Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr13
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: 55873576
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1239791 characters in sequence are not A, C, G, or T
File 73 of 182
Found at i:22036062 original size:20 final size:19
Alignment explanation
Indices: 22036014--22036063 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
22036004 TAACAGAAAT
* *
22036014 TTATCCGTATCAACAGTAA
1 TTATCCATATCAACAATAA
*
22036033 CTTATACATATCAACAATAA
1 -TTATCCATATCAACAATAA
22036053 TTCATCCATAT
1 TT-ATCCATAT
22036064 AATTACATAG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.40, C:0.22, G:0.04, T:0.34
Consensus pattern (19 bp):
TTATCCATATCAACAATAA
Found at i:22036267 original size:23 final size:25
Alignment explanation
Indices: 22036212--22036272 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 25
22036202 GAGCCATGAT
22036212 CGGTAAGCTCATTCCGAGCTGATAAA
1 CGGTAAGCTCATTCCGAGCTGA-AAA
*
22036238 CGATAAGCTC-TAT-CGAGCTG-AAA
1 CGGTAAGCTCAT-TCCGAGCTGAAAA
22036261 CGGTAAGCTCAT
1 CGGTAAGCTCAT
22036273 AAAAGCTGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
23 12 0.39
24 1 0.03
25 8 0.26
26 10 0.32
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (25 bp):
CGGTAAGCTCATTCCGAGCTGAAAA
Found at i:22036305 original size:26 final size:24
Alignment explanation
Indices: 22036213--22036306 Score: 84
Period size: 26 Copynumber: 3.8 Consensus size: 24
22036203 AGCCATGATC
*
22036213 GGTAAGCTCATTCCGAGCTGATAAA
1 GGTAAGCTCA-TACGAGCTGATAAA
* *
22036238 CGATAAGCTC-TATCGAGCTGA-AAC
1 -GGTAAGCTCATA-CGAGCTGATAAA
**
22036262 GGTAAGCTCATAAAAGCTGATATATA
1 GGTAAGCTCATACGAGCTGATA-A-A
22036288 GGTAAGCTCATACGAGCTG
1 GGTAAGCTCATACGAGCTG
22036307 TGGTGAGCCC
Statistics
Matches: 54, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
23 14 0.26
24 6 0.11
25 9 0.17
26 25 0.46
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.23
Consensus pattern (24 bp):
GGTAAGCTCATACGAGCTGATAAA
Found at i:22038029 original size:44 final size:45
Alignment explanation
Indices: 22037979--22038069 Score: 139
Period size: 47 Copynumber: 2.0 Consensus size: 45
22037969 ACTACCAATA
*
22037979 AAAATAAATTAATAA-TTTTATTGTTTTTTAATGATATTGTTAAT
1 AAAATAAATTAATAATTTTTATTGTTTTTCAATGATATTGTTAAT
*
22038023 AAAATAAATTAATAATTTTTTTTTTGTTTTTCAATGATATTGTTAAT
1 AAAATAAATTAATAA--TTTTTATTGTTTTTCAATGATATTGTTAAT
22038070 TGATTTTTAG
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
44 15 0.36
47 27 0.64
ACGTcount: A:0.38, C:0.01, G:0.07, T:0.54
Consensus pattern (45 bp):
AAAATAAATTAATAATTTTTATTGTTTTTCAATGATATTGTTAAT
Found at i:22038511 original size:25 final size:25
Alignment explanation
Indices: 22038472--22038544 Score: 101
Period size: 25 Copynumber: 2.9 Consensus size: 25
22038462 CCTCTACTAC
*
22038472 TTCTTTGATCCTCTACTGGTGCTGG
1 TTCTTTGTTCCTCTACTGGTGCTGG
* *
22038497 TTCTTTGTTCTTCTACTGGTGTTGG
1 TTCTTTGTTCCTCTACTGGTGCTGG
* *
22038522 TTATTTGTTCCTCTGCTGGTGCT
1 TTCTTTGTTCCTCTACTGGTGCT
22038545 TTGTTCCTCT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.05, C:0.21, G:0.23, T:0.51
Consensus pattern (25 bp):
TTCTTTGTTCCTCTACTGGTGCTGG
Found at i:22041035 original size:190 final size:190
Alignment explanation
Indices: 22040707--22041092 Score: 763
Period size: 190 Copynumber: 2.0 Consensus size: 190
22040697 AATCCTATAA
*
22040707 AAAGAACCGTTGATGCATCGGATGAATGGTGGGAGAGTAGGCTCCAGGTACATTAATAATTTTAA
1 AAAGGACCGTTGATGCATCGGATGAATGGTGGGAGAGTAGGCTCCAGGTACATTAATAATTTTAA
22040772 ATATTTTTTATTTTTTTTCTTATTTATGATGTTGTTGATAATTATTGTTATTAAACTATCATTTT
66 ATATTTTTTATTTTTTTTCTTATTTATGATGTTGTTGATAATTATTGTTATTAAACTATCATTTT
22040837 ATATGTAGGTTGTGCCTGAAGCTAAAAACTTTAGAACATCGGGCATTGATCTTGAATTCG
131 ATATGTAGGTTGTGCCTGAAGCTAAAAACTTTAGAACATCGGGCATTGATCTTGAATTCG
22040897 AAAGGACCGTTGATGCATCGGATGAATGGTGGGAGAGTAGGCTCCAGGTACATTAATAATTTTAA
1 AAAGGACCGTTGATGCATCGGATGAATGGTGGGAGAGTAGGCTCCAGGTACATTAATAATTTTAA
22040962 ATATTTTTTATTTTTTTTCTTATTTATGATGTTGTTGATAATTATTGTTATTAAACTATCATTTT
66 ATATTTTTTATTTTTTTTCTTATTTATGATGTTGTTGATAATTATTGTTATTAAACTATCATTTT
22041027 ATATGTAGGTTGTGCCTGAAGCTAAAAACTTTAGAACATCGGGCATTGATCTTGAATTCG
131 ATATGTAGGTTGTGCCTGAAGCTAAAAACTTTAGAACATCGGGCATTGATCTTGAATTCG
22041087 AAAGGA
1 AAAGGA
22041093 AGTTGGATCA
Statistics
Matches: 195, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
190 195 1.00
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (190 bp):
AAAGGACCGTTGATGCATCGGATGAATGGTGGGAGAGTAGGCTCCAGGTACATTAATAATTTTAA
ATATTTTTTATTTTTTTTCTTATTTATGATGTTGTTGATAATTATTGTTATTAAACTATCATTTT
ATATGTAGGTTGTGCCTGAAGCTAAAAACTTTAGAACATCGGGCATTGATCTTGAATTCG
Found at i:22041252 original size:18 final size:18
Alignment explanation
Indices: 22041229--22041276 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
22041219 AAAATATGAG
* *
22041229 AAATGATGTTTACATTTT
1 AAATGATGTTCACATTTC
22041247 AAATGATGTTCACATTTC
1 AAATGATGTTCACATTTC
22041265 AAATGATGTTCA
1 AAATGATGTTCA
22041277 AATTGATGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.42
Consensus pattern (18 bp):
AAATGATGTTCACATTTC
Found at i:22041851 original size:72 final size:72
Alignment explanation
Indices: 22041697--22041869 Score: 233
Period size: 72 Copynumber: 2.4 Consensus size: 72
22041687 AACAACAATG
* * * * *
22041697 CTAAACTAGTTTTATCAATAGTTATTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTA
1 CTAAATTAGTTTTATCAATAGTTGTTTATGTTTGGTCTTTAGATATTGAATTTATATTCTACTTA
22041762 TTTATGT
66 TTTATGT
* * *
22041769 GT-AATCTAGTTTTATTAAAAGTTGTTTATGTTTGGTCTTTAGATATTGAATTTATATTCTACTT
1 CTAAAT-TAGTTTTATCAATAGTTGTTTATGTTTGGTCTTTAGATATTGAATTTATATTCTACTT
*
22041833 ATTT-TTT
65 ATTTATGT
22041840 ACTAAATTAGTTTTATCAATAGTTGTTTAT
1 -CTAAATTAGTTTTATCAATAGTTGTTTAT
22041870 ATGTGATTTT
Statistics
Matches: 86, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
71 4 0.05
72 79 0.92
73 3 0.03
ACGTcount: A:0.27, C:0.06, G:0.13, T:0.54
Consensus pattern (72 bp):
CTAAATTAGTTTTATCAATAGTTGTTTATGTTTGGTCTTTAGATATTGAATTTATATTCTACTTA
TTTATGT
Found at i:22048465 original size:28 final size:28
Alignment explanation
Indices: 22048432--22048507 Score: 75
Period size: 28 Copynumber: 2.7 Consensus size: 28
22048422 AACTTTTAGA
*
22048432 TAAAAAGAAATAAATAATAATTTAAATAC
1 TAAAATGAAA-AAATAATAATTTAAATAC
* *
22048461 TAAAATGAGAGAGAATAAT--TTTAAATAT
1 TAAAATGA-A-AAAATAATAATTTAAATAC
*
22048489 TAAAATGAAAAAGTAATAA
1 TAAAATGAAAAAATAATAA
22048508 ACGAGGAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
26 6 0.16
27 1 0.03
28 16 0.42
29 7 0.18
30 7 0.18
31 1 0.03
ACGTcount: A:0.62, C:0.01, G:0.09, T:0.28
Consensus pattern (28 bp):
TAAAATGAAAAAATAATAATTTAAATAC
Found at i:22048899 original size:12 final size:12
Alignment explanation
Indices: 22048882--22048908 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
22048872 TCTATAATTT
22048882 TTAAAAATTAAA
1 TTAAAAATTAAA
22048894 TTAAAAATTAAA
1 TTAAAAATTAAA
22048906 TTA
1 TTA
22048909 TTTTTGAAAG
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:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
TTAAAAATTAAA
Found at i:22051175 original size:6 final size:6
Alignment explanation
Indices: 22051158--22051188 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
22051148 ATGAACAAGT
*
22051158 TGTATA TCTATA TGTATA TGTATA TGTATA T
1 TGTATA TGTATA TGTATA TGTATA TGTATA T
22051189 CGATTTCAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.32, C:0.03, G:0.13, T:0.52
Consensus pattern (6 bp):
TGTATA
Found at i:22055360 original size:52 final size:52
Alignment explanation
Indices: 22055299--22055403 Score: 174
Period size: 52 Copynumber: 2.0 Consensus size: 52
22055289 TAATAATCTA
*
22055299 AACAACATAATAACTAACTATTTAAAATTAAATAATTTAATAATAGTTTCTT
1 AACAACATAATAACTAACTATTTAAAATTAAATAATTTAATAACAGTTTCTT
* * *
22055351 AACATCATAATAACTAACTGTTTAAAATTAAATAATTTAATAACATTTTCTT
1 AACAACATAATAACTAACTATTTAAAATTAAATAATTTAATAACAGTTTCTT
22055403 A
1 A
22055404 CCATTTGTTA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.49, C:0.10, G:0.02, T:0.39
Consensus pattern (52 bp):
AACAACATAATAACTAACTATTTAAAATTAAATAATTTAATAACAGTTTCTT
Found at i:22055572 original size:14 final size:14
Alignment explanation
Indices: 22055526--22055591 Score: 55
Period size: 14 Copynumber: 4.7 Consensus size: 14
22055516 TGAAATTGGG
* *
22055526 AATTTAGAATAAAA
1 AATTGAGAATAAGA
* *
22055540 AATCGAGAAT-TGA
1 AATTGAGAATAAGA
22055553 CAATTGAGAATAA-A
1 -AATTGAGAATAAGA
*
22055567 AGATTGAGAACAAGA
1 A-ATTGAGAATAAGA
22055582 AATTGAGAAT
1 AATTGAGAAT
22055592 CAAATTGCAA
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
13 2 0.05
14 36 0.90
15 2 0.05
ACGTcount: A:0.55, C:0.05, G:0.18, T:0.23
Consensus pattern (14 bp):
AATTGAGAATAAGA
Found at i:22055575 original size:28 final size:28
Alignment explanation
Indices: 22055509--22055576 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 28
22055499 ACAAATTTAA
** *
22055509 AAAAAATTGA-AATTGGGAATTTAGAAT
1 AAAAAATTGAGAATTGACAATTGAGAAT
*
22055536 AAAAAATCGAGAATTGACAATTGAGAAT
1 AAAAAATTGAGAATTGACAATTGAGAAT
*
22055564 AAAAGATTGAGAA
1 AAAAAATTGAGAA
22055577 CAAGAAATTG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
27 9 0.26
28 25 0.74
ACGTcount: A:0.54, C:0.03, G:0.19, T:0.24
Consensus pattern (28 bp):
AAAAAATTGAGAATTGACAATTGAGAAT
Found at i:22060930 original size:412 final size:412
Alignment explanation
Indices: 22060166--22060989 Score: 1630
Period size: 412 Copynumber: 2.0 Consensus size: 412
22060156 AATGAACTCT
22060166 TATTTTTTATTAAAGAAGAATGCTCGAATGTTAGATTTAACGAAGAAAATCGGAATCCAATACGT
1 TATTTTTTATTAAAGAAGAATGCTCGAATGTTAGATTTAACGAAGAAAATCGGAATCCAATACGT
22060231 TATGGCTCAATTTTCTTGAAAATCCTAAATACAAACATTATCCCTATTTTGAAAAAGTTTGATTT
66 TATGGCTCAATTTTCTTGAAAATCCTAAATACAAACATTATCCCTATTTTGAAAAAGTTTGATTT
22060296 TAAAAATCGAGTAAAAAAATGTAATGTTATGCTACATTAAATATATAATGCATTAATAAATACTA
131 TAAAAATCGAGTAAAAAAATGTAATGTTATGCTACATTAAATATATAATGCATTAATAAATACTA
22060361 CGATAGCATAGAAATAATGCAAATATATGAACAAATAAATAAAATAATGGCATGCAAAACATCAA
196 CGATAGCATAGAAATAATGCAAATATATGAACAAATAAATAAAATAATGGCATGCAAAACATCAA
22060426 ACAAATGGGCAAGATAATAAAAAAATATGTAAACCTAAATTAATAGACAAATGATTGAAATAAAC
261 ACAAATGGGCAAGATAATAAAAAAATATGTAAACCTAAATTAATAGACAAATGATTGAAATAAAC
22060491 AAAAAAATGTATACATGTACCCATAAAGATATATAAGTTTAAAATAATTAAAATAATATCAAAAT
326 AAAAAAATGTATACATGTACCCATAAAGATATATAAGTTTAAAATAATTAAAATAATATCAAAAT
22060556 TAATTACATAAAACATGTGTCC
391 TAATTACATAAAACATGTGTCC
22060578 TATTTTTTATTAAAGAAGAATGCTCGAATGTTAGATTTAACGAAGAAAATCGGAATCCAATACGT
1 TATTTTTTATTAAAGAAGAATGCTCGAATGTTAGATTTAACGAAGAAAATCGGAATCCAATACGT
22060643 TATGGCTCAATTTTCTTGAAAATCCTAAATACAAACATTATCCCTATTTTGAAAAAGTTTGATTT
66 TATGGCTCAATTTTCTTGAAAATCCTAAATACAAACATTATCCCTATTTTGAAAAAGTTTGATTT
22060708 TAAAAATCGAGTAAAAAAATGTAATGTTATGCTACATTAAATATATAATGCATTAATAAATACTA
131 TAAAAATCGAGTAAAAAAATGTAATGTTATGCTACATTAAATATATAATGCATTAATAAATACTA
*
22060773 CGATAGCATAGAAATAATGCAAATATATGAACAAATAAATAAAATAATGGCATGCAAAATATCAA
196 CGATAGCATAGAAATAATGCAAATATATGAACAAATAAATAAAATAATGGCATGCAAAACATCAA
*
22060838 ATAAATGGGCAAGATAATAAAAAAATATGTAAACCTAAATTAATAGACAAATGATTGAAATAAAC
261 ACAAATGGGCAAGATAATAAAAAAATATGTAAACCTAAATTAATAGACAAATGATTGAAATAAAC
22060903 AAAAAAATGTATACATGTACCCATAAAGATATATAAGTTTAAAATAATTAAAATAATATCAAAAT
326 AAAAAAATGTATACATGTACCCATAAAGATATATAAGTTTAAAATAATTAAAATAATATCAAAAT
22060968 TAATTACATAAAACATGTGTCC
391 TAATTACATAAAACATGTGTCC
22060990 ATAAATATAC
Statistics
Matches: 410, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
412 410 1.00
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.30
Consensus pattern (412 bp):
TATTTTTTATTAAAGAAGAATGCTCGAATGTTAGATTTAACGAAGAAAATCGGAATCCAATACGT
TATGGCTCAATTTTCTTGAAAATCCTAAATACAAACATTATCCCTATTTTGAAAAAGTTTGATTT
TAAAAATCGAGTAAAAAAATGTAATGTTATGCTACATTAAATATATAATGCATTAATAAATACTA
CGATAGCATAGAAATAATGCAAATATATGAACAAATAAATAAAATAATGGCATGCAAAACATCAA
ACAAATGGGCAAGATAATAAAAAAATATGTAAACCTAAATTAATAGACAAATGATTGAAATAAAC
AAAAAAATGTATACATGTACCCATAAAGATATATAAGTTTAAAATAATTAAAATAATATCAAAAT
TAATTACATAAAACATGTGTCC
Found at i:22075993 original size:52 final size:52
Alignment explanation
Indices: 22075932--22076036 Score: 174
Period size: 52 Copynumber: 2.0 Consensus size: 52
22075922 TAATAATCTA
*
22075932 AACAACATAATAACTAACTATTTAAAATTAAATAATTTAATAATAGTTTCTT
1 AACAACATAATAACTAACTATTTAAAATTAAATAATTTAATAACAGTTTCTT
* * *
22075984 AACATCATAATAACTAACTGTTTAAAATTAAATAATTTAATAACATTTTCTT
1 AACAACATAATAACTAACTATTTAAAATTAAATAATTTAATAACAGTTTCTT
22076036 A
1 A
22076037 CCATTTGTTA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.49, C:0.10, G:0.02, T:0.39
Consensus pattern (52 bp):
AACAACATAATAACTAACTATTTAAAATTAAATAATTTAATAACAGTTTCTT
Found at i:22076205 original size:14 final size:14
Alignment explanation
Indices: 22076159--22076224 Score: 55
Period size: 14 Copynumber: 4.7 Consensus size: 14
22076149 TGAAATTGGG
* *
22076159 AATTTAGAATAAAA
1 AATTGAGAATAAGA
* *
22076173 AATCGAGAAT-TGA
1 AATTGAGAATAAGA
22076186 CAATTGAGAATAA-A
1 -AATTGAGAATAAGA
*
22076200 AGATTGAGAACAAGA
1 A-ATTGAGAATAAGA
22076215 AATTGAGAAT
1 AATTGAGAAT
22076225 CAAATTGCAA
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
13 2 0.05
14 36 0.90
15 2 0.05
ACGTcount: A:0.55, C:0.05, G:0.18, T:0.23
Consensus pattern (14 bp):
AATTGAGAATAAGA
Found at i:22076208 original size:28 final size:28
Alignment explanation
Indices: 22076142--22076209 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 28
22076132 ACAAATTTAA
** *
22076142 AAAAAATTGA-AATTGGGAATTTAGAAT
1 AAAAAATTGAGAATTGACAATTGAGAAT
*
22076169 AAAAAATCGAGAATTGACAATTGAGAAT
1 AAAAAATTGAGAATTGACAATTGAGAAT
*
22076197 AAAAGATTGAGAA
1 AAAAAATTGAGAA
22076210 CAAGAAATTG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
27 9 0.26
28 25 0.74
ACGTcount: A:0.54, C:0.03, G:0.19, T:0.24
Consensus pattern (28 bp):
AAAAAATTGAGAATTGACAATTGAGAAT
Found at i:22082176 original size:11 final size:11
Alignment explanation
Indices: 22082160--22082185 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
22082150 ATTTGGACTC
22082160 TATTATTTATT
1 TATTATTTATT
22082171 TATTATTTATT
1 TATTATTTATT
22082182 TATT
1 TATT
22082186 TGTTTGCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TATTATTTATT
Found at i:22083436 original size:21 final size:20
Alignment explanation
Indices: 22083398--22083446 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 20
22083388 GAAAATAACA
22083398 AAAAAACAAAAAAGAATC-T
1 AAAAAACAAAAAAGAATCAT
22083417 AAAAAACGAAAAAAGAAATCGAT
1 AAAAAAC-AAAAAAG-AATC-AT
22083440 AAAAAAC
1 AAAAAAC
22083447 TTTTCAAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 7 0.27
20 7 0.27
21 4 0.15
23 8 0.31
ACGTcount: A:0.73, C:0.10, G:0.08, T:0.08
Consensus pattern (20 bp):
AAAAAACAAAAAAGAATCAT
Found at i:22085484 original size:33 final size:33
Alignment explanation
Indices: 22085424--22085496 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
22085414 ACCAAAATTT
* *
22085424 TATTTT-AAAATTTTTAAAAAATAAAAAATATA
1 TATTTTAAAAATATTTAAAAAATAAAAAATAAA
*
22085456 TATTTTAAAAATATTT-AAAATTAAAAAAATAAA
1 TATTTTAAAAATATTTAAAAAAT-AAAAAATAAA
22085489 TATATTTA
1 TAT-TTTA
22085497 TTATATTTGG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
32 11 0.31
33 20 0.57
34 4 0.11
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (33 bp):
TATTTTAAAAATATTTAAAAAATAAAAAATAAA
Found at i:22094393 original size:62 final size:62
Alignment explanation
Indices: 22094322--22094447 Score: 234
Period size: 62 Copynumber: 2.0 Consensus size: 62
22094312 ATAATTTTGT
22094322 AAAAAGAAAATGAATTTTTAATAATTTTGTAATTGAATTTGTGGGATGCGTTGCATTTATCG
1 AAAAAGAAAATGAATTTTTAATAATTTTGTAATTGAATTTGTGGGATGCGTTGCATTTATCG
* *
22094384 AAAAAGAAAATGAATTTTTAATAATTTTGTAATTGAATTTGTGGGGTGTGTTGCATTTATCG
1 AAAAAGAAAATGAATTTTTAATAATTTTGTAATTGAATTTGTGGGATGCGTTGCATTTATCG
22094446 AA
1 AA
22094448 TTCTTTGCAG
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.36, C:0.04, G:0.20, T:0.40
Consensus pattern (62 bp):
AAAAAGAAAATGAATTTTTAATAATTTTGTAATTGAATTTGTGGGATGCGTTGCATTTATCG
Found at i:22098062 original size:28 final size:28
Alignment explanation
Indices: 22098031--22098088 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
22098021 TAAAATATTA
**
22098031 TTAAAATACTTTTTTAAT-TTTTTTAATT
1 TTAAAATA-TTTTAAAATATTTTTTAATT
*
22098059 TTAAAATATTTTAAAATATTTTTTATTT
1 TTAAAATATTTTAAAATATTTTTTAATT
22098087 TT
1 TT
22098089 GTTTTAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 7 0.27
28 19 0.73
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (28 bp):
TTAAAATATTTTAAAATATTTTTTAATT
Found at i:22098065 original size:39 final size:38
Alignment explanation
Indices: 22097986--22098106 Score: 145
Period size: 39 Copynumber: 3.0 Consensus size: 38
22097976 ATTTTTTTAT
*
22097986 TTTTAAAATACTTTTTTTAAAAATTATTTTAATTTTAAAATA
1 TTTTAAAATAC-TTTTTT---AATTTTTTTAATTTTAAAATA
22098028 TTATTAAAATACTTTTTTAATTTTTTTAATTTTAAAATA
1 TT-TTAAAATACTTTTTTAATTTTTTTAATTTTAAAATA
*
22098067 TTTTAAAATA-TTTTTTATTTTTGTTTTAATTTTTAAAATA
1 TTTTAAAATACTTTTTTA-ATTT-TTTTAA-TTTTAAAATA
22098107 AATTTTTGGT
Statistics
Matches: 73, Mismatches: 2, Indels: 10
0.86 0.02 0.12
Matches are distributed among these distances:
37 7 0.10
38 11 0.15
39 28 0.38
40 10 0.14
42 8 0.11
43 9 0.12
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.60
Consensus pattern (38 bp):
TTTTAAAATACTTTTTTAATTTTTTTAATTTTAAAATA
Found at i:22098069 original size:10 final size:10
Alignment explanation
Indices: 22098056--22098080 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
22098046 AATTTTTTTA
22098056 ATTTTAAAAT
1 ATTTTAAAAT
22098066 ATTTTAAAAT
1 ATTTTAAAAT
22098076 ATTTT
1 ATTTT
22098081 TTATTTTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
ATTTTAAAAT
Found at i:22100175 original size:24 final size:24
Alignment explanation
Indices: 22100143--22100188 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
22100133 AAAAAATTAT
22100143 TTTAAAAATAAAAAAATAAAAAAA
1 TTTAAAAATAAAAAAATAAAAAAA
**
22100167 TTTAAAAATTTAAAAATAAAAA
1 TTTAAAAATAAAAAAATAAAAA
22100189 TAAAAAACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (24 bp):
TTTAAAAATAAAAAAATAAAAAAA
Found at i:22100195 original size:8 final size:8
Alignment explanation
Indices: 22100146--22100188 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
22100136 AAATTATTTT
22100146 AAAAATAA
1 AAAAATAA
22100154 AAAAATAA
1 AAAAATAA
**
22100162 AAAAATTT
1 AAAAATAA
**
22100170 AAAAATTT
1 AAAAATAA
22100178 AAAAATAA
1 AAAAATAA
22100186 AAA
1 AAA
22100189 TAAAAAACAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 31 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (8 bp):
AAAAATAA
Found at i:22100571 original size:20 final size:19
Alignment explanation
Indices: 22100542--22100590 Score: 73
Period size: 18 Copynumber: 2.6 Consensus size: 19
22100532 TAAAAAGATT
22100542 GAAAATATTAAAGATGAGTA
1 GAAAATATTAAA-ATGAGTA
*
22100562 GAAAAAATT-AAATGAGTA
1 GAAAATATTAAAATGAGTA
22100580 GAAAATATTAA
1 GAAAATATTAA
22100591 GGGTGAGGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 15 0.58
19 3 0.12
20 8 0.31
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.24
Consensus pattern (19 bp):
GAAAATATTAAAATGAGTA
Found at i:22100860 original size:13 final size:14
Alignment explanation
Indices: 22100842--22100874 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
22100832 AAGCAATAGA
22100842 TAATATTTGA-TAT
1 TAATATTTGATTAT
*
22100855 TAATATTTTATTAT
1 TAATATTTGATTAT
22100869 TAATAT
1 TAATAT
22100875 AACAATATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (14 bp):
TAATATTTGATTAT
Found at i:22104605 original size:7 final size:7
Alignment explanation
Indices: 22104593--22104652 Score: 102
Period size: 7 Copynumber: 8.4 Consensus size: 7
22104583 TTAACGTAGC
22104593 TTTAGGG
1 TTTAGGG
22104600 TTTAGGG
1 TTTAGGG
22104607 TTTAGGG
1 TTTAGGG
22104614 TTTTAGGG
1 -TTTAGGG
22104622 TTTAGGG
1 TTTAGGG
*
22104629 TTTATGG
1 TTTAGGG
22104636 TTTAGGG
1 TTTAGGG
22104643 TTTAGGG
1 TTTAGGG
22104650 TTT
1 TTT
22104653 GCAAAAGGGT
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
7 43 0.86
8 7 0.14
ACGTcount: A:0.13, C:0.00, G:0.38, T:0.48
Consensus pattern (7 bp):
TTTAGGG
Found at i:22104618 original size:22 final size:21
Alignment explanation
Indices: 22104593--22104652 Score: 102
Period size: 22 Copynumber: 2.8 Consensus size: 21
22104583 TTAACGTAGC
22104593 TTTAGGGTTTAGGGTTTAGGG
1 TTTAGGGTTTAGGGTTTAGGG
*
22104614 TTTTAGGGTTTAGGGTTTATGG
1 -TTTAGGGTTTAGGGTTTAGGG
22104636 TTTAGGGTTTAGGGTTT
1 TTTAGGGTTTAGGGTTT
22104653 GCAAAAGGGT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
21 17 0.46
22 20 0.54
ACGTcount: A:0.13, C:0.00, G:0.38, T:0.48
Consensus pattern (21 bp):
TTTAGGGTTTAGGGTTTAGGG
Found at i:22105616 original size:5 final size:5
Alignment explanation
Indices: 22105606--22105677 Score: 64
Period size: 5 Copynumber: 14.8 Consensus size: 5
22105596 TGTTAAAAAA
* *
22105606 ATATT ATATT ATAGTA ATGATT ATGTT -T-TT ATATT ATATT ATTATT
1 ATATT ATATT ATA-TT AT-ATT ATATT ATATT ATATT ATATT A-TATT
22105652 A-A-T ATATT ATATT ATATT ATA-T ATAT
1 ATATT ATATT ATATT ATATT ATATT ATAT
22105678 ACATAAAACA
Statistics
Matches: 56, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
3 4 0.07
4 8 0.14
5 32 0.57
6 11 0.20
7 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (5 bp):
ATATT
Found at i:22105659 original size:19 final size:19
Alignment explanation
Indices: 22105635--22105677 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
22105625 ATTATGTTTT
22105635 TATATTATATTATTATTA-A
1 TATATTATATTA-TATTATA
22105654 TATATTATATTATATTATA
1 TATATTATATTATATTATA
22105673 TATAT
1 TATAT
22105678 ACATAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATATTATATTATATTATA
Found at i:22105946 original size:13 final size:13
Alignment explanation
Indices: 22105928--22105959 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
22105918 TTTCCAGCAA
22105928 TTATGAATTTATT
1 TTATGAATTTATT
22105941 TTATGAATTTATT
1 TTATGAATTTATT
*
22105954 TGATGA
1 TTATGA
22105960 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:22106134 original size:50 final size:50
Alignment explanation
Indices: 22106054--22106238 Score: 361
Period size: 50 Copynumber: 3.7 Consensus size: 50
22106044 ATTTGGGTAA
*
22106054 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
22106104 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
22106154 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
22106204 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGC
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGC
22106239 TTTGGCATGT
Statistics
Matches: 134, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
50 134 1.00
ACGTcount: A:0.26, C:0.24, G:0.33, T:0.17
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:22109734 original size:16 final size:16
Alignment explanation
Indices: 22109704--22109733 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
22109694 CAAAAATTGT
22109704 AAAAAGGAGAAAAAAG
1 AAAAAGGAGAAAAAAG
22109720 AAAAAGG-GAAAAAA
1 AAAAAGGAGAAAAAA
22109734 ACCCTCCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (16 bp):
AAAAAGGAGAAAAAAG
Found at i:22117643 original size:6 final size:6
Alignment explanation
Indices: 22117627--22117667 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
22117617 TTATAGGCAT
*
22117627 ATATAC TTATAC ATATAC ATATAC ATATAC ATATAC ATATA
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATA
22117668 TAGGCCTGCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.37
Consensus pattern (6 bp):
ATATAC
Found at i:22128630 original size:26 final size:26
Alignment explanation
Indices: 22128582--22128635 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 26
22128572 GATTCTTTTT
* * *
22128582 AAAAGATTAAAGGTGAAATTTAACTAA
1 AAAAGAATAAAAGTCAAATTTAA-TAA
22128609 AAAAGAATAAAAGTCAAA-TTAATAA
1 AAAAGAATAAAAGTCAAATTTAATAA
22128634 AA
1 AA
22128636 TATATAAGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 5 0.21
26 4 0.17
27 15 0.62
ACGTcount: A:0.63, C:0.04, G:0.11, T:0.22
Consensus pattern (26 bp):
AAAAGAATAAAAGTCAAATTTAATAA
Found at i:22128922 original size:15 final size:15
Alignment explanation
Indices: 22128904--22128949 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
22128894 ATTGATTTTT
22128904 ATATTATAAAAATAA
1 ATATTATAAAAATAA
**
22128919 ATATT-TGGCAAA-AA
1 ATATTAT-AAAAATAA
22128933 ATATTATAAAAATAA
1 ATATTATAAAAATAA
22128948 AT
1 AT
22128950 TTAATTATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 6
0.71 0.12 0.18
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (15 bp):
ATATTATAAAAATAA
Found at i:22131289 original size:29 final size:29
Alignment explanation
Indices: 22131234--22131289 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
22131224 GGCCATTTTT
* *
22131234 AATTATTAAATATAAACTTATTTTTTTGA
1 AATTATTAAATATAAAATTATTATTTTGA
*
22131263 AATTATTAAATATAAAATTGTTATTTT
1 AATTATTAAATATAAAATTATTATTTT
22131290 ATCACGTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.52
Consensus pattern (29 bp):
AATTATTAAATATAAAATTATTATTTTGA
Found at i:22131356 original size:13 final size:13
Alignment explanation
Indices: 22131338--22131362 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22131328 AAAACAAATA
22131338 TAAACATATCCCG
1 TAAACATATCCCG
22131351 TAAACATATCCC
1 TAAACATATCCC
22131363 ATCTGTCGCT
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:0.40, C:0.32, G:0.04, T:0.24
Consensus pattern (13 bp):
TAAACATATCCCG
Found at i:22132110 original size:72 final size:71
Alignment explanation
Indices: 22131989--22132138 Score: 169
Period size: 72 Copynumber: 2.1 Consensus size: 71
22131979 AGGCGGGCGT
* * *
22131989 TGAATTGCTACCAAAGCTTTTAGATGATTCTACAATGGCCAACAGGATGGGCATGAATATGGAGG
1 TGAATTGCTACCAAAGCTTATAGAAGATTCTACAATGGCCAACAGGATGGGCA-GAATATGGAGA
22132054 TGAACAC
65 TGAACAC
* * * * *
22132061 TGAATTGCTACCATATCTTATAGAAGATTCTACAA-GTGCTAA-AGAGATGGGTAGACTATGGAG
1 TGAATTGCTACCAAAGCTTATAGAAGATTCTACAATG-GCCAACAG-GATGGGCAGAATATGGAG
**
22132124 ATGAACGT
64 ATGAACAC
22132132 TGAATTG
1 TGAATTG
22132139 TTACTAAGAT
Statistics
Matches: 66, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
71 24 0.36
72 42 0.64
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (71 bp):
TGAATTGCTACCAAAGCTTATAGAAGATTCTACAATGGCCAACAGGATGGGCAGAATATGGAGAT
GAACAC
Found at i:22132978 original size:31 final size:30
Alignment explanation
Indices: 22132909--22132984 Score: 118
Period size: 29 Copynumber: 2.5 Consensus size: 30
22132899 TTCTTTGTTC
22132909 CTAAGAAAAAAAGTTGAATCTTGTGAGTGG
1 CTAAGAAAAAAAGTTGAATCTTGTGAGTGG
22132939 -TAAGAAAAAAAGTTGAATCTTGTGAGTGG
1 CTAAGAAAAAAAGTTGAATCTTGTGAGTGG
*
22132968 TCTAATAAAAATAAGTT
1 -CTAAGAAAAA-AAGTT
22132985 ACCTTGTTCT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
29 29 0.69
31 8 0.19
32 5 0.12
ACGTcount: A:0.43, C:0.05, G:0.22, T:0.29
Consensus pattern (30 bp):
CTAAGAAAAAAAGTTGAATCTTGTGAGTGG
Found at i:22136442 original size:2 final size:2
Alignment explanation
Indices: 22136433--22136479 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
22136423 GAGTGTGTTT
22136433 GA GA -A GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
22136474 GA GA GA
1 GA GA GA
22136480 CAATCGAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:22150639 original size:12 final size:12
Alignment explanation
Indices: 22150622--22150646 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
22150612 GGTGTTCATT
22150622 CGGTTAACCGAC
1 CGGTTAACCGAC
22150634 CGGTTAACCGAC
1 CGGTTAACCGAC
22150646 C
1 C
22150647 CGAAATTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:22150821 original size:9 final size:9
Alignment explanation
Indices: 22150807--22150849 Score: 68
Period size: 9 Copynumber: 4.8 Consensus size: 9
22150797 TTTGGTTAAA
22150807 AATTACCCG
1 AATTACCCG
22150816 AATTACCCG
1 AATTACCCG
*
22150825 AATTAACCG
1 AATTACCCG
*
22150834 AATTAACCG
1 AATTACCCG
22150843 AATTACC
1 AATTACC
22150850 GAAAAATACC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.40, C:0.28, G:0.09, T:0.23
Consensus pattern (9 bp):
AATTACCCG
Found at i:22158134 original size:16 final size:16
Alignment explanation
Indices: 22158105--22158144 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
22158095 AATTTACATG
* *
22158105 AACTCGAAACTATCTT
1 AACTCAAAACTATCCT
*
22158121 AACTCAAAATTATCCT
1 AACTCAAAACTATCCT
22158137 AACTCAAA
1 AACTCAAA
22158145 TAGACTATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.45, C:0.25, G:0.03, T:0.28
Consensus pattern (16 bp):
AACTCAAAACTATCCT
Found at i:22158509 original size:16 final size:16
Alignment explanation
Indices: 22158472--22158513 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
22158462 TTAATCATAT
*
22158472 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
22158488 TT-AAATATATTATAA
1 TTAAAATATATTATAA
22158503 TTAAAATATAT
1 TTAAAATATAT
22158514 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:22158520 original size:14 final size:15
Alignment explanation
Indices: 22158481--22158522 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
22158471 TTTAAACATA
*
22158481 ATTATTATTAAATAT
1 ATTATAATTAAATAT
22158496 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
22158510 A-TATAATTTAATA
1 ATTATAATTAAATA
22158523 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:22158639 original size:18 final size:17
Alignment explanation
Indices: 22158612--22158646 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
22158602 TTAATATTAA
*
22158612 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
22158630 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
22158647 TTAAAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:22158658 original size:54 final size:54
Alignment explanation
Indices: 22158585--22158748 Score: 155
Period size: 54 Copynumber: 3.2 Consensus size: 54
22158575 GATACTATAA
* *
22158585 AATATAATTTGAAATAATTAATATTAAATATATTTTAATTAAAATATATAATTT
1 AATAAAATTTAAAATAATTAATATTAAATATATTTTAATTAAAATATATAATTT
* * * * *
22158639 AATAAAATTTAAAATAATTAAAACT-AATAAATTTT-CTT---ATAT-GAATTT
1 AATAAAATTTAAAATAATTAATATTAAATATATTTTAATTAAAATATATAATTT
* * * *
22158687 -GTATAATTTAAAATAATTATTATTAAATATAATTTAA-TAATAATATATAATTT
1 AATAAAATTTAAAATAATTAATATTAAATATATTTTAATTAA-AATATATAATTT
*
22158740 CATAAAATT
1 AATAAAATT
22158749 CTTGATAATA
Statistics
Matches: 84, Mismatches: 18, Indels: 16
0.71 0.15 0.14
Matches are distributed among these distances:
47 19 0.23
48 14 0.17
49 4 0.05
52 6 0.07
53 14 0.17
54 27 0.32
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (54 bp):
AATAAAATTTAAAATAATTAATATTAAATATATTTTAATTAAAATATATAATTT
Found at i:22158696 original size:47 final size:46
Alignment explanation
Indices: 22158629--22158979 Score: 173
Period size: 47 Copynumber: 7.7 Consensus size: 46
22158619 TTAATTAAAA
*
22158629 TATAT-AATTTAATAAAATTTAAAATAATTAAAACTAATAAATTTTCT
1 TATATGAATTT-ATATAATTTAAAATAATTAAAA-TAATAAATTTTCT
* * * *
22158676 TATATGAATTTGTATAATTTAAAATAATT--ATTATTAAATATAAT-T
1 TATATGAATTTATATAATTTAAAATAATTAAAATAATAAAT-T-TTCT
* * ***
22158721 TA-AT-AATAATATATAATTTCATAA-AATTCTTGATAATAAATTTTCT
1 TATATGAAT-TTATATAATTT-AAAATAATT-AAAATAATAAATTTTCT
* *
22158767 TATATGAATTTATATAATTTAAAATAATT--AATATTAAATATAAT-T
1 TATATGAATTTATATAATTTAAAATAATTAAAATAATAAAT-T-TTCT
* * ***
22158812 TA-AT-AATGATATATAATTTCATAAA-ATTTTTGATAATAAATTTTCT
1 TATATGAAT-TTATATAATTT-A-AAATAATTAAAATAATAAATTTTCT
* * * *
22158858 TATATGAACTTATACAATTTAAAATAATT--AATATTAAATATAAT-T
1 TATATGAATTTATATAATTTAAAATAATTAAAATAATAAAT-T-TTCT
* * ***
22158903 TA-AT-AATGATATATAATTTCATAA-AATTCTTGATAATAAATTTTCT
1 TATATGAAT-TTATATAATTT-AAAATAATT-AAAATAATAAATTTTCT
*
22158949 TATATGAATTTATACAATTTAAAATAATTAA
1 TATATGAATTTATATAATTTAAAATAATTAA
22158980 TATTAAATAT
Statistics
Matches: 229, Mismatches: 41, Indels: 69
0.68 0.12 0.20
Matches are distributed among these distances:
43 8 0.03
44 65 0.28
45 29 0.13
46 28 0.12
47 86 0.38
48 13 0.06
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (46 bp):
TATATGAATTTATATAATTTAAAATAATTAAAATAATAAATTTTCT
Found at i:22158758 original size:91 final size:91
Alignment explanation
Indices: 22158663--22159033 Score: 661
Period size: 91 Copynumber: 4.1 Consensus size: 91
22158653 TAATTAAAAC
* * *
22158663 TAATAAATTTTCTTATATGAATTTGTATAATTTAAAATAATTATTATTAAATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
22158728 AATATATAATTTCATAAAATTCTTGA
66 GATATATAATTTCATAAAATTCTTGA
*
22158754 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
22158819 GATATATAATTTCATAAAATTTTTGA
66 GATATATAATTTCATAAAATTCTTGA
*
22158845 TAATAAATTTTCTTATATGAACTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
22158910 GATATATAATTTCATAAAATTCTTGA
66 GATATATAATTTCATAAAATTCTTGA
22158936 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
* *
22159001 GATATATAAGTTCATAAAATTCTTAA
66 GATATATAATTTCATAAAATTCTTGA
22159027 TAATAAA
1 TAATAAA
22159034 ATTTACTAAA
Statistics
Matches: 270, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
91 270 1.00
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (91 bp):
TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
GATATATAATTTCATAAAATTCTTGA
Found at i:22159027 original size:47 final size:47
Alignment explanation
Indices: 22158695--22159033 Score: 230
Period size: 47 Copynumber: 7.4 Consensus size: 47
22158685 TTGTATAATT
* * * *
22158695 TAAAATAATTATTATTAAATATAATTTAATAATAATATATAATTTCA
1 TAAAATTATTAATAATAAATATAATTTAATAATGATATATAATTTCA
* * * *
22158742 TAAAATTCTTGATAATAAAT-T-TTCTTATATGAAT-TTATATAA-TT--
1 TAAAATTATTAATAATAAATATAAT-TTA-AT-AATGATATATAATTTCA
* *
22158786 TAAAATAATTAATATTAAATATAATTTAATAATGATATATAATTTCA
1 TAAAATTATTAATAATAAATATAATTTAATAATGATATATAATTTCA
* * * *
22158833 TAAAATTTTTGATAATAAAT-T--TTCTTAT-ATGA-ACTTATACAATT--
1 TAAAATTATTAATAATAAATATAATT-TAATAATGATA--TATA-ATTTCA
* *
22158877 TAAAATAATTAATATTAAATATAATTTAATAATGATATATAATTTCA
1 TAAAATTATTAATAATAAATATAATTTAATAATGATATATAATTTCA
* * * * *
22158924 TAAAATTCTTGATAATAAAT-T--TTCTTAT-ATGAATTTATACAATT--
1 TAAAATTATTAATAATAAATATAATT-TAATAATG-ATATATA-ATTTCA
* * *
22158968 TAAAATAATTAATATTAAATATAATTTAATAATGATATATAAGTTCA
1 TAAAATTATTAATAATAAATATAATTTAATAATGATATATAATTTCA
*
22159015 TAAAATTCTTAATAATAAA
1 TAAAATTATTAATAATAAA
22159034 ATTTACTAAA
Statistics
Matches: 221, Mismatches: 42, Indels: 58
0.69 0.13 0.18
Matches are distributed among these distances:
43 4 0.02
44 68 0.31
45 31 0.14
46 31 0.14
47 83 0.38
48 4 0.02
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.45
Consensus pattern (47 bp):
TAAAATTATTAATAATAAATATAATTTAATAATGATATATAATTTCA
Found at i:22159387 original size:87 final size:88
Alignment explanation
Indices: 22159238--22159416 Score: 308
Period size: 87 Copynumber: 2.0 Consensus size: 88
22159228 CTTGATCACA
*
22159238 GCCGTGTGAACCCCCACATCTTCTTTCTCCTCGCCTGTTCTTGTGATCGGCGCTGTTTAGCAATA
1 GCCGTGAGAACCCCCACA--TTCTTTCTCCTCGCCTGTTCTTGTGATCGGCGCTGTTTAGCAATA
22159303 TCAATCCCCTCCTTGCACTTATTCT
64 TCAATCCCCTCCTTGCACTTATTCT
22159328 GCCGTGAGAACCCCCACA-TCTTTCTCCTCGCCTGTTCTTGTGA-CAGGCGCTGTTTAGCAATAT
1 GCCGTGAGAACCCCCACATTCTTTCTCCTCGCCTGTTCTTGTGATC-GGCGCTGTTTAGCAATAT
22159391 CAATCCCCTCCTTGCACTTATTCT
65 CAATCCCCTCCTTGCACTTATTCT
22159415 GC
1 GC
22159417 TCTTTAAGCC
Statistics
Matches: 87, Mismatches: 1, Indels: 5
0.94 0.01 0.05
Matches are distributed among these distances:
86 1 0.01
87 69 0.79
90 17 0.20
ACGTcount: A:0.16, C:0.35, G:0.16, T:0.34
Consensus pattern (88 bp):
GCCGTGAGAACCCCCACATTCTTTCTCCTCGCCTGTTCTTGTGATCGGCGCTGTTTAGCAATATC
AATCCCCTCCTTGCACTTATTCT
Found at i:22161767 original size:14 final size:14
Alignment explanation
Indices: 22161748--22161775 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
22161738 ACTCGGTGAA
22161748 GAAATTATTGAGAT
1 GAAATTATTGAGAT
22161762 GAAATTATTGAGAT
1 GAAATTATTGAGAT
22161776 TTGAGATCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.21, T:0.36
Consensus pattern (14 bp):
GAAATTATTGAGAT
Found at i:22164462 original size:64 final size:64
Alignment explanation
Indices: 22164394--22164521 Score: 204
Period size: 64 Copynumber: 2.0 Consensus size: 64
22164384 CGAAATCGGC
* * * *
22164394 CCATTGTTAGCTCTAATCTCAGCCATATTATGAAAATT-AACCTTTGATAACACTTATGTGAAAT
1 CCATTATTAGCTCTAATCTCAACCATATTATG-AAATTAAACCTTTGATAACACCTACGTGAAAT
22164458 CCATTATTAGCTCTAATCTCAACCATATTATGAAATTAAACCTTTGATAACACCTACGTGAAAT
1 CCATTATTAGCTCTAATCTCAACCATATTATGAAATTAAACCTTTGATAACACCTACGTGAAAT
22164522 TAATGTAGAT
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
63 5 0.08
64 54 0.92
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.34
Consensus pattern (64 bp):
CCATTATTAGCTCTAATCTCAACCATATTATGAAATTAAACCTTTGATAACACCTACGTGAAAT
Found at i:22165394 original size:17 final size:17
Alignment explanation
Indices: 22165374--22165407 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
22165364 TTTAAAAAGT
22165374 AATAT-AATAGAATTTAA
1 AATATAAATAG-ATTTAA
22165391 AATATAAATAGATTTAA
1 AATATAAATAGATTTAA
22165408 GCAAAATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (17 bp):
AATATAAATAGATTTAA
Found at i:22171533 original size:5 final size:5
Alignment explanation
Indices: 22171523--22171569 Score: 94
Period size: 5 Copynumber: 9.4 Consensus size: 5
22171513 GAATTAAGTA
22171523 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TA
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TA
22171570 AAAATAAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 42 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:22175962 original size:38 final size:37
Alignment explanation
Indices: 22175893--22175965 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 37
22175883 TTTTCATAAT
* *
22175893 TTCACTTTTTCACTTTTAATCACTATTCAATTCAAAA
1 TTCACTTTTCCACTTTTAATCAATATTCAATTCAAAA
22175930 TTCACTTTTCCA-TTTTCAAGTCAATATTCAATTCAA
1 TTCACTTTTCCACTTTT-AA-TCAATATTCAATTCAA
22175966 TTCCACACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
36 4 0.12
37 13 0.41
38 15 0.47
ACGTcount: A:0.32, C:0.22, G:0.01, T:0.45
Consensus pattern (37 bp):
TTCACTTTTCCACTTTTAATCAATATTCAATTCAAAA
Found at i:22175996 original size:23 final size:22
Alignment explanation
Indices: 22175953--22175996 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
22175943 TTTCAAGTCA
22175953 ATATTCAATTCAATTCCACACAT
1 ATATTCAATTCAATT-CACACAT
22175976 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
22175997 TTAATCGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACAT
Found at i:22176129 original size:23 final size:23
Alignment explanation
Indices: 22176096--22176147 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
22176086 CTAAGTGCCA
*
22176096 CACTGATATGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
*
22176119 CACTGAAATGTAGCTGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
22176142 CACTGA
1 CACTGA
22176148 CGAAGCTACC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGAAATGTAGCCGAAGCTAC
Found at i:22176154 original size:15 final size:15
Alignment explanation
Indices: 22176134--22176162 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
22176124 AAATGTAGCT
22176134 GAAGCTACCACTGAC
1 GAAGCTACCACTGAC
22176149 GAAGCTACCACTGA
1 GAAGCTACCACTGA
22176163 TCAATAACAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.31, G:0.21, T:0.14
Consensus pattern (15 bp):
GAAGCTACCACTGAC
Found at i:22176968 original size:375 final size:375
Alignment explanation
Indices: 22176278--22177025 Score: 1451
Period size: 375 Copynumber: 2.0 Consensus size: 375
22176268 TGATCTCTAA
22176278 TGACATGTCACTTGTATCCACTTCTATTCCTAAGTTCAACCGGGAATTTACACTTAACACTTTAT
1 TGACATGTCACTTGTATCCACTTCTATTCCTAAGTTCAACCGGGAATTTACACTTAACACTTTAT
22176343 TTTCAACACTTTATCACTTGAATAATTCATGAACAATTTTCCGTCCACATTCAATATTGATTCAC
66 TTTCAACACTTTATCACTTGAATAATTCATGAACAATTTTCCGTCCACATTCAATATTGATTCAC
* *
22176408 ATATCAAATAAAATTCACAATTTATAAAAGTATATTACTATTATTTACACATAACTTACTTTGAT
131 ATATCAAATAAAATTCAAAATTTATAAAAGTATATTACTATTATTTACACATAACTTACCTTGAT
* *
22176473 GCAACAATATAAAAATTTAGCAATTTAGTCTTTAATCTTTTCTTTTCTCCGGTCAATGTCGATTC
196 GCAACAATATAAAAATTTAGCAATTTAGTCTTGAATCTTTTCTTTTCTCCGGTCAATGTCAATTC
22176538 CACTTCTTTCTTGATCTATAATAACACATTTGACTTATTTAGTACTCACATTTATCAAAACAGTC
261 CACTTCTTTCTTGATCTATAATAACACATTTGACTTATTTAGTACTCACATTTATCAAAACAGTC
*
22176603 CTTGACTCAAATTTTGGCAAAATTACAATTTTGCCCCTAAACTTTTGCTG
326 CTTGACTCAAATTTTGGCAAAATTACAATTTTGCCCATAAACTTTTGCTG
22176653 TGACATGTCACTTGTATCCACTTCTATTCCTAAGTTCAACCGGGAATTTACACTTAACACTTTAT
1 TGACATGTCACTTGTATCCACTTCTATTCCTAAGTTCAACCGGGAATTTACACTTAACACTTTAT
22176718 TTTCAACACTTTATCACTTGAATAATTCATGAACAATTTTCCGTCCACATTCAATATTGATTCAC
66 TTTCAACACTTTATCACTTGAATAATTCATGAACAATTTTCCGTCCACATTCAATATTGATTCAC
22176783 ATATCAAATAAAATTCAAAATTTATAAAAGTATATTACTATTATTTACACATAACTTACCTTGAT
131 ATATCAAATAAAATTCAAAATTTATAAAAGTATATTACTATTATTTACACATAACTTACCTTGAT
22176848 GCAACAATATAAAAATTTAGCAATTTAGTCTTGAATCTTTTCTTTTCTCCGGTCAATGTCAATTC
196 GCAACAATATAAAAATTTAGCAATTTAGTCTTGAATCTTTTCTTTTCTCCGGTCAATGTCAATTC
22176913 CACTTCTTTCTTGATCTATAATAACACATTTGACTTATTTAGTACTCACATTTATCAAAACAGTC
261 CACTTCTTTCTTGATCTATAATAACACATTTGACTTATTTAGTACTCACATTTATCAAAACAGTC
22176978 CTTGACTCAAATTTTGGCAAAATTACAATTTTGCCCATAAACTTTTGC
326 CTTGACTCAAATTTTGGCAAAATTACAATTTTGCCCATAAACTTTTGC
22177026 ATATTTACAC
Statistics
Matches: 368, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
375 368 1.00
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.39
Consensus pattern (375 bp):
TGACATGTCACTTGTATCCACTTCTATTCCTAAGTTCAACCGGGAATTTACACTTAACACTTTAT
TTTCAACACTTTATCACTTGAATAATTCATGAACAATTTTCCGTCCACATTCAATATTGATTCAC
ATATCAAATAAAATTCAAAATTTATAAAAGTATATTACTATTATTTACACATAACTTACCTTGAT
GCAACAATATAAAAATTTAGCAATTTAGTCTTGAATCTTTTCTTTTCTCCGGTCAATGTCAATTC
CACTTCTTTCTTGATCTATAATAACACATTTGACTTATTTAGTACTCACATTTATCAAAACAGTC
CTTGACTCAAATTTTGGCAAAATTACAATTTTGCCCATAAACTTTTGCTG
Found at i:22177203 original size:10 final size:9
Alignment explanation
Indices: 22177176--22177205 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
22177166 ATCGATTATG
22177176 TCGTTTTAC
1 TCGTTTTAC
22177185 TCGTTTTAC
1 TCGTTTTAC
22177194 TCGTTTTTAC
1 TCG-TTTTAC
22177204 TC
1 TC
22177206 AAAATCGCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.60
10 8 0.40
ACGTcount: A:0.10, C:0.23, G:0.10, T:0.57
Consensus pattern (9 bp):
TCGTTTTAC
Found at i:22178521 original size:35 final size:35
Alignment explanation
Indices: 22178452--22178523 Score: 108
Period size: 35 Copynumber: 2.1 Consensus size: 35
22178442 TGTGACATAA
* * * *
22178452 CAACAAATATGTTAGGTGTTTGTAGATTTGATATG
1 CAACAAATATGTTAAGTGTTTGTACATCTAATATG
22178487 CAACAAATATGTTAAGTGTTTGTACATCTAATATG
1 CAACAAATATGTTAAGTGTTTGTACATCTAATATG
22178522 CA
1 CA
22178524 GTGGACACCA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.38
Consensus pattern (35 bp):
CAACAAATATGTTAAGTGTTTGTACATCTAATATG
Found at i:22180352 original size:19 final size:21
Alignment explanation
Indices: 22180328--22180376 Score: 75
Period size: 19 Copynumber: 2.4 Consensus size: 21
22180318 ATAATTATAA
*
22180328 TGATTTAAAAAA-ATAA-ATT
1 TGATTTAAAAAATAAAAGATT
22180347 TGATTTAAAAAATAAAAGATT
1 TGATTTAAAAAATAAAAGATT
22180368 TGATTTAAA
1 TGATTTAAA
22180377 CCCCAATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 12 0.44
20 3 0.11
21 12 0.44
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (21 bp):
TGATTTAAAAAATAAAAGATT
Found at i:22189596 original size:15 final size:16
Alignment explanation
Indices: 22189566--22189598 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
22189556 TGATAAATTG
*
22189566 AAAATTAAGTATTGAA
1 AAAATTAAGTAGTGAA
22189582 AAAATTAAGT-GTGAA
1 AAAATTAAGTAGTGAA
22189597 AA
1 AA
22189599 GGTTAATTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.58, C:0.00, G:0.15, T:0.27
Consensus pattern (16 bp):
AAAATTAAGTAGTGAA
Found at i:22191006 original size:7 final size:7
Alignment explanation
Indices: 22190994--22191021 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
22190984 CAAAATACAG
22190994 CCATTGC
1 CCATTGC
22191001 CCATTGC
1 CCATTGC
22191008 CCATTGC
1 CCATTGC
22191015 CCATTGC
1 CCATTGC
22191022 ATGCATCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.43, G:0.14, T:0.29
Consensus pattern (7 bp):
CCATTGC
Found at i:22191451 original size:17 final size:17
Alignment explanation
Indices: 22191420--22191453 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
22191410 GCTCTTTGTC
* *
22191420 TTTTCCATTTTCTTTCT
1 TTTTCCATCTGCTTTCT
22191437 TTTTCCATCTGCTTTCT
1 TTTTCCATCTGCTTTCT
22191454 CTCTCTGCCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.26, G:0.03, T:0.65
Consensus pattern (17 bp):
TTTTCCATCTGCTTTCT
Found at i:22202830 original size:15 final size:16
Alignment explanation
Indices: 22202800--22202843 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
22202790 TTTTTTAAAT
22202800 ATTTATAT-TATTTATA
1 ATTTATATAT-TTTATA
22202816 ATTTA-ATATTTTATA
1 ATTTATATATTTTATA
*
22202831 TTTTATATATTTT
1 ATTTATATATTTT
22202844 TTATTTATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
ATTTATATATTTTATA
Found at i:22202850 original size:15 final size:15
Alignment explanation
Indices: 22202799--22202851 Score: 54
Period size: 16 Copynumber: 3.5 Consensus size: 15
22202789 TTTTTTTAAA
*
22202799 TATTTATATTATTTAT
1 TATTTATA-TATTTTT
* *
22202815 AATTTA-ATATTTTA
1 TATTTATATATTTTT
22202829 TATTTTATATATTTTT
1 TA-TTTATATATTTTT
22202845 TATTTAT
1 TATTTAT
22202852 TAAAATTTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
14 6 0.20
15 10 0.33
16 14 0.47
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TATTTATATATTTTT
Found at i:22206681 original size:21 final size:21
Alignment explanation
Indices: 22206655--22206703 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
22206645 TTTTTAAAAG
*
22206655 ATTATTTAT-TTTTATTTTAAT
1 ATTATTTATATTATATTTT-AT
*
22206676 ATTATTAATATTATATTTTAT
1 ATTATTTATATTATATTTTAT
22206697 ATTATTT
1 ATTATTT
22206704 TGGATAGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 16 0.67
22 8 0.33
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
ATTATTTATATTATATTTTAT
Found at i:22208641 original size:22 final size:23
Alignment explanation
Indices: 22208601--22208643 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
22208591 ACCAGGGCAA
*
22208601 AAAAAATTCAAGTATCAAATTAG
1 AAAAAATTCAAGTACCAAATTAG
*
22208624 AAAAAATT-AGGTACCAAATT
1 AAAAAATTCAAGTACCAAATT
22208644 GAACATTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.56, C:0.09, G:0.09, T:0.26
Consensus pattern (23 bp):
AAAAAATTCAAGTACCAAATTAG
Found at i:22209611 original size:29 final size:29
Alignment explanation
Indices: 22209568--22209623 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
22209558 TAGATGAAGT
* *
22209568 AAAATACAATCTGAGTTTTAGTACTTTAA
1 AAAATACAATATGAGTTCTAGTACTTTAA
22209597 AAAATACAATATGAGTTCTAGTACTTT
1 AAAATACAATATGAGTTCTAGTACTTT
22209624 CAGCCATCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.38
Consensus pattern (29 bp):
AAAATACAATATGAGTTCTAGTACTTTAA
Found at i:22218829 original size:36 final size:34
Alignment explanation
Indices: 22218725--22218830 Score: 88
Period size: 36 Copynumber: 3.0 Consensus size: 34
22218715 ACCTAATGCA
* * *
22218725 TCATTGGTATGTCCAAAGTAATATGCGTTTCACGCC
1 TCATCGGTATGTCCAAAGTAATATGAG-CTC-CGCC
** * *
22218761 TCATCGGTATAAACCGAAGTAATGTGTA-CTCCGCAC
1 TCATCGGTAT-GTCCAAAGTAATATG-AGCTCCGC-C
22218797 TTCATCGGTATGTCCAAAGTAATATGAGCTCCGC
1 -TCATCGGTATGTCCAAAGTAATATGAGCTCCGC
22218831 GCCTCATTAG
Statistics
Matches: 54, Mismatches: 11, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
35 4 0.07
36 29 0.54
37 21 0.39
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (34 bp):
TCATCGGTATGTCCAAAGTAATATGAGCTCCGCC
Found at i:22225241 original size:28 final size:27
Alignment explanation
Indices: 22225181--22225265 Score: 104
Period size: 25 Copynumber: 3.2 Consensus size: 27
22225171 TTAATTCATG
* * *
22225181 AATTTAATTACTAATTAATTCTA-TTT
1 AATTTAATTATTAAATAATTTTATTTT
22225207 AA-TTAATTATTAAATAATTTTATTTCT
1 AATTTAATTATTAAATAATTTTATTT-T
22225234 AATTTAATTATTAAATAA-TTTATTTT
1 AATTTAATTATTAAATAATTTTATTTT
22225260 CAATTT
1 -AATTT
22225266 CATACTTGCT
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
25 17 0.33
26 5 0.10
27 15 0.29
28 15 0.29
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (27 bp):
AATTTAATTATTAAATAATTTTATTTT
Found at i:22225687 original size:16 final size:17
Alignment explanation
Indices: 22225660--22225695 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
22225650 TAATAAATTA
*
22225660 ATTATAATTATTTTTAT
1 ATTATAATTATTTATAT
22225677 ATTAT-ATTATTTATAT
1 ATTATAATTATTTATAT
22225693 ATT
1 ATT
22225696 TAAAAAGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTATAATTATTTATAT
Found at i:22227628 original size:29 final size:29
Alignment explanation
Indices: 22227596--22227652 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
22227586 CATGCATGTC
*
22227596 AACCCCTTGTATGCGAACACC-TATAGGCG
1 AACCCCTTGCATGCGAA-ACCTTATAGGCG
*
22227625 AACCCCTTGCATGTGAAACCTTATAGGC
1 AACCCCTTGCATGCGAAACCTTATAGGC
22227653 AAGCCTTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 22 0.88
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (29 bp):
AACCCCTTGCATGCGAAACCTTATAGGCG
Found at i:22232347 original size:28 final size:27
Alignment explanation
Indices: 22232307--22232364 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
22232297 TAATACTATA
22232307 ATATAAATATTAAAAAAT-ATAAGATAT
1 ATATAAATATTAAAAAATGA-AAGATAT
* *
22232334 ATATAAAGTTTTAATAAATGAAAGATAT
1 ATATAAA-TATTAAAAAATGAAAGATAT
22232362 ATA
1 ATA
22232365 AATTTATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 7 0.26
28 19 0.70
29 1 0.04
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (27 bp):
ATATAAATATTAAAAAATGAAAGATAT
Found at i:22239818 original size:20 final size:19
Alignment explanation
Indices: 22239786--22239842 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 19
22239776 AATTAAAAAG
*
22239786 AAAATTCAGAATAATTT-TA
1 AAAATTCAAAAT-ATTTATA
22239805 AAAGATTCAAAATATTTATA
1 AAA-ATTCAAAATATTTATA
22239825 AAAATTTCAAAAATATTT
1 AAAA-TTC-AAAATATTT
22239843 TTTTTAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
19 8 0.24
20 16 0.48
21 9 0.27
ACGTcount: A:0.54, C:0.05, G:0.04, T:0.37
Consensus pattern (19 bp):
AAAATTCAAAATATTTATA
Found at i:22240328 original size:3 final size:3
Alignment explanation
Indices: 22240299--22240345 Score: 53
Period size: 3 Copynumber: 16.0 Consensus size: 3
22240289 ACTCGTTAAA
**
22240299 AAT AAT AA- AAT -AT AAT TTT ATAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT
22240343 AAT
1 AAT
22240346 TACATTTAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
2 4 0.11
3 31 0.84
4 2 0.05
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:22243590 original size:13 final size:13
Alignment explanation
Indices: 22243572--22243598 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
22243562 TTCGTGTTTA
22243572 CCGGTTAGTGACT
1 CCGGTTAGTGACT
22243585 CCGGTTAGTGACT
1 CCGGTTAGTGACT
22243598 C
1 C
22243599 TTGGTGACAT
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:0.15, C:0.26, G:0.30, T:0.30
Consensus pattern (13 bp):
CCGGTTAGTGACT
Found at i:22245115 original size:4 final size:4
Alignment explanation
Indices: 22245106--22245131 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
22245096 TAACCCGCAA
22245106 ACAT ACAT ACAT ACAT ACAT ACAT AC
1 ACAT ACAT ACAT ACAT ACAT ACAT AC
22245132 TTAGGTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (4 bp):
ACAT
Found at i:22246532 original size:5 final size:5
Alignment explanation
Indices: 22246522--22246547 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
22246512 AGCATTTATT
22246522 ATAAA ATAAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA A
22246548 ATTGTAATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:22246779 original size:25 final size:24
Alignment explanation
Indices: 22246738--22246784 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 24
22246728 ATTTAATTTA
22246738 TAATTATTATTTTAAAATATTGTGC
1 TAATTATTATTTTAAAAT-TTGTGC
22246763 TAATT-TTATTTTAAAAATTTGT
1 TAATTATTATTTT-AAAATTTGT
22246785 ATTCATTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.55
Consensus pattern (24 bp):
TAATTATTATTTTAAAATTTGTGC
Found at i:22255338 original size:29 final size:30
Alignment explanation
Indices: 22255306--22255369 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
22255296 TTGTAACTTT
*
22255306 TAATAATTGGATGACC-AAAACAAATTTAG
1 TAATAATTGGATGACCAAAAACAAATTTAC
* * *
22255335 TAATAGTTGGGTGACCAAAAATAAATTTAC
1 TAATAATTGGATGACCAAAAACAAATTTAC
22255365 TAATA
1 TAATA
22255370 TAGTTTACCC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 14 0.47
30 16 0.53
ACGTcount: A:0.47, C:0.09, G:0.14, T:0.30
Consensus pattern (30 bp):
TAATAATTGGATGACCAAAAACAAATTTAC
Found at i:22260835 original size:38 final size:37
Alignment explanation
Indices: 22260793--22260866 Score: 89
Period size: 38 Copynumber: 2.0 Consensus size: 37
22260783 AATTATTTAT
22260793 ATTTAGTCA-TATAATAAATTA-TTAATATAATTAATATA
1 ATTTA-TCATTATAATAAATTATTTAATAT--TTAATATA
* *
22260831 ATTTATTATTTTAATAAATTATTTAATATTTAATAT
1 ATTTATCATTATAATAAATTATTTAATATTTAATAT
22260867 TTAAATTTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
37 9 0.28
38 16 0.50
39 7 0.22
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (37 bp):
ATTTATCATTATAATAAATTATTTAATATTTAATATA
Found at i:22260852 original size:16 final size:19
Alignment explanation
Indices: 22260804--22260865 Score: 60
Period size: 18 Copynumber: 3.3 Consensus size: 19
22260794 TTTAGTCATA
22260804 TAATAAATTATTAATATAAT
1 TAATAAATTATTAATAT-AT
22260824 TAATATAATTTATT-AT-T-T
1 TAATA-AA-TTATTAATATAT
22260842 TAATAAATTATTTAATAT-T
1 TAATAAATTA-TTAATATAT
22260861 TAATA
1 TAATA
22260866 TTTAAATTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
16 3 0.08
17 4 0.11
18 8 0.22
19 7 0.19
20 6 0.16
21 4 0.11
22 5 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TAATAAATTATTAATATAT
Found at i:22261463 original size:19 final size:20
Alignment explanation
Indices: 22261439--22261484 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
22261429 CATCCAAACA
22261439 CCAGAAAA-TAT-TAATTTTT
1 CCAGAAAAGTATGTAA-TTTT
*
22261458 CCAGAAAAGTATGTCATTTT
1 CCAGAAAAGTATGTAATTTT
22261478 CCAGAAA
1 CCAGAAA
22261485 TCAATTTCCG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 8 0.33
20 14 0.58
21 2 0.08
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.33
Consensus pattern (20 bp):
CCAGAAAAGTATGTAATTTT
Found at i:22267854 original size:9 final size:9
Alignment explanation
Indices: 22267840--22267867 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
22267830 GGTATTGTAT
22267840 GCAGCAGTA
1 GCAGCAGTA
22267849 GCAGCAGTA
1 GCAGCAGTA
22267858 GCAGCAGTA
1 GCAGCAGTA
22267867 G
1 G
22267868 GTGTGTTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.21, G:0.36, T:0.11
Consensus pattern (9 bp):
GCAGCAGTA
Found at i:22269611 original size:18 final size:18
Alignment explanation
Indices: 22269579--22269633 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 18
22269569 AAAATAAAGT
*
22269579 TAAATATAT-TAAAATTA
1 TAAATAAATATAAAATTA
22269596 TAAATAAATATAAAA-TA
1 TAAATAAATATAAAATTA
* *
22269613 TAGAAAAAACAT-AAATTA
1 TA-AATAAATATAAAATTA
22269631 TAA
1 TAA
22269634 TTTTTTATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
17 16 0.50
18 16 0.50
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (18 bp):
TAAATAAATATAAAATTA
Found at i:22269828 original size:23 final size:23
Alignment explanation
Indices: 22269802--22269846 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
22269792 TTAAAATTAT
22269802 ATATTTTAAAATTTTATAAAAAA
1 ATATTTTAAAATTTTATAAAAAA
* * *
22269825 ATATTTTTAATTTTTTTAAAAA
1 ATATTTTAAAATTTTATAAAAA
22269847 GTATATATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAATTTTATAAAAAA
Found at i:22270074 original size:32 final size:32
Alignment explanation
Indices: 22270038--22270098 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
22270028 TAAAATTAAT
*
22270038 TGCCATGTGGCATTTTTTCATTGGCCAAAACA
1 TGCCATGTGCCATTTTTTCATTGGCCAAAACA
*
22270070 TGCCATGTGCCGTTTTTTCATTGGCCAAA
1 TGCCATGTGCCATTTTTTCATTGGCCAAA
22270099 GTTGCCTAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.36
Consensus pattern (32 bp):
TGCCATGTGCCATTTTTTCATTGGCCAAAACA
Found at i:22272326 original size:15 final size:15
Alignment explanation
Indices: 22272298--22272331 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
22272288 CTGATTACAC
22272298 TTAAGGTTTAATTAA
1 TTAAGGTTTAATTAA
* *
22272313 TTAAGTTTTTATTAA
1 TTAAGGTTTAATTAA
22272328 TTAA
1 TTAA
22272332 TTATGATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (15 bp):
TTAAGGTTTAATTAA
Found at i:22275716 original size:19 final size:19
Alignment explanation
Indices: 22275692--22275745 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
22275682 AATTTTTGAG
22275692 GATATGAAATCTTAGATAT
1 GATATGAAATCTTAGATAT
* *
22275711 GATATGCAATCCTAGATAT
1 GATATGAAATCTTAGATAT
*
22275730 GATATGTAATCTTAGA
1 GATATGAAATCTTAGA
22275746 AGATACGATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (19 bp):
GATATGAAATCTTAGATAT
Found at i:22276343 original size:25 final size:25
Alignment explanation
Indices: 22276292--22276343 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
22276282 AATTTTGTTA
**
22276292 ATGTAATTATTATTATTATTTTCAT
1 ATGTAATTATTATTATTATTAGCAT
22276317 ATGTAATTATTATTATT-TTAGCTAT
1 ATGTAATTATTATTATTATTAGC-AT
22276342 AT
1 AT
22276344 ATATATGTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 3 0.12
25 21 0.88
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.58
Consensus pattern (25 bp):
ATGTAATTATTATTATTATTAGCAT
Found at i:22276942 original size:19 final size:20
Alignment explanation
Indices: 22276903--22276942 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
22276893 TTCTAGGCCT
* *
22276903 TTGTAATATTTATTATTGCA
1 TTGTAATATTTAATATAGCA
22276923 TTGT-ATATTTAATATAGCA
1 TTGTAATATTTAATATAGCA
22276942 T
1 T
22276943 CACATCATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.53
Consensus pattern (20 bp):
TTGTAATATTTAATATAGCA
Found at i:22277298 original size:98 final size:98
Alignment explanation
Indices: 22277183--22277377 Score: 345
Period size: 98 Copynumber: 2.0 Consensus size: 98
22277173 CTAAAAACAA
* * * *
22277183 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTTTTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGAGTGTGATTTC
22277248 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
*
22277281 TAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGAGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGAGTGTGATTTC
22277346 TTAAATCTTGGATAAGTGGATGTTCTTTTAAA
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAA
22277378 ATTTTATTGT
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 92 1.00
ACGTcount: A:0.28, C:0.10, G:0.24, T:0.37
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGAGTGTGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:22278277 original size:22 final size:23
Alignment explanation
Indices: 22278237--22278280 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
22278227 CAAACAAACC
22278237 TGTTGCTGTTTCCACTGTTTTGG
1 TGTTGCTGTTTCCACTGTTTTGG
*
22278260 TGTTGCT-TTTTCACTGTTTTG
1 TGTTGCTGTTTCCACTGTTTTG
22278281 CTGCTATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.05, C:0.16, G:0.23, T:0.57
Consensus pattern (23 bp):
TGTTGCTGTTTCCACTGTTTTGG
Found at i:22278613 original size:11 final size:11
Alignment explanation
Indices: 22278575--22278630 Score: 69
Period size: 11 Copynumber: 5.2 Consensus size: 11
22278565 TATATTTTTT
22278575 ATATTTT-AAA
1 ATATTTTAAAA
*
22278585 ATATTTCAAAA
1 ATATTTTAAAA
22278596 ATATTTTAAAA
1 ATATTTTAAAA
*
22278607 ATATTTTTAAA
1 ATATTTTAAAA
* *
22278618 TTTTTTTAAAA
1 ATATTTTAAAA
22278629 AT
1 AT
22278631 TGGTGTTTAT
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
10 6 0.16
11 32 0.84
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (11 bp):
ATATTTTAAAA
Found at i:22286436 original size:31 final size:31
Alignment explanation
Indices: 22286398--22286457 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
22286388 AAAAGATAGA
*
22286398 TTATTATATTATACTTCGTAGATGAATTGGT
1 TTATTATATTATACTTCGAAGATGAATTGGT
*
22286429 TTATTATATTATACTTCGAAGATTAATTG
1 TTATTATATTATACTTCGAAGATGAATTG
22286458 TCAAAAGTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.32, C:0.07, G:0.13, T:0.48
Consensus pattern (31 bp):
TTATTATATTATACTTCGAAGATGAATTGGT
Found at i:22290413 original size:19 final size:20
Alignment explanation
Indices: 22290389--22290426 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
22290379 AAAAAATTCG
22290389 GGTAATTCGGGT-ATTTTTC
1 GGTAATTCGGGTAATTTTTC
22290408 GGTAATTCGGGTAATTTTT
1 GGTAATTCGGGTAATTTTT
22290427 AACCAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.18, C:0.08, G:0.26, T:0.47
Consensus pattern (20 bp):
GGTAATTCGGGTAATTTTTC
Found at i:22294317 original size:35 final size:35
Alignment explanation
Indices: 22294278--22294346 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
22294268 TTTCCTAGTG
*
22294278 AAAATGAACATGATTCTCATGGTTGAGCTGAAGTA
1 AAAATGAACATGACTCTCATGGTTGAGCTGAAGTA
*
22294313 AAAATGAACATGACTCTCATGGTTGAGTTGAAGT
1 AAAATGAACATGACTCTCATGGTTGAGCTGAAGT
22294347 TGAAATTGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.29
Consensus pattern (35 bp):
AAAATGAACATGACTCTCATGGTTGAGCTGAAGTA
Found at i:22296220 original size:13 final size:13
Alignment explanation
Indices: 22296202--22296234 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
22296192 TTCCCTAAAT
22296202 AATGAAAAGGAAA
1 AATGAAAAGGAAA
*
22296215 AATGAAAATGAAA
1 AATGAAAAGGAAA
22296228 AA-GAAAA
1 AATGAAAA
22296235 TAAATAACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.09
Consensus pattern (13 bp):
AATGAAAAGGAAA
Found at i:22302849 original size:17 final size:17
Alignment explanation
Indices: 22302827--22302862 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
22302817 GACCACTCTC
*
22302827 CCTTAGATGATACATAT
1 CCTTAGATGACACATAT
22302844 CCTTAGATGACACATAT
1 CCTTAGATGACACATAT
22302861 CC
1 CC
22302863 ACTTAGTGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.33, C:0.25, G:0.11, T:0.31
Consensus pattern (17 bp):
CCTTAGATGACACATAT
Found at i:22302908 original size:91 final size:91
Alignment explanation
Indices: 22302753--22303008 Score: 503
Period size: 91 Copynumber: 2.8 Consensus size: 91
22302743 GTTTACTCAC
22302753 CCTTAGATGACACATATCCACTTAGTGTACCGAACAAAATAAATTAATACAAGAGAATCCAATTG
1 CCTTAGATGACACATATCCACTTAGTGTACCGAACAAAATAAATTAATACAAGAGAATCCAATTG
22302818 ACCACTCTCCCTTAGATGATACATAT
66 ACCACTCTCCCTTAGATGATACATAT
22302844 CCTTAGATGACACATATCCACTTAGTGTACCGAACAAAATAAATTAATACAAGAGAATCCAATTG
1 CCTTAGATGACACATATCCACTTAGTGTACCGAACAAAATAAATTAATACAAGAGAATCCAATTG
22302909 ACCACTCTCCCTTAGATGATACATAT
66 ACCACTCTCCCTTAGATGATACATAT
*
22302935 CCTTAGATGACACATATCCACTTAGTGTACCGAACAAAATAAATTAATACAAGAGAATCCAATTT
1 CCTTAGATGACACATATCCACTTAGTGTACCGAACAAAATAAATTAATACAAGAGAATCCAATTG
22303000 ACCACTCTC
66 ACCACTCTC
22303009 GTATAAGGAA
Statistics
Matches: 164, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 164 1.00
ACGTcount: A:0.40, C:0.23, G:0.11, T:0.26
Consensus pattern (91 bp):
CCTTAGATGACACATATCCACTTAGTGTACCGAACAAAATAAATTAATACAAGAGAATCCAATTG
ACCACTCTCCCTTAGATGATACATAT
Found at i:22302940 original size:17 final size:17
Alignment explanation
Indices: 22302918--22302953 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
22302908 GACCACTCTC
*
22302918 CCTTAGATGATACATAT
1 CCTTAGATGACACATAT
22302935 CCTTAGATGACACATAT
1 CCTTAGATGACACATAT
22302952 CC
1 CC
22302954 ACTTAGTGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.33, C:0.25, G:0.11, T:0.31
Consensus pattern (17 bp):
CCTTAGATGACACATAT
Found at i:22309097 original size:14 final size:14
Alignment explanation
Indices: 22309080--22309106 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
22309070 ACATCCTTAA
22309080 GTTAAAATTTATAT
1 GTTAAAATTTATAT
22309094 GTTAAAATTTATA
1 GTTAAAATTTATA
22309107 ATTCAGTCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (14 bp):
GTTAAAATTTATAT
Found at i:22309156 original size:33 final size:33
Alignment explanation
Indices: 22309119--22309185 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
22309109 TCAGTCACAT
22309119 TTAAATTTAATAAAATACAAAGTTGAAAAAACA
1 TTAAATTTAATAAAATACAAAGTTGAAAAAACA
22309152 TTAAATTTAATAAAATACAAAGTTGAAAAAACA
1 TTAAATTTAATAAAATACAAAGTTGAAAAAACA
22309185 T
1 T
22309186 ACTTAAGAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.60, C:0.06, G:0.06, T:0.28
Consensus pattern (33 bp):
TTAAATTTAATAAAATACAAAGTTGAAAAAACA
Found at i:22318393 original size:26 final size:27
Alignment explanation
Indices: 22318360--22318422 Score: 110
Period size: 27 Copynumber: 2.4 Consensus size: 27
22318350 AATAAAAAAA
22318360 ACCAAAATATTAT-AAGTTTTTTATTT
1 ACCAAAATATTATAAAGTTTTTTATTT
*
22318386 ACCAAAATATTATAAATTTTTTTATTT
1 ACCAAAATATTATAAAGTTTTTTATTT
22318413 ACCAAAATAT
1 ACCAAAATAT
22318423 ACCAAAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
26 13 0.37
27 22 0.63
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.46
Consensus pattern (27 bp):
ACCAAAATATTATAAAGTTTTTTATTT
Found at i:22318525 original size:27 final size:27
Alignment explanation
Indices: 22318495--22318567 Score: 69
Period size: 27 Copynumber: 2.7 Consensus size: 27
22318485 CCCTGGTCAG
22318495 GCCAAGGTGATTGGCGGCAACAAAT-GT
1 GCCAA-GTGATTGGCGGCAACAAATGGT
** *
22318522 GCCAAAGCCATTGGCGGC-ACCAATGGT
1 GCC-AAGTGATTGGCGGCAACAAATGGT
*
22318549 GCCATACTGATTGGCGGCA
1 GCCA-AGTGATTGGCGGCA
22318568 CTACTCGTGT
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
26 6 0.17
27 28 0.78
28 2 0.06
ACGTcount: A:0.26, C:0.25, G:0.32, T:0.18
Consensus pattern (27 bp):
GCCAAGTGATTGGCGGCAACAAATGGT
Found at i:22318671 original size:11 final size:11
Alignment explanation
Indices: 22318655--22318696 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
22318645 GAGGTGCTAC
22318655 GAAAAAGAAGA
1 GAAAAAGAAGA
22318666 GAAAAAG-AGA
1 GAAAAAGAAGA
*
22318676 GAAAGAGAAGA
1 GAAAAAGAAGA
22318687 GAAAAAGAAG
1 GAAAAAGAAG
22318697 GTATTTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (11 bp):
GAAAAAGAAGA
Found at i:22318684 original size:21 final size:21
Alignment explanation
Indices: 22318655--22318694 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
22318645 GAGGTGCTAC
22318655 GAAAAAGAAGAGAAAAAGAGA
1 GAAAAAGAAGAGAAAAAGAGA
*
22318676 GAAAGAGAAGAGAAAAAGA
1 GAAAAAGAAGAGAAAAAGA
22318695 AGGTATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (21 bp):
GAAAAAGAAGAGAAAAAGAGA
Found at i:22318835 original size:3 final size:3
Alignment explanation
Indices: 22318829--22318867 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
22318819 TATTATTATA
*
22318829 GTT GTT GTT GTT GTT GTT ATT GTT GTT GTT GTT GTT GTT
1 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT
22318868 AGTATTAAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.03, C:0.00, G:0.31, T:0.67
Consensus pattern (3 bp):
GTT
Found at i:22319723 original size:18 final size:18
Alignment explanation
Indices: 22319679--22319723 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
22319669 TTGATATGGT
*
22319679 TGGTGGTGAAGAAGAAGG
1 TGGTGGCGAAGAAGAAGG
* * *
22319697 TGCTAGCGAAGAAGAATG
1 TGGTGGCGAAGAAGAAGG
22319715 TGGTGGCGA
1 TGGTGGCGA
22319724 TCATTGGGAT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.31, C:0.07, G:0.44, T:0.18
Consensus pattern (18 bp):
TGGTGGCGAAGAAGAAGG
Found at i:22323531 original size:11 final size:11
Alignment explanation
Indices: 22323514--22323557 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
22323504 AATCATTTAA
22323514 TAATAAAATAT
1 TAATAAAATAT
* *
22323525 TACTAAAAATCT
1 TAAT-AAAATAT
22323537 TAATAAAATAT
1 TAATAAAATAT
*
22323548 TAATTAAATA
1 TAATAAAATA
22323558 ACATTTAACT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (11 bp):
TAATAAAATAT
Found at i:22324401 original size:11 final size:11
Alignment explanation
Indices: 22324385--22324411 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
22324375 GTTTATGCTT
22324385 AAATTGTATCC
1 AAATTGTATCC
22324396 AAATTGTATCC
1 AAATTGTATCC
22324407 AAATT
1 AAATT
22324412 AAGTTATAAA
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:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (11 bp):
AAATTGTATCC
Found at i:22328407 original size:41 final size:41
Alignment explanation
Indices: 22328342--22328528 Score: 142
Period size: 40 Copynumber: 4.7 Consensus size: 41
22328332 AAAATTACCT
* *
22328342 TTTTTTCTTTTTTTTTTCCT-TCC-TTCCTTCCCTCTTCTTC
1 TTTTTTCTTTCTTTTCTCCTCTCCTTTCCTT-CCTCTTCTTC
* * * *
22328382 TTTTTTTTTTCTTTTCTCTTCTCCTTTCCTTTTCTTTTCTTC
1 TTTTTTCTTTCTTTTCTCCTCTCCTTTCC-TTCCTCTTCTTC
* *
22328424 -TTTTTCTTTCTTTTTTCCTCTCCTTTCC-TCTTCTTCTTC
1 TTTTTTCTTTCTTTTCTCCTCTCCTTTCCTTCCTCTTCTTC
* * * * *
22328463 TTTCTTTCTGT-TTTTCGCTTCTCCTGTCCTT-TTCTTTCCTTC
1 TTT-TTTCTTTCTTTTCTCCTCTCCTTTCCTTCCTC-TT-CTTC
22328505 -TTTTTCTTTC--TT-TCCTCTCCTTTC
1 TTTTTTCTTTCTTTTCTCCTCTCCTTTC
22328529 TTTCTTTCTT
Statistics
Matches: 117, Mismatches: 21, Indels: 20
0.74 0.13 0.13
Matches are distributed among these distances:
38 9 0.08
39 10 0.09
40 41 0.35
41 39 0.33
42 16 0.14
43 2 0.02
ACGTcount: A:0.00, C:0.31, G:0.02, T:0.67
Consensus pattern (41 bp):
TTTTTTCTTTCTTTTCTCCTCTCCTTTCCTTCCTCTTCTTC
Found at i:22328408 original size:24 final size:24
Alignment explanation
Indices: 22328373--22328440 Score: 75
Period size: 23 Copynumber: 2.8 Consensus size: 24
22328363 CCTTCCTTCC
22328373 CTCTTCTTCTTTTTTTTTTCTTTT
1 CTCTTCTTCTTTTTTTTTTCTTTT
* **
22328397 CTCTTC-TCCTTTCCTTTTCTTTT
1 CTCTTCTTCTTTTTTTTTTCTTTT
* *
22328420 CTTCTTTTTCTTTCTTTTTTC
1 C-TCTTCTTCTTTTTTTTTTC
22328441 CTCTCCTTTC
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
23 15 0.44
24 10 0.29
25 9 0.26
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (24 bp):
CTCTTCTTCTTTTTTTTTTCTTTT
Done.