543 TAAAA-AATCAATAAAAATATGTTTG
1 TAAAACAATCAACAAAAATATGTTTG
55546568 AAATTTTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 8 0.35
28 10 0.43
29 5 0.22
ACGTcount: A:0.52, C:0.09, G:0.06, T:0.33
Consensus pattern (28 bp):
TAAAACAATCAACAAAAATATGTTTGTC
Found at i:55547469 original size:28 final size:28
Alignment explanation
Indices: 55547433--55547506 Score: 132
Period size: 28 Copynumber: 2.6 Consensus size: 28
55547423 CAGTAACAGT
55547433 ACAGTGTGGGCCTTAG-CTCGATATAGTA
1 ACAGTGTGGGCCTTAGCCT-GATATAGTA
55547461 ACAGTGTGGGCCTTAGCCTGATATAGTA
1 ACAGTGTGGGCCTTAGCCTGATATAGTA
55547489 ACAGTGTGGGCCTTAGCC
1 ACAGTGTGGGCCTTAGCC
55547507 CAATACAGTA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
28 43 0.96
29 2 0.04
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.27
Consensus pattern (28 bp):
ACAGTGTGGGCCTTAGCCTGATATAGTA
Found at i:55547516 original size:28 final size:28
Alignment explanation
Indices: 55547428--55547516 Score: 126
Period size: 28 Copynumber: 3.2 Consensus size: 28
55547418 CTATGCAGTA
*
55547428 ACAGT-ACAGTGTGGGCCTTAGCTCGAT
1 ACAGTAACAGTGTGGGCCTTAGCCCGAT
* *
55547455 ATAGTAACAGTGTGGGCCTTAGCCTGAT
1 ACAGTAACAGTGTGGGCCTTAGCCCGAT
* *
55547483 ATAGTAACAGTGTGGGCCTTAGCCCAAT
1 ACAGTAACAGTGTGGGCCTTAGCCCGAT
55547511 ACAGTA
1 ACAGTA
55547517 TTAGTACAGT
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
27 4 0.07
28 51 0.93
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (28 bp):
ACAGTAACAGTGTGGGCCTTAGCCCGAT
Found at i:55547896 original size:27 final size:27
Alignment explanation
Indices: 55547866--55548249 Score: 230
Period size: 27 Copynumber: 14.3 Consensus size: 27
55547856 GGGTAGAACA
* *
55547866 GTCATTTTACCCTAAGGGGGTATTTTG
1 GTCATTTTACCCTAAGAGGGTATTTCG
*
55547893 GTCATTTTACCCTTTAG-GGGTATTTCG
1 GTCATTTTACCC-TAAGAGGGTATTTCG
* * *
55547920 ATTATTTTACCCTTCA-AGGGTATTTCG
1 GTCATTTTACCC-TAAGAGGGTATTTCG
* * * **
55547947 ATCATTTTACTCTTCA-AGGGTATTTTA
1 GTCATTTTAC-CCTAAGAGGGTATTTCG
* *
55547974 GTCATTTTACCCTTCA-AGTGTATTTCG
1 GTCATTTTACCC-TAAGAGGGTATTTCG
** *
55548001 GTCATTTTACCCTTCGAGGGTAATTCG
1 GTCATTTTACCCTAAGAGGGTATTTCG
* * * ***
55548028 GTTATTTTATCGTTTTAGGGTATTTCG
1 GTCATTTTACCCTAAGAGGGTATTTCG
* * ** *
55548055 ATCATTTTACCATTTGAGGGTATTTTG
1 GTCATTTTACCCTAAGAGGGTATTTCG
* *
55548082 GTCATTTTACCCTATA-AAGGTATTTTG
1 GTCATTTTACCCTA-AGAGGGTATTTCG
** *
55548109 GTCATTTTACCCATTGGA-GGTATTTTG
1 GTCATTTTACCC-TAAGAGGGTATTTCG
*
55548136 GTCATTTTACCC-ATCGAGGGTATTTCG
1 GTCATTTTACCCTA-AGAGGGTATTTCG
* * *
55548163 GTCATTTTACCC-ATCGAGGGAATTTTG
1 GTCATTTTACCCTA-AGAGGGTATTTCG
* * * *
55548190 GTCATTTTACCAT-CGGGGGCATTTCG
1 GTCATTTTACCCTAAGAGGGTATTTCG
* * *
55548216 ATCATTTTACCC-ATTGAGGGTATTTTG
1 GTCATTTTACCCTA-AGAGGGTATTTCG
55548243 GTCATTT
1 GTCATTT
55548250 GCCCACGAAT
Statistics
Matches: 291, Mismatches: 53, Indels: 26
0.79 0.14 0.07
Matches are distributed among these distances:
26 24 0.08
27 261 0.90
28 6 0.02
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (27 bp):
GTCATTTTACCCTAAGAGGGTATTTCG
Found at i:55547928 original size:54 final size:52
Alignment explanation
Indices: 55547866--55548249 Score: 282
Period size: 54 Copynumber: 7.1 Consensus size: 52
55547856 GGGTAGAACA
* *
55547866 GTCATTTTACCCTAAGGGGGTATTTTGGTCATTTTACCCTTTAGGGGTATTTCG
1 GTCATTTTACCCTAA-AGGGTATTTCGGTCATTTTACCCTTT-GGGGTATTTCG
* * * * * ** **
55547920 ATTATTTTACCCTTCAAGGGTATTTCGATCATTTTACTCTTCAAGGGTATTTTA
1 GTCATTTTACCC-TAAAGGGTATTTCGGTCATTTTACCCTT-TGGGGTATTTCG
* * * *
55547974 GTCATTTTACCCTTCAAGTGTATTTCGGTCATTTTACCCTTCGAGGGTAATTCG
1 GTCATTTTACCC-TAAAGGGTATTTCGGTCATTTTACCCTTTG-GGGTATTTCG
* ** ** * * *
55548028 GTTATTTTATCGTTTTAGGGTATTTCGATCATTTTACCATTTGAGGGTATTTTG
1 GTCATTTTA-CCCTAAAGGGTATTTCGGTCATTTTACCCTTTG-GGGTATTTCG
* * * *
55548082 GTCATTTTACCCTATAAAGGTATTTTGGTCATTTTACCCATTGGAGGTATTTTG
1 GTCATTTTACCCTA-AAGGGTATTTCGGTCATTTTACCCTTTGG-GGTATTTCG
** * * * *
55548136 GTCATTTTACCCATCGAGGGTATTTCGGTCATTTTACCCATCGAGGGAATTTTG
1 GTCATTTTACCC-TAAAGGGTATTTCGGTCATTTTACCCTTTG-GGGTATTTCG
* *** * * * *
55548190 GTCATTTTACCATCGGGGGCATTTCGATCATTTTACCCATTGAGGGTATTTTG
1 GTCATTTTACCCTAAAGGGTATTTCGGTCATTTTACCCTTTG-GGGTATTTCG
55548243 GTCATTT
1 GTCATTT
55548250 GCCCACGAAT
Statistics
Matches: 268, Mismatches: 54, Indels: 17
0.79 0.16 0.05
Matches are distributed among these distances:
53 46 0.17
54 217 0.81
55 5 0.02
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (52 bp):
GTCATTTTACCCTAAAGGGTATTTCGGTCATTTTACCCTTTGGGGTATTTCG
Found at i:55547997 original size:81 final size:82
Alignment explanation
Indices: 55547883--55548249 Score: 334
Period size: 81 Copynumber: 4.5 Consensus size: 82
55547873 TACCCTAAGG
* * * * *
55547883 GGGTATTTTGGTCATTTTACCCTTTAGGGGTATTTCGATTATTTTACCCTTCAAGGGTATTTCGA
1 GGGTATTTTGGTCATTTTACCCTTCAAGGGTATTTCGGTCATTTTACCCTTCAAGGGTATTTCGG
55547948 TCATTTTACTC-TTCAA
66 TCATTTTACTCATTCAA
* * * *
55547964 GGGTATTTTAGTCATTTTACCCTTCAAGTGTATTTCGGTCATTTTACCCTTCGAGGGTAATTCGG
1 GGGTATTTTGGTCATTTTACCCTTCAAGGGTATTTCGGTCATTTTACCCTTCAAGGGTATTTCGG
* * **
55548029 TTATTTTA-TCGTTTTA
66 TCATTTTACTCATTCAA
* * * ** * * *
55548045 GGGTATTTCGATCATTTTACCATTTGAGGGTATTTTGGTCATTTTACCCTAT-AAAGGTATTTTG
1 GGGTATTTTGGTCATTTTACCCTTCAAGGGTATTTCGGTCATTTTACCCT-TCAAGGGTATTTCG
* **
55548109 GTCATTTTACCCATTGGA
65 GTCATTTTACTCATTCAA
* * * * * *
55548127 -GGTATTTTGGTCATTTTACCCATCGAGGGTATTTCGGTCATTTTACCCATCGAGGGAATTTTGG
1 GGGTATTTTGGTCATTTTACCCTTCAAGGGTATTTCGGTCATTTTACCCTTCAAGGGTATTTCGG
**
55548191 TCATTTTAC-CA-TCGG
66 TCATTTTACTCATTCAA
* * * * *
55548206 GGGCATTTCGATCATTTTACCCATT-GAGGGTATTTTGGTCATTT
1 GGGTATTTTGGTCATTTTACCC-TTCAAGGGTATTTCGGTCATTT
55548250 GCCCACGAAT
Statistics
Matches: 234, Mismatches: 46, Indels: 13
0.80 0.16 0.04
Matches are distributed among these distances:
79 2 0.01
80 41 0.18
81 186 0.79
82 5 0.02
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.44
Consensus pattern (82 bp):
GGGTATTTTGGTCATTTTACCCTTCAAGGGTATTTCGGTCATTTTACCCTTCAAGGGTATTTCGG
TCATTTTACTCATTCAA
Found at i:55552853 original size:28 final size:28
Alignment explanation
Indices: 55552817--55552873 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
55552807 TATATATGGG
55552817 AAAGAATCCATTTACATGATATAAAACT
1 AAAGAATCCATTTACATGATATAAAACT
55552845 AAAGAATCCATTTACATGATATAAAACT
1 AAAGAATCCATTTACATGATATAAAACT
55552873 A
1 A
55552874 GTGTATGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.51, C:0.14, G:0.07, T:0.28
Consensus pattern (28 bp):
AAAGAATCCATTTACATGATATAAAACT
Found at i:55555099 original size:4 final size:4
Alignment explanation
Indices: 55555090--55555133 Score: 61
Period size: 4 Copynumber: 11.0 Consensus size: 4
55555080 CTTACATTAG
* * *
55555090 TATT TATT TATT TATC CATC TATT TATT TATT TATT TATT TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT
55555134 GGCTTGTTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.25, C:0.07, G:0.00, T:0.68
Consensus pattern (4 bp):
TATT
Found at i:55559707 original size:15 final size:15
Alignment explanation
Indices: 55559684--55559714 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
55559674 TACAACAATG
*
55559684 GTTTGAAGTGAAGAT
1 GTTTCAAGTGAAGAT
55559699 GTTTCAAGTGAAGAT
1 GTTTCAAGTGAAGAT
55559714 G
1 G
55559715 AATACTCTAC
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:0.32, C:0.03, G:0.32, T:0.32
Consensus pattern (15 bp):
GTTTCAAGTGAAGAT
Found at i:55565690 original size:103 final size:104
Alignment explanation
Indices: 55565511--55565775 Score: 424
Period size: 103 Copynumber: 2.6 Consensus size: 104
55565501 AACCGTTATT
* * * *
55565511 GGTGGATCTCGCACTTAGCACCACCACTTAATCGGGGAATCAGCACTTAGCAACCCCTTGGGGGA
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
** *
55565576 ATCAGCACATAGCAACCCCCTTT-TTATTTCAGAGATAC
66 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
*
55565614 GGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
55565679 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
66 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
* **
55565718 GGTGGATATCGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
55565776 TTATGTACAA
Statistics
Matches: 149, Mismatches: 12, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
103 83 0.56
104 66 0.44
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (104 bp):
GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
Found at i:55566137 original size:30 final size:29
Alignment explanation
Indices: 55566103--55566167 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
55566093 TAATCCACCA
55566103 CCCAACTTTTTGAAAAATTACAATTTTGCC
1 CCCAAC-TTTTGAAAAATTACAATTTTGCC
* * * *
55566133 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGAAAAATTACAATTTTGCC
55566163 CCCAA
1 CCCAA
55566168 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 2 0.07
30 25 0.83
31 3 0.10
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (29 bp):
CCCAACTTTTGAAAAATTACAATTTTGCC
Found at i:55566141 original size:31 final size:30
Alignment explanation
Indices: 55566110--55566167 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
55566100 CCACCCAACT
55566110 TTTTGAAAAATTACAATTTTGCCCCCAAAC
1 TTTTGAAAAATTACAATTTTGCCCCCAAAC
* * * *
55566140 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGAAAAATTACAATTTTGCCCCCAA
55566168 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (30 bp):
TTTTGAAAAATTACAATTTTGCCCCCAAAC
Found at i:55573178 original size:103 final size:104
Alignment explanation
Indices: 55572999--55573263 Score: 415
Period size: 103 Copynumber: 2.6 Consensus size: 104
55572989 AACCGTTATT
* * * *
55572999 GGTGGATCTCGCACTTAGCACCACCACTTAATCGGGGAATCAGCACTTAGCAACCCCTTGGGGGA
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
** *
55573064 ATCAGCACATAGCAACCCCCTTT-TTATTTCAGAGATAC
66 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
*
55573102 GGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
55573167 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
66 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
* * **
55573206 GGTGGATATCGCACATAGCACCACCAATGAATCGGGGAATCATCACACAGCAACCCCT
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
55573264 TTATGTACAA
Statistics
Matches: 148, Mismatches: 13, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
103 83 0.56
104 65 0.44
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (104 bp):
GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
Found at i:55573625 original size:30 final size:29
Alignment explanation
Indices: 55573591--55573655 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
55573581 TAATCCACCA
55573591 CCCAACTTTTTGAAAAATTACAATTTTGCC
1 CCCAAC-TTTTGAAAAATTACAATTTTGCC
* * * *
55573621 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGAAAAATTACAATTTTGCC
55573651 CCCAA
1 CCCAA
55573656 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 2 0.07
30 25 0.83
31 3 0.10
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (29 bp):
CCCAACTTTTGAAAAATTACAATTTTGCC
Found at i:55573629 original size:31 final size:30
Alignment explanation
Indices: 55573598--55573655 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
55573588 CCACCCAACT
55573598 TTTTGAAAAATTACAATTTTGCCCCCAAAC
1 TTTTGAAAAATTACAATTTTGCCCCCAAAC
* * * *
55573628 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGAAAAATTACAATTTTGCCCCCAA
55573656 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (30 bp):
TTTTGAAAAATTACAATTTTGCCCCCAAAC
Found at i:55578245 original size:10 final size:10
Alignment explanation
Indices: 55578172--55578245 Score: 51
Period size: 10 Copynumber: 7.3 Consensus size: 10
55578162 TTTTATCGTC
55578172 TTTT-ATAAT
1 TTTTAATAAT
*
55578181 TTCTAATAAT
1 TTTTAATAAT
*
55578191 TTTTTATAATT
1 TTTTAATAA-T
* *
55578202 TTTTTACAAT
1 TTTTAATAAT
* *
55578212 ATTTAACAAT
1 TTTTAATAAT
* *
55578222 TTCTAACAATT
1 TTTTAATAA-T
55578233 TTTTAATAAT
1 TTTTAATAAT
55578243 TTT
1 TTT
55578246 ATTATGTATT
Statistics
Matches: 52, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
9 3 0.06
10 32 0.62
11 17 0.33
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.58
Consensus pattern (10 bp):
TTTTAATAAT
Found at i:55579460 original size:15 final size:17
Alignment explanation
Indices: 55579437--55579481 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 17
55579427 ATAATTGATG
*
55579437 AATAAATTTATA-GA-T
1 AATATATTTATATGACT
55579452 AATATATTTATATGATCT
1 AATATATTTATATGA-CT
55579470 AATATA-TTATAT
1 AATATATTTATAT
55579482 TAATATTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 11 0.42
16 2 0.08
17 6 0.23
18 7 0.27
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (17 bp):
AATATATTTATATGACT
Found at i:55583249 original size:45 final size:45
Alignment explanation
Indices: 55583198--55583287 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
55583188 TTTAATTTTG
*
55583198 TCACTAAATTTGATTTGTTCAATATAGATTTTGGTGACTTAAAAC
1 TCACTAAATTTGATTTGTTCAATATACATTTTGGTGACTTAAAAC
*
55583243 TCACTAAATTTGATTTTTTCAATATACATTTTGGTGACTTAAAAC
1 TCACTAAATTTGATTTGTTCAATATACATTTTGGTGACTTAAAAC
55583288 AAAATTAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.43
Consensus pattern (45 bp):
TCACTAAATTTGATTTGTTCAATATACATTTTGGTGACTTAAAAC
Found at i:55586501 original size:29 final size:29
Alignment explanation
Indices: 55586463--55586519 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
55586453 GTATTATAGG
*
55586463 AAATGGATTAAATTAGTCTTTTTATTAGT
1 AAATGGATTAAATTAATCTTTTTATTAGT
* **
55586492 AAATGTATTATTTTAATCTTTTTATTAG
1 AAATGGATTAAATTAATCTTTTTATTAG
55586520 GTATGAATGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.33, C:0.04, G:0.11, T:0.53
Consensus pattern (29 bp):
AAATGGATTAAATTAATCTTTTTATTAGT
Found at i:55593577 original size:36 final size:36
Alignment explanation
Indices: 55593509--55593578 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
55593499 ATAGGGCTTG
* ** *
55593509 ATCACATATATAGGTTTGCATGATCTTAGGGTTCGC
1 ATCACATATATAAGTACGCATGATCATAGGGTTCGC
55593545 ATCACATATATAAGTACGCATGATACAT-GGGTTC
1 ATCACATATATAAGTACGCATGAT-CATAGGGTTC
55593579 ACTCAACATG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 27 0.93
37 2 0.07
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (36 bp):
ATCACATATATAAGTACGCATGATCATAGGGTTCGC
Found at i:55598665 original size:20 final size:20
Alignment explanation
Indices: 55598640--55598685 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
55598630 GTACTGGATC
* *
55598640 ACACTTTGGTTCTTCTCTTT
1 ACACTTTGGTGCCTCTCTTT
55598660 ACACTTTGGTGCCTCTCTTT
1 ACACTTTGGTGCCTCTCTTT
*
55598680 GCACTT
1 ACACTT
55598686 CAGTGCCACT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.11, C:0.28, G:0.13, T:0.48
Consensus pattern (20 bp):
ACACTTTGGTGCCTCTCTTT
Found at i:55598691 original size:20 final size:20
Alignment explanation
Indices: 55598653--55598717 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 20
55598643 CTTTGGTTCT
* **
55598653 TCTCTTTACACTTTGGTGCC
1 TCTCTTTGCACTTCAGTGCC
55598673 TCTCTTTGCACTTCAGTGCCAC
1 TCTCTTTGCACTTCAGTG-C-C
* * *
55598695 TGTATTTGCACTACAGTGCC
1 TCTCTTTGCACTTCAGTGCC
55598715 TCT
1 TCT
55598718 ATTAGCATTT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 16 0.44
ACGTcount: A:0.14, C:0.31, G:0.15, T:0.40
Consensus pattern (20 bp):
TCTCTTTGCACTTCAGTGCC
Found at i:55601398 original size:17 final size:16
Alignment explanation
Indices: 55601360--55601402 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
55601350 TAAATAGTGG
55601360 AAGATGGA-ATGAATA
1 AAGATGGATATGAATA
55601375 AACGATGGATATGACATA
1 AA-GATGGATATGA-ATA
*
55601393 TAGATGGATA
1 AAGATGGATA
55601403 AGTGTCTGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 2 0.08
16 6 0.25
17 12 0.50
18 4 0.17
ACGTcount: A:0.47, C:0.05, G:0.26, T:0.23
Consensus pattern (16 bp):
AAGATGGATATGAATA
Found at i:55606051 original size:20 final size:23
Alignment explanation
Indices: 55606020--55606063 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
55606010 TTGCTTGAAC
55606020 TTAAGTACATTTT-GTT-GCATT
1 TTAAGTACATTTTAGTTAGCATT
55606041 TTAAG-ACATTTTAGTTAGCATT
1 TTAAGTACATTTTAGTTAGCATT
55606063 T
1 T
55606064 CTAATATTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.33
21 8 0.38
22 6 0.29
ACGTcount: A:0.27, C:0.09, G:0.14, T:0.50
Consensus pattern (23 bp):
TTAAGTACATTTTAGTTAGCATT
Found at i:55612603 original size:17 final size:16
Alignment explanation
Indices: 55612565--55612607 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
55612555 TAAATAGTGG
55612565 AAGATGGA-ATGAATA
1 AAGATGGATATGAATA
55612580 AACGATGGATATGACATA
1 AA-GATGGATATGA-ATA
*
55612598 TAGATGGATA
1 AAGATGGATA
55612608 AGTGTCTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 2 0.08
16 6 0.25
17 12 0.50
18 4 0.17
ACGTcount: A:0.47, C:0.05, G:0.26, T:0.23
Consensus pattern (16 bp):
AAGATGGATATGAATA
Found at i:55612703 original size:20 final size:23
Alignment explanation
Indices: 55612672--55612715 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
55612662 TTGTTTGTAC
55612672 TTAAGTACATTTT-GTT-GCATT
1 TTAAGTACATTTTAGTTAGCATT
55612693 TTAAG-ACATTTTAGTTAGCATT
1 TTAAGTACATTTTAGTTAGCATT
55612715 T
1 T
55612716 CTAATATTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.33
21 8 0.38
22 6 0.29
ACGTcount: A:0.27, C:0.09, G:0.14, T:0.50
Consensus pattern (23 bp):
TTAAGTACATTTTAGTTAGCATT
Found at i:55614405 original size:30 final size:30
Alignment explanation
Indices: 55614369--55614428 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
55614359 TAGGCTAGAT
55614369 AAGTACATCCAGATAAAATATTCAAGTATC
1 AAGTACATCCAGATAAAATATTCAAGTATC
55614399 AAGTACATCCAGATAAAATATTCAAGTATC
1 AAGTACATCCAGATAAAATATTCAAGTATC
55614429 TTGAAACTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.47, C:0.17, G:0.10, T:0.27
Consensus pattern (30 bp):
AAGTACATCCAGATAAAATATTCAAGTATC
Found at i:55631312 original size:46 final size:46
Alignment explanation
Indices: 55631240--55631484 Score: 388
Period size: 46 Copynumber: 5.4 Consensus size: 46
55631230 GTGATAAGCG
55631240 GTGACAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAA
1 GTGACAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAA
*
55631286 GTGAGAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAA
1 GTGACAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAA
* * *
55631332 GTGACAAAGTGATAAGTGGTAGCCTTAGCTACCCTTATCTAATCAA
1 GTGACAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAA
* *
55631378 GTGAGAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAA
1 GTGACAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAA
*
55631424 GTGACAAAGTGATAAGTGGTAGC-CTAGCTACACTTATCTGATC-A
1 GTGACAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAA
* *
55631468 GGGAC-AGGTGATAAGTG
1 GTGACAAAGTGATAAGTG
55631485 ATCATACGTA
Statistics
Matches: 187, Mismatches: 12, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
43 11 0.06
44 5 0.03
45 19 0.10
46 152 0.81
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (46 bp):
GTGACAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAA
Found at i:55633649 original size:15 final size:15
Alignment explanation
Indices: 55633609--55633657 Score: 82
Period size: 15 Copynumber: 3.3 Consensus size: 15
55633599 ATATACTTAG
55633609 ATTAAATCTTAATTA
1 ATTAAATCTTAATTA
*
55633624 ATCAAAT-TTAATTA
1 ATTAAATCTTAATTA
55633638 ATTAAATCTTAATTA
1 ATTAAATCTTAATTA
55633653 ATTAA
1 ATTAA
55633658 CCTTAATCAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
14 13 0.42
15 18 0.58
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTAAATCTTAATTA
Found at i:55633662 original size:14 final size:14
Alignment explanation
Indices: 55633609--55633664 Score: 67
Period size: 14 Copynumber: 3.9 Consensus size: 14
55633599 ATATACTTAG
55633609 ATTAAATCTTAATTA
1 ATTAAA-CTTAATTA
* *
55633624 ATCAAATTTAATTA
1 ATTAAACTTAATTA
55633638 ATTAAATCTTAATTA
1 ATTAAA-CTTAATTA
*
55633653 ATTAACCTTAAT
1 ATTAAACTTAAT
55633665 CACAATTAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
14 18 0.51
15 17 0.49
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTAAACTTAATTA
Done.