Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001700.1 Hibiscus syriacus cultivar Beakdansim tig00003398_pilon, whole genome shotgun sequence
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: 2632955
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 11
Found at i:2378230 original size:25 final size:23
Alignment explanation
Indices: 2378197--2378251 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
2378187 AATCAACAAA
*
2378197 TTTTCAAAATAAAAGTCATAATTAT
1 TTTTTAAAATAAAA-T-ATAATTAT
* *
2378222 TTTTTAAAATAATATTTAATTAT
1 TTTTTAAAATAAAATATAATTAT
2378245 TTTTTAA
1 TTTTTAA
2378252 TAAAATGGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 14 0.52
24 1 0.04
25 12 0.44
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (23 bp):
TTTTTAAAATAAAATATAATTAT
Found at i:2381372 original size:29 final size:29
Alignment explanation
Indices: 2381310--2381376 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
2381300 GGACAAAAGG
2381310 TTTTATAAATTATAATAAAGTACAAAAAT
1 TTTTATAAATTATAATAAAGTACAAAAAT
* ** *
2381339 GTTTATAAATTATAATAAAGTGTAAAACT
1 TTTTATAAATTATAATAAAGTACAAAAAT
2381368 TTTTATAAA
1 TTTTATAAA
2381377 ATAAAGTATA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.51, C:0.03, G:0.06, T:0.40
Consensus pattern (29 bp):
TTTTATAAATTATAATAAAGTACAAAAAT
Found at i:2381436 original size:27 final size:27
Alignment explanation
Indices: 2381388--2381440 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
2381378 TAAAGTATAC
* **
2381388 TTTTTTTTATAAATTATGATAAAGGAA
1 TTTTTTTTATAAAATACAATAAAGGAA
2381415 TTTTTTTTATAAAATACAATAAAGGA
1 TTTTTTTTATAAAATACAATAAAGGA
2381441 CAACTTCTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.45
Consensus pattern (27 bp):
TTTTTTTTATAAAATACAATAAAGGAA
Found at i:2381621 original size:22 final size:22
Alignment explanation
Indices: 2381591--2381655 Score: 85
Period size: 22 Copynumber: 3.0 Consensus size: 22
2381581 AGCGCGTACA
*
2381591 AATGGTGGAAGAAGGCTGCACG
1 AATGCTGGAAGAAGGCTGCACG
*
2381613 AATGCTGGAAGTAGGCTGCACG
1 AATGCTGGAAGAAGGCTGCACG
* **
2381635 AATGCTAGAAGCGGGCTGCAC
1 AATGCTGGAAGAAGGCTGCAC
2381656 AGTCGCTGAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.29, C:0.18, G:0.37, T:0.15
Consensus pattern (22 bp):
AATGCTGGAAGAAGGCTGCACG
Found at i:2382302 original size:30 final size:30
Alignment explanation
Indices: 2382268--2382328 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
2382258 TCGCTTGTAC
* *
2382268 TAACTTGTTTTTCTTTTTTGTTTGTGTTAT
1 TAACTCGTTTTTCTCTTTTGTTTGTGTTAT
2382298 TAACTCGTTTTTCTCTTTTGTTTGTGTTAT
1 TAACTCGTTTTTCTCTTTTGTTTGTGTTAT
2382328 T
1 T
2382329 TTTCATCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.10, C:0.10, G:0.13, T:0.67
Consensus pattern (30 bp):
TAACTCGTTTTTCTCTTTTGTTTGTGTTAT
Found at i:2387169 original size:17 final size:17
Alignment explanation
Indices: 2387147--2387180 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2387137 CTCTGGCCCA
2387147 AAAAGTCAAATTTTATG
1 AAAAGTCAAATTTTATG
*
2387164 AAAAGTCATATTTTATG
1 AAAAGTCAAATTTTATG
2387181 TTTTTCGACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (17 bp):
AAAAGTCAAATTTTATG
Found at i:2390503 original size:15 final size:14
Alignment explanation
Indices: 2390470--2390507 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
2390460 ATGATTGATG
2390470 TATATCATATATGAA
1 TATAT-ATATATGAA
*
2390485 TATATATATATGTA
1 TATATATATATGAA
2390499 T-TATATATA
1 TATATATATA
2390508 ATTATAGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 8 0.36
14 9 0.41
15 5 0.23
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (14 bp):
TATATATATATGAA
Found at i:2391549 original size:2 final size:2
Alignment explanation
Indices: 2391542--2391584 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2391532 AAATACTCAA
2391542 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2391584 A
1 A
2391585 AATTTCGATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2392629 original size:13 final size:13
Alignment explanation
Indices: 2392574--2392624 Score: 75
Period size: 13 Copynumber: 3.8 Consensus size: 13
2392564 AGTCAATCCG
2392574 TTGACTTTGACCA
1 TTGACTTTGACCA
*
2392587 TTGATTTTGACCA
1 TTGACTTTGACCA
*
2392600 TTGACTTTGACCC
1 TTGACTTTGACCA
2392613 TTGACTGTTGAC
1 TTGACT-TTGAC
2392625 TTTGAGCAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
13 29 0.85
14 5 0.15
ACGTcount: A:0.20, C:0.22, G:0.18, T:0.41
Consensus pattern (13 bp):
TTGACTTTGACCA
Found at i:2393537 original size:27 final size:28
Alignment explanation
Indices: 2393506--2393571 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 28
2393496 ATTGGATTTA
*
2393506 TAAAATTCCCTTAAAGTGTAAAATAACC
1 TAAAATACCCTTAAAGTGTAAAATAACC
* *
2393534 -AAAACACCCCTAAAGTGTAAAATAACC
1 TAAAATACCCTTAAAGTGTAAAATAACC
*
2393561 TAAAATGCCCT
1 TAAAATACCCT
2393572 CAAACTCCGA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
27 24 0.77
28 7 0.23
ACGTcount: A:0.47, C:0.23, G:0.08, T:0.23
Consensus pattern (28 bp):
TAAAATACCCTTAAAGTGTAAAATAACC
Found at i:2395762 original size:157 final size:157
Alignment explanation
Indices: 2395456--2395769 Score: 612
Period size: 157 Copynumber: 2.0 Consensus size: 157
2395446 GTCCATCGGT
2395456 ATTCTTCGTTTCTCCGTCGTCACCGGCGCGTGGAGGGGTGACACTGTCAAAGTTTCTAACGTTTC
1 ATTCTTCGTTTCTCCGTCGTCACCGGCGCGTGGAGGGGTGACACTGTCAAAGTTTCTAACGTTTC
2395521 AGAATCGAGCTGTCCGCCGTTCAAAATTGTGAACCGAGCTTTGTAAGTGCCTCAAAATCGATTAA
66 AGAATCGAGCTGTCCGCCGTTCAAAATTGTGAACCGAGCTTTGTAAGTGCCTCAAAATCGATTAA
2395586 AATAATTTTTAGGAA-TTTTTCGGGAA
131 AATAATTTTTAGGAATTTTTTCGGGAA
2395612 ATTCTTCGTTTCTCCGTCGTCCACCGGCGCGTGGAGGGGTGACACTGTCAAAGTTTCTAACGTTT
1 ATTCTTCGTTTCTCCGTCGT-CACCGGCGCGTGGAGGGGTGACACTGTCAAAGTTTCTAACGTTT
2395677 CAGAATCGAGCTGTCCGCCGTTCAAAATTGTGAACCGAGCTTTGTAAGTGCCTCAAAATCGATTA
65 CAGAATCGAGCTGTCCGCCGTTCAAAATTGTGAACCGAGCTTTGTAAGTGCCTCAAAATCGATTA
2395742 AAATAATTTTTAGGAATTTTTTCGGGAA
130 AAATAATTTTTAGGAATTTTTTCGGGAA
2395770 TTTATCGACA
Statistics
Matches: 156, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
156 20 0.13
157 125 0.80
158 11 0.07
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.32
Consensus pattern (157 bp):
ATTCTTCGTTTCTCCGTCGTCACCGGCGCGTGGAGGGGTGACACTGTCAAAGTTTCTAACGTTTC
AGAATCGAGCTGTCCGCCGTTCAAAATTGTGAACCGAGCTTTGTAAGTGCCTCAAAATCGATTAA
AATAATTTTTAGGAATTTTTTCGGGAA
Found at i:2408754 original size:17 final size:17
Alignment explanation
Indices: 2408731--2408769 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
2408721 TGGTTGGAAC
2408731 ATACTCGTATCCGATAT
1 ATACTCGTATCCGATAT
*
2408748 GTACTCGTATCCGATAT
1 ATACTCGTATCCGATAT
2408765 ATACT
1 ATACT
2408770 ATGTCGTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.36
Consensus pattern (17 bp):
ATACTCGTATCCGATAT
Found at i:2409537 original size:3 final size:3
Alignment explanation
Indices: 2409529--2409621 Score: 60
Period size: 3 Copynumber: 32.3 Consensus size: 3
2409519 ATGACTTAAG
*
2409529 ATA ATA ATA ATAA ATA ATA ATGA A-A ATA ATA AT- TTA A-A CATA TATA
1 ATA ATA ATA AT-A ATA ATA AT-A ATA ATA ATA ATA ATA ATA -ATA -ATA
*
2409575 A-A A-A ATA ATA ATA A-A ATA A-A ATT ATA ATA ATA ATCA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA
2409616 A-A ATA A
1 ATA ATA A
2409622 ATTAAAATCA
Statistics
Matches: 73, Mismatches: 5, Indels: 24
0.72 0.05 0.24
Matches are distributed among these distances:
2 16 0.22
3 46 0.63
4 11 0.15
ACGTcount: A:0.68, C:0.02, G:0.01, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:2409559 original size:22 final size:22
Alignment explanation
Indices: 2409531--2409644 Score: 87
Period size: 22 Copynumber: 5.1 Consensus size: 22
2409521 GACTTAAGAT
2409531 AATAATAAT-AAATAATAATGAA
1 AATAATAATAAAATAATAAT-AA
2409553 AATAATAATTTAAACATATATAA-AA
1 AATAATAA--TAAA-ATA-ATAATAA
*
2409578 AATAATAATAAAATAA-AATTAT
1 AATAATAATAAAATAATAA-TAA
2409600 AATAATAATCAAAATAA-AATAA
1 AATAATAAT-AAAATAATAATAA
* * *
2409622 ATTAA-AAT-CAATAATATTAA
1 AATAATAATAAAATAATAATAA
2409642 AAT
1 AAT
2409645 GAAAAATATA
Statistics
Matches: 77, Mismatches: 6, Indels: 20
0.75 0.06 0.19
Matches are distributed among these distances:
19 5 0.06
20 8 0.10
21 4 0.05
22 27 0.35
23 13 0.17
24 1 0.01
25 12 0.16
26 3 0.04
27 4 0.05
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.30
Consensus pattern (22 bp):
AATAATAATAAAATAATAATAA
Found at i:2409560 original size:28 final size:26
Alignment explanation
Indices: 2409529--2409652 Score: 80
Period size: 25 Copynumber: 4.7 Consensus size: 26
2409519 ATGACTTAAG
2409529 ATAATAATAATAAATAATAATGAAAATA
1 ATAATAA-AATAAATAATAAT-AAAATA
** *
2409557 ATAATTTAA-ACATATATAA-AAAATA
1 ATAATAAAATAAATA-ATAATAAAATA
*
2409582 ATAATAAAATAAAATTATAATAATAATCA
1 ATAATAAAAT-AAATAATAATAA-AAT-A
*
2409611 A-AATAAAATAAATTAA-AAT-CAATA
1 ATAATAAAATAAA-TAATAATAAAATA
*
2409635 ATATTAAAATGAAA-AATA
1 ATAATAAAAT-AAATAATA
2409653 TATTAAATGA
Statistics
Matches: 76, Mismatches: 10, Indels: 23
0.70 0.09 0.21
Matches are distributed among these distances:
24 4 0.05
25 24 0.32
26 11 0.14
27 17 0.22
28 18 0.24
29 2 0.03
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (26 bp):
ATAATAAAATAAATAATAATAAAATA
Found at i:2409594 original size:5 final size:5
Alignment explanation
Indices: 2409576--2409629 Score: 54
Period size: 5 Copynumber: 10.0 Consensus size: 5
2409566 ACATATATAA
* *
2409576 AAAAT AATAAT AAAAT AAAATT ATAAT AATAAT CAAAAT AAAAT AAATT
1 AAAAT AA-AAT AAAAT AAAA-T AAAAT AA-AAT -AAAAT AAAAT AAAAT
2409625 AAAAT
1 AAAAT
2409630 CAATAATATT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 24 0.59
6 15 0.37
7 2 0.05
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (5 bp):
AAAAT
Found at i:2409635 original size:31 final size:30
Alignment explanation
Indices: 2409576--2409676 Score: 87
Period size: 31 Copynumber: 3.2 Consensus size: 30
2409566 ACATATATAA
* *
2409576 AAAATAATAATAAAATAAAATTATAATAATAATC
1 AAAATAA-AATAAATTAAAA-T-CAATAAT-ATC
*
2409610 AAAATAAAATAAATTAAAATCAATAATATT
1 AAAATAAAATAAATTAAAATCAATAATATC
* * *
2409640 AAAATGAAAAATATATT-AAATGAAAAATATC
1 AAAAT--AAAATAAATTAAAATCAATAATATC
2409671 AAAATA
1 AAAATA
2409677 TCAAAATATT
Statistics
Matches: 58, Mismatches: 7, Indels: 9
0.78 0.09 0.12
Matches are distributed among these distances:
29 1 0.02
30 7 0.12
31 22 0.38
32 10 0.17
33 11 0.19
34 7 0.12
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.28
Consensus pattern (30 bp):
AAAATAAAATAAATTAAAATCAATAATATC
Found at i:2409658 original size:32 final size:32
Alignment explanation
Indices: 2409607--2409701 Score: 85
Period size: 32 Copynumber: 3.1 Consensus size: 32
2409597 TATAATAATA
* *
2409607 ATCAAAAT--AAAATAAATTAAAATCAATAAT
1 ATCAAAATACAAAATATATTAAAATCAAAAAT
* *
2409637 ATTAAAATGA-AAAATATATT-AAATGAAAAAT
1 ATCAAAAT-ACAAAATATATTAAAATCAAAAAT
2409668 ATCAAAATATCAAAATAT-TTAAAAT-ATAAAAT
1 ATCAAAATA-CAAAATATATTAAAATCA-AAAAT
2409700 AT
1 AT
2409702 ATAAATTAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
30 8 0.15
31 19 0.35
32 27 0.50
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.29
Consensus pattern (32 bp):
ATCAAAATACAAAATATATTAAAATCAAAAAT
Found at i:2409676 original size:8 final size:8
Alignment explanation
Indices: 2409663--2409701 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
2409653 TATTAAATGA
2409663 AAAATATC
1 AAAATATC
2409671 AAAATATC
1 AAAATATC
*
2409679 AAAATATTT
1 AAAATA-TC
2409688 AAAATAT-
1 AAAATATC
2409695 AAAATAT
1 AAAATAT
2409702 ATAAATTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
7 7 0.24
8 15 0.52
9 7 0.24
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (8 bp):
AAAATATC
Found at i:2409706 original size:16 final size:16
Alignment explanation
Indices: 2409563--2409706 Score: 77
Period size: 16 Copynumber: 8.8 Consensus size: 16
2409553 AATAATAATT
*
2409563 TAAACATATATAAAAAA
1 TAAA-ATATATAAAATA
*
2409580 TAATAATAAAATAAAATTA
1 TAA-AAT-ATATAAAA-TA
*
2409599 TAATAATA-ATCAAA-A
1 TAA-AATATATAAAATA
*
2409614 TAAAATAAATTAAAATCA
1 TAAAATATA-TAAAAT-A
*
2409632 -ATAATAT-TAAAATGA
1 TAAAATATATAAAAT-A
*
2409647 -AAAATATATTAAATGA
1 TAAAATATATAAAAT-A
*
2409663 -AAAATAT-CAAAATA
1 TAAAATATATAAAATA
*
2409677 TCAAAATATTTAAAATA
1 T-AAAATATATAAAATA
2409694 TAAAATATATAAA
1 TAAAATATATAAA
2409707 TTAATCCCTT
Statistics
Matches: 103, Mismatches: 13, Indels: 23
0.74 0.09 0.17
Matches are distributed among these distances:
14 5 0.05
15 22 0.21
16 36 0.35
17 22 0.21
18 10 0.10
19 8 0.08
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.29
Consensus pattern (16 bp):
TAAAATATATAAAATA
Found at i:2409707 original size:24 final size:24
Alignment explanation
Indices: 2409634--2409707 Score: 66
Period size: 24 Copynumber: 3.1 Consensus size: 24
2409624 TAAAATCAAT
*
2409634 AATA-TTAAAATGA-AAAATATATT
1 AATATTTAAAAT-ATAAAATATATA
**
2409657 AA-ATGAAAAATATCAAAATATCA-A
1 AATATTTAAAATAT-AAAATAT-ATA
2409681 AATATTTAAAATATAAAATATATA
1 AATATTTAAAATATAAAATATATA
2409705 AAT
1 AAT
2409708 TAATCCCTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
22 2 0.05
23 8 0.20
24 20 0.50
25 10 0.25
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (24 bp):
AATATTTAAAATATAAAATATATA
Found at i:2410162 original size:13 final size:13
Alignment explanation
Indices: 2410144--2410179 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
2410134 ATTTCGACCG
2410144 GCCACCGTCGTCA
1 GCCACCGTCGTCA
*
2410157 GCCACCGTCGTCG
1 GCCACCGTCGTCA
2410170 GCCACCGTCG
1 GCCACCGTCG
2410180 CCGGTGGCTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.11, C:0.47, G:0.28, T:0.14
Consensus pattern (13 bp):
GCCACCGTCGTCA
Found at i:2410801 original size:3 final size:3
Alignment explanation
Indices: 2410789--2410852 Score: 69
Period size: 3 Copynumber: 21.3 Consensus size: 3
2410779 AATATAATTT
*
2410789 ATA A-A ATA ATA ATA ATA AGT- TTA ATA ATA ATA ATA TATA ATA ATA
1 ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA -ATA ATA ATA
* *
2410834 ATA AAA ATA AAA ATA ATA A
1 ATA ATA ATA ATA ATA ATA A
2410853 AAGCAAACTG
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
2 3 0.06
3 44 0.86
4 4 0.08
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:2410849 original size:31 final size:31
Alignment explanation
Indices: 2410794--2410852 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
2410784 AATTTATAAA
*** *
2410794 ATAATAATAATAAGTTTAATAATAATAATAT
1 ATAATAATAATAAAAATAAAAATAATAATAT
2410825 ATAATAATAATAAAAATAAAAATAATAA
1 ATAATAATAATAAAAATAAAAATAATAA
2410853 AAGCAAACTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (31 bp):
ATAATAATAATAAAAATAAAAATAATAATAT
Found at i:2411043 original size:45 final size:45
Alignment explanation
Indices: 2410979--2411125 Score: 258
Period size: 45 Copynumber: 3.3 Consensus size: 45
2410969 GATGGAAATA
* *
2410979 TTGAAAACATCATGCACTGAAGGACGTACAGATGACCCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
2411024 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
*
2411069 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
*
2411114 TTGAAAATATCA
1 TTGAAAACATCA
2411126 AAAATCTCCC
Statistics
Matches: 98, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 98 1.00
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (45 bp):
TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
Found at i:2411156 original size:76 final size:76
Alignment explanation
Indices: 2411059--2411277 Score: 388
Period size: 76 Copynumber: 2.9 Consensus size: 76
2411049 TTACAGATGA
2411059 CCCGAAGG--TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAAT
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAAT
2411122 ATCAAAAATCT
66 ATCAAAAATCT
*
2411133 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGGTGACCCGAAGGCTTTGAAAAT
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAAT
2411198 ATCAAAAATCT
66 ATCAAAAATCT
* * *
2411209 CCCGAAGGCTTTTTGAAAACATCATGCATTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAAC
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAAT
2411274 ATCA
66 ATCA
2411278 TGCACTGAAG
Statistics
Matches: 138, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
74 8 0.06
76 130 0.94
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.24
Consensus pattern (76 bp):
CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAAT
ATCAAAAATCT
Found at i:2411268 original size:121 final size:121
Alignment explanation
Indices: 2410979--2411392 Score: 471
Period size: 121 Copynumber: 3.4 Consensus size: 121
2410969 GATGGAAATA
* * *
2410979 TTGAAAACATCATGCACTGAAGGACGTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGA
1 TTGAAAACATCATGCACTGAAGGGCTTACAAATGACCCGAAGGTTTTGAAAACATCATGCACTGA
* * *** *
2411044 AGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCA-CT---GAAGGGCTTA
66 AGGGCTTACAGATGACCCGAAGGCTTTGAAAATATCAAAAATCTCCCGAA-GGCTTT
** ** * * ** **** * * **
2411097 CAGATGAC-CCGAAGGCTTTGAAAATATCAAAAATCTCCCGAAGGCTTTTTGAAAACATCATGCA
1 TTGAAAACATC--ATGCACTGAAGGGCTTACAAATGACCCGAAGG--TTTTGAAAACATCATGCA
*
2411161 CTGAAGGGCTTACAGGTGACCCGAAGGCTTTGAAAATATCAAAAATCTCCCGAAGGCTTT
62 CTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAATATCAAAAATCTCCCGAAGGCTTT
* *
2411221 TTGAAAACATCATGCATTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGA
1 TTGAAAACATCATGCACTGAAGGGCTTACAAATGACCCGAAGGTTTTGAAAACATCATGCACTGA
2411286 AGGGCTTACAGATGACCCGAAGGCTTTGAAAATATCAAAAAGT-TCCCGAAGGCTTT
66 AGGGCTTACAGATGACCCGAAGGCTTTGAAAATATCAAAAA-TCTCCCGAAGGCTTT
*
2411342 TTGAAAACATCATGCACTGAAGGGCTTACAAATGACCCGAAGGCTTTGAAA
1 TTGAAAACATCATGCACTGAAGGGCTTACAAATGACCCGAAGGTTTTGAAA
2411393 TTATCAAAAA
Statistics
Matches: 241, Mismatches: 45, Indels: 17
0.80 0.15 0.06
Matches are distributed among these distances:
117 1 0.00
118 4 0.02
119 19 0.08
121 180 0.75
122 3 0.01
123 21 0.09
124 9 0.04
125 4 0.02
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (121 bp):
TTGAAAACATCATGCACTGAAGGGCTTACAAATGACCCGAAGGTTTTGAAAACATCATGCACTGA
AGGGCTTACAGATGACCCGAAGGCTTTGAAAATATCAAAAATCTCCCGAAGGCTTT
Found at i:2411276 original size:45 final size:45
Alignment explanation
Indices: 2411209--2411322 Score: 183
Period size: 45 Copynumber: 2.5 Consensus size: 45
2411199 TCAAAAATCT
*
2411209 CCCGAAGGCTTTTTGAAAACATCATGCATTGAAGGGCTTACAGATGA
1 CCCGAAGG--TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
2411256 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
* *
2411301 CCCGAAGGCTTTGAAAATATCA
1 CCCGAAGGTTTTGAAAACATCA
2411323 AAAAGTTCCC
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
45 56 0.88
47 8 0.12
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.24
Consensus pattern (45 bp):
CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
Found at i:2411344 original size:76 final size:76
Alignment explanation
Indices: 2411256--2411460 Score: 369
Period size: 76 Copynumber: 2.7 Consensus size: 76
2411246 TTACAGATGA
2411256 CCCGAAGG--TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAAT
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAAT
*
2411319 ATCAAAAAGTT
66 ATCAAAAAGCT
* *
2411330 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAAATGACCCGAAGGCTTTGAAATT
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAAT
2411395 ATCAAAAAGCT
66 ATCAAAAAGCT
2411406 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
2411461 ATTTAAGATC
Statistics
Matches: 125, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
74 8 0.06
76 117 0.94
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.22
Consensus pattern (76 bp):
CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAAT
ATCAAAAAGCT
Found at i:2411357 original size:197 final size:197
Alignment explanation
Indices: 2411014--2411460 Score: 819
Period size: 197 Copynumber: 2.3 Consensus size: 197
2411004 GTACAGATGA
2411014 CCCGAAGG--TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAAC
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAAC
2411077 ATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAATATCAAAAATCTCCCGAAGGC
66 ATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAATATCAAAAATCTCCCGAAGGC
** *
2411142 TTTTTGAAAACATCATGCACTGAAGGGCTTACAGGTGACCCGAAGGCTTTGAAAATATCAAAAAT
131 TTTTTGAAAACATCATGCACTGAAGGGCTTACAAATGACCCGAAGGCTTTGAAAATATCAAAAAG
2411207 CT
196 CT
*
2411209 CCCGAAGGCTTTTTGAAAACATCATGCATTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAAC
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAAC
2411274 ATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAATATCAAAAAGT-TCCCGAAGG
66 ATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAATATCAAAAA-TCTCCCGAAGG
*
2411338 CTTTTTGAAAACATCATGCACTGAAGGGCTTACAAATGACCCGAAGGCTTTGAAATTATCAAAAA
130 CTTTTTGAAAACATCATGCACTGAAGGGCTTACAAATGACCCGAAGGCTTTGAAAATATCAAAAA
2411403 GCT
195 GCT
2411406 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
2411461 ATTTAAGATC
Statistics
Matches: 243, Mismatches: 6, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
195 8 0.03
197 234 0.96
198 1 0.00
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.23
Consensus pattern (197 bp):
CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAAC
ATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAATATCAAAAATCTCCCGAAGGC
TTTTTGAAAACATCATGCACTGAAGGGCTTACAAATGACCCGAAGGCTTTGAAAATATCAAAAAG
CT
Found at i:2417390 original size:22 final size:22
Alignment explanation
Indices: 2417365--2417413 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
2417355 AAGTAAACAT
2417365 AAAAATAC-AAATGCAAAGATGC
1 AAAAATACAAAATGCAAA-ATGC
* *
2417387 -AAAATGCAAAATGCAAAATTC
1 AAAAATACAAAATGCAAAATGC
2417408 AAAAAT
1 AAAAAT
2417414 GTAAATATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.61, C:0.12, G:0.10, T:0.16
Consensus pattern (22 bp):
AAAAATACAAAATGCAAAATGC
Found at i:2417395 original size:7 final size:7
Alignment explanation
Indices: 2417373--2417411 Score: 60
Period size: 7 Copynumber: 5.4 Consensus size: 7
2417363 ATAAAAATAC
2417373 AAATGCA
1 AAATGCA
2417380 AAGATGCA
1 AA-ATGCA
2417388 AAATGCA
1 AAATGCA
2417395 AAATGCA
1 AAATGCA
*
2417402 AAATTCA
1 AAATGCA
2417409 AAA
1 AAA
2417412 ATGTAAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
7 23 0.77
8 7 0.23
ACGTcount: A:0.59, C:0.13, G:0.13, T:0.15
Consensus pattern (7 bp):
AAATGCA
Found at i:2417575 original size:15 final size:16
Alignment explanation
Indices: 2417550--2417579 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2417540 GTAAATACAA
2417550 ACGTAAAAATGCAAAG
1 ACGTAAAAATGCAAAG
2417566 ACGT-AAAATGCAAA
1 ACGTAAAAATGCAAA
2417580 TGCATGTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.57, C:0.13, G:0.17, T:0.13
Consensus pattern (16 bp):
ACGTAAAAATGCAAAG
Found at i:2420566 original size:11 final size:11
Alignment explanation
Indices: 2420506--2420567 Score: 56
Period size: 11 Copynumber: 5.5 Consensus size: 11
2420496 GACTTAAGAT
*
2420506 AATAGTAAT-A
1 AATAATAATAA
*
2420516 AATAATAATGA
1 AATAATAATAA
2420527 AATAATAATTTAA
1 AATAATAA--TAA
2420540 ACATATATAA-AA
1 A-ATA-ATAATAA
2420552 AATAATAATAA
1 AATAATAATAA
2420563 AATAA
1 AATAA
2420568 AAATTATACT
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
10 12 0.27
11 19 0.43
12 3 0.07
13 3 0.07
14 3 0.07
15 4 0.09
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (11 bp):
AATAATAATAA
Found at i:2421845 original size:3 final size:3
Alignment explanation
Indices: 2421833--2421899 Score: 84
Period size: 3 Copynumber: 22.3 Consensus size: 3
2421823 AATATAATTT
*
2421833 ATA A-A ATA ATA ATA ATA AGT- TTA ATA ATA ATA ATA TATA ATA ATA
1 ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA -ATA ATA ATA
*
2421878 ATA ATA ATA ATA AAA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA A
2421900 AAGCAAACTG
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
2 3 0.05
3 49 0.88
4 4 0.07
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2423679 original size:38 final size:39
Alignment explanation
Indices: 2423569--2423664 Score: 158
Period size: 39 Copynumber: 2.5 Consensus size: 39
2423559 TTAAAGGGGG
*
2423569 GAATTTAAGAGTCACTTGGGAGTTAGAGTGTTTTATTGT
1 GAATTTAAGAGTCTCTTGGGAGTTAGAGTGTTTTATTGT
* *
2423608 GAAATTAAGATTCTCTTGGGAGTTAGAGTGTTTTATTGT
1 GAATTTAAGAGTCTCTTGGGAGTTAGAGTGTTTTATTGT
2423647 GAATTTAAGAGT-TCTTGG
1 GAATTTAAGAGTCTCTTGG
2423665 AAGATGGAGA
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
38 6 0.12
39 46 0.88
ACGTcount: A:0.26, C:0.05, G:0.27, T:0.42
Consensus pattern (39 bp):
GAATTTAAGAGTCTCTTGGGAGTTAGAGTGTTTTATTGT
Found at i:2426212 original size:39 final size:39
Alignment explanation
Indices: 2426101--2426212 Score: 127
Period size: 40 Copynumber: 2.8 Consensus size: 39
2426091 AGACAAATTT
* *
2426101 CCCTATGCAC-AAGGCAAAGGAGCATACAGTAAAGTTTTC
1 CCCTATGCACGAA-GCAAATGAGCATACAGTAAGGTTTTC
* * * *
2426140 CCCTATGCATGATGCAAAATGGGCATGCAGTAAGGTTTTC
1 CCCTATGCACGAAGC-AAATGAGCATACAGTAAGGTTTTC
* *
2426180 CCCTATGCACGAAGCAAATGAGCTTACGGTAAG
1 CCCTATGCACGAAGCAAATGAGCATACAGTAAG
2426213 AACGCACACT
Statistics
Matches: 59, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
39 25 0.42
40 34 0.58
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.22
Consensus pattern (39 bp):
CCCTATGCACGAAGCAAATGAGCATACAGTAAGGTTTTC
Found at i:2426301 original size:39 final size:39
Alignment explanation
Indices: 2426180--2426301 Score: 104
Period size: 39 Copynumber: 3.1 Consensus size: 39
2426170 TAAGGTTTTC
* * *
2426180 CCCTATGCACGAAGCAAATGAG-CTTACGGTAAGAACGC-A
1 CCCTACGCACAAAGAAAATGAGTC-TACGGTAAGAAC-CTA
* ** * * * *
2426219 CACTGTGCACAAAGCAAATGAGTCTACTGTAAGAACTTT
1 CCCTACGCACAAAGAAAATGAGTCTACGGTAAGAACCTA
* *
2426258 CCCTACGCACAAAGAAAATGAGTCTGCGGTAAGGACCTA
1 CCCTACGCACAAAGAAAATGAGTCTACGGTAAGAACCTA
2426297 CCCTA
1 CCCTA
2426302 GCCATAGCAT
Statistics
Matches: 66, Mismatches: 15, Indels: 4
0.78 0.18 0.05
Matches are distributed among these distances:
39 65 0.98
40 1 0.02
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.19
Consensus pattern (39 bp):
CCCTACGCACAAAGAAAATGAGTCTACGGTAAGAACCTA
Found at i:2427045 original size:26 final size:27
Alignment explanation
Indices: 2427016--2427093 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 27
2427006 GACATTTTTA
**
2427016 TCATTTTAGAGCTT-AGAGTATTTTGG
1 TCATTTTAGAGCTTAAGAGTATTTCAG
** *
2427042 TCATTTTAGAATTTAAGGGTATTTCAG
1 TCATTTTAGAGCTTAAGAGTATTTCAG
*
2427069 TCATTTTAGAG-TTCAAGGGTATTTC
1 TCATTTTAGAGCTT-AAGAGTATTTC
2427094 GATCCTTTCA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
26 14 0.32
27 30 0.68
ACGTcount: A:0.26, C:0.09, G:0.21, T:0.45
Consensus pattern (27 bp):
TCATTTTAGAGCTTAAGAGTATTTCAG
Found at i:2427071 original size:27 final size:27
Alignment explanation
Indices: 2427041--2427093 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
2427031 GAGTATTTTG
*
2427041 GTCATTTTAGAATTTAAGGGTATTTCA
1 GTCATTTTAGAATTCAAGGGTATTTCA
*
2427068 GTCATTTTAGAGTTCAAGGGTATTTC
1 GTCATTTTAGAATTCAAGGGTATTTC
2427094 GATCCTTTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.26, C:0.09, G:0.21, T:0.43
Consensus pattern (27 bp):
GTCATTTTAGAATTCAAGGGTATTTCA
Found at i:2430726 original size:24 final size:24
Alignment explanation
Indices: 2430699--2430765 Score: 98
Period size: 24 Copynumber: 2.8 Consensus size: 24
2430689 ATTTGAATTA
*
2430699 TGATTTGATACTTGACATGGATTC
1 TGATATGATACTTGACATGGATTC
* * *
2430723 TGATATGATACTTTACCTGGATTT
1 TGATATGATACTTGACATGGATTC
2430747 TGATATGATACTTGACATG
1 TGATATGATACTTGACATG
2430766 AATTATATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.27, C:0.12, G:0.19, T:0.42
Consensus pattern (24 bp):
TGATATGATACTTGACATGGATTC
Found at i:2430779 original size:24 final size:24
Alignment explanation
Indices: 2430692--2430771 Score: 97
Period size: 24 Copynumber: 3.3 Consensus size: 24
2430682 ATTTTCGATT
*
2430692 TGAATTATGATTTGATACTTGACA
1 TGAATTATGATATGATACTTGACA
* * * *
2430716 TGGATTCTGATATGATACTTTACC
1 TGAATTATGATATGATACTTGACA
* *
2430740 TGGATTTTGATATGATACTTGACA
1 TGAATTATGATATGATACTTGACA
2430764 TGAATTAT
1 TGAATTAT
2430772 ATTTTGATTT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.30, C:0.10, G:0.17, T:0.42
Consensus pattern (24 bp):
TGAATTATGATATGATACTTGACA
Found at i:2435642 original size:24 final size:24
Alignment explanation
Indices: 2435615--2435733 Score: 168
Period size: 24 Copynumber: 5.0 Consensus size: 24
2435605 TTCGATTTGA
*
2435615 ATTCTAATATGATACTTGACATGG
1 ATTCTGATATGATACTTGACATGG
2435639 ATTCTGATATGATA-TCTGACATGG
1 ATTCTGATATGATACT-TGACATGG
* *
2435663 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATATGATACTTGACATGG
* *
2435687 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATATGATACTTGACATGG
*
2435711 ATTTTGATATGATACTTGACATG
1 ATTCTGATATGATACTTGACATG
2435734 AATTATATTT
Statistics
Matches: 87, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
23 1 0.01
24 85 0.98
25 1 0.01
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.40
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACATGG
Found at i:2435668 original size:12 final size:12
Alignment explanation
Indices: 2435631--2435669 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
2435621 ATATGATACT
2435631 TGACATGGATTC
1 TGACATGGATTC
*
2435643 TGATAT-GATATC
1 TGACATGGAT-TC
2435655 TGACATGGATTC
1 TGACATGGATTC
2435667 TGA
1 TGA
2435670 TCTGATACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 3 0.13
12 17 0.74
13 3 0.13
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (12 bp):
TGACATGGATTC
Found at i:2439267 original size:123 final size:123
Alignment explanation
Indices: 2439048--2439293 Score: 483
Period size: 123 Copynumber: 2.0 Consensus size: 123
2439038 CCATATCTAA
2439048 TGAAAGAATAAGGTCATCACTCATCAGAATCCCCAACTGCCTCCCTATAACTCAATTTGAATCAC
1 TGAAAGAATAAGGTCATCACTCATCAGAATCCCCAACTGCCTCCCTATAACTCAATTTGAATCAC
2439113 TTTTAAGGGAATATAACTCGACTTGGTTGTTCCAATCTGCCATCAACCCTTCAACTAG
66 TTTTAAGGGAATATAACTCGACTTGGTTGTTCCAATCTGCCATCAACCCTTCAACTAG
*
2439171 TGAAAGAATAAGGTCATCACTCATCATAATCCCCAACTGCCTCCCTATAACTCAATTTGAATCAC
1 TGAAAGAATAAGGTCATCACTCATCAGAATCCCCAACTGCCTCCCTATAACTCAATTTGAATCAC
2439236 TTTTAAGGGAATATAACTCGACTTGGTTGTTCCAATCTGCCATCAACCCTTCAACTAG
66 TTTTAAGGGAATATAACTCGACTTGGTTGTTCCAATCTGCCATCAACCCTTCAACTAG
2439294 ATTATCTTCA
Statistics
Matches: 122, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
123 122 1.00
ACGTcount: A:0.32, C:0.27, G:0.13, T:0.29
Consensus pattern (123 bp):
TGAAAGAATAAGGTCATCACTCATCAGAATCCCCAACTGCCTCCCTATAACTCAATTTGAATCAC
TTTTAAGGGAATATAACTCGACTTGGTTGTTCCAATCTGCCATCAACCCTTCAACTAG
Found at i:2444308 original size:23 final size:22
Alignment explanation
Indices: 2444281--2444343 Score: 58
Period size: 25 Copynumber: 2.8 Consensus size: 22
2444271 TATATATTAT
2444281 TTTAATATTTATTATTTTTATAA
1 TTTAATATTTATTATTTTTA-AA
*
2444304 TTTAAACACTTT-TATATTTTTAAA
1 TTT-AATA-TTTAT-TATTTTTAAA
*
2444328 GTTAAT-TTTATTATTT
1 TTTAATATTTATTATTT
2444344 ATTACAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
21 8 0.24
22 1 0.03
23 5 0.15
24 8 0.24
25 11 0.33
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (22 bp):
TTTAATATTTATTATTTTTAAA
Found at i:2449185 original size:157 final size:156
Alignment explanation
Indices: 2448892--2449198 Score: 456
Period size: 157 Copynumber: 2.0 Consensus size: 156
2448882 TAAAATTCAG
* * *
2448892 AAACCATAGTAATCCCTCCAGCCCAACACATCATAATGTGTAGGTTCCCCAGAACCATACACCCA
1 AAACCATAGTAATCCCTCCAACCAAACACATCATAATGTGTAGGTTCCCCAGAACCATACACACA
* * * *
2448957 CCGTCACATTGAGTAAGTCCATGAGCACAAAGCAGAGGAGCCTGCAAGTATACTTCCTCCAACAA
66 CCGTCACATCGAGTAAGGCCATAAGCACAAAGCAGAGGAGCCTGCAAGTATACATCCTCCAACAA
*
2449022 TACCCCCCTAAATAAAACATTTATTTA
131 TACCCCCC-AAATAAAAAATTTATTTA
*
2449049 AAACCATAGTAATCCCTTCAACCAAACACATCATAATGTGTAGGTTCCCCAGAACCATACACACA
1 AAACCATAGTAATCCCTCCAACCAAACACATCATAATGTGTAGGTTCCCCAGAACCATACACACA
* * * * *
2449114 CCGTCACATCGAGTAAGGCCTTAAGCATAAAGTC-GATGAGCTTGCAAGTATTCAT-CTCCAACA
66 CCGTCACATCGAGTAAGGCCATAAGCACAAAG-CAGAGGAGCCTGCAAGTATACATCCTCCAACA
2449177 ATACCCCCCAAATAAAAAATTT
130 ATACCCCCCAAATAAAAAATTT
2449199 TCCATCCGTA
Statistics
Matches: 135, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
155 12 0.09
156 17 0.13
157 105 0.78
158 1 0.01
ACGTcount: A:0.37, C:0.29, G:0.12, T:0.21
Consensus pattern (156 bp):
AAACCATAGTAATCCCTCCAACCAAACACATCATAATGTGTAGGTTCCCCAGAACCATACACACA
CCGTCACATCGAGTAAGGCCATAAGCACAAAGCAGAGGAGCCTGCAAGTATACATCCTCCAACAA
TACCCCCCAAATAAAAAATTTATTTA
Found at i:2454944 original size:30 final size:30
Alignment explanation
Indices: 2454890--2454959 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
2454880 AAAAATAGTT
* * *
2454890 AAATTTTAATTTGACCTCTGAATTTAGACA
1 AAATATTAATTTGACCTCTAAATTTACACA
*
2454920 AAATATTAATTTGACCT-TAAAATTTACATA
1 AAATATTAATTTGACCTCT-AAATTTACACA
*
2454950 AAATAGTAAT
1 AAATATTAAT
2454960 ATAACTCTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 1 0.03
30 33 0.97
ACGTcount: A:0.44, C:0.10, G:0.07, T:0.39
Consensus pattern (30 bp):
AAATATTAATTTGACCTCTAAATTTACACA
Found at i:2457515 original size:16 final size:16
Alignment explanation
Indices: 2457496--2457561 Score: 53
Period size: 16 Copynumber: 3.9 Consensus size: 16
2457486 TGCAATGTTC
2457496 TACATGATCTATGTGT
1 TACATGATCTATGTGT
* *
2457512 TACATTTTATCCTACGTGT
1 TACA--TGAT-CTATGTGT
*
2457531 TACATTATCTATGTGTT
1 TACATGATCTATGTG-T
*
2457548 TATATG-TCTATGTG
1 TACATGATCTATGTG
2457562 ATAAGCTATG
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
16 18 0.44
17 9 0.22
18 3 0.07
19 11 0.27
ACGTcount: A:0.23, C:0.14, G:0.15, T:0.48
Consensus pattern (16 bp):
TACATGATCTATGTGT
Found at i:2457691 original size:23 final size:23
Alignment explanation
Indices: 2457648--2457762 Score: 95
Period size: 23 Copynumber: 5.0 Consensus size: 23
2457638 CAAGAGTCAT
** *
2457648 GTGGTCCTTCGGGACAATTCTAC
1 GTGGTCCTTCAAGACATTTCTAC
* *
2457671 GTTGTCCTTCAAGATATTTCTAC
1 GTGGTCCTTCAAGACATTTCTAC
*
2457694 GTGGTCCTTCAGGACATTTCTAC
1 GTGGTCCTTCAAGACATTTCTAC
* *** * *
2457717 GCGGTCCTTTGGGACATATCTAT
1 GTGGTCCTTCAAGACATTTCTAC
* **
2457740 GTGGTCATTCGGGACATTTCTAC
1 GTGGTCCTTCAAGACATTTCTAC
2457763 ATGGGTCTTT
Statistics
Matches: 74, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 74 1.00
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (23 bp):
GTGGTCCTTCAAGACATTTCTAC
Found at i:2457701 original size:46 final size:46
Alignment explanation
Indices: 2457648--2457762 Score: 131
Period size: 46 Copynumber: 2.5 Consensus size: 46
2457638 CAAGAGTCAT
* ** * *
2457648 GTGGTCCTTCGGGACAATTCTACGTTGTCCTTCAAGATATTTCTAC
1 GTGGTCCTTCGGGACATTTCTACGCGGTCCTTCAAGACATATCTAC
* *** *
2457694 GTGGTCCTTCAGGACATTTCTACGCGGTCCTTTGGGACATATCTAT
1 GTGGTCCTTCGGGACATTTCTACGCGGTCCTTCAAGACATATCTAC
*
2457740 GTGGTCATTCGGGACATTTCTAC
1 GTGGTCCTTCGGGACATTTCTAC
2457763 ATGGGTCTTT
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
46 57 1.00
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (46 bp):
GTGGTCCTTCGGGACATTTCTACGCGGTCCTTCAAGACATATCTAC
Found at i:2458063 original size:27 final size:27
Alignment explanation
Indices: 2458025--2458078 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
2458015 CATTATATGT
2458025 CTCACTAAGTCAAAGACTTAGCGTGTG
1 CTCACTAAGTCAAAGACTTAGCGTGTG
*
2458052 CTCATTAAGTCAAAGACTTAGCGTGTG
1 CTCACTAAGTCAAAGACTTAGCGTGTG
2458079 AGTGTTTCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (27 bp):
CTCACTAAGTCAAAGACTTAGCGTGTG
Found at i:2470323 original size:23 final size:23
Alignment explanation
Indices: 2470297--2470389 Score: 82
Period size: 23 Copynumber: 4.0 Consensus size: 23
2470287 GGTTCTACGC
**
2470297 GGTCCTTTAGGACAATTCTATGT
1 GGTCCTTCGGGACAATTCTATGT
* * *
2470320 GGTCCATT-GGGACATTTCTACGC
1 GGTCC-TTCGGGACAATTCTATGT
* *
2470343 AGTCATTCGGGAC-ATATCTATGT
1 GGTCCTTCGGGACAAT-TCTATGT
*
2470366 GGTCCTTCGGGACATTTCTATGT
1 GGTCCTTCGGGACAATTCTATGT
2470389 G
1 G
2470390 ACATTTCGGT
Statistics
Matches: 54, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
22 3 0.06
23 48 0.89
24 3 0.06
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.35
Consensus pattern (23 bp):
GGTCCTTCGGGACAATTCTATGT
Found at i:2471112 original size:3 final size:3
Alignment explanation
Indices: 2471106--2471147 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
2471096 TGTTGTGTAT
2471106 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2471148 TTATGATAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2471734 original size:44 final size:43
Alignment explanation
Indices: 2471652--2471735 Score: 123
Period size: 43 Copynumber: 1.9 Consensus size: 43
2471642 CAGTTCCTTT
* *
2471652 TTATATTGCAAATGTAACATTAAATTGTTTCTATTTCAGTGTG
1 TTATATTGAAAATGTAACATCAAATTGTTTCTATTTCAGTGTG
**
2471695 TTATATTGAAAATGTGGCATCAAATGTGTTTCTATTTCAGT
1 TTATATTGAAAATGTAACATCAAAT-TGTTTCTATTTCAGT
2471736 TTCTGTTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 21 0.58
44 15 0.42
ACGTcount: A:0.30, C:0.10, G:0.15, T:0.45
Consensus pattern (43 bp):
TTATATTGAAAATGTAACATCAAATTGTTTCTATTTCAGTGTG
Found at i:2475988 original size:15 final size:15
Alignment explanation
Indices: 2475968--2475998 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2475958 ACTCAAAACC
2475968 AATGTAATAAAGTCT
1 AATGTAATAAAGTCT
*
2475983 AATGTAATCAAGTCT
1 AATGTAATAAAGTCT
2475998 A
1 A
2475999 GGAGGGCGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.32
Consensus pattern (15 bp):
AATGTAATAAAGTCT
Found at i:2483188 original size:21 final size:21
Alignment explanation
Indices: 2483164--2483218 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
2483154 TTTATCTTTT
2483164 GGGCACTAAGAATTAAATAAA
1 GGGCACTAAGAATTAAATAAA
*
2483185 GGGCACTAAGAATTATATAAA
1 GGGCACTAAGAATTAAATAAA
*
2483206 GGGCACTACGAAT
1 GGGCACTAAGAAT
2483219 ATAATAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.45, C:0.13, G:0.22, T:0.20
Consensus pattern (21 bp):
GGGCACTAAGAATTAAATAAA
Found at i:2483225 original size:21 final size:20
Alignment explanation
Indices: 2483164--2483225 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 20
2483154 TTTATCTTTT
2483164 GGGCACTAAGAATTAAATAAA
1 GGGCACTAAGAATT-AATAAA
2483185 GGGCACTAAGAATTATATAAA
1 GGGCACTAAGAATTA-ATAAA
*
2483206 GGGCACTACGAATATAATAA
1 GGGCACTAAGAAT-TAATAA
2483226 TATAGTCGCA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
20 1 0.03
21 35 0.92
22 2 0.05
ACGTcount: A:0.48, C:0.11, G:0.19, T:0.21
Consensus pattern (20 bp):
GGGCACTAAGAATTAATAAA
Found at i:2483866 original size:59 final size:59
Alignment explanation
Indices: 2483774--2483889 Score: 187
Period size: 59 Copynumber: 2.0 Consensus size: 59
2483764 AGATTGTTGA
* * * *
2483774 TAAATAGTTTTAAAAGAGTGACTAATATGTAATTAATTTCTGTTATGGTGCTATTTTTG
1 TAAATAATTTTAAAAGAATGACTAATACGTAATTAATTTCGGTTATGGTGCTATTTTTG
*
2483833 TAAATAATTTTAAAAGAATGACTAATACGTAATTAATTTCGGTTATGGTGGTATTTT
1 TAAATAATTTTAAAAGAATGACTAATACGTAATTAATTTCGGTTATGGTGCTATTTT
2483890 ATTGTTAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
59 52 1.00
ACGTcount: A:0.34, C:0.05, G:0.16, T:0.44
Consensus pattern (59 bp):
TAAATAATTTTAAAAGAATGACTAATACGTAATTAATTTCGGTTATGGTGCTATTTTTG
Found at i:2483933 original size:29 final size:28
Alignment explanation
Indices: 2483889--2484145 Score: 379
Period size: 29 Copynumber: 9.0 Consensus size: 28
2483879 GGTGGTATTT
*
2483889 TATTGTTAAAAAGTGTTAGTTTCGTAAA
1 TATTGTTAAAAGGTGTTAGTTTCGTAAA
*
2483917 TAATGTTAAGAAGGTGTTAGTTTCGTAAA
1 TATTGTTAA-AAGGTGTTAGTTTCGTAAA
*
2483946 TATTGTTAAGAAGGTGTTAGTTTCATAAA
1 TATTGTTAA-AAGGTGTTAGTTTCGTAAA
* *
2483975 TATTGTTCAACAGGTGTTAGTTTTGTAAA
1 TATTGTT-AAAAGGTGTTAGTTTCGTAAA
2484004 TATTGTTAAGAAGGTGTTAGTTTCGTAAA
1 TATTGTTAA-AAGGTGTTAGTTTCGTAAA
*
2484033 TATTGTTAAAAAGGTGTTAGCTTCGTAAA
1 TATTGTT-AAAAGGTGTTAGTTTCGTAAA
* *
2484062 TATTGTTAAAAAGTGTTAGTTTTGTAAA
1 TATTGTTAAAAGGTGTTAGTTTCGTAAA
2484090 TATTGTTAAGAAGGTGTTAGTTTCGTAAA
1 TATTGTTAA-AAGGTGTTAGTTTCGTAAA
*
2484119 TATTTTTAAAAGGTGTTAGTTTCGTAA
1 TATTGTTAAAAGGTGTTAGTTTCGTAA
2484146 TTAATTCTGT
Statistics
Matches: 208, Mismatches: 16, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
28 55 0.26
29 149 0.72
30 4 0.02
ACGTcount: A:0.33, C:0.04, G:0.21, T:0.42
Consensus pattern (28 bp):
TATTGTTAAAAGGTGTTAGTTTCGTAAA
Found at i:2484047 original size:87 final size:86
Alignment explanation
Indices: 2483889--2484141 Score: 418
Period size: 87 Copynumber: 2.9 Consensus size: 86
2483879 GGTGGTATTT
* *
2483889 TATTGTTAAAAAGTGTTAGTTTCGTAAATAATGTTAAGAAGGTGTTAGTTTCGTAAATATTGTTA
1 TATTGTTAAAAAGTGTTAGTTTTGTAAATATTGTTAAGAAGGTGTTAGTTTCGTAAATATTGTTA
*
2483954 AGAAGGTGTTAGTTTCATAAA
66 AAAAGGTGTTAGTTTCATAAA
* *
2483975 TATTGTTCAACAGGTGTTAGTTTTGTAAATATTGTTAAGAAGGTGTTAGTTTCGTAAATATTGTT
1 TATTGTT-AAAAAGTGTTAGTTTTGTAAATATTGTTAAGAAGGTGTTAGTTTCGTAAATATTGTT
* *
2484040 AAAAAGGTGTTAGCTTCGTAAA
65 AAAAAGGTGTTAGTTTCATAAA
*
2484062 TATTGTTAAAAAGTGTTAGTTTTGTAAATATTGTTAAGAAGGTGTTAGTTTCGTAAATATT-TTT
1 TATTGTTAAAAAGTGTTAGTTTTGTAAATATTGTTAAGAAGGTGTTAGTTTCGTAAATATTGTTA
2484126 AAAAGGTGTTAGTTTC
66 AAAAGGTGTTAGTTTC
2484142 GTAATTAATT
Statistics
Matches: 155, Mismatches: 11, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
85 17 0.11
86 59 0.38
87 79 0.51
ACGTcount: A:0.32, C:0.04, G:0.21, T:0.43
Consensus pattern (86 bp):
TATTGTTAAAAAGTGTTAGTTTTGTAAATATTGTTAAGAAGGTGTTAGTTTCGTAAATATTGTTA
AAAAGGTGTTAGTTTCATAAA
Found at i:2487723 original size:59 final size:59
Alignment explanation
Indices: 2487631--2487764 Score: 189
Period size: 59 Copynumber: 2.3 Consensus size: 59
2487621 TAGATTGTTG
* * * * *
2487631 ATAAATAGTTTTAAAAGAGTGACTAATATGTAATTAATTTCTGTTATGGTGCTATTTTT
1 ATAAATAATTTTAAAAGAATGACAAATACGTAATTAATTTCGGTTATGGTGCTATTTTT
*
2487690 ATAAATAATTTTAAAAGAATGACAAATACGTAATTAATTTCGGTTATGGTGGTATTTTT
1 ATAAATAATTTTAAAAGAATGACAAATACGTAATTAATTTCGGTTATGGTGCTATTTTT
*
2487749 GTAAAT-ATTGTTAAAA
1 ATAAATAATT-TTAAAA
2487765 AGTGTTAGTT
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
58 3 0.04
59 64 0.96
ACGTcount: A:0.38, C:0.04, G:0.15, T:0.43
Consensus pattern (59 bp):
ATAAATAATTTTAAAAGAATGACAAATACGTAATTAATTTCGGTTATGGTGCTATTTTT
Found at i:2487808 original size:29 final size:28
Alignment explanation
Indices: 2487749--2488010 Score: 371
Period size: 29 Copynumber: 9.1 Consensus size: 28
2487739 TGGTATTTTT
*
2487749 GTAAATATTGTTAAAAAGTGTTAGTTTC
1 GTAAATATTGTTAAAAGGTGTTAGTTTC
2487777 GTAAATATTGTTAAGAAGGTGTTAGTTTC
1 GTAAATATTGTTAA-AAGGTGTTAGTTTC
2487806 GTAAATATTGTTAAGAAGGTGTTAGTTTC
1 GTAAATATTGTTAA-AAGGTGTTAGTTTC
* * *
2487835 ATAAATATTGTTCAACAGGTGTTAGTTTT
1 GTAAATATTGTT-AAAAGGTGTTAGTTTC
*
2487864 GTAAATATTGTTAAGAAGGTGATAGTTTC
1 GTAAATATTGTTAA-AAGGTGTTAGTTTC
* *
2487893 GTAAATATTGTTAAAAACGTGTTAGCTTC
1 GTAAATATTGTT-AAAAGGTGTTAGTTTC
* *
2487922 GTAAATATTGTTAAAAAGAGTTAGTTTC
1 GTAAATATTGTTAAAAGGTGTTAGTTTC
*
2487950 GTAAATATTGTTAAGAAGGTGCTAGTTTC
1 GTAAATATTGTTAA-AAGGTGTTAGTTTC
*
2487979 GTAAATATTTTTAAAAGGTGTTAGTTTC
1 GTAAATATTGTTAAAAGGTGTTAGTTTC
2488007 GTAA
1 GTAA
2488011 TTAATTCTGC
Statistics
Matches: 210, Mismatches: 19, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
28 60 0.29
29 146 0.70
30 4 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.41
Consensus pattern (28 bp):
GTAAATATTGTTAAAAGGTGTTAGTTTC
Found at i:2496715 original size:17 final size:15
Alignment explanation
Indices: 2496680--2496760 Score: 59
Period size: 14 Copynumber: 5.7 Consensus size: 15
2496670 TTTAAAATAA
2496680 TTAA-AATAATATAT
1 TTAATAATAATATAT
2496694 TTAATAATAATATAT
1 TTAATAATAATATAT
* *
2496709 CT-ATAATAATTTA-
1 TTAATAATAATATAT
**
2496722 TTATATTTTAA-ATGA-
1 TTA-ATAATAATAT-AT
2496737 TTAA-AATAATATAT
1 TTAATAATAATATAT
2496751 TT-ATAATAAT
1 TTAATAATAAT
2496761 TTGTTACATT
Statistics
Matches: 52, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
13 6 0.12
14 26 0.50
15 20 0.38
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (15 bp):
TTAATAATAATATAT
Found at i:2499991 original size:19 final size:19
Alignment explanation
Indices: 2499967--2500071 Score: 111
Period size: 19 Copynumber: 5.2 Consensus size: 19
2499957 GCGATTTTGA
2499967 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTT
2499986 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTT
*
2500005 AAAATGTGTTGCGAGAGTTT
1 AAAATGTGTTGCGATAG-TT
* *
2500025 GAAAAACGTGTTGTTGTGATAGTG
1 --AAAA--TG-TGTTGCGATAGTT
* *
2500049 AAAAAGTGTTGCGATAGTG
1 AAAATGTGTTGCGATAGTT
2500068 AAAA
1 AAAA
2500072 ATCCAAAATA
Statistics
Matches: 74, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
19 51 0.69
20 3 0.04
22 8 0.11
24 3 0.04
25 9 0.12
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (19 bp):
AAAATGTGTTGCGATAGTT
Found at i:2500429 original size:20 final size:20
Alignment explanation
Indices: 2500404--2500457 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
2500394 TGCAATACCA
2500404 AATCGCGTTGCGATAATCAG
1 AATCGCGTTGCGATAATCAG
* *
2500424 AATCGCGTTGCGATAGTCAT
1 AATCGCGTTGCGATAATCAG
*
2500444 TATCGCGTTGCGAT
1 AATCGCGTTGCGAT
2500458 TATGTTGATC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (20 bp):
AATCGCGTTGCGATAATCAG
Found at i:2513225 original size:15 final size:15
Alignment explanation
Indices: 2513205--2513250 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
2513195 AGGCAACCCA
*
2513205 ATTTTTCTTTTTTTT
1 ATTTTTATTTTTTTT
*
2513220 ATTTTTATTTTTGTT
1 ATTTTTATTTTTTTT
*
2513235 CTTTTTATTTTATTTT
1 ATTTTTATTTT-TTTT
2513251 TCCTTGATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
15 23 0.88
16 3 0.12
ACGTcount: A:0.11, C:0.04, G:0.02, T:0.83
Consensus pattern (15 bp):
ATTTTTATTTTTTTT
Found at i:2513229 original size:21 final size:20
Alignment explanation
Indices: 2513205--2513252 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 20
2513195 AGGCAACCCA
*
2513205 ATTTTTCTTTTTTTTATTTTT
1 ATTTTTCTTCTTTTTA-TTTT
*
2513226 ATTTTTGTTCTTTTTATTTT
1 ATTTTTCTTCTTTTTATTTT
2513246 ATTTTTC
1 ATTTTTC
2513253 CTTGATTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.10, C:0.06, G:0.02, T:0.81
Consensus pattern (20 bp):
ATTTTTCTTCTTTTTATTTT
Found at i:2522415 original size:15 final size:14
Alignment explanation
Indices: 2522391--2522434 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
2522381 TTTAAAATAA
2522391 TTAAAATAATATAT
1 TTAAAATAATATAT
2522405 TTAATAATAATATAT
1 TTAA-AATAATATAT
* * *
2522420 CTACAATAATTTAT
1 TTAAAATAATATAT
2522434 T
1 T
2522435 ATATTTTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (14 bp):
TTAAAATAATATAT
Found at i:2522451 original size:23 final size:20
Alignment explanation
Indices: 2522424--2522484 Score: 59
Period size: 23 Copynumber: 2.9 Consensus size: 20
2522414 ATATATCTAC
2522424 AATAATTTATTATATTTTAAAT
1 AATAATTTATTATATTTT--AT
** *
2522446 GAATAAAATAATATATTTTAT
1 -AATAATTTATTATATTTTAT
*
2522467 AATAATTTATTACATTTT
1 AATAATTTATTATATTTT
2522485 TACTATTAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
20 14 0.45
21 2 0.06
23 15 0.48
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (20 bp):
AATAATTTATTATATTTTAT
Found at i:2522476 original size:43 final size:42
Alignment explanation
Indices: 2522410--2522506 Score: 117
Period size: 43 Copynumber: 2.3 Consensus size: 42
2522400 TATATTTAAT
* *
2522410 AATAATATA-TCTACAATAATTTATTATATTTTAAATGAATAA
1 AATAATATATTTTACAATAATTTATTACATTTTAAAT-AATAA
* * * *
2522452 AATAATATATTTTATAATAATTTATTACATTTTTACTATTAA
1 AATAATATATTTTACAATAATTTATTACATTTTAAATAATAA
2522494 AA-AATATATTTTA
1 AATAATATATTTTA
2522507 ACATTATAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
41 11 0.23
42 15 0.31
43 22 0.46
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (42 bp):
AATAATATATTTTACAATAATTTATTACATTTTAAATAATAA
Found at i:2522492 original size:57 final size:59
Alignment explanation
Indices: 2522372--2522480 Score: 163
Period size: 57 Copynumber: 1.9 Consensus size: 59
2522362 ATATACAATA
2522372 TATTAGTATTTTAAAATAATTAAAATAATATATTTAATAATAATATATCTACAATAATT
1 TATTAGTATTTTAAAATAATTAAAATAATATATTTAATAATAATATATCTACAATAATT
* *
2522431 TATTA-TATTTT-AAATGAA-TAAAATAATATATTTTATAATAATTTAT-TACA
1 TATTAGTATTTTAAAAT-AATTAAAATAATATATTTAATAATAATATATCTACA
2522481 TTTTTACTAT
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
56 4 0.09
57 30 0.64
58 8 0.17
59 5 0.11
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.46
Consensus pattern (59 bp):
TATTAGTATTTTAAAATAATTAAAATAATATATTTAATAATAATATATCTACAATAATT
Found at i:2522504 original size:21 final size:21
Alignment explanation
Indices: 2522480--2522520 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2522470 AATTTATTAC
*
2522480 ATTTTTACTATTA-AAAAATAT
1 ATTTTAAC-ATTATAAAAATAT
2522501 ATTTTAACATTATAAAAATA
1 ATTTTAACATTATAAAAATA
2522521 GAAACCCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (21 bp):
ATTTTAACATTATAAAAATAT
Found at i:2524440 original size:15 final size:16
Alignment explanation
Indices: 2524420--2524453 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2524410 TAAATTGATA
*
2524420 TATTA-TTTTATTATT
1 TATTATTTTTATAATT
2524435 TATTATTTTTATAATT
1 TATTATTTTTATAATT
2524451 TAT
1 TAT
2524454 ACACTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TATTATTTTTATAATT
Found at i:2528757 original size:20 final size:22
Alignment explanation
Indices: 2528722--2528765 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
2528712 AATAATTTGT
*
2528722 TACATTTTTACTATTA-AAAAA
1 TACATTTTAACTATTATAAAAA
2528743 TACATTTTAAC-ATTATAAAAA
1 TACATTTTAACTATTATAAAAA
2528764 TA
1 TA
2528766 AAAACCCTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (22 bp):
TACATTTTAACTATTATAAAAA
Found at i:2531051 original size:167 final size:169
Alignment explanation
Indices: 2530773--2531108 Score: 649
Period size: 167 Copynumber: 2.0 Consensus size: 169
2530763 TCGTCTAATT
*
2530773 TGATACGGCCAAATTTATTATAAAAGCCTTGATTAATTTTTAAAAAATACTTTATAAAAGTAGGT
1 TGATACGGCAAAATTTATTATAAAAGCCTTGATTAATTTTTAAAAAATACTTTATAAAAGTAGGT
2530838 CTCCTAATTTCGGGTTGATTATGATTAAATTAACATAAGAGAGTACATGTCATTATCAACATTAA
66 CTCCTAATTTCGGGTTGATTATGATTAAATTAACATAAGAGAGTACATGTCATTATCAACATTAA
2530903 ATATTTTTTACTTCCTATTCTTTGAGGTTAATTTTTTTA
131 ATATTTTTTACTTCCTATTCTTTGAGGTTAATTTTTTTA
2530942 TGATACGGCAAAATTTA-TAT-AAAGCCTTGATTAATTTTTAAAAAATACTTTATAAAAGTAGGT
1 TGATACGGCAAAATTTATTATAAAAGCCTTGATTAATTTTTAAAAAATACTTTATAAAAGTAGGT
2531005 CTCCTAATTTCGGGTTGATTATGATTAAATTAACATAAGAGAGTACATGTCATTATCAACATTAA
66 CTCCTAATTTCGGGTTGATTATGATTAAATTAACATAAGAGAGTACATGTCATTATCAACATTAA
2531070 ATATTTTTTACTTCCTATTCTTTGAGGTTAATTTTTTTA
131 ATATTTTTTACTTCCTATTCTTTGAGGTTAATTTTTTTA
2531109 CATTAGTGCA
Statistics
Matches: 166, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
167 147 0.89
168 3 0.02
169 16 0.10
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.42
Consensus pattern (169 bp):
TGATACGGCAAAATTTATTATAAAAGCCTTGATTAATTTTTAAAAAATACTTTATAAAAGTAGGT
CTCCTAATTTCGGGTTGATTATGATTAAATTAACATAAGAGAGTACATGTCATTATCAACATTAA
ATATTTTTTACTTCCTATTCTTTGAGGTTAATTTTTTTA
Found at i:2531608 original size:26 final size:26
Alignment explanation
Indices: 2531552--2531600 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
2531542 ATGTCACTTA
*
2531552 TAAAATGATTTATCAGTATACAAAAG
1 TAAAATGATTTATCAGAATACAAAAG
2531578 TAAAATAGATTT-TCAGAAT-CAAA
1 TAAAAT-GATTTATCAGAATACAAA
2531601 TATTAAAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 4 0.19
26 12 0.57
27 5 0.24
ACGTcount: A:0.51, C:0.08, G:0.10, T:0.31
Consensus pattern (26 bp):
TAAAATGATTTATCAGAATACAAAAG
Found at i:2532250 original size:24 final size:24
Alignment explanation
Indices: 2532223--2532320 Score: 72
Period size: 24 Copynumber: 4.1 Consensus size: 24
2532213 TATATCAAAA
* *
2532223 ATCAAAACATAATCCAGTTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* *
2532247 ATCATATCAAAATCCAGGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* * *
2532271 ATTC-GATCAGAATCCAGGTCAAGT
1 A-TCAAAACAAAATCCAGGTCAAGT
* * * * *
2532295 ATCCAATCAGAATCCAAGTCAGGT
1 ATCAAAACAAAATCCAGGTCAAGT
2532319 AT
1 AT
2532321 TATAATATAA
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
23 2 0.03
24 59 0.94
25 2 0.03
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.24
Consensus pattern (24 bp):
ATCAAAACAAAATCCAGGTCAAGT
Found at i:2556114 original size:2 final size:2
Alignment explanation
Indices: 2556109--2556148 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
2556099 AAAAATACGA
2556109 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2556149 ATTATTAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2559492 original size:44 final size:44
Alignment explanation
Indices: 2559423--2559590 Score: 232
Period size: 44 Copynumber: 3.8 Consensus size: 44
2559413 TATAAAATTT
* * *
2559423 CTTATCATTTATTCGATAAGATCGTAAGCTTATTTATCAATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTATCAATATA
*
2559467 CTTACCATTTGTTCCATAAGCTCGTAAGCTTATTT-TACAAATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTAT-C-AATATA
* *
2559512 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATG
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTA-TTTATCAATATA
*
2559557 CTTGCCA-TTATTCCATAAGCTCGTAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
2559591 GCATGCTCAC
Statistics
Matches: 112, Mismatches: 8, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
43 4 0.04
44 56 0.50
45 48 0.43
46 4 0.04
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.41
Consensus pattern (44 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTATCAATATA
Found at i:2559527 original size:45 final size:44
Alignment explanation
Indices: 2559423--2559590 Score: 241
Period size: 45 Copynumber: 3.8 Consensus size: 44
2559413 TATAAAATTT
* * *
2559423 CTTATCATTTATTCGATAAGATCGTAAGCTTA-TTTATCAATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTA-CAATATA
*
2559467 CTTACCATTTGTTCCATAAGCTCGTAAGCTTATTTTACAAATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC-AATATA
*
2559512 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATG
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTA-CAATATA
*
2559557 CTTGCCA-TTATTCCATAAGCTCGTAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
2559591 GCATGCTCAC
Statistics
Matches: 114, Mismatches: 7, Indels: 6
0.90 0.06 0.05
Matches are distributed among these distances:
44 56 0.49
45 57 0.50
46 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.41
Consensus pattern (44 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACAATATA
Found at i:2559545 original size:21 final size:21
Alignment explanation
Indices: 2559520--2559589 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 21
2559510 TACTTACCAT
2559520 TTATTCCATAAGCTCGTAAGC
1 TTATTCCATAAGCTCGTAAGC
* * **
2559541 TTATTTTACCAATATGCTTGCCA--
1 TTA--TT-CC-ATAAGCTCGTAAGC
2559564 TTATTCCATAAGCTCGTAAGC
1 TTATTCCATAAGCTCGTAAGC
2559585 TTATT
1 TTATT
2559590 TGCATGCTCA
Statistics
Matches: 35, Mismatches: 8, Indels: 12
0.64 0.15 0.22
Matches are distributed among these distances:
19 8 0.23
20 2 0.06
21 10 0.29
23 5 0.14
24 2 0.06
25 8 0.23
ACGTcount: A:0.27, C:0.21, G:0.11, T:0.40
Consensus pattern (21 bp):
TTATTCCATAAGCTCGTAAGC
Found at i:2559579 original size:89 final size:89
Alignment explanation
Indices: 2559423--2559590 Score: 257
Period size: 89 Copynumber: 1.9 Consensus size: 89
2559413 TATAAAATTT
* * * *
2559423 CTTATCATTTATTCGATAAGATCGTAAGCTTATTTATCAATATACTTACCATTTGTTCCATAAGC
1 CTTACCATTTATTCCATAAGATCGTAAGCTTATTTACCAATATACTTACCATTTATTCCATAAGC
2559488 TCGTAAGCTTATTTTACAAATATA
66 TCGTAAGCTTATTTTACAAATATA
* * *
2559512 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATGCTTGCCA-TTATTCCATAAG
1 CTTACCATTTATTCCATAAGATCGTAAGCTTA-TTTACCAATATACTTACCATTTATTCCATAAG
2559576 CTCGTAAGCTTATTT
65 CTCGTAAGCTTATTT
2559591 GCATGCTCAC
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
89 55 0.77
90 16 0.23
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.41
Consensus pattern (89 bp):
CTTACCATTTATTCCATAAGATCGTAAGCTTATTTACCAATATACTTACCATTTATTCCATAAGC
TCGTAAGCTTATTTTACAAATATA
Found at i:2559739 original size:40 final size:39
Alignment explanation
Indices: 2559695--2559816 Score: 172
Period size: 40 Copynumber: 3.1 Consensus size: 39
2559685 ACCGTAGTGC
* *
2559695 TACACATAATGTCGTGCCTACAATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCAC-ATATACACCGAAGTGTAT
* *
2559735 TACACATAAGGTCGTGCCCATCATATACTCCAAAGTGTAT
1 TACACATAAGGTCGTGCCCA-CATATACACCGAAGTGTAT
*
2559775 TACACATAAGGTCGTGCCCACCATATACATCGAAGTGTAT
1 TACACATAAGGTCGTGCCCA-CATATACACCGAAGTGTAT
2559815 TA
1 TA
2559817 TGAACCTGCA
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
40 72 0.99
41 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.27
Consensus pattern (39 bp):
TACACATAAGGTCGTGCCCACATATACACCGAAGTGTAT
Found at i:2573261 original size:162 final size:162
Alignment explanation
Indices: 2572994--2573313 Score: 640
Period size: 162 Copynumber: 2.0 Consensus size: 162
2572984 CAGTCTGTTG
2572994 TAAGTGGGATACTCTATTGTTTCAGTTTATTCAGTTTGTTTGCAGTGGAAGCACACACATGGTTT
1 TAAGTGGGATACTCTATTGTTTCAGTTTATTCAGTTTGTTTGCAGTGGAAGCACACACATGGTTT
2573059 TCAGTTCGGAAGTTAGGCAGAAATAACTTCCATCCCTTAAAACCCAAACATGACATGTAATTTAA
66 TCAGTTCGGAAGTTAGGCAGAAATAACTTCCATCCCTTAAAACCCAAACATGACATGTAATTTAA
2573124 TAAAATATAAGATTTAGTTATCACATGTAATT
131 TAAAATATAAGATTTAGTTATCACATGTAATT
2573156 TAAGTGGGATACTCTATTGTTTCAGTTTATTCAGTTTGTTTGCAGTGGAAGCACACACATGGTTT
1 TAAGTGGGATACTCTATTGTTTCAGTTTATTCAGTTTGTTTGCAGTGGAAGCACACACATGGTTT
2573221 TCAGTTCGGAAGTTAGGCAGAAATAACTTCCATCCCTTAAAACCCAAACATGACATGTAATTTAA
66 TCAGTTCGGAAGTTAGGCAGAAATAACTTCCATCCCTTAAAACCCAAACATGACATGTAATTTAA
2573286 TAAAATATAAGATTTAGTTATCACATGT
131 TAAAATATAAGATTTAGTTATCACATGT
2573314 TATGCAATTT
Statistics
Matches: 158, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
162 158 1.00
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (162 bp):
TAAGTGGGATACTCTATTGTTTCAGTTTATTCAGTTTGTTTGCAGTGGAAGCACACACATGGTTT
TCAGTTCGGAAGTTAGGCAGAAATAACTTCCATCCCTTAAAACCCAAACATGACATGTAATTTAA
TAAAATATAAGATTTAGTTATCACATGTAATT
Found at i:2577214 original size:3 final size:3
Alignment explanation
Indices: 2577206--2577268 Score: 69
Period size: 3 Copynumber: 21.7 Consensus size: 3
2577196 GTCATATTTC
* * *
2577206 ATT ATT ATT A-T ATT ATC ATT ATT ATT ACT ATT -TT -TT AAT ATTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT
2577249 ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT AT
2577269 ATTTATAGGG
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
2 6 0.12
3 43 0.84
4 2 0.04
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:2577535 original size:18 final size:18
Alignment explanation
Indices: 2577512--2577558 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
2577502 AGTTCTTCAA
2577512 CCGCCACGCGCCAAGCTG
1 CCGCCACGCGCCAAGCTG
*
2577530 CCGCCACACGCCAAGCTG
1 CCGCCACGCGCCAAGCTG
**
2577548 CTACCACGCGC
1 CCGCCACGCGC
2577559 TTCCCACGTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.19, C:0.51, G:0.23, T:0.06
Consensus pattern (18 bp):
CCGCCACGCGCCAAGCTG
Found at i:2584423 original size:23 final size:23
Alignment explanation
Indices: 2584393--2584514 Score: 190
Period size: 23 Copynumber: 5.3 Consensus size: 23
2584383 GTCGAGGGTC
2584393 CTATGTGGTCCTTTGGGACAAAA
1 CTATGTGGTCCTTTGGGACAAAA
* *
2584416 CTATGTGGTTCTTCGGGACAAAA
1 CTATGTGGTCCTTTGGGACAAAA
*
2584439 CTATGTGGTCCTTTAGGACAAAA
1 CTATGTGGTCCTTTGGGACAAAA
* *
2584462 CTATGTGGTCCTTTAGGACAAAC
1 CTATGTGGTCCTTTGGGACAAAA
*
2584485 CTATGTGGTCCTTCGGGACAAAA
1 CTATGTGGTCCTTTGGGACAAAA
2584508 CTATGTG
1 CTATGTG
2584515 CTCGTTCAAG
Statistics
Matches: 90, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 90 1.00
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (23 bp):
CTATGTGGTCCTTTGGGACAAAA
Found at i:2584460 original size:46 final size:46
Alignment explanation
Indices: 2584393--2584536 Score: 193
Period size: 46 Copynumber: 3.2 Consensus size: 46
2584383 GTCGAGGGTC
* *
2584393 CTATGTGGTCCTTTGGGACAAAACTATGTGGTTCTTCGGGACAAAA
1 CTATGTGGTCCTTTGGGACAAAACTATGTGGTCCTTCAGGACAAAA
* * *
2584439 CTATGTGGTCCTTTAGGACAAAACTATGTGGTCCTTTAGGACAAAC
1 CTATGTGGTCCTTTGGGACAAAACTATGTGGTCCTTCAGGACAAAA
* * * *
2584485 CTATGTGGTCCTTCGGGACAAAACTATGTGCTCGTTCAAGAC-AAA
1 CTATGTGGTCCTTTGGGACAAAACTATGTGGTCCTTCAGGACAAAA
2584530 -TATGTGG
1 CTATGTGG
2584537 CACTTCGATG
Statistics
Matches: 86, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
44 7 0.08
45 2 0.02
46 77 0.90
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (46 bp):
CTATGTGGTCCTTTGGGACAAAACTATGTGGTCCTTCAGGACAAAA
Found at i:2584527 original size:23 final size:23
Alignment explanation
Indices: 2584393--2584536 Score: 175
Period size: 23 Copynumber: 6.3 Consensus size: 23
2584383 GTCGAGGGTC
**
2584393 CTATGTGGTCCTTTGGGACAAAA
1 CTATGTGGTCCTTCAGGACAAAA
* *
2584416 CTATGTGGTTCTTCGGGACAAAA
1 CTATGTGGTCCTTCAGGACAAAA
*
2584439 CTATGTGGTCCTTTAGGACAAAA
1 CTATGTGGTCCTTCAGGACAAAA
* *
2584462 CTATGTGGTCCTTTAGGACAAAC
1 CTATGTGGTCCTTCAGGACAAAA
*
2584485 CTATGTGGTCCTTCGGGACAAAA
1 CTATGTGGTCCTTCAGGACAAAA
* * *
2584508 CTATGTGCTCGTTCAAGAC-AAA
1 CTATGTGGTCCTTCAGGACAAAA
2584530 -TATGTGG
1 CTATGTGG
2584537 CACTTCGATG
Statistics
Matches: 107, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
21 6 0.06
22 3 0.03
23 98 0.92
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (23 bp):
CTATGTGGTCCTTCAGGACAAAA
Found at i:2584528 original size:69 final size:68
Alignment explanation
Indices: 2584393--2584536 Score: 209
Period size: 69 Copynumber: 2.1 Consensus size: 68
2584383 GTCGAGGGTC
* * * * *
2584393 CTATGTGGTCCTTTGGGACAAAACTATGTGGTTCTTCGGGACAAAACTATGTGGTCCTTTAGGAC
1 CTATGTGGTCCTTTAGGACAAAACTATGTGGTCCTTCGGGACAAAACTATGTGCTCCTTCAAGAC
2584458 AAAA
66 -AAA
* *
2584462 CTATGTGGTCCTTTAGGACAAACCTATGTGGTCCTTCGGGACAAAACTATGTGCTCGTTCAAGAC
1 CTATGTGGTCCTTTAGGACAAAACTATGTGGTCCTTCGGGACAAAACTATGTGCTCCTTCAAGAC
2584527 AAA
66 AAA
2584530 -TATGTGG
1 CTATGTGG
2584537 CACTTCGATG
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
67 7 0.10
68 3 0.04
69 58 0.85
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (68 bp):
CTATGTGGTCCTTTAGGACAAAACTATGTGGTCCTTCGGGACAAAACTATGTGCTCCTTCAAGAC
AAA
Found at i:2587965 original size:19 final size:20
Alignment explanation
Indices: 2587928--2587966 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
2587918 TACACTTTTC
*
2587928 ATTCTATATTAATTTGTTTA
1 ATTCTATATTAATTGGTTTA
*
2587948 ATTC-ATATTCATTGGTTTA
1 ATTCTATATTAATTGGTTTA
2587967 TTTAGCCCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.56
Consensus pattern (20 bp):
ATTCTATATTAATTGGTTTA
Found at i:2588085 original size:24 final size:24
Alignment explanation
Indices: 2588061--2588158 Score: 110
Period size: 23 Copynumber: 4.2 Consensus size: 24
2588051 AATTGCAACG
* * *
2588061 TAGAATTTATCCAAAAGGACCACG
1 TAGAATTTGTCCAGAAGGACCACA
* *
2588085 TAGAATTTGTCCCGAAGGTCCACA
1 TAGAATTTGTCCAGAAGGACCACA
*
2588109 TAG-ATTTGTCCTGAAGGACCACA
1 TAGAATTTGTCCAGAAGGACCACA
* *
2588132 TAGAA-TTGTCCCGAAGGAACACA
1 TAGAATTTGTCCAGAAGGACCACA
2588155 TAGA
1 TAGA
2588159 TATGTCCCAA
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
23 41 0.64
24 23 0.36
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.22
Consensus pattern (24 bp):
TAGAATTTGTCCAGAAGGACCACA
Found at i:2588119 original size:23 final size:23
Alignment explanation
Indices: 2588075--2588181 Score: 124
Period size: 23 Copynumber: 4.6 Consensus size: 23
2588065 ATTTATCCAA
*
2588075 AAGGACCACGTAGAATTTGTCCCG
1 AAGGACCACATAG-ATTTGTCCCG
* *
2588099 AAGGTCCACATAGATTTGTCCTG
1 AAGGACCACATAGATTTGTCCCG
*
2588122 AAGGACCACATAGAATTGTCCCG
1 AAGGACCACATAGATTTGTCCCG
* * *
2588145 AAGGAACACATAGATATGTCCCA
1 AAGGACCACATAGATTTGTCCCG
* *
2588168 AAAGACCACGTAGA
1 AAGGACCACATAGA
2588182 ACCCTCGACT
Statistics
Matches: 70, Mismatches: 13, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
23 59 0.84
24 11 0.16
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.20
Consensus pattern (23 bp):
AAGGACCACATAGATTTGTCCCG
Found at i:2588175 original size:46 final size:47
Alignment explanation
Indices: 2588071--2588182 Score: 145
Period size: 46 Copynumber: 2.4 Consensus size: 47
2588061 TAGAATTTAT
** *
2588071 CCAAAAGGACCACGTAGAATTTGTCCCGAAGGTCCACATAGATTTGTC
1 CCAAAA-GACCACGTAGAATTTGTCCCGAAGGAACACATAGATATGTC
** * *
2588119 CTGAAGGACCACATAGAA-TTGTCCCGAAGGAACACATAGATATGTC
1 CCAAAAGACCACGTAGAATTTGTCCCGAAGGAACACATAGATATGTC
2588165 CCAAAAGACCACGTAGAA
1 CCAAAAGACCACGTAGAA
2588183 CCCTCGACTC
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
46 39 0.74
47 11 0.21
48 3 0.06
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.19
Consensus pattern (47 bp):
CCAAAAGACCACGTAGAATTTGTCCCGAAGGAACACATAGATATGTC
Found at i:2599647 original size:2 final size:2
Alignment explanation
Indices: 2599640--2599674 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2599630 GGCGATGATA
2599640 AT AT AT 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 AT AT AT A
2599675 CACACACAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2601832 original size:230 final size:229
Alignment explanation
Indices: 2601392--2601836 Score: 567
Period size: 230 Copynumber: 1.9 Consensus size: 229
2601382 AAGTTAAAAG
*
2601392 ATGAGAAACATTTCTCATTTAAATCTAAAATTGAAATATTTGAAAAGTAAGAAAAGTTTCTTATC
1 ATGAGAAACATTTCTCATTTAAATCTAAAATTGAAATATTTGAAAAGTAAGAAAAGTTTATTATC
* * * * *
2601457 TCGTAAACTATTTCCAAAATTGTTAAGTCATTCGGGGAATTAGTAAGTCTTTCGAGCATGATGGT
66 TAGTAAACTATTTCCAAAATTGATAAGTCATTCAGGCAATTAGTAAGTCTTTCGAGCATGATGCT
* * *
2601522 TAAATCCTTTGGGTCATCTGTAAGCCTTACGAGCAAGATGATAAGTCATTTGGGCAATCCATAAG
131 TAAATCCTTCGGGTCATCTATAAGCCTTACGAACAAGATGATAAGTCATTTGGGCAATCCATAAG
2601587 ACCTTTGGCCAGGATGTTTTCACATGTCTCTCAA
196 ACCTTTGGCCAGGATGTTTTCACATGTCTCTCAA
* * * *
2601621 ATGAGAAA-AGTTTTTCATTTAAATCTTAAAATTGAATTTTTTGAAAAGTAAGGAAAGTTTATTA
1 ATGAGAAACA-TTTCTCATTTAAATC-TAAAATTGAAATATTTGAAAAGTAAGAAAAGTTTATTA
* * * * * * * * * *
2601685 -CTTAGTAAACTA-TTCCCAATTTAGATATGTCCTTTAGTCCATTAGTAAGTCTTTTGATCATTA
64 TC-TAGTAAACTATTTCCAAAATT-GATAAGTCATTCAGGCAATTAGTAAGTCTTTCGAGCATGA
* *
2601748 TGCTTAAATCCTTCGGGTCATCTATAAGCCTTTCGAACAAGATGATAAGTC-TTTCGGGCCATCC
127 TGCTTAAATCCTTCGGGTCATCTATAAGCCTTACGAACAAGATGATAAGTCATTT-GGGCAATCC
*
2601812 ATAAGTCCTTTAGG-CAGGATGTTTT
191 ATAAGACCTTT-GGCCAGGATGTTTT
2601837 TGCATGCTTT
Statistics
Matches: 184, Mismatches: 26, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
228 1 0.01
229 34 0.18
230 147 0.80
231 2 0.01
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (229 bp):
ATGAGAAACATTTCTCATTTAAATCTAAAATTGAAATATTTGAAAAGTAAGAAAAGTTTATTATC
TAGTAAACTATTTCCAAAATTGATAAGTCATTCAGGCAATTAGTAAGTCTTTCGAGCATGATGCT
TAAATCCTTCGGGTCATCTATAAGCCTTACGAACAAGATGATAAGTCATTTGGGCAATCCATAAG
ACCTTTGGCCAGGATGTTTTCACATGTCTCTCAA
Found at i:2602418 original size:132 final size:133
Alignment explanation
Indices: 2602215--2602573 Score: 451
Period size: 132 Copynumber: 2.7 Consensus size: 133
2602205 CGTATTTGAT
* * * * * *
2602215 TTTTCCCTTAATAAGAAGTGGAACATGTCCCT-TTTT-TA-ATTTGATATTCCCTGTGTAACAGT
1 TTTTCCCTCAAGAAGAAGTGAAACATATCCCTCTTTTCAAGATTTGATATTCCCTGAGTAACAGT
* * *
2602277 GGAACAAGTCTGCCTCGATTCAATCTTCCCTAAACAATAGTGGAATGAATCAACA-TCCT-AGAT
66 GGAACAAGTCTACCTCGATTCAATCTTCCCTAAACAATAATGGAATGAAT-AAAAGTCCTCAGAT
2602340 CTAA
130 CTAA
* * *
2602344 TTTTCCCTCAAGAAGAAGTGAAACAAATCCCTCTTTTCAAGATTTGATACTCCTTGAGTAACAGT
1 TTTTCCCTCAAGAAGAAGTGAAACATATCCCTCTTTTCAAGATTTGATATTCCCTGAGTAACAGT
* * * * *
2602409 GGAATAAGTCTACCTTGATTCAATCTTCCCTGAAGAATAATGGAGTGAATAAAAGTCCTCAGATC
66 GGAACAAGTCTACCTCGATTCAATCTTCCCTAAACAATAATGGAATGAATAAAAGTCCTCAGATC
*
2602474 TGA
131 TAA
** * *
2602477 TTTTCCCTCAAGAAGAA-CCATAACATATCCCTCTCTTTCAAGATTTGATATTCCGTGAGTGACA
1 TTTTCCCTCAAGAAGAAGTGA-AACATATCCCTCT-TTTCAAGATTTGATATTCCCTGAGTAACA
2602541 GTGGAACAAGTCTACCTCGATTCAATCTTCCCT
64 GTGGAACAAGTCTACCTCGATTCAATCTTCCCT
2602574 GAGGAACAAC
Statistics
Matches: 197, Mismatches: 26, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
129 27 0.14
130 4 0.02
131 4 0.02
132 69 0.35
133 36 0.18
134 57 0.29
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (133 bp):
TTTTCCCTCAAGAAGAAGTGAAACATATCCCTCTTTTCAAGATTTGATATTCCCTGAGTAACAGT
GGAACAAGTCTACCTCGATTCAATCTTCCCTAAACAATAATGGAATGAATAAAAGTCCTCAGATC
TAA
Found at i:2602608 original size:134 final size:132
Alignment explanation
Indices: 2602253--2602611 Score: 434
Period size: 134 Copynumber: 2.7 Consensus size: 132
2602243 CCCTTTTTTA
* * * * *
2602253 ATTTGATATTCCCTGTGTAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTAAACAATAGT
1 ATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTACCTCGATTCAATCTTCCCTGAAGAATAAT
* * * **
2602318 GGAATGAATCAACATCCTAGATCTAATTTTCCCTCAAGAAGAAGTGAAACAAATCCCTCTTTTCA
66 GGAATGAATCAACGTCCTCGATCTGATTTTCCCTCAAGAAGAAGCCAAACAAATCCCTCTTTTCA
2602383 AG
131 AG
* * * *
2602385 ATTTGATACTCCTTGAGTAACAGTGGAATAAGTCTACCTTGATTCAATCTTCCCTGAAGAATAAT
1 ATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTACCTCGATTCAATCTTCCCTGAAGAATAAT
* * * *
2602450 GGAGTGAATAAAAGTCCTCAGATCTGATTTTCCCTCAAGAAGAA-CCATAACATATCCCTCTCTT
66 GGAATGAATCAACGTCCTC-GATCTGATTTTCCCTCAAGAAGAAGCCA-AACAAATCCCTCT-TT
2602514 TCAAG
128 TCAAG
* * * * *
2602519 ATTTGATATTCCGTGAGTGACAGTGGAACAAGTCTACCTCGATTCAATCTTCCCTGAGGAACAAC
1 ATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTACCTCGATTCAATCTTCCCTGAAGAATAAT
* *
2602584 GGAAT-AAGTCGACGTTTCTCGATCTGAT
66 GGAATGAA-TCAACG-TCCTCGATCTGAT
2602612 CTACCGGAGA
Statistics
Matches: 191, Mismatches: 31, Indels: 8
0.83 0.13 0.03
Matches are distributed among these distances:
132 71 0.37
133 37 0.19
134 79 0.41
135 4 0.02
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (132 bp):
ATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTACCTCGATTCAATCTTCCCTGAAGAATAAT
GGAATGAATCAACGTCCTCGATCTGATTTTCCCTCAAGAAGAAGCCAAACAAATCCCTCTTTTCA
AG
Found at i:2602782 original size:3 final size:3
Alignment explanation
Indices: 2602774--2602850 Score: 102
Period size: 3 Copynumber: 25.7 Consensus size: 3
2602764 TCATAATTTT
** **
2602774 TTA TTA TTA -TA TTA CCA TTA TTA TTA CCA TTTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
2602819 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2602851 TTCAGGGTAC
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
2 2 0.03
3 61 0.95
4 1 0.02
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:2604555 original size:2 final size:2
Alignment explanation
Indices: 2604548--2604577 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2604538 AGTATTTTTA
2604548 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2604578 GTTAAATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2606633 original size:29 final size:29
Alignment explanation
Indices: 2606577--2606633 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
2606567 TGGTTAAATT
* *
2606577 TTAATTTGACCTCTGAATTTAGACAAAAA
1 TTAATTTGACCTCTAAATTTACACAAAAA
*
2606606 TTAATTTGACCT-TAAAATTTACATAAAA
1 TTAATTTGACCTCT-AAATTTACACAAAA
2606634 TACTAATCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 1 0.04
29 23 0.96
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (29 bp):
TTAATTTGACCTCTAAATTTACACAAAAA
Found at i:2608213 original size:23 final size:23
Alignment explanation
Indices: 2608169--2608226 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
2608159 AATTTTAATC
*
2608169 AAAATATTAATTATTAAAATTTTT
1 AAAATA-TAATTATTAAAATTTCT
* * *
2608193 AAAATATATTTATTCATATTTCT
1 AAAATATAATTATTAAAATTTCT
2608216 AATAATATAAT
1 AA-AATATAAT
2608227 ATAATATTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
23 15 0.54
24 13 0.46
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (23 bp):
AAAATATAATTATTAAAATTTCT
Found at i:2608233 original size:22 final size:22
Alignment explanation
Indices: 2608208--2608254 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
2608198 ATATTTATTC
*
2608208 ATATTTCT-AATAATATAATATA
1 ATATTT-TGAATAATATAATAAA
*
2608230 ATATTTTGAATATTATAATAAA
1 ATATTTTGAATAATATAATAAA
2608252 ATA
1 ATA
2608255 ATCAATTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (22 bp):
ATATTTTGAATAATATAATAAA
Found at i:2608424 original size:27 final size:27
Alignment explanation
Indices: 2608345--2608429 Score: 91
Period size: 27 Copynumber: 3.1 Consensus size: 27
2608335 AATAAAATTT
* *
2608345 ATATTATTTATA-ATTTCATAGAAATA
1 ATATTATTTATATATTTAATATAAATA
* * * *
2608371 ATATTATTTAAATATTAAAAATGAATA
1 ATATTATTTATATATTTAATATAAATA
2608398 ATATTATTTATATATTTAATATTAATATA
1 ATATTATTTATATATTTAATA-TAA-ATA
2608427 ATA
1 ATA
2608430 ATATAATAAT
Statistics
Matches: 46, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
26 11 0.24
27 27 0.59
28 2 0.04
29 6 0.13
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.47
Consensus pattern (27 bp):
ATATTATTTATATATTTAATATAAATA
Found at i:2608593 original size:28 final size:30
Alignment explanation
Indices: 2608526--2608607 Score: 87
Period size: 28 Copynumber: 2.7 Consensus size: 30
2608516 AATATAATTT
*
2608526 ATAATATTTTTATTTCAATAAAATATACCAATA
1 ATAATATTTTTA-TT-AATAAATTATA-CAATA
*
2608559 TTAATATTTTTATTAATAAATTATA-AA-A
1 ATAATATTTTTATTAATAAATTATACAATA
* *
2608587 ATAATATTTTAAATAATAAAT
1 ATAATATTTTTATTAATAAAT
2608608 AAATTATTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
28 19 0.43
29 2 0.05
31 10 0.23
32 2 0.05
33 11 0.25
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (30 bp):
ATAATATTTTTATTAATAAATTATACAATA
Found at i:2608633 original size:20 final size:21
Alignment explanation
Indices: 2608575--2608633 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
2608565 TTTTTATTAA
* * *
2608575 TAAATTATAAAAATAATATTT
1 TAAATAATAATAATATTATTT
2608596 TAAATAATAAATAA-ATTATTT
1 TAAATAAT-AATAATATTATTT
2608617 TAAA-AATAATAATATTA
1 TAAATAATAATAATATTA
2608634 ACTTTTATGA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
19 5 0.15
20 7 0.21
21 17 0.52
22 4 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TAAATAATAATAATATTATTT
Found at i:2608702 original size:14 final size:14
Alignment explanation
Indices: 2608680--2608714 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
2608670 CAAACATCGT
*
2608680 AAAACGTTTTCCAG
1 AAAATGTTTTCCAG
*
2608694 AAAATGTTTTTCAG
1 AAAATGTTTTCCAG
2608708 AAAATGT
1 AAAATGT
2608715 AATTCATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.34
Consensus pattern (14 bp):
AAAATGTTTTCCAG
Found at i:2625451 original size:8 final size:7
Alignment explanation
Indices: 2625437--2625490 Score: 54
Period size: 8 Copynumber: 7.1 Consensus size: 7
2625427 ATTACACCTG
2625437 AAGAAAA
1 AAGAAAA
2625444 ATAGAAAA
1 A-AGAAAA
*
2625452 AGATAAAA
1 A-AGAAAA
2625460 AAGATAAA
1 AAGA-AAA
*
2625468 AAGATAA
1 AAGAAAA
2625475 AAGAAAA
1 AAGAAAA
2625482 AATGAAAA
1 AA-GAAAA
2625490 A
1 A
2625491 TGAATTAAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
7 13 0.33
8 26 0.67
ACGTcount: A:0.78, C:0.00, G:0.13, T:0.09
Consensus pattern (7 bp):
AAGAAAA
Found at i:2625460 original size:9 final size:9
Alignment explanation
Indices: 2625448--2625476 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
2625438 AGAAAAATAG
2625448 AAAAAGATA
1 AAAAAGATA
2625457 AAAAAGAT-
1 AAAAAGATA
2625465 AAAAAGATA
1 AAAAAGATA
2625474 AAA
1 AAA
2625477 GAAAAAATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.79, C:0.00, G:0.10, T:0.10
Consensus pattern (9 bp):
AAAAAGATA
Found at i:2627115 original size:3 final size:3
Alignment explanation
Indices: 2627107--2627253 Score: 80
Period size: 3 Copynumber: 45.7 Consensus size: 3
2627097 CTGGAACCTG
* *
2627107 TTA TTA TTA TTGG TTA TTA TTGG TTA TTA TTA TTA TTA TTA TTTA TTAA
1 TTA TTA TTA TT-A TTA TTA TT-A TTA TTA TTA TTA TTA TTA -TTA TT-A
* * * ** * *
2627156 TGA -TA TTA TTA ATA TATA TTAA TTA TTA TTA TCA TTAA TCG TTG TCA
1 TTA TTA TTA TTA TTA T-TA TT-A TTA TTA TTA TTA TT-A TTA TTA TTA
* * *
2627203 TTA TTTA TTA TTA CTTA TTG TTA TTAA TTG TTAA TTA TTC TTA TTA TTA
1 TTA -TTA TTA TTA -TTA TTA TTA TT-A TTA TT-A TTA TTA TTA TTA TTA
2627252 TT
1 TT
2627254 TAAAATACTA
Statistics
Matches: 110, Mismatches: 22, Indels: 24
0.71 0.14 0.15
Matches are distributed among these distances:
2 1 0.01
3 81 0.74
4 28 0.25
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:2627152 original size:10 final size:10
Alignment explanation
Indices: 2627110--2627253 Score: 60
Period size: 10 Copynumber: 13.8 Consensus size: 10
2627100 GAACCTGTTA
**
2627110 TTATTATTGG
1 TTATTATTAT
**
2627120 TTATTATTGG
1 TTATTATTAT
2627130 TTATTATTA-
1 TTATTATTAT
2627139 TTATTATTAT
1 TTATTATTAT
*
2627149 TTATTAATGAT
1 TTATT-ATTAT
2627160 ATTATTAATATAT
1 -TTATT-AT-TAT
2627173 ATTAATTATTA-
1 -TT-ATTATTAT
*
2627184 TTATCATTAAT
1 TTATTATT-AT
* *
2627195 CGTTGTCATTAT
1 --TTATTATTAT
*
2627207 TTATTATTAC
1 TTATTATTAT
*
2627217 TTATTGTTAT
1 TTATTATTAT
* * *
2627227 TAATTGTTAA
1 TTATTATTAT
*
2627237 TTATTCTTA-
1 TTATTATTAT
2627246 TTATTATT
1 TTATTATT
2627254 TAAAATACTA
Statistics
Matches: 110, Mismatches: 15, Indels: 19
0.76 0.10 0.13
Matches are distributed among these distances:
9 21 0.19
10 56 0.51
11 4 0.04
12 12 0.11
13 14 0.13
14 3 0.03
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.60
Consensus pattern (10 bp):
TTATTATTAT
Found at i:2627152 original size:29 final size:28
Alignment explanation
Indices: 2627107--2627185 Score: 86
Period size: 29 Copynumber: 2.8 Consensus size: 28
2627097 CTGGAACCTG
** *
2627107 TTATTATTATTGGTTATTATTGGTTATTA
1 TTATTATTATTAATTATTATT-GATATTA
* *
2627136 TTATTATTATTATTTATTAATGATATTA
1 TTATTATTATTAATTATTATTGATATTA
*
2627164 TTAATATATATTAATTATTATT
1 TTATTAT-TATTAATTATTATT
2627186 ATCATTAATC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
28 12 0.29
29 30 0.71
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (28 bp):
TTATTATTATTAATTATTATTGATATTA
Found at i:2627626 original size:17 final size:17
Alignment explanation
Indices: 2627585--2627626 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
2627575 CAGTAGGAAA
*
2627585 AATAACCCAAATCAGTT
1 AATAAACCAAATCAGTT
*
2627602 AATCAACCAAATCAGTCT
1 AATAAACCAAATCAGT-T
2627620 AA-AAACC
1 AATAAACC
2627627 CAATAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.50, C:0.26, G:0.05, T:0.19
Consensus pattern (17 bp):
AATAAACCAAATCAGTT
Done.