Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr10
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: 21822658
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.32
Warning! 1067834 characters in sequence are not A, C, G, or T
File 11 of 59
Found at i:4098899 original size:2 final size:2
Alignment explanation
Indices: 4098892--4098918 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4098882 GAAATCCAGA
4098892 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
4098919 GAAACACATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4099495 original size:4 final size:4
Alignment explanation
Indices: 4099486--4099516 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
4099476 GGCTATGATT
*
4099486 TTTA TTTA TTTA TTTA CTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
4099517 TGGCTTTGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:4100355 original size:78 final size:77
Alignment explanation
Indices: 4100273--4100420 Score: 287
Period size: 78 Copynumber: 1.9 Consensus size: 77
4100263 TATATAAGGA
4100273 GTAGCTTGAATTTTCATTTAAAAAAACAAAGACAATATTTTTCAAAGTTTTTAAATTATTTAAGA
1 GTAGCTTGAATTTTCATTTAAAAAAACAAAGACAATATTTTTCAAAGTTTTTAAATTATTTAAGA
4100338 AAATTAATATTT
66 AAATTAATATTT
4100350 NGTAGCTTGAATTTTCATTTAAAAAAACAAAGACAATATTTTTCAAAGTTTTTAAATTATTTAAG
1 -GTAGCTTGAATTTTCATTTAAAAAAACAAAGACAATATTTTTCAAAGTTTTTAAATTATTTAAG
4100415 AAAATT
65 AAAATT
4100421 CAAATAAGTT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 70 1.00
ACGTcount: A:0.44, C:0.07, G:0.08, T:0.41
Consensus pattern (77 bp):
GTAGCTTGAATTTTCATTTAAAAAAACAAAGACAATATTTTTCAAAGTTTTTAAATTATTTAAGA
AAATTAATATTT
Found at i:4100736 original size:19 final size:21
Alignment explanation
Indices: 4100714--4100752 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
4100704 AAAAAATAAA
*
4100714 AATTTATT-AAAAA-ATTTTC
1 AATTAATTCAAAAATATTTTC
4100733 AATTAATTCAAAAATATTTT
1 AATTAATTCAAAAATATTTT
4100753 TACATATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 5 0.29
21 5 0.29
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (21 bp):
AATTAATTCAAAAATATTTTC
Found at i:4100906 original size:5 final size:6
Alignment explanation
Indices: 4100890--4100919 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
4100880 AATAATTACC
4100890 GAAAAA GAAAAA GAAAAA GAAAAA GTAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA G-AAAA
4100920 TCCCTATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.83
7 4 0.17
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (6 bp):
GAAAAA
Found at i:4102461 original size:18 final size:17
Alignment explanation
Indices: 4102440--4102479 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 17
4102430 TTATATCAAT
4102440 ATCATGTGATATAAAATG
1 ATCAT-TGATATAAAATG
4102458 ATCAATTGATATAAAATG
1 ATC-ATTGATATAAAATG
4102476 ATCA
1 ATCA
4102480 ATGACAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 1 0.05
18 18 0.86
19 2 0.10
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.33
Consensus pattern (17 bp):
ATCATTGATATAAAATG
Found at i:4102480 original size:18 final size:18
Alignment explanation
Indices: 4102446--4102481 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
4102436 CAATATCATG
4102446 TGATATAAAATGATCAAT
1 TGATATAAAATGATCAAT
4102464 TGATATAAAATGATCAAT
1 TGATATAAAATGATCAAT
4102482 GACAATTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.06, G:0.11, T:0.33
Consensus pattern (18 bp):
TGATATAAAATGATCAAT
Found at i:4103702 original size:29 final size:30
Alignment explanation
Indices: 4103668--4103728 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
4103658 AAATTTTTGA
* * *
4103668 ATTTTTGTTTTTAATTAAATAAGTTTTTAT
1 ATTTTTATTTTAAATCAAATAAGTTTTTAT
* *
4103698 ATTTTTATTTTAAATCGAATGAGTTTTTAT
1 ATTTTTATTTTAAATCAAATAAGTTTTTAT
4103728 A
1 A
4103729 ACTAACGATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.02, G:0.08, T:0.59
Consensus pattern (30 bp):
ATTTTTATTTTAAATCAAATAAGTTTTTAT
Found at i:4105282 original size:38 final size:37
Alignment explanation
Indices: 4105229--4105305 Score: 127
Period size: 38 Copynumber: 2.1 Consensus size: 37
4105219 TAAAAAGAAA
*
4105229 AAGAAAAATCATTTTCATCTGGTTTACTTTTAACTAC
1 AAGAAAAATCATTTTCATCTCGTTTACTTTTAACTAC
*
4105266 AAGAAAAAGTCATTTTCATCTCGTTTACTTTTAATTAC
1 AAGAAAAA-TCATTTTCATCTCGTTTACTTTTAACTAC
4105304 AA
1 AA
4105306 AGCTTTAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
37 8 0.22
38 29 0.78
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (37 bp):
AAGAAAAATCATTTTCATCTCGTTTACTTTTAACTAC
Found at i:4112164 original size:2 final size:2
Alignment explanation
Indices: 4112153--4112182 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
4112143 AGTTTTTAAA
4112153 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4112183 AATTTTAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4112506 original size:96 final size:95
Alignment explanation
Indices: 4112389--4112587 Score: 382
Period size: 96 Copynumber: 2.1 Consensus size: 95
4112379 CATTTCGATT
4112389 TATTAATT-TTTTTGGATTCGAAATGATTTTGCTCATCCTACAAACAAAATCTAAGCAAACAACA
1 TATTAATTGTTTTTGGATTCGAAATGATTTTGCTCATCCTACAAACAAAATCTAAGCAAACAACA
4112453 CTTAGCTTAGAAGTGTAACTTATTTGACTA
66 CTTAGCTTAGAAGTGTAACTTATTTGACTA
4112483 TATTAATTGNTTTTTGGATTCGAAATGATTTTGCTCATCCTACAAACAAAATCTAAGCAAACAAC
1 TATTAATTG-TTTTTGGATTCGAAATGATTTTGCTCATCCTACAAACAAAATCTAAGCAAACAAC
4112548 ACTTAGCTTAGAAGTGTAACTTATTTGACTA
65 ACTTAGCTTAGAAGTGTAACTTATTTGACTA
4112579 TATTAATTG
1 TATTAATTG
4112588 CTCTCACTAC
Statistics
Matches: 103, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
94 8 0.08
96 95 0.92
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (95 bp):
TATTAATTGTTTTTGGATTCGAAATGATTTTGCTCATCCTACAAACAAAATCTAAGCAAACAACA
CTTAGCTTAGAAGTGTAACTTATTTGACTA
Found at i:4140964 original size:2 final size:2
Alignment explanation
Indices: 4140957--4140995 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
4140947 ATGCCCAAAA
*
4140957 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4140996 NNNNNNNNNN
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:4151296 original size:57 final size:57
Alignment explanation
Indices: 4151232--4151346 Score: 212
Period size: 57 Copynumber: 2.0 Consensus size: 57
4151222 AATCATATCC
*
4151232 TTGTATTTTTATCCCTTTTTTAAGTGAAAAATTCGATTATTTCGAACAAATATCTCT
1 TTGTATTTTTATCCCTGTTTTAAGTGAAAAATTCGATTATTTCGAACAAATATCTCT
*
4151289 TTGTATTTTTATCCCTGTTTTAAGTGAAAAATTCTATTATTTCGAACAAATATCTCT
1 TTGTATTTTTATCCCTGTTTTAAGTGAAAAATTCGATTATTTCGAACAAATATCTCT
4151346 T
1 T
4151347 CAAACAAAAT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.30, C:0.14, G:0.09, T:0.48
Consensus pattern (57 bp):
TTGTATTTTTATCCCTGTTTTAAGTGAAAAATTCGATTATTTCGAACAAATATCTCT
Found at i:4157179 original size:18 final size:18
Alignment explanation
Indices: 4157146--4157180 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4157136 CAAAAGTTAT
*
4157146 GTTTGTTCAACCAATTAA
1 GTTTGTTCAAACAATTAA
*
4157164 GTTTGTTCAAATAATTA
1 GTTTGTTCAAACAATTA
4157181 TATTGGAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.43
Consensus pattern (18 bp):
GTTTGTTCAAACAATTAA
Found at i:4161563 original size:9 final size:9
Alignment explanation
Indices: 4161551--4161622 Score: 55
Period size: 9 Copynumber: 7.9 Consensus size: 9
4161541 TTTTATATCT
4161551 TTTATTTTA
1 TTTATTTTA
4161560 TTTA-TTTA
1 TTTATTTTA
4161568 TTTTATTTTA
1 -TTTATTTTA
4161578 TTTA-TTTA
1 TTTATTTTA
4161586 TCTT-TTATTA
1 T-TTATT-TTA
4161596 -TTATTATTA
1 TTTATT-TTA
4161605 TTATATTTT-
1 TT-TATTTTA
4161614 TTATATTTT
1 TT-TATTTT
4161623 TTTCTTATCC
Statistics
Matches: 55, Mismatches: 0, Indels: 16
0.77 0.00 0.23
Matches are distributed among these distances:
8 11 0.20
9 30 0.55
10 10 0.18
11 4 0.07
ACGTcount: A:0.24, C:0.01, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTATTTTA
Found at i:4161571 original size:18 final size:18
Alignment explanation
Indices: 4161550--4161625 Score: 79
Period size: 18 Copynumber: 4.2 Consensus size: 18
4161540 ATTTTATATC
4161550 TTTTATTTTATTTATTTA
1 TTTTATTTTATTTATTTA
4161568 TTTTATTTTATTTATTTA
1 TTTTATTTTATTTATTTA
4161586 TCTTTTATTATTA-TTA-TTA
1 --TTTTATT-TTATTTATTTA
*
4161605 TTATATTTT-TTATATTT-
1 TTTTATTTTATT-TATTTA
4161622 TTTT
1 TTTT
4161626 CTTATCCTAA
Statistics
Matches: 50, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
16 3 0.06
17 11 0.22
18 20 0.40
19 3 0.06
20 10 0.20
21 3 0.06
ACGTcount: A:0.22, C:0.01, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTATTTTATTTATTTA
Found at i:4161577 original size:14 final size:14
Alignment explanation
Indices: 4161551--4161617 Score: 68
Period size: 14 Copynumber: 4.7 Consensus size: 14
4161541 TTTTATATCT
4161551 TTTATTTTA-TTTA
1 TTTATTTTATTTTA
4161564 TTTATTTTATTTTA
1 TTTATTTTATTTTA
*
4161578 TTTATTTATCTTTTA
1 TTTATTT-TATTTTA
4161593 -TTATTATTATTATTA
1 TTTATT-TTATT-TTA
4161608 TATT-TTTTAT
1 T-TTATTTTAT
4161618 ATTTTTTTCT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
13 9 0.20
14 19 0.41
15 14 0.30
16 2 0.04
17 2 0.04
ACGTcount: A:0.24, C:0.01, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTATTTTATTTTA
Found at i:4161623 original size:9 final size:9
Alignment explanation
Indices: 4161541--4161624 Score: 53
Period size: 9 Copynumber: 8.4 Consensus size: 9
4161531 CTAATTATCA
*
4161541 TTTTATATC
1 TTTTATATT
4161550 TTTTAT-TT
1 TTTTATATT
4161558 TATTTATTTATT
1 T-TTTA--TATT
*
4161570 TTATTTTATT
1 TT-TTATATT
*
4161580 TATTTATCTT
1 T-TTTATATT
4161590 TTATTATTATT
1 TT-TTA-TATT
4161601 ATTATTATATT
1 -TT-TTATATT
4161612 TTTTATATT
1 TTTTATATT
4161621 TTTT
1 TTTT
4161625 TCTTATCCTA
Statistics
Matches: 61, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
8 2 0.03
9 22 0.36
10 16 0.26
11 10 0.16
12 11 0.18
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTTATATT
Found at i:4161790 original size:10 final size:9
Alignment explanation
Indices: 4161764--4161818 Score: 53
Period size: 9 Copynumber: 6.2 Consensus size: 9
4161754 TCTCATCATT
*
4161764 TTTTTACTA
1 TTTTTATTA
4161773 TTTTTATTA
1 TTTTTATTA
4161782 -TTTTA-TA
1 TTTTTATTA
4161789 TTTTATATT-
1 TTTT-TATTA
*
4161798 TCTTTATTA
1 TTTTTATTA
4161807 TTTTTTATTA
1 -TTTTTATTA
4161817 TT
1 TT
4161819 ATATCCTTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
7 2 0.05
8 12 0.32
9 15 0.39
10 9 0.24
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTTTATTA
Found at i:4161836 original size:27 final size:26
Alignment explanation
Indices: 4161775--4161830 Score: 80
Period size: 25 Copynumber: 2.2 Consensus size: 26
4161765 TTTTACTATT
* *
4161775 TTTATTATTTTATATT-TTATATTTC
1 TTTATTATTTTTTATTATTATATTCC
4161800 TTTATTATTTTTTATTATTATA-TCC
1 TTTATTATTTTTTATTATTATATTCC
4161825 TTTATT
1 TTTATT
4161831 TTATTTCTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 23 0.82
26 5 0.18
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.71
Consensus pattern (26 bp):
TTTATTATTTTTTATTATTATATTCC
Found at i:4162119 original size:19 final size:18
Alignment explanation
Indices: 4162092--4162127 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
4162082 TTATGGAATA
*
4162092 TTATTATTATTTTCTTTTT
1 TTATCATTATTTT-TTTTT
4162111 TTATCATTATTTTTTTT
1 TTATCATTATTTTTTTT
4162128 ATATTTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.78
Consensus pattern (18 bp):
TTATCATTATTTTTTTTT
Found at i:4165614 original size:22 final size:22
Alignment explanation
Indices: 4165589--4165642 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
4165579 ACCAATTTCG
*
4165589 CAATACTTAAAAACCAGTGACA
1 CAATACTTAAAAACCAGTAACA
* * **
4165611 CAATGCCTAAAAACCAGTAATG
1 CAATACTTAAAAACCAGTAACA
4165633 CAATACTTAA
1 CAATACTTAA
4165643 TAACTAATTG
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.48, C:0.22, G:0.09, T:0.20
Consensus pattern (22 bp):
CAATACTTAAAAACCAGTAACA
Found at i:4167289 original size:60 final size:62
Alignment explanation
Indices: 4167164--4167299 Score: 179
Period size: 60 Copynumber: 2.2 Consensus size: 62
4167154 AAAAAAAAAC
* * **
4167164 TTTTAAGCA-TTTTGAGCATTTTGGAGTGATTTTTTATACACAAAAAAAAAATCTTTGAGTG
1 TTTTGAGCATTTTTAAGCATTTTGGAGTGATTTTTTATACACAAAAAAAAAATCTTTGAGCA
* * *
4167225 TTTTGAGCATTTTTAAGTATTTTGGAGTG-TTTTTTATATAC-AAAGAAAAATCTTTGAGCA
1 TTTTGAGCATTTTTAAGCATTTTGGAGTGATTTTTTATACACAAAAAAAAAATCTTTGAGCA
4167285 TTTTGAGCAGTTTTT
1 TTTTGAGCA-TTTTT
4167300 GCCAAGTAGG
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
60 25 0.38
61 24 0.36
62 17 0.26
ACGTcount: A:0.31, C:0.07, G:0.17, T:0.45
Consensus pattern (62 bp):
TTTTGAGCATTTTTAAGCATTTTGGAGTGATTTTTTATACACAAAAAAAAAATCTTTGAGCA
Found at i:4167477 original size:22 final size:22
Alignment explanation
Indices: 4167398--4167487 Score: 90
Period size: 22 Copynumber: 4.1 Consensus size: 22
4167388 GTTTTGGTGG
* * * *
4167398 TTTTTAGGCATTGCGTAACTAA
1 TTTTTAAGCATTGTGTGACTGA
** * *
4167420 TTTTTAAGCATTACGTTACTAA
1 TTTTTAAGCATTGTGTGACTGA
*
4167442 TTTTTAGGCATTGTGTGACTGA
1 TTTTTAAGCATTGTGTGACTGA
*
4167464 TTTTTAAGTATTGTGTGACTGA
1 TTTTTAAGCATTGTGTGACTGA
4167486 TT
1 TT
4167488 GGAAGACATT
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 58 1.00
ACGTcount: A:0.24, C:0.10, G:0.19, T:0.47
Consensus pattern (22 bp):
TTTTTAAGCATTGTGTGACTGA
Found at i:4167498 original size:22 final size:22
Alignment explanation
Indices: 4167450--4167521 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 22
4167440 AATTTTTAGG
*
4167450 CATTGTGTGACTGATTTTTAAG-
1 CATTGTGTGACTGA-TTGTAAGA
* *
4167472 TATTGTGTGACTGATTGGAAGA
1 CATTGTGTGACTGATTGTAAGA
* * *
4167494 CATTGCGCGACTGGTTAGTAAGA
1 CATTGTGTGACTGATT-GTAAGA
4167517 CATTG
1 CATTG
4167522 CATGACTAGT
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
21 5 0.12
22 25 0.62
23 10 0.25
ACGTcount: A:0.25, C:0.11, G:0.28, T:0.36
Consensus pattern (22 bp):
CATTGTGTGACTGATTGTAAGA
Found at i:4167520 original size:23 final size:23
Alignment explanation
Indices: 4167490--4167543 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
4167480 GACTGATTGG
* *
4167490 AAGACATTGCGCGACTGGTTAGT
1 AAGACATTGCACGACTAGTTAGT
*
4167513 AAGACATTGCATGACTAGTTAGT
1 AAGACATTGCACGACTAGTTAGT
*
4167536 AAGGCATT
1 AAGACATT
4167544 ACGTGATTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (23 bp):
AAGACATTGCACGACTAGTTAGT
Found at i:4167632 original size:22 final size:22
Alignment explanation
Indices: 4167583--4167641 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 22
4167573 TTAGTTGTTG
* *
4167583 CTTAAAAATCAGTCACATAATG
1 CTTAAAAATCAGTCACACAATA
* * *
4167605 CCTAAAAATCAGTTACGCAATA
1 CTTAAAAATCAGTCACACAATA
*
4167627 CTT-AAAATCAATCAC
1 CTTAAAAATCAGTCAC
4167642 GGAATGCCTA
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 10 0.34
22 19 0.66
ACGTcount: A:0.46, C:0.22, G:0.07, T:0.25
Consensus pattern (22 bp):
CTTAAAAATCAGTCACACAATA
Found at i:4167653 original size:21 final size:21
Alignment explanation
Indices: 4167587--4167654 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
4167577 TTGTTGCTTA
**
4167587 AAAATCAGTCACATAATGCCT
1 AAAATCAGTCACGCAATGCCT
* * *
4167608 AAAAATCAGTTACGCAATACTT
1 -AAAATCAGTCACGCAATGCCT
* *
4167630 AAAATCAATCACGGAATGCCT
1 AAAATCAGTCACGCAATGCCT
4167651 AAAA
1 AAAA
4167655 ACTAGAAACG
Statistics
Matches: 36, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
21 20 0.56
22 16 0.44
ACGTcount: A:0.47, C:0.21, G:0.10, T:0.22
Consensus pattern (21 bp):
AAAATCAGTCACGCAATGCCT
Found at i:4168990 original size:15 final size:15
Alignment explanation
Indices: 4168968--4169019 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 15
4168958 GTTAATATTT
4168968 TTTAATTTT-TTATA
1 TTTAATTTTATTATA
4168982 TTATAATTTTAATTATA
1 TT-TAATTTT-ATTATA
*
4168999 TTTAATATTATTATTA
1 TTTAATTTTATTA-TA
4169015 TTTAA
1 TTTAA
4169020 AAAATGATTG
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
14 2 0.06
15 11 0.33
16 13 0.39
17 7 0.21
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTAATTTTATTATA
Found at i:4168992 original size:21 final size:24
Alignment explanation
Indices: 4168967--4169009 Score: 65
Period size: 21 Copynumber: 1.9 Consensus size: 24
4168957 TGTTAATATT
4168967 TTTTAATT-T-TTT-ATATTATAA
1 TTTTAATTATATTTAATATTATAA
4168988 TTTTAATTATATTTAATATTAT
1 TTTTAATTATATTTAATATTAT
4169010 TATTATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
22 1 0.05
23 3 0.16
24 7 0.37
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (24 bp):
TTTTAATTATATTTAATATTATAA
Found at i:4170851 original size:2 final size:2
Alignment explanation
Indices: 4170844--4170868 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4170834 TCAAATTTAT
4170844 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
4170869 GCATGGTTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4174407 original size:2 final size:2
Alignment explanation
Indices: 4174400--4174481 Score: 110
Period size: 2 Copynumber: 40.0 Consensus size: 2
4174390 TAAAAGTCAA
* *
4174400 AT AT AT AT TT AT AT AT AT GAT TT GAT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT -AT AT -AT AT AT AT AT AT AT AT AT AT
* *
4174444 AT AT AT AT AT AT AT AT AT GT AT GT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4174482 GTATGTATGA
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
2 67 0.96
3 3 0.04
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
AT
Found at i:4174428 original size:24 final size:24
Alignment explanation
Indices: 4174400--4174492 Score: 108
Period size: 22 Copynumber: 4.1 Consensus size: 24
4174390 TAAAAGTCAA
* *
4174400 ATATATATTTATATATATGATTTG
1 ATATATATATATATATATGATATG
4174424 --ATATATATATATATAT-ATAT-
1 ATATATATATATATATATGATATG
4174444 ATATATATATATATATATG-TATG
1 ATATATATATATATATATGATATG
*
4174467 TATATATATATATATGTATG-TATG
1 -ATATATATATATATATATGATATG
4174491 AT
1 AT
4174493 TTGAAAAAAT
Statistics
Matches: 61, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
21 3 0.05
22 34 0.56
23 2 0.03
24 22 0.36
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.51
Consensus pattern (24 bp):
ATATATATATATATATATGATATG
Found at i:4174490 original size:8 final size:8
Alignment explanation
Indices: 4174427--4174490 Score: 65
Period size: 8 Copynumber: 8.0 Consensus size: 8
4174417 TGATTTGATA
*
4174427 TATATATA
1 TATATATG
*
4174435 TATATATA
1 TATATATG
*
4174443 TATATATA
1 TATATATG
*
4174451 TATATATA
1 TATATATG
*
4174459 TATGTATG
1 TATATATG
*
4174467 TATATATA
1 TATATATG
4174475 TATATATG
1 TATATATG
*
4174483 TATGTATG
1 TATATATG
4174491 ATTTGAAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 50 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (8 bp):
TATATATG
Found at i:4176150 original size:22 final size:22
Alignment explanation
Indices: 4176120--4176175 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 22
4176110 TGTGACTTAA
* *
4176120 TCATCATGTGACTAGTTTTTAG
1 TCATTATGTGACTAGGTTTTAG
*
4176142 TCATTATGTGA-TTGGTTTTAG
1 TCATTATGTGACTAGGTTTTAG
* *
4176163 GCATTACGTGACT
1 TCATTATGTGACT
4176176 TAATTTCTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
21 17 0.61
22 11 0.39
ACGTcount: A:0.21, C:0.12, G:0.21, T:0.45
Consensus pattern (22 bp):
TCATTATGTGACTAGGTTTTAG
Found at i:4176241 original size:23 final size:23
Alignment explanation
Indices: 4176210--4176309 Score: 123
Period size: 23 Copynumber: 4.4 Consensus size: 23
4176200 ATTTTTAAGC
*
4176210 AATGCCTTACTAACTAGTCACGT
1 AATGCCTTACTAACAAGTCACGT
*
4176233 AATGTCTTACTAACAAGTCACGT
1 AATGCCTTACTAACAAGTCACGT
*
4176256 AATGCCTTACTAACAAGTCACGC
1 AATGCCTTACTAACAAGTCACGT
* * *
4176279 AATG-CTTA-TCAACTAGTCATGC
1 AATGCCTTACT-AACAAGTCACGT
4176301 AATGCCTTA
1 AATGCCTTA
4176310 TCAGAAACTA
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
21 1 0.01
22 18 0.26
23 50 0.72
ACGTcount: A:0.33, C:0.25, G:0.13, T:0.29
Consensus pattern (23 bp):
AATGCCTTACTAACAAGTCACGT
Found at i:4176277 original size:46 final size:45
Alignment explanation
Indices: 4176208--4176361 Score: 139
Period size: 46 Copynumber: 3.2 Consensus size: 45
4176198 TGATTTTTAA
* *
4176208 GCAATGCCTTACTAACTAGTCACGTAATGTCTTA-CTAACAAGTCAC
1 GCAATGCCTTACTAACAAGTCACGCAATG-CTTATC-AACAAGTCAC
* * *
4176254 GTAATGCCTTACTAACAAGTCACGCAATGCTTATCAACTAGTCAT
1 GCAATGCCTTACTAACAAGTCACGCAATGCTTATCAACAAGTCAC
* * * *
4176299 GCAATGCCTTATCAGAAACTAGCCACGCAATGCCTTATCAAAAACTAGTCAC
1 GCAATGCCTTA-C--TAACAAGTCACGCAATG-CTTATC---AACAAGTCAC
4176351 GCAATGCCTTA
1 GCAATGCCTTA
4176362 TCAGAAACTA
Statistics
Matches: 90, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
45 22 0.24
46 28 0.31
48 14 0.16
49 6 0.07
52 20 0.22
ACGTcount: A:0.34, C:0.27, G:0.14, T:0.26
Consensus pattern (45 bp):
GCAATGCCTTACTAACAAGTCACGCAATGCTTATCAACAAGTCAC
Found at i:4176318 original size:26 final size:26
Alignment explanation
Indices: 4176271--4176409 Score: 171
Period size: 26 Copynumber: 5.5 Consensus size: 26
4176261 CTTACTAACA
4176271 AGTCACGCAATG-CTTATC---AACT
1 AGTCACGCAATGCCTTATCAAAAACT
* *
4176293 AGTCATGCAATGCCTTATCAGAAACT
1 AGTCACGCAATGCCTTATCAAAAACT
*
4176319 AGCCACGCAATGCCTTATCAAAAACT
1 AGTCACGCAATGCCTTATCAAAAACT
*
4176345 AGTCACGCAATGCCTTATCAGAAACT
1 AGTCACGCAATGCCTTATCAAAAACT
* * *
4176371 AGT-GCGTAATGCCTTATCAAAAATT
1 AGTCACGCAATGCCTTATCAAAAACT
*
4176396 AGTCATGCAATGCC
1 AGTCACGCAATGCC
4176410 CAAAGTCATG
Statistics
Matches: 99, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
22 11 0.11
23 6 0.06
25 21 0.21
26 61 0.62
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (26 bp):
AGTCACGCAATGCCTTATCAAAAACT
Found at i:4176406 original size:51 final size:52
Alignment explanation
Indices: 4176274--4176409 Score: 192
Period size: 51 Copynumber: 2.7 Consensus size: 52
4176264 ACTAACAAGT
4176274 CACGCAATG-CTTATC---AACTAGTCATGCAATGCCTTATCAGAAACTAGC
1 CACGCAATGCCTTATCAAAAACTAGTCATGCAATGCCTTATCAGAAACTAGC
*
4176322 CACGCAATGCCTTATCAAAAACTAGTCACGCAATGCCTTATCAGAAACTAG-
1 CACGCAATGCCTTATCAAAAACTAGTCATGCAATGCCTTATCAGAAACTAGC
** * *
4176373 TGCGTAATGCCTTATCAAAAATTAGTCATGCAATGCC
1 CACGCAATGCCTTATCAAAAACTAGTCATGCAATGCC
4176410 CAAAGTCATG
Statistics
Matches: 78, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
48 9 0.12
49 6 0.08
51 32 0.41
52 31 0.40
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.25
Consensus pattern (52 bp):
CACGCAATGCCTTATCAAAAACTAGTCATGCAATGCCTTATCAGAAACTAGC
Found at i:4176472 original size:26 final size:25
Alignment explanation
Indices: 4176443--4176530 Score: 78
Period size: 26 Copynumber: 3.6 Consensus size: 25
4176433 CTACTCACGT
*
4176443 AATGCCTTAACAAAAACTAGTCATGC
1 AATGCCTTATCAAAAACTAGTCA-GC
* *
4176469 AATGCC----CAAAATC-AGTCACC
1 AATGCCTTATCAAAAACTAGTCAGC
*
4176489 AATGCCTTATCAGAAACTAGTCACGC
1 AATGCCTTATCAAAAACTAGTCA-GC
*
4176515 AATACCTTATCAAAAA
1 AATGCCTTATCAAAAA
4176531 TCAGTCAAGT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
20 7 0.14
21 5 0.10
22 6 0.12
24 5 0.10
25 5 0.10
26 21 0.43
ACGTcount: A:0.42, C:0.26, G:0.10, T:0.22
Consensus pattern (25 bp):
AATGCCTTATCAAAAACTAGTCAGC
Found at i:4176536 original size:26 final size:25
Alignment explanation
Indices: 4176476--4176537 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 25
4176466 TGCAATGCCC
*
4176476 AAAATCAGTCACCAATGCCTTATCA
1 AAAATCAGTCACCAATACCTTATCA
*
4176501 GAAA-CTAGTCACGCAATACCTTATCA
1 AAAATC-AGTCAC-CAATACCTTATCA
4176527 AAAATCAGTCA
1 AAAATCAGTCA
4176538 AGTAATGCCC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
24 1 0.03
25 9 0.29
26 20 0.65
27 1 0.03
ACGTcount: A:0.42, C:0.26, G:0.10, T:0.23
Consensus pattern (25 bp):
AAAATCAGTCACCAATACCTTATCA
Found at i:4176537 original size:72 final size:72
Alignment explanation
Indices: 4176345--4176559 Score: 250
Period size: 72 Copynumber: 3.1 Consensus size: 72
4176335 ATCAAAAACT
* *
4176345 AGTCACGCAATGCCTTATCAGAAACTAGT-GCGTAATGCCTTATCAAAAATTAGTCATGCAATGC
1 AGTCAC-CAATGCCTTATCAGAAACTAGTCACGTAATGCCTTATCAAAAATCAGTCATGCAATGC
4176409 CCAAAGTC
65 CCAAAGTC
* * * *
4176417 A-T--GCAATGCC-TA-C--CAACTACTCACGTAATGCCTTAACAAAAA-CTAGTCATGCAATGC
1 AGTCACCAATGCCTTATCAGAAACTAGTCACGTAATGCCTTATCAAAAATC-AGTCATGCAATGC
*
4176474 CCAAAATC
65 CCAAAGTC
* * * *
4176482 AGTCACCAATGCCTTATCAGAAACTAGTCACGCAATACCTTATCAAAAATCAGTCAAGTAATGCC
1 AGTCACCAATGCCTTATCAGAAACTAGTCACGTAATGCCTTATCAAAAATCAGTCATGCAATGCC
4176547 CAAAGTC
66 CAAAGTC
4176554 AGTCAC
1 AGTCAC
4176560 GTAATATCCA
Statistics
Matches: 117, Mismatches: 16, Indels: 20
0.76 0.10 0.13
Matches are distributed among these distances:
64 6 0.05
65 39 0.33
66 2 0.02
67 2 0.02
68 14 0.12
69 2 0.02
70 1 0.01
71 1 0.01
72 49 0.42
73 1 0.01
ACGTcount: A:0.37, C:0.27, G:0.13, T:0.23
Consensus pattern (72 bp):
AGTCACCAATGCCTTATCAGAAACTAGTCACGTAATGCCTTATCAAAAATCAGTCATGCAATGCC
CAAAGTC
Found at i:4176555 original size:21 final size:21
Alignment explanation
Indices: 4176531--4176578 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
4176521 TTATCAAAAA
*
4176531 TCAGTCAAGTAATGCCCAAAG
1 TCAGTCAAGTAATACCCAAAG
* *
4176552 TCAGTCACGTAATATCCAAAG
1 TCAGTCAAGTAATACCCAAAG
4176573 TCAGTC
1 TCAGTC
4176579 CATGCAATGC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (21 bp):
TCAGTCAAGTAATACCCAAAG
Found at i:4180512 original size:24 final size:24
Alignment explanation
Indices: 4180485--4180542 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
4180475 CCTGGAAGTG
4180485 GCAATATGGCTCAATTGAGGAAGA
1 GCAATATGGCTCAATTGAGGAAGA
4180509 GCAATATGGCTCAATTGAGGAAGA
1 GCAATATGGCTCAATTGAGGAAGA
4180533 GCAATTATGG
1 GCAA-TATGG
4180543 ACTATGTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 28 0.85
25 5 0.15
ACGTcount: A:0.36, C:0.12, G:0.29, T:0.22
Consensus pattern (24 bp):
GCAATATGGCTCAATTGAGGAAGA
Found at i:4180722 original size:125 final size:125
Alignment explanation
Indices: 4180509--4180747 Score: 347
Period size: 125 Copynumber: 1.9 Consensus size: 125
4180499 TTGAGGAAGA
* * * *
4180509 GCAATATGGCTCAATTGAGGAAGAGCAATTATGGACTATGTATTGTACTCGTTTTTCCTTTTGAT
1 GCAACATGGCTCAATTGAGGAAGAGCAATTATGGACTATGCATTGTACTAGTTTTTCCTTCTGAT
* *
4180574 CGATTTTTGTCCCACTAGA-TTTTTCTGGCTTAAGGTTTTTAATGAGGCAATTCAGAAGTG
66 CGATTTGTATCCCACTAGATTTTTTC-GGCTTAAGGTTTTTAATGAGGCAATTCAGAAGTG
* * *
4180634 GCAACATGGCTCAATTGAAGGGA-AGCAATTATGGACTATGCGTTGTACTATTTTTTCCTTCTGA
1 GCAACATGGCTCAATTG-AGGAAGAGCAATTATGGACTATGCATTGTACTAGTTTTTCCTTCTGA
* *
4180698 TCGATTTGTATTCCACTAGGTTTTTTCGGCTTAAGGTTTTTAATGAGGCA
65 TCGATTTGTATCCCACTAGATTTTTTCGGCTTAAGGTTTTTAATGAGGCA
4180748 GTACCATGGA
Statistics
Matches: 101, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
125 91 0.90
126 10 0.10
ACGTcount: A:0.24, C:0.15, G:0.22, T:0.39
Consensus pattern (125 bp):
GCAACATGGCTCAATTGAGGAAGAGCAATTATGGACTATGCATTGTACTAGTTTTTCCTTCTGAT
CGATTTGTATCCCACTAGATTTTTTCGGCTTAAGGTTTTTAATGAGGCAATTCAGAAGTG
Found at i:4181438 original size:10 final size:10
Alignment explanation
Indices: 4181423--4181454 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
4181413 GTATTTTTTT
4181423 AAAATTAATA
1 AAAATTAATA
4181433 AAAATTAATA
1 AAAATTAATA
4181443 AAAATTATATA
1 AAAATTA-ATA
4181454 A
1 A
4181455 TAATAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 17 0.81
11 4 0.19
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
AAAATTAATA
Found at i:4186997 original size:21 final size:21
Alignment explanation
Indices: 4186958--4186998 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
4186948 TCTTTGACTT
* *
4186958 CTTTTTTCTTTTTAATTTTCC
1 CTTTTCTCTTTTGAATTTTCC
*
4186979 CTTTTCTCTTTTGATTTTTC
1 CTTTTCTCTTTTGAATTTTC
4186999 TTTGGATAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.07, C:0.20, G:0.02, T:0.71
Consensus pattern (21 bp):
CTTTTCTCTTTTGAATTTTCC
Found at i:4194459 original size:13 final size:12
Alignment explanation
Indices: 4194432--4194465 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
4194422 ATTTTTCATG
4194432 AAAAATAATTA-
1 AAAAATAATTAT
*
4194443 AAAAGTAATTAT
1 AAAAATAATTAT
4194455 AAAAATAATTA
1 AAAAATAATTA
4194466 CTACATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (12 bp):
AAAAATAATTAT
Found at i:4206993 original size:19 final size:19
Alignment explanation
Indices: 4206969--4207008 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
4206959 TGGGTTGGAG
4206969 GGAGTATGTTGGAGATGAA
1 GGAGTATGTTGGAGATGAA
4206988 GGAGTATGTTGGAGATGAA
1 GGAGTATGTTGGAGATGAA
4207007 GG
1 GG
4207009 TGCAGTGATT
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:0.30, C:0.00, G:0.45, T:0.25
Consensus pattern (19 bp):
GGAGTATGTTGGAGATGAA
Found at i:4208636 original size:50 final size:50
Alignment explanation
Indices: 4208575--4208674 Score: 182
Period size: 50 Copynumber: 2.0 Consensus size: 50
4208565 AAATAGACCC
*
4208575 TACGTAGATTTAAAATCAATACCCCCAATAAACTTAAAACCCCCACATAA
1 TACGTACATTTAAAATCAATACCCCCAATAAACTTAAAACCCCCACATAA
*
4208625 TACGTACATTTAAAATCAATACCCCTAATAAACTTAAAACCCCCACATAA
1 TACGTACATTTAAAATCAATACCCCCAATAAACTTAAAACCCCCACATAA
4208675 ATCGACACTA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.46, C:0.28, G:0.03, T:0.23
Consensus pattern (50 bp):
TACGTACATTTAAAATCAATACCCCCAATAAACTTAAAACCCCCACATAA
Found at i:4228370 original size:14 final size:14
Alignment explanation
Indices: 4228351--4228380 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
4228341 GTTTAAGCAG
4228351 AATTCTACTTGCTT
1 AATTCTACTTGCTT
*
4228365 AATTCTAGTTGCTT
1 AATTCTACTTGCTT
4228379 AA
1 AA
4228381 ATTTAAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.17, G:0.10, T:0.47
Consensus pattern (14 bp):
AATTCTACTTGCTT
Found at i:4229455 original size:21 final size:21
Alignment explanation
Indices: 4229431--4229471 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
4229421 GGATGATGGC
*
4229431 AATGAGCTTGAAATAGAAGGA
1 AATGACCTTGAAATAGAAGGA
*
4229452 AATGACCTTGAAATTGAAGG
1 AATGACCTTGAAATAGAAGG
4229472 GCGTGACATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.07, G:0.27, T:0.22
Consensus pattern (21 bp):
AATGACCTTGAAATAGAAGGA
Found at i:4232386 original size:20 final size:20
Alignment explanation
Indices: 4232363--4232403 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
4232353 AATGGTGTGA
4232363 ATGTGGTTTGAATGGGAATG
1 ATGTGGTTTGAATGGGAATG
*
4232383 ATGTGGTTTGGATGGGAATG
1 ATGTGGTTTGAATGGGAATG
4232403 A
1 A
4232404 AAAAAAGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.24, C:0.00, G:0.41, T:0.34
Consensus pattern (20 bp):
ATGTGGTTTGAATGGGAATG
Found at i:4233283 original size:25 final size:25
Alignment explanation
Indices: 4233253--4233315 Score: 83
Period size: 25 Copynumber: 2.5 Consensus size: 25
4233243 AAAGAAAAGA
4233253 AATAGAAAATAAATGAGCATGACCC
1 AATAGAAAATAAATGAGCATGACCC
* * *
4233278 AATAGAAAATAAGTGGGCATGGCCC
1 AATAGAAAATAAATGAGCATGACCC
4233303 AATATG-AAATAAA
1 AATA-GAAAATAAA
4233316 AATAAATGGA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
25 32 0.97
26 1 0.03
ACGTcount: A:0.51, C:0.13, G:0.19, T:0.17
Consensus pattern (25 bp):
AATAGAAAATAAATGAGCATGACCC
Found at i:4238042 original size:18 final size:19
Alignment explanation
Indices: 4238001--4238042 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
4237991 TCTACGCCCT
*
4238001 ACTCACTGAGTTGATGATT
1 ACTCACTGAGTTGATGATG
*
4238020 A-TCACTGAGTTTATGA-G
1 ACTCACTGAGTTGATGATG
4238037 ACTCAC
1 ACTCAC
4238043 ACCCCTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 1 0.05
18 18 0.90
19 1 0.05
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (19 bp):
ACTCACTGAGTTGATGATG
Found at i:4242149 original size:20 final size:20
Alignment explanation
Indices: 4242126--4242166 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
4242116 AATGGTGTGA
4242126 ATGTGG-TTTGAATGGGAATG
1 ATGTGGTTTTG-ATGGGAATG
4242146 ATGTGGTTTTGATGGGAATG
1 ATGTGGTTTTGATGGGAATG
4242166 A
1 A
4242167 AGAAAAGTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.24, C:0.00, G:0.39, T:0.37
Consensus pattern (20 bp):
ATGTGGTTTTGATGGGAATG
Found at i:4244579 original size:25 final size:25
Alignment explanation
Indices: 4244522--4244584 Score: 83
Period size: 25 Copynumber: 2.5 Consensus size: 25
4244512 TCCATTTATT
4244522 TTTA-TTTCATATTGGGCCATGCCCA
1 TTTATTTTC-TATTGGGCCATGCCCA
* *
4244547 CTTATTTTCTATTGGGTCATGCCCA
1 TTTATTTTCTATTGGGCCATGCCCA
*
4244572 TTTATTTTTTATT
1 TTTATTTTCTATT
4244585 TATTTTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
25 29 0.88
26 4 0.12
ACGTcount: A:0.17, C:0.19, G:0.13, T:0.51
Consensus pattern (25 bp):
TTTATTTTCTATTGGGCCATGCCCA
Found at i:4244612 original size:6 final size:6
Alignment explanation
Indices: 4244590--4244648 Score: 50
Period size: 6 Copynumber: 9.7 Consensus size: 6
4244580 TTATTTATTT
* * *
4244590 TTTTTC TTTTT- TCTTTC TTTTTC TCTCTTGC ATGTTTC TTTTTC TTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC T-T-TTTC -TTTTTC TTTTTC TTTTTC
4244640 TTTTT- TTTT
1 TTTTTC TTTT
4244649 CCAACCTATT
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
5 8 0.19
6 27 0.63
7 4 0.09
8 3 0.07
9 1 0.02
ACGTcount: A:0.02, C:0.17, G:0.03, T:0.78
Consensus pattern (6 bp):
TTTTTC
Found at i:4244886 original size:34 final size:34
Alignment explanation
Indices: 4244824--4244900 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 34
4244814 CACAAAGCTG
4244824 TCCAATTTTTTTACACAAACTACTAGCAAACTA-C
1 TCCAATTTTTTTACACAAACTACTAGCAAAC-AGC
* * *
4244858 TCCAATTTTTTTGCACAAATTGGC-AGCAAACAGC
1 TCCAATTTTTTTACACAAACT-ACTAGCAAACAGC
4244892 TCCAATTTT
1 TCCAATTTT
4244901 CAGTAGCCAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
33 1 0.03
34 36 0.95
35 1 0.03
ACGTcount: A:0.34, C:0.25, G:0.08, T:0.34
Consensus pattern (34 bp):
TCCAATTTTTTTACACAAACTACTAGCAAACAGC
Found at i:4245027 original size:22 final size:22
Alignment explanation
Indices: 4245001--4245054 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
4244991 TTTCAGCACC
4245001 AAAATCAGCCATA-ATAACCTCA
1 AAAATCAGCCA-ACATAACCTCA
4245023 AAAATTCCAG-CAACATAACCTCA
1 AAAA-T-CAGCCAACATAACCTCA
*
4245046 AAATTCAGC
1 AAAATCAGC
4245055 TTTATTACCT
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
21 3 0.11
22 6 0.22
23 15 0.56
24 3 0.11
ACGTcount: A:0.48, C:0.28, G:0.06, T:0.19
Consensus pattern (22 bp):
AAAATCAGCCAACATAACCTCA
Found at i:4245397 original size:20 final size:20
Alignment explanation
Indices: 4245372--4245409 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
4245362 TGACTTTTCT
4245372 TCATTCCCATCCAAACCATA
1 TCATTCCCATCCAAACCATA
*
4245392 TCATTCCCATTCAAACCA
1 TCATTCCCATCCAAACCA
4245410 CATTCACACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.39, G:0.00, T:0.26
Consensus pattern (20 bp):
TCATTCCCATCCAAACCATA
Found at i:4246601 original size:13 final size:13
Alignment explanation
Indices: 4246583--4246607 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4246573 TTTTCAAAAA
4246583 ATTTTATAAAATT
1 ATTTTATAAAATT
4246596 ATTTTATAAAAT
1 ATTTTATAAAAT
4246608 CTCATTTTCC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTTTATAAAATT
Found at i:4269637 original size:10 final size:11
Alignment explanation
Indices: 4269622--4269650 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
4269612 CTGAAATTGA
4269622 TGATATTTT-G
1 TGATATTTTGG
4269632 TGATATTTTGG
1 TGATATTTTGG
4269643 TGATATTT
1 TGATATTT
4269651 GATGTTTGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.50
11 9 0.50
ACGTcount: A:0.21, C:0.00, G:0.21, T:0.59
Consensus pattern (11 bp):
TGATATTTTGG
Found at i:4274023 original size:11 final size:11
Alignment explanation
Indices: 4273994--4274026 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
4273984 GTAGCTAAAA
4273994 TTGATGATATT
1 TTGATGATATT
4274005 TT-ATGATATT
1 TTGATGATATT
4274015 TTGATGATATT
1 TTGATGATATT
4274026 T
1 T
4274027 GATATTTGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (11 bp):
TTGATGATATT
Found at i:4274027 original size:10 final size:10
Alignment explanation
Indices: 4273994--4274029 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
4273984 GTAGCTAAAA
4273994 TTGATGATAT
1 TTGATGATAT
*
4274004 TTTATGATATT
1 TTGATGATA-T
4274015 TTGATGATAT
1 TTGATGATAT
4274025 TTGAT
1 TTGAT
4274030 ATTTGGTGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.28, C:0.00, G:0.17, T:0.56
Consensus pattern (10 bp):
TTGATGATAT
Found at i:4281919 original size:10 final size:11
Alignment explanation
Indices: 4281901--4281937 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
4281891 GCGGCTGAAA
4281901 TTGATGATATT
1 TTGATGATATT
4281912 TT-ATGATATT
1 TTGATGATATT
*
4281922 TTGGTGATA-T
1 TTGATGATATT
4281932 TTGATG
1 TTGATG
4281938 TTTGGTGAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
10 16 0.70
11 7 0.30
ACGTcount: A:0.24, C:0.00, G:0.22, T:0.54
Consensus pattern (11 bp):
TTGATGATATT
Found at i:4284754 original size:20 final size:20
Alignment explanation
Indices: 4284729--4284774 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
4284719 CTTCTAAACC
4284729 TCAAATCATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
*
4284749 TCAAATTATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
4284769 TCAAAT
1 TCAAAT
4284775 GGGGTCAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.46, C:0.22, G:0.04, T:0.28
Consensus pattern (20 bp):
TCAAATCATACTCCAATAAG
Found at i:4287983 original size:15 final size:16
Alignment explanation
Indices: 4287963--4287994 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
4287953 TGTTATTATG
4287963 ATTA-TTTATTTTTAA
1 ATTATTTTATTTTTAA
4287978 ATTATTTTATTTTTAA
1 ATTATTTTATTTTTAA
4287994 A
1 A
4287995 CATTAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
ATTATTTTATTTTTAA
Found at i:4288135 original size:25 final size:25
Alignment explanation
Indices: 4288107--4288183 Score: 97
Period size: 25 Copynumber: 3.2 Consensus size: 25
4288097 TTATTTATTC
4288107 ATTTATATTTAAATATTAATAATTT
1 ATTTATATTTAAATATTAATAATTT
* *
4288132 ATTTTTATTTTAATATTAATAATTT
1 ATTTATATTTAAATATTAATAATTT
* *
4288157 A--T-CATTTAAATATTAATATTTT
1 ATTTATATTTAAATATTAATAATTT
4288179 ATTTA
1 ATTTA
4288184 ATANNNNNNN
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
22 18 0.41
23 1 0.02
24 1 0.02
25 24 0.55
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (25 bp):
ATTTATATTTAAATATTAATAATTT
Found at i:4288157 original size:19 final size:19
Alignment explanation
Indices: 4288135--4288186 Score: 61
Period size: 22 Copynumber: 2.6 Consensus size: 19
4288125 ATAATTTATT
4288135 TTTATTTTAATATTAATAA
1 TTTATTTTAATATTAATAA
*
4288154 TTTATCATTTAAATATTAATAT
1 TTTAT--TTT-AATATTAATAA
4288176 TTTA-TTTAATA
1 TTTATTTTAATA
4288187 NNNNNNNNNN
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 4 0.14
19 8 0.28
21 3 0.10
22 14 0.48
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTATTTTAATATTAATAA
Found at i:4288451 original size:27 final size:27
Alignment explanation
Indices: 4288421--4288523 Score: 83
Period size: 27 Copynumber: 4.0 Consensus size: 27
4288411 TTTATTTTTT
*
4288421 AAATATTAATAATTTATAATTGATTTA
1 AAATATTAATAATTTATAATTAATTTA
**
4288448 AAATATTAATAATTGGTAAGTTAATTTA
1 AAATATTAATAATTTATAA-TTAATTTA
* * *
4288476 TAAT-TT-A-AATATTATTA-TGA-TTA
1 AAATATTAATAAT-TTATAATTAATTTA
*
4288499 AAATATTAATACTTT-TAATTAATTT
1 AAATATTAATAATTTATAATTAATTT
4288524 TTAAATTTAA
Statistics
Matches: 57, Mismatches: 12, Indels: 15
0.68 0.14 0.18
Matches are distributed among these distances:
23 6 0.11
24 6 0.11
25 8 0.14
26 8 0.14
27 19 0.33
28 10 0.18
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.49
Consensus pattern (27 bp):
AAATATTAATAATTTATAATTAATTTA
Found at i:4288503 original size:51 final size:50
Alignment explanation
Indices: 4288445--4288543 Score: 130
Period size: 51 Copynumber: 2.0 Consensus size: 50
4288435 TATAATTGAT
4288445 TTAAAATATTAATAATTGGTAAGTTAATTTAT-AATTT-AAATATTATTATGA
1 TTAAAATATTAATAATT-GTAA-TTAATTTATAAATTTAAAATATT-TTATGA
* * *
4288496 TTAAAATATTAATACTTTTAATTAATTTTTAAATTTAAAATATTTTAT
1 TTAAAATATTAATAATTGTAATTAATTTATAAATTTAAAATATTTTAT
4288544 AATATATAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
49 8 0.19
50 12 0.28
51 23 0.53
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (50 bp):
TTAAAATATTAATAATTGTAATTAATTTATAAATTTAAAATATTTTATGA
Found at i:4293621 original size:2 final size:2
Alignment explanation
Indices: 4293614--4293689 Score: 100
Period size: 2 Copynumber: 37.5 Consensus size: 2
4293604 CATTGTACAA
* * *
4293614 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AC AT TT AGT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
4293657 A- AT NAT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4293690 ACATTTTCCT
Statistics
Matches: 67, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
1 1 0.01
2 62 0.93
3 4 0.06
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.46
Consensus pattern (2 bp):
AT
Found at i:4296558 original size:129 final size:127
Alignment explanation
Indices: 4296328--4296650 Score: 297
Period size: 129 Copynumber: 2.5 Consensus size: 127
4296318 CTACATCTTT
* * * * * *
4296328 ATCAGTGAAAAGCTCATCCAACTTGCTAATTTCACTT-ATGTTGCTAATTCCTCATAGCTGATCC
1 ATCAATGACAAGCTCAACCAAGTTGCTAATTTCA-TTGTTGTTGCTAA-TCC-CATAGTTGATCC
* * * * * * * *
4296392 AATTTCTTGAAAGACTCATCATCGTTTAATTCCTCATATCCACCCAATAGCTCATCCACATTCGA
63 AATTCCTTCAAACACTCACCATCGATTAATGCCTCATATCCACCCAATAACTCATCCACACTCGA
* * * * *
4296457 ATCAGTGACAGGTTCAACCGATTTGCTAATTTCATTGTTGTTGCTAATCCCATGTAGTTGATCCA
1 ATCAATGACAAGCTCAACCAAGTTGCTAATTTCATTGTTGTTGCTAATCCCA--TAGTTGATCCA
* * * * * * * **
4296522 ATTCCTTCTAACAGTCACCATCGATTAATGCCTCATATTCACGCAATAATTCATCTACGCTCTT
64 ATTCCTTCAAACACTCACCATCGATTAATGCCTCATATCCACCCAATAACTCATCCACACTCGA
* * *
4296586 ATCAATGACAAGCTCATCCAAGTTGCTAATTTGATCGTTGTTGCTAATCCCCAATAGTTGATCCA
1 ATCAATGACAAGCTCAACCAAGTTGCTAATTTCATTGTTGTTGCTAAT-CCC-ATAGTTGATCCA
4296651 CCTCATTGAA
Statistics
Matches: 156, Mismatches: 33, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
127 2 0.01
128 5 0.03
129 145 0.93
130 3 0.02
131 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.34
Consensus pattern (127 bp):
ATCAATGACAAGCTCAACCAAGTTGCTAATTTCATTGTTGTTGCTAATCCCATAGTTGATCCAAT
TCCTTCAAACACTCACCATCGATTAATGCCTCATATCCACCCAATAACTCATCCACACTCGA
Found at i:4297691 original size:14 final size:14
Alignment explanation
Indices: 4297672--4297701 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
4297662 GTTTAAGCAG
4297672 AATTCTACTTGCTT
1 AATTCTACTTGCTT
*
4297686 AATTCTAGTTGCTT
1 AATTCTACTTGCTT
4297700 AA
1 AA
4297702 AACGCGTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.17, G:0.10, T:0.47
Consensus pattern (14 bp):
AATTCTACTTGCTT
Found at i:4300821 original size:2 final size:2
Alignment explanation
Indices: 4300814--4300845 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
4300804 TCATCATTTC
4300814 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4300846 ACTATCAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4312910 original size:6 final size:6
Alignment explanation
Indices: 4312901--4312927 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
4312891 TGTGGATGTG
4312901 TGTTTC TGTTTC TGTTTC TGTTTC TGT
1 TGTTTC TGTTTC TGTTTC TGTTTC TGT
4312928 ATCTTTGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.19, T:0.67
Consensus pattern (6 bp):
TGTTTC
Found at i:4328326 original size:6 final size:6
Alignment explanation
Indices: 4328315--4328345 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
4328305 CCTTGTGGAT
*
4328315 TTTCTG TTTCTG TTTCTC TTTCTG TTTCTG T
1 TTTCTG TTTCTG TTTCTG TTTCTG TTTCTG T
4328346 ATCTTTGTTT
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:0.00, C:0.19, G:0.13, T:0.68
Consensus pattern (6 bp):
TTTCTG
Found at i:4331196 original size:14 final size:14
Alignment explanation
Indices: 4331179--4331208 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
4331169 GTTTATGCAG
4331179 AATTCTACATGCTT
1 AATTCTACATGCTT
*
4331193 AATTCTACTTGCTT
1 AATTCTACATGCTT
4331207 AA
1 AA
4331209 AACGCCTCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.43
Consensus pattern (14 bp):
AATTCTACATGCTT
Found at i:4337802 original size:37 final size:39
Alignment explanation
Indices: 4337752--4337829 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 39
4337742 ATCTTAAAGC
* *
4337752 TAATATATAATTGAATTA-AAGATAAGTTTATT-AAATT
1 TAATATATAATTGAATTAGAAGATAAATTAATTAAAATT
* *
4337789 TAATATGTCATTGAATTAGAAGATAAATTAATTAAAATT
1 TAATATATAATTGAATTAGAAGATAAATTAATTAAAATT
4337828 TA
1 TA
4337830 TTTTCATAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 16 0.46
38 12 0.34
39 7 0.20
ACGTcount: A:0.49, C:0.01, G:0.09, T:0.41
Consensus pattern (39 bp):
TAATATATAATTGAATTAGAAGATAAATTAATTAAAATT
Found at i:4340553 original size:23 final size:23
Alignment explanation
Indices: 4340510--4340564 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
4340500 TTTTTTATTG
* *
4340510 TTTTTAAA-AAATATAATAATAAT
1 TTTTTAAATTAATATAAAAAT-AT
4340533 TTTTTAAATTAATA-AAAAATAT
1 TTTTTAAATTAATATAAAAATAT
*
4340555 ATTTTAAATT
1 TTTTTAAATT
4340565 TTTTATAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 11 0.39
23 13 0.46
24 4 0.14
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TTTTTAAATTAATATAAAAATAT
Found at i:4359790 original size:22 final size:22
Alignment explanation
Indices: 4359726--4359897 Score: 95
Period size: 22 Copynumber: 7.7 Consensus size: 22
4359716 TCAAAATAAC
*
4359726 TTTTACTATAA-TTAATAATAT
1 TTTTATTATAATTTAATAATAT
* * * **
4359747 TTTCACTAAAATACAA-ACATAT
1 TTTTATTATAATTTAATA-ATAT
4359769 TTTTATTATAATTTAATAATAT
1 TTTTATTATAATTTAATAATAT
* *
4359791 TTTTATTAGAAGTTAATTAA-ACT
1 TTTTATTATAATTTAA-TAATA-T
*
4359814 TTTTATTATAATTAAATAATAT
1 TTTTATTATAATTTAATAATAT
* * **
4359836 TTAATATTAAAAGATAA-AATAT
1 TT-TTATTATAATTTAATAATAT
4359858 ATTATTCATTA-AATTTAAATAATACT
1 -TT-TT-ATTATAATTT-AATAATA-T
*
4359884 CTTTATTAT-ATTTA
1 TTTTATTATAATTTA
4359898 TTATATTCAA
Statistics
Matches: 115, Mismatches: 23, Indels: 25
0.71 0.14 0.15
Matches are distributed among these distances:
21 10 0.09
22 48 0.42
23 43 0.37
24 8 0.07
25 5 0.04
26 1 0.01
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (22 bp):
TTTTATTATAATTTAATAATAT
Found at i:4359794 original size:23 final size:23
Alignment explanation
Indices: 4359768--4359897 Score: 85
Period size: 23 Copynumber: 5.7 Consensus size: 23
4359758 TACAAACATA
4359768 TTTTTATTATAATTTAATAATA-
1 TTTTTATTATAATTTAATAATAC
* *
4359790 TTTTTATTAGAAGTTAATTAA-AC
1 TTTTTATTATAATTTAA-TAATAC
*
4359813 TTTTTATTATAATTAAATAATA-
1 TTTTTATTATAATTTAATAATAC
* * **
4359835 TTTAATATTAAAAGATAA-AATA-
1 TTT-TTATTATAATTTAATAATAC
4359857 TATTATTCATTA-AATTTAAATAATAC
1 T-TT-TT-ATTATAATTT-AATAATAC
*
4359883 TCTTTATTAT-ATTTA
1 TTTTTATTATAATTTA
4359898 TTATATTCAA
Statistics
Matches: 84, Mismatches: 14, Indels: 20
0.71 0.12 0.17
Matches are distributed among these distances:
22 28 0.33
23 42 0.50
24 8 0.10
25 5 0.06
26 1 0.01
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (23 bp):
TTTTTATTATAATTTAATAATAC
Found at i:4360488 original size:18 final size:20
Alignment explanation
Indices: 4360448--4360491 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
4360438 AGAGAAAATC
* *
4360448 TAATGATAAGATTCAAAATA
1 TAATGATAAGAGTCAAAAAA
4360468 TAATGATAA-AGT-AAAAAA
1 TAATGATAAGAGTCAAAAAA
4360486 TAATGA
1 TAATGA
4360492 ATATTCGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 11 0.50
19 2 0.09
20 9 0.41
ACGTcount: A:0.59, C:0.02, G:0.11, T:0.27
Consensus pattern (20 bp):
TAATGATAAGAGTCAAAAAA
Found at i:4361441 original size:31 final size:31
Alignment explanation
Indices: 4361378--4361442 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
4361368 TATACATCAA
* **
4361378 TATATATAATATTATATATTATTTTTAAATT
1 TATATAAAATATTATATATTATTACTAAATT
*
4361409 TATATAAAATA-TATATTTTATTACTAATATT
1 TATATAAAATATTATATATTATTACTAA-ATT
4361440 TAT
1 TAT
4361443 TTTATATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 13 0.45
31 16 0.55
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (31 bp):
TATATAAAATATTATATATTATTACTAAATT
Found at i:4371668 original size:29 final size:29
Alignment explanation
Indices: 4371626--4371684 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
4371616 GTTCCTATGC
4371626 ATTTGAAGTTATTATTCACTATGTAACAT
1 ATTTGAAGTTATTATTCACTATGTAACAT
4371655 ATTTGAAGTTATTATTCACTATGTAACAT
1 ATTTGAAGTTATTATTCACTATGTAACAT
4371684 A
1 A
4371685 ATCCTGTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (29 bp):
ATTTGAAGTTATTATTCACTATGTAACAT
Found at i:4392853 original size:125 final size:125
Alignment explanation
Indices: 4392631--4392878 Score: 469
Period size: 125 Copynumber: 2.0 Consensus size: 125
4392621 TGTCGTTCAC
* *
4392631 AAGATTTAGGACTTATTTTTCCGAGAATATCATCAATGATTGATGCTTAACTATTGATTTATTAA
1 AAGATTTAGGACTTATTTTTCCAAGAATATCATCAATGATTGATGCTTAACTATGGATTTATTAA
*
4392696 TTGAACTTGATGACCGTAGAGCCTGACTTGTAATTTTGAAGTCAACTGTGTCAATGCCAG
66 TTAAACTTGATGACCGTAGAGCCTGACTTGTAATTTTGAAGTCAACTGTGTCAATGCCAG
4392756 AAGATTTAGGACTTATTTTTCCAAGAATATCATCAATGATTGATGCTTAACTATGGATTTATTAA
1 AAGATTTAGGACTTATTTTTCCAAGAATATCATCAATGATTGATGCTTAACTATGGATTTATTAA
4392821 TTAAACTTGATGACCGTAGAGCCTGACTTGTAATTTTGAAGTCAACTGTGTCAATGCC
66 TTAAACTTGATGACCGTAGAGCCTGACTTGTAATTTTGAAGTCAACTGTGTCAATGCC
4392879 TTAAGTGATT
Statistics
Matches: 120, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
125 120 1.00
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.37
Consensus pattern (125 bp):
AAGATTTAGGACTTATTTTTCCAAGAATATCATCAATGATTGATGCTTAACTATGGATTTATTAA
TTAAACTTGATGACCGTAGAGCCTGACTTGTAATTTTGAAGTCAACTGTGTCAATGCCAG
Found at i:4394235 original size:36 final size:37
Alignment explanation
Indices: 4394187--4394261 Score: 98
Period size: 36 Copynumber: 2.1 Consensus size: 37
4394177 GCTTTTCATC
** *
4394187 TTTTTTCTTTTTTTGGTATAATATTGGAAATGTAGCA
1 TTTTTTCTTTTTTTGAAAGAATATTGGAAATGTAGCA
**
4394224 TTTTTT-TTTTTTTGAAAGGCTATTGGAAATGTAGCA
1 TTTTTTCTTTTTTTGAAAGAATATTGGAAATGTAGCA
4394260 TT
1 TT
4394262 AATATATGAG
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
36 27 0.82
37 6 0.18
ACGTcount: A:0.24, C:0.05, G:0.17, T:0.53
Consensus pattern (37 bp):
TTTTTTCTTTTTTTGAAAGAATATTGGAAATGTAGCA
Found at i:4394845 original size:57 final size:57
Alignment explanation
Indices: 4394756--4394870 Score: 203
Period size: 57 Copynumber: 2.0 Consensus size: 57
4394746 CCTATGGCTG
* *
4394756 TTCTAGTTGCTGGTTTTACGTACTTGCTTCCATGTTACCTGTTTATGAATTATGACT
1 TTCTAGTTGCTGGTTTTACGTACTTGCGTCCATGTTACCTGTTCATGAATTATGACT
*
4394813 TTCTAGTTGCTGGTTTTATGTACTTGCGTCCATGTTACCTGTTCATGAATTATGACT
1 TTCTAGTTGCTGGTTTTACGTACTTGCGTCCATGTTACCTGTTCATGAATTATGACT
4394870 T
1 T
4394871 ATGCAGTTAT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.17, C:0.17, G:0.18, T:0.47
Consensus pattern (57 bp):
TTCTAGTTGCTGGTTTTACGTACTTGCGTCCATGTTACCTGTTCATGAATTATGACT
Found at i:4397732 original size:31 final size:31
Alignment explanation
Indices: 4397692--4397755 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
4397682 GTCAAAGAAC
4397692 GAAAAATCTACTAATTACAAACTGATTCTCA
1 GAAAAATCTACTAATTACAAACTGATTCTCA
*
4397723 GAAAGATCTACTAATTACAAACTGATTCTCA
1 GAAAAATCTACTAATTACAAACTGATTCTCA
4397754 GA
1 GA
4397756 GCATATTACA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.44, C:0.19, G:0.09, T:0.28
Consensus pattern (31 bp):
GAAAAATCTACTAATTACAAACTGATTCTCA
Found at i:4404045 original size:16 final size:16
Alignment explanation
Indices: 4404017--4404049 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4404007 TGTTTGTTTG
4404017 ATTTGATTTTTTTTTA
1 ATTTGATTTTTTTTTA
4404033 ATTT-ATTTATTTTTTA
1 ATTTGATTT-TTTTTTA
4404049 A
1 A
4404050 AAATAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (16 bp):
ATTTGATTTTTTTTTA
Found at i:4405923 original size:2 final size:2
Alignment explanation
Indices: 4405916--4405947 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4405906 GCTAACAAAT
4405916 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
4405948 TAGAAGTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4406224 original size:2 final size:2
Alignment explanation
Indices: 4406217--4406250 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4406207 GTAAGTAAGA
4406217 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
4406251 TTAGAAGGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4407204 original size:21 final size:21
Alignment explanation
Indices: 4407151--4407215 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
4407141 AAATTACTTC
*
4407151 AATGATTTTTGAACTTCTTTG
1 AATGATTTTTGAACTTGTTTG
* * **
4407172 AGTAATCCTTGAACTTGTTTG
1 AATGATTTTTGAACTTGTTTG
*
4407193 AATGATTTTTGAAATTGTTTG
1 AATGATTTTTGAACTTGTTTG
4407214 AA
1 AA
4407216 AATGTTTATG
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.28, C:0.08, G:0.17, T:0.48
Consensus pattern (21 bp):
AATGATTTTTGAACTTGTTTG
Found at i:4407374 original size:43 final size:44
Alignment explanation
Indices: 4407303--4407409 Score: 148
Period size: 44 Copynumber: 2.5 Consensus size: 44
4407293 AAAAATAATC
*
4407303 TAAAC-TGTTTAAATGA-TCTTTGAACTTGTTTGAATA-ATTTT
1 TAAACTTGTTTAAATGAGTTTTTGAACTTGTTTGAATAGATTTT
* *
4407344 TAAAGTTGTTTAAATGAGTTTTTGAACTTGTTTGAATAGTTTTT
1 TAAACTTGTTTAAATGAGTTTTTGAACTTGTTTGAATAGATTTT
* *
4407388 TAAACTTTTTTAAATAAGTTTT
1 TAAACTTGTTTAAATGAGTTTT
4407410 GAAGTGCCTA
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
41 4 0.07
42 11 0.19
43 19 0.33
44 23 0.40
ACGTcount: A:0.31, C:0.05, G:0.13, T:0.51
Consensus pattern (44 bp):
TAAACTTGTTTAAATGAGTTTTTGAACTTGTTTGAATAGATTTT
Found at i:4407469 original size:22 final size:22
Alignment explanation
Indices: 4407439--4407499 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 22
4407429 ATGTGAAAAG
4407439 TTTC-AAAATTATTTGAATGAGT
1 TTTCGAAAATTATTTGAATGA-T
*
4407461 TTT-GAAAATTGCTTT-AATGAT
1 TTTCGAAAATT-ATTTGAATGAT
*
4407482 TTTCG-AACTTATTTGAAT
1 TTTCGAAAATTATTTGAAT
4407500 AGCTTTTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
20 3 0.09
21 11 0.34
22 15 0.47
23 3 0.09
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.48
Consensus pattern (22 bp):
TTTCGAAAATTATTTGAATGAT
Found at i:4407511 original size:21 final size:21
Alignment explanation
Indices: 4407487--4407531 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
4407477 ATGATTTTCG
*
4407487 AACTTATTTGAA-TAGCTTTTA
1 AACTTATTTAAATTAG-TTTTA
*
4407508 AACTTGTTTAAATTAGTTTTA
1 AACTTATTTAAATTAGTTTTA
4407529 AAC
1 AAC
4407532 CTCCCTTACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.47
Consensus pattern (21 bp):
AACTTATTTAAATTAGTTTTA
Found at i:4422819 original size:35 final size:35
Alignment explanation
Indices: 4422752--4422838 Score: 113
Period size: 35 Copynumber: 2.5 Consensus size: 35
4422742 CTTTACTGAA
* *
4422752 GTGAAGGCAATGAAGACTTGGCACGCGTAGATT-C
1 GTGAAGTCAATGAAGACTTGGCACGCGCAGATTAC
* *
4422786 GGTGAAGTCAATGAAGACTTGGCATGTGCAGATTAC
1 -GTGAAGTCAATGAAGACTTGGCACGCGCAGATTAC
*
4422822 GTGAAGTCAACGAAGAC
1 GTGAAGTCAATGAAGAC
4422839 GAAGCTCCAC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 45 0.98
36 1 0.02
ACGTcount: A:0.32, C:0.16, G:0.31, T:0.21
Consensus pattern (35 bp):
GTGAAGTCAATGAAGACTTGGCACGCGCAGATTAC
Found at i:4449152 original size:38 final size:39
Alignment explanation
Indices: 4449101--4449183 Score: 159
Period size: 38 Copynumber: 2.2 Consensus size: 39
4449091 AGGGTTGTTG
4449101 AGTTGAGTGCCTTGGAGGAAGCTCACCAAGCTAAGTGT-
1 AGTTGAGTGCCTTGGAGGAAGCTCACCAAGCTAAGTGTA
4449139 AGTTGAGTGCCTTGGAGGAAGCTCACCAAGCTAAGTGTA
1 AGTTGAGTGCCTTGGAGGAAGCTCACCAAGCTAAGTGTA
4449178 AGTTGA
1 AGTTGA
4449184 AATGAATTAG
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
38 38 0.86
39 6 0.14
ACGTcount: A:0.28, C:0.17, G:0.31, T:0.24
Consensus pattern (39 bp):
AGTTGAGTGCCTTGGAGGAAGCTCACCAAGCTAAGTGTA
Found at i:4465190 original size:2 final size:2
Alignment explanation
Indices: 4465183--4465211 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4465173 AATGATCAGA
4465183 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4465212 AAATAATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4468680 original size:25 final size:27
Alignment explanation
Indices: 4468635--4468689 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
4468625 TTATATTAGA
*
4468635 TTTCATTTTCTAAATCCTTAACATT-C
1 TTTCATTTTCTAAATCCTTAAAATTAC
* *
4468661 TTTCTTTTTCTAAAT-TTTAAAATTAC
1 TTTCATTTTCTAAATCCTTAAAATTAC
4468687 TTT
1 TTT
4468690 TCAAGATGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 7 0.28
26 18 0.72
ACGTcount: A:0.27, C:0.16, G:0.00, T:0.56
Consensus pattern (27 bp):
TTTCATTTTCTAAATCCTTAAAATTAC
Found at i:4476215 original size:7 final size:7
Alignment explanation
Indices: 4476198--4476252 Score: 58
Period size: 7 Copynumber: 7.7 Consensus size: 7
4476188 TATTATTTGC
4476198 TATTTTAT
1 TATTTT-T
4476206 TATTTTT
1 TATTTTT
4476213 TATCTTTT
1 TAT-TTTT
*
4476221 TATTATT
1 TATTTTT
*
4476228 TATTTAT
1 TATTTTT
4476235 TA-TTTT
1 TATTTTT
*
4476241 TATTTAT
1 TATTTTT
4476248 TATTT
1 TATTT
4476253 CGTTTTATAG
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
6 5 0.12
7 22 0.55
8 13 0.32
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (7 bp):
TATTTTT
Found at i:4476260 original size:13 final size:11
Alignment explanation
Indices: 4476202--4476252 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
4476192 ATTTGCTATT
*
4476202 TTATTATTTT-
1 TTATTTTTTTA
*
4476212 TTATCTTTTTA
1 TTATTTTTTTA
*
4476223 TTATTTATTTA
1 TTATTTTTTTA
4476234 TTATTTTTATTTA
1 TTA-TTTT-TTTA
4476247 TTATTT
1 TTATTT
4476253 CGTTTTATAG
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
10 8 0.24
11 12 0.36
12 6 0.18
13 7 0.21
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (11 bp):
TTATTTTTTTA
Found at i:4476484 original size:33 final size:31
Alignment explanation
Indices: 4476421--4476502 Score: 85
Period size: 33 Copynumber: 2.6 Consensus size: 31
4476411 AAAAAATGTA
*
4476421 TTTTATTATTTA-TTTAATATTTCTATTTCT
1 TTTTATTATTTATTTTTATATTTCTATTTCT
* *
4476451 TTTTATTATTATATTTTTTTATTTCTTTATTCT
1 TTTTATTATT-TATTTTTATATTTCTAT-TTCT
* *
4476484 TCTTCATAATTTATTTTTA
1 T-TTTATTATTTATTTTTA
4476503 CTTTTTATAA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
30 10 0.24
31 2 0.05
32 11 0.26
33 12 0.29
34 7 0.17
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.71
Consensus pattern (31 bp):
TTTTATTATTTATTTTTATATTTCTATTTCT
Found at i:4476860 original size:13 final size:13
Alignment explanation
Indices: 4476842--4476880 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
4476832 AACCTTTTCC
4476842 TTCTTTTTTTCTT
1 TTCTTTTTTTCTT
*
4476855 TTCTTTATTTCTT
1 TTCTTTTTTTCTT
*
4476868 TTC-ATTTTTCTT
1 TTCTTTTTTTCTT
4476880 T
1 T
4476881 CTTCTTCTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 8 0.35
13 15 0.65
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.79
Consensus pattern (13 bp):
TTCTTTTTTTCTT
Found at i:4476936 original size:22 final size:21
Alignment explanation
Indices: 4476906--4476999 Score: 71
Period size: 22 Copynumber: 4.2 Consensus size: 21
4476896 CCGCTCCCTC
*
4476906 TTCTTCTTCTCTCTTTCTTTCT
1 TTCTCCTTCTCTCTTTCTTT-T
*
4476928 TTCTCCTTCTCATTCTTCCCTTTT
1 TTCTCCTTCTC--TCTT-TCTTTT
* * *
4476952 TTCCCCTTATTTCTTTCTCTTT
1 TTCTCCTTCTCTCTTTCT-TTT
* *
4476974 TTCTTCTTTTCTCTTTCTTCTT
1 TTCTCCTTCTCTCTTTCTT-TT
4476996 TTCT
1 TTCT
4477000 TTCTCCTTCT
Statistics
Matches: 57, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
21 3 0.05
22 37 0.65
24 13 0.23
25 4 0.07
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (21 bp):
TTCTCCTTCTCTCTTTCTTTT
Found at i:4477466 original size:13 final size:13
Alignment explanation
Indices: 4477450--4477493 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
4477440 TTTTTTAATT
*
4477450 TTTTATTATTTTG
1 TTTTATTATTTTA
4477463 TTTTA-TATTTTA
1 TTTTATTATTTTA
*
4477475 TTATTATTTTTTTA
1 TT-TTATTATTTTA
4477489 TTTTA
1 TTTTA
4477494 GAGGTGTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 8 0.30
13 11 0.41
14 8 0.30
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.77
Consensus pattern (13 bp):
TTTTATTATTTTA
Found at i:4477473 original size:20 final size:19
Alignment explanation
Indices: 4477450--4477493 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
4477440 TTTTTTAATT
4477450 TTTTATTATT-TTGTTTTATA
1 TTTTATTATTATT-TTTT-TA
4477470 TTTTATTATTATTTTTTTA
1 TTTTATTATTATTTTTTTA
4477489 TTTTA
1 TTTTA
4477494 GAGGTGTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.30
20 14 0.61
21 2 0.09
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.77
Consensus pattern (19 bp):
TTTTATTATTATTTTTTTA
Found at i:4477478 original size:23 final size:21
Alignment explanation
Indices: 4477437--4477484 Score: 69
Period size: 23 Copynumber: 2.2 Consensus size: 21
4477427 TCTCTTCTTC
*
4477437 TTTTTTTTTAATTTTTTATTA
1 TTTTGTTTTAATTTTTTATTA
4477458 TTTTGTTTTATATTTTATTATTA
1 TTTTGTTTTA-ATTTT-TTATTA
4477481 TTTT
1 TTTT
4477485 TTTATTTTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 9 0.38
22 5 0.21
23 10 0.42
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (21 bp):
TTTTGTTTTAATTTTTTATTA
Found at i:4477489 original size:11 final size:11
Alignment explanation
Indices: 4477437--4477490 Score: 58
Period size: 11 Copynumber: 4.9 Consensus size: 11
4477427 TCTCTTCTTC
4477437 TTTTTTT-TTA
1 TTTTTTTATTA
*
4477447 ATTTTTTATTA
1 TTTTTTTATTA
4477458 TTTTGTTT-TATA
1 TTTT-TTTAT-TA
*
4477470 TTTTATTATTA
1 TTTTTTTATTA
4477481 TTTTTTTATT
1 TTTTTTTATT
4477491 TTAGAGGTGT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
10 6 0.17
11 20 0.56
12 10 0.28
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.80
Consensus pattern (11 bp):
TTTTTTTATTA
Found at i:4479764 original size:57 final size:57
Alignment explanation
Indices: 4479695--4479865 Score: 252
Period size: 57 Copynumber: 3.0 Consensus size: 57
4479685 TTCTTTCCTC
* * *
4479695 AAGGTGGAGAAAATATGTTTCCCAAAGCCAAAAACATGAAGAAGATGTTAACTTATT
1 AAGGTGGAGAAAATATGTTTCCTAAAGCCAAAAGCATGAAGAAGATGCTAACTTATT
* **
4479752 AAGGTGGAGAAAATATTTTTTGTAAAGCCAAAAGCATGAAGAAGATGCTAACTTATT
1 AAGGTGGAGAAAATATGTTTCCTAAAGCCAAAAGCATGAAGAAGATGCTAACTTATT
* **
4479809 AAAGTGGAGAAGAATATGTTTCCTAAAGATAAAAGCATGAAGAAGATGCTAACTTAT
1 AAGGTGGAGAA-AATATGTTTCCTAAAGCCAAAAGCATGAAGAAGATGCTAACTTAT
4479866 GAATGACAAA
Statistics
Matches: 101, Mismatches: 12, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
57 61 0.60
58 40 0.40
ACGTcount: A:0.44, C:0.10, G:0.20, T:0.26
Consensus pattern (57 bp):
AAGGTGGAGAAAATATGTTTCCTAAAGCCAAAAGCATGAAGAAGATGCTAACTTATT
Found at i:4480706 original size:19 final size:20
Alignment explanation
Indices: 4480669--4480707 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
4480659 GTTTAGTTGA
4480669 TGTTTTTGCTTTTTGCTATT
1 TGTTTTTGCTTTTTGCTATT
4480689 TGTTTTT-CTATTTT-CTATT
1 TGTTTTTGCT-TTTTGCTATT
4480708 CATTTTCTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.08, C:0.10, G:0.10, T:0.72
Consensus pattern (20 bp):
TGTTTTTGCTTTTTGCTATT
Found at i:4485240 original size:58 final size:57
Alignment explanation
Indices: 4485139--4485250 Score: 161
Period size: 58 Copynumber: 1.9 Consensus size: 57
4485129 CTTTTCTTAG
* ** * *
4485139 GGTGGAGAAGAATATGTTTTTTAAAACCAAAGCATGAAGAAGATGCTAACTTATTAA
1 GGTGGAGAAGAATATGATTCCTAAAACAAAAGCATGAAGAAGATACTAACTTATTAA
*
4485196 GGTGGAGAAGAATATGATTCCTAAAGCTAAAAGCATGAAGAAGATACTAACTTAT
1 GGTGGAGAAGAATATGATTCCTAAAAC-AAAAGCATGAAGAAGATACTAACTTAT
4485251 GAGTGACAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
57 23 0.48
58 25 0.52
ACGTcount: A:0.43, C:0.10, G:0.21, T:0.26
Consensus pattern (57 bp):
GGTGGAGAAGAATATGATTCCTAAAACAAAAGCATGAAGAAGATACTAACTTATTAA
Found at i:4490622 original size:17 final size:17
Alignment explanation
Indices: 4490600--4490633 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
4490590 AACAGCAGTA
4490600 GAATAATTCAGCTTATG
1 GAATAATTCAGCTTATG
4490617 GAATAATTCAGCTTATG
1 GAATAATTCAGCTTATG
4490634 CAGATACATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (17 bp):
GAATAATTCAGCTTATG
Found at i:4491065 original size:19 final size:20
Alignment explanation
Indices: 4491037--4491074 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
4491027 ATTTGCAGGG
4491037 AAAGAGAGAAAAAGCAAAGA
1 AAAGAGAGAAAAAGCAAAGA
*
4491057 AAAGA-AGAAAGAGCAAAG
1 AAAGAGAGAAAAAGCAAAG
4491075 GGCTGAGGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.68, C:0.05, G:0.26, T:0.00
Consensus pattern (20 bp):
AAAGAGAGAAAAAGCAAAGA
Found at i:4495190 original size:11 final size:11
Alignment explanation
Indices: 4495174--4495224 Score: 54
Period size: 11 Copynumber: 4.8 Consensus size: 11
4495164 AAAAAGAGGA
4495174 AAAAGAAAATC
1 AAAAGAAAATC
*
4495185 AAAAGAAAATA
1 AAAAGAAAATC
*
4495196 AAAAGAGGAA-C
1 AAAAGA-AAATC
4495207 --AAGAAAATC
1 AAAAGAAAATC
4495216 AAAAGAAAA
1 AAAAGAAAA
4495225 CAAGAATGGC
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
8 2 0.06
9 5 0.16
11 23 0.72
12 2 0.06
ACGTcount: A:0.75, C:0.06, G:0.14, T:0.06
Consensus pattern (11 bp):
AAAAGAAAATC
Found at i:4495194 original size:31 final size:31
Alignment explanation
Indices: 4495159--4495224 Score: 123
Period size: 31 Copynumber: 2.1 Consensus size: 31
4495149 CCATAAAGGA
4495159 AAAATAAAAAGAGGAAAAAGAAAATCAAAAG
1 AAAATAAAAAGAGGAAAAAGAAAATCAAAAG
*
4495190 AAAATAAAAAGAGGAACAAGAAAATCAAAAG
1 AAAATAAAAAGAGGAAAAAGAAAATCAAAAG
4495221 AAAA
1 AAAA
4495225 CAAGAATGGC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.74, C:0.05, G:0.15, T:0.06
Consensus pattern (31 bp):
AAAATAAAAAGAGGAAAAAGAAAATCAAAAG
Found at i:4495228 original size:19 final size:20
Alignment explanation
Indices: 4495187--4495230 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
4495177 AGAAAATCAA
*
4495187 AAGAAAATAAAAAGAGGAAC
1 AAGAAAATAAAAAGAGAAAC
*
4495207 AAGAAAATCAAAAGA-AAAC
1 AAGAAAATAAAAAGAGAAAC
4495226 AAGAA
1 AAGAA
4495231 TGGCACCCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.73, C:0.07, G:0.16, T:0.05
Consensus pattern (20 bp):
AAGAAAATAAAAAGAGAAAC
Found at i:4496845 original size:8 final size:8
Alignment explanation
Indices: 4496832--4496865 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
4496822 ATCTCAAAAA
4496832 ACATATAT
1 ACATATAT
4496840 ACATATAT
1 ACATATAT
*
4496848 ACATATGT
1 ACATATAT
4496856 ACATATAT
1 ACATATAT
4496864 AC
1 AC
4496866 GTACATATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.47, C:0.15, G:0.03, T:0.35
Consensus pattern (8 bp):
ACATATAT
Found at i:4496871 original size:12 final size:12
Alignment explanation
Indices: 4496832--4496875 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
4496822 ATCTCAAAAA
*
4496832 ACATATATACAT
1 ACATATATACGT
* * *
4496844 ATATACATATGT
1 ACATATATACGT
4496856 ACATATATACGT
1 ACATATATACGT
4496868 ACATATAT
1 ACATATAT
4496876 TAATATTTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.45, C:0.14, G:0.05, T:0.36
Consensus pattern (12 bp):
ACATATATACGT
Done.