Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007984.1 Hibiscus syriacus cultivar Beakdansim tig00110429_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: 12923621
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 65
Found at i:2714964 original size:15 final size:15
Alignment explanation
Indices: 2714944--2714976 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2714934 GGTTATTTTG
*
2714944 ATTAAAAATTAAAAT
1 ATTAAAAACTAAAAT
2714959 ATTAAAAACTAAAAT
1 ATTAAAAACTAAAAT
2714974 ATT
1 ATT
2714977 CCTAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (15 bp):
ATTAAAAACTAAAAT
Found at i:2715375 original size:21 final size:22
Alignment explanation
Indices: 2715349--2715395 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
2715339 TATATAAAAT
*
2715349 TAAAATTACATCATTTCCAC-G
1 TAAAATTACATCATTTACACAG
2715370 TAAAATTACATCATTTACACAG
1 TAAAATTACATCATTTACACAG
2715392 TAAA
1 TAAA
2715396 TATATAAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 19 0.79
22 5 0.21
ACGTcount: A:0.45, C:0.19, G:0.04, T:0.32
Consensus pattern (22 bp):
TAAAATTACATCATTTACACAG
Found at i:2715477 original size:30 final size:31
Alignment explanation
Indices: 2715433--2715509 Score: 120
Period size: 30 Copynumber: 2.5 Consensus size: 31
2715423 AAAGAAAACA
*
2715433 TAAGTTTTGGTCACTTACGTTATTG-TTTAT
1 TAAGTTTTGGTCACTTACGTTATAGTTTTAT
* *
2715463 TAAGTTATGTTCACTTACGTTATAGTTTTAT
1 TAAGTTTTGGTCACTTACGTTATAGTTTTAT
2715494 TAAGTTTTGGTCACTT
1 TAAGTTTTGGTCACTT
2715510 GGATGTAGTA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 22 0.54
31 19 0.46
ACGTcount: A:0.22, C:0.10, G:0.16, T:0.52
Consensus pattern (31 bp):
TAAGTTTTGGTCACTTACGTTATAGTTTTAT
Found at i:2715484 original size:15 final size:15
Alignment explanation
Indices: 2715443--2715485 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
2715433 TAAGTTTTGG
2715443 TCACTTACGTTATTGT
1 TCACTTACGTTA-TGT
* *
2715459 TTA-TTAAGTTATGT
1 TCACTTACGTTATGT
2715473 TCACTTACGTTAT
1 TCACTTACGTTAT
2715486 AGTTTTATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
14 5 0.23
15 15 0.68
16 2 0.09
ACGTcount: A:0.23, C:0.14, G:0.12, T:0.51
Consensus pattern (15 bp):
TCACTTACGTTATGT
Found at i:2716937 original size:31 final size:31
Alignment explanation
Indices: 2716827--2716936 Score: 148
Period size: 31 Copynumber: 3.5 Consensus size: 31
2716817 TTCATCGTTC
*
2716827 AAGTGACCAAAACTTAACAAAACGATAATGT
1 AAGTGACCAAAACTTAACAAAACGATAACGT
*
2716858 AAGTGATCAAAACTTAACAAAACGATAACGT
1 AAGTGACCAAAACTTAACAAAACGATAACGT
* * * **
2716889 AAGTGTCTAAAACTTAATAAAATAATAACGT
1 AAGTGACCAAAACTTAACAAAACGATAACGT
*
2716920 AAGTGACCAAAAATTAA
1 AAGTGACCAAAACTTAA
2716937 TCCATGCTTT
Statistics
Matches: 68, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 68 1.00
ACGTcount: A:0.53, C:0.14, G:0.12, T:0.22
Consensus pattern (31 bp):
AAGTGACCAAAACTTAACAAAACGATAACGT
Found at i:2717465 original size:22 final size:22
Alignment explanation
Indices: 2717428--2717483 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
2717418 TAATAAATTT
*
2717428 AAAT-ATTAATTA-TTATAATA
1 AAATAATTAAATATTTATAATA
* *
2717448 AAATAATTAAATATTTATTATC
1 AAATAATTAAATATTTATAATA
2717470 AAATAATTAAATAT
1 AAATAATTAAATAT
2717484 ATACTATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 4 0.13
21 7 0.23
22 20 0.65
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
AAATAATTAAATATTTATAATA
Found at i:2717467 original size:28 final size:26
Alignment explanation
Indices: 2717409--2717468 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 26
2717399 TTATTAAAGA
2717409 AATTATTATTAATAAATTTAAATATT
1 AATTATTATTAATAAATTTAAATATT
2717435 AATTATTA-TAATAAAATAATTAAATATT
1 AATTATTATTAAT-AAAT--TTAAATATT
*
2717463 TATTAT
1 AATTAT
2717469 CAAATAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 4 0.13
26 12 0.40
28 14 0.47
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
AATTATTATTAATAAATTTAAATATT
Found at i:2724525 original size:22 final size:22
Alignment explanation
Indices: 2724500--2724544 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
2724490 GTCGGGTAAC
*
2724500 TCAACAAACCAACA-CCATATAG
1 TCAACAAAACAACATCCA-ATAG
2724522 TCAACAAAACAACATCCAATAG
1 TCAACAAAACAACATCCAATAG
2724544 T
1 T
2724545 TGGGGGATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.51, C:0.29, G:0.04, T:0.16
Consensus pattern (22 bp):
TCAACAAAACAACATCCAATAG
Found at i:2726311 original size:23 final size:23
Alignment explanation
Indices: 2726255--2726307 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
2726245 AACAGAATTG
2726255 GAAGATAATATTATTCATCATTA
1 GAAGATAATATTATTCATCATTA
* *
2726278 GAAGATAATATTATTTATCTTTA
1 GAAGATAATATTATTCATCATTA
2726301 GAA-ATAA
1 GAAGATAA
2726308 ATATAAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
22 4 0.14
23 24 0.86
ACGTcount: A:0.45, C:0.06, G:0.09, T:0.40
Consensus pattern (23 bp):
GAAGATAATATTATTCATCATTA
Found at i:2726318 original size:23 final size:23
Alignment explanation
Indices: 2726255--2726318 Score: 60
Period size: 23 Copynumber: 2.8 Consensus size: 23
2726245 AACAGAATTG
* *
2726255 GAAGATAATAT-TATTCATCATTA
1 GAAGATAATATAAATT-ATCTTTA
* *
2726278 GAAGATAATATTATTTATCTTTA
1 GAAGATAATATAAATTATCTTTA
2726301 GAA-ATAAATATAAATTAT
1 GAAGAT-AATATAAATTAT
2726319 GAGACTTCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
22 2 0.06
23 30 0.88
24 2 0.06
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.41
Consensus pattern (23 bp):
GAAGATAATATAAATTATCTTTA
Found at i:2728173 original size:2 final size:2
Alignment explanation
Indices: 2728168--2728192 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2728158 TATAAACATC
2728168 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
2728193 CGATTCGGTC
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2728532 original size:13 final size:13
Alignment explanation
Indices: 2728516--2728542 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2728506 ATAACTCAAA
2728516 TATTTAACTTAAT
1 TATTTAACTTAAT
2728529 TATTTAACTTAAT
1 TATTTAACTTAAT
2728542 T
1 T
2728543 TTAGATAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (13 bp):
TATTTAACTTAAT
Found at i:2730290 original size:19 final size:19
Alignment explanation
Indices: 2730261--2730305 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
2730251 CTTTCCTAAA
*
2730261 ATTTT-AAAA-TTATCATAT
1 ATTTTAAAAATTTAT-ATAC
2730279 ATTTTAAAAATTTATATAC
1 ATTTTAAAAATTTATATAC
2730298 ATTTTAAA
1 ATTTTAAA
2730306 TCTTTTTTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 5 0.21
19 15 0.62
20 4 0.17
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTTTAAAAATTTATATAC
Found at i:2735441 original size:4 final size:4
Alignment explanation
Indices: 2735432--2735588 Score: 106
Period size: 4 Copynumber: 37.2 Consensus size: 4
2735422 ACACTCTTTC
* * *
2735432 AAAT AAAT AATT AAAAT AAAAT AAAT -ATT CAAAT AAACT AAAT AACT
1 AAAT AAAT AAAT -AAAT -AAAT AAAT AAAT -AAAT AAA-T AAAT AAAT
* * * *
2735479 AAAT AAAAT AAAT AAAT AAAT AATT GAATT AAAT AAAA AAAT -AAT CTAAT
1 AAAT -AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AAAT -AAAT
*
2735529 AAAA AAATT AAAAT AAA- AAACT AAAT AAAT AAAAT AAAT AAAT AACA-
1 AAAT AAA-T -AAAT AAAT AAA-T AAAT AAAT -AAAT AAAT AAAT AA-AT
2735576 AAAT AAAT AAAT A
1 AAAT AAAT AAAT A
2735589 CTCTTGGATT
Statistics
Matches: 125, Mismatches: 13, Indels: 30
0.74 0.08 0.18
Matches are distributed among these distances:
3 9 0.07
4 79 0.63
5 34 0.27
6 3 0.02
ACGTcount: A:0.71, C:0.04, G:0.01, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:2735465 original size:30 final size:31
Alignment explanation
Indices: 2735430--2735585 Score: 126
Period size: 30 Copynumber: 5.0 Consensus size: 31
2735420 TCACACTCTT
*
2735430 TCAAATAAAT-AATTAAAATAAAATAAATAT
1 TCAAATAAATAAATTAAAATAAAATAAATAA
*
2735460 TCAAATAAACTAAATAACTAAATAAAATAAATAAA
1 TCAAATAAA-TAAATTA--AAATAAAATAAAT-AA
* *
2735495 T-AAATAATTGAATT-AAATAAAA-AAATAA
1 TCAAATAAATAAATTAAAATAAAATAAATAA
* * *
2735523 TCTAATAAAAAAATTAAAATAAAA-AACTAAA
1 TCAAATAAATAAATTAAAATAAAATAAAT-AA
* *
2735554 T-AAATAAAATAAATAAATAACAAAATAAATAA
1 TCAAAT-AAATAAATTAA-AATAAAATAAATAA
2735586 ATACTCTTGG
Statistics
Matches: 100, Mismatches: 15, Indels: 20
0.74 0.11 0.15
Matches are distributed among these distances:
28 3 0.03
29 13 0.13
30 31 0.31
31 13 0.13
32 12 0.12
33 7 0.07
34 19 0.19
35 2 0.02
ACGTcount: A:0.70, C:0.04, G:0.01, T:0.25
Consensus pattern (31 bp):
TCAAATAAATAAATTAAAATAAAATAAATAA
Found at i:2735493 original size:17 final size:17
Alignment explanation
Indices: 2735432--2735588 Score: 122
Period size: 17 Copynumber: 8.8 Consensus size: 17
2735422 ACACTCTTTC
*
2735432 AAATAAATAATTAAAATA
1 AAATAAATAAAT-AAATA
*
2735450 AAATAAAT-ATTCAAATA
1 AAATAAATAAAT-AAATA
* *
2735467 AACTAAATAACTAAATA
1 AAATAAATAAATAAATA
2735484 AAATAAATAAATAAATA
1 AAATAAATAAATAAATA
*
2735501 ATTGAATTAAATAAAAAAATA
1 A---AA-TAAATAAATAAATA
*
2735522 ATCTAATAAAAAAATTAAAATA
1 A---AATAAATAAA-T-AAATA
*
2735544 AAA-AACTAAATAAATA
1 AAATAAATAAATAAATA
*
2735560 AAATAAATAAAT-AACA
1 AAATAAATAAATAAATA
2735576 AAATAAATAAATA
1 AAATAAATAAATA
2735589 CTCTTGGATT
Statistics
Matches: 116, Mismatches: 14, Indels: 19
0.78 0.09 0.13
Matches are distributed among these distances:
16 23 0.20
17 44 0.38
18 15 0.13
19 2 0.02
20 9 0.08
21 17 0.15
22 6 0.05
ACGTcount: A:0.71, C:0.04, G:0.01, T:0.25
Consensus pattern (17 bp):
AAATAAATAAATAAATA
Found at i:2735529 original size:29 final size:29
Alignment explanation
Indices: 2735478--2735588 Score: 118
Period size: 29 Copynumber: 3.8 Consensus size: 29
2735468 ACTAAATAAC
***
2735478 TAAATAAAATAAATAAATAAATAATTGAAT
1 TAAATAAAA-AAATAAATAAATAAAAAAAT
*
2735508 TAAATAAAAAAAT-AATCTAATAAAAAAAT
1 TAAATAAAAAAATAAAT-AAATAAAAAAAT
*
2735537 TAAAATAAAAAACTAAATAAATAAAATAAA-
1 T-AAATAAAAAAATAAATAAATAAAA-AAAT
*
2735567 TAAATAACAAAATAAATAAATA
1 TAAATAAAAAAATAAATAAATA
2735589 CTCTTGGATT
Statistics
Matches: 69, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
28 3 0.04
29 32 0.46
30 28 0.41
31 6 0.09
ACGTcount: A:0.72, C:0.03, G:0.01, T:0.24
Consensus pattern (29 bp):
TAAATAAAAAAATAAATAAATAAAAAAAT
Found at i:2765608 original size:53 final size:53
Alignment explanation
Indices: 2765538--2765656 Score: 202
Period size: 53 Copynumber: 2.2 Consensus size: 53
2765528 AATACTCCTA
*
2765538 AGCGTTAACTACAACCCTTGGTGTGTCAAACTGTTGTTGTAGGAATACCTCTC
1 AGCGTTAACTATAACCCTTGGTGTGTCAAACTGTTGTTGTAGGAATACCTCTC
* *
2765591 AGCGTTAACTATAACCCTTGGTGTGTCAAACTGTTGTTTTAGGAATACCTCTT
1 AGCGTTAACTATAACCCTTGGTGTGTCAAACTGTTGTTGTAGGAATACCTCTC
*
2765644 AGCGTAAACTATA
1 AGCGTTAACTATA
2765657 GGCGTTGTCT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 62 1.00
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (53 bp):
AGCGTTAACTATAACCCTTGGTGTGTCAAACTGTTGTTGTAGGAATACCTCTC
Found at i:2773553 original size:21 final size:21
Alignment explanation
Indices: 2773520--2773581 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
2773510 TGTATCAAGT
*
2773520 TCTTT-GTGGAGGCCATGAAA
1 TCTTTCGTCGAGGCCATGAAA
2773540 TCTTTCGTCGAGGCCATGAAA
1 TCTTTCGTCGAGGCCATGAAA
*
2773561 TATTTCGTCGAGGCCAT-AAA
1 TCTTTCGTCGAGGCCATGAAA
2773581 T
1 T
2773582 TCCTGCAATG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
20 9 0.23
21 30 0.77
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (21 bp):
TCTTTCGTCGAGGCCATGAAA
Found at i:2776218 original size:75 final size:75
Alignment explanation
Indices: 2776053--2776262 Score: 242
Period size: 75 Copynumber: 2.8 Consensus size: 75
2776043 CAAAGCCAAA
* * * * **
2776053 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCCTGAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGATT--CCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
2776118 TTTGGCTCAGAG
64 TTTGGCTCAGAG
* * *
2776130 ATTTCTAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACATTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
* * *
2776195 TTGTTCCGAG
66 TGGCTCAGAG
* * * *
2776205 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCCTA
1 AATTCCAGAATGCTCGGAGGGAACCGAT-TCCCCCATAGGAGGAACCGATTCCCCCCTA
2776263 TTCAACGGTC
Statistics
Matches: 114, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
75 84 0.74
76 6 0.05
77 24 0.21
ACGTcount: A:0.25, C:0.30, G:0.23, T:0.21
Consensus pattern (75 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
TGGCTCAGAG
Found at i:2784718 original size:75 final size:75
Alignment explanation
Indices: 2784533--2784738 Score: 245
Period size: 74 Copynumber: 2.7 Consensus size: 75
2784523 CAAAGCCAAA
* * * * **
2784533 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCCTGAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGA-TCCCCCCCATAGGAGGAACCGATT-CCCCCTAAACAG
*
2784598 TTTGGCTCTGAG
64 TTTGGCTCCGAG
* * *
2784610 ATTTCCAGAATGCTCGGAGGGAACCGAT-TCCCCCATAGGAGGAACCGATTCCCCCTAAACATTT
1 AATTCCAGAATGCTCGGAGGGAACCGATCCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
* *
2784674 TTGTTCCGAG
66 TGGCTCCGAG
* * *
2784684 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCC
1 AATTCCAGAATGCTCGGAGGGAACCGATCCCCCCCATAGGAGGAACCGATTCCCCC
2784739 CTATTCAACG
Statistics
Matches: 111, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
74 60 0.54
75 27 0.24
76 1 0.01
77 23 0.21
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.21
Consensus pattern (75 bp):
AATTCCAGAATGCTCGGAGGGAACCGATCCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
TGGCTCCGAG
Found at i:2787918 original size:21 final size:23
Alignment explanation
Indices: 2787889--2787930 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
2787879 GGGTACTAGG
2787889 TTTATAATT-TTTTATTTTTTTC
1 TTTATAATTATTTTATTTTTTTC
2787911 TTTA-AATTATTTTATTTTTT
1 TTTATAATTATTTTATTTTTT
2787931 AATATATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.76
Consensus pattern (23 bp):
TTTATAATTATTTTATTTTTTTC
Found at i:2787922 original size:17 final size:17
Alignment explanation
Indices: 2787900--2787932 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2787890 TTATAATTTT
2787900 TTATTTT-TTTCTTTAAA
1 TTATTTTATTT-TTTAAA
2787917 TTATTTTATTTTTTAA
1 TTATTTTATTTTTTAA
2787933 TATATATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (17 bp):
TTATTTTATTTTTTAAA
Found at i:2788003 original size:21 final size:22
Alignment explanation
Indices: 2787979--2788023 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
2787969 TATAATATAT
* *
2787979 AATTCACA-CATAAAATTTAAA
1 AATTCAAATCATAAAATTGAAA
*
2788000 AATTCAAATTATAAAATTGAAA
1 AATTCAAATCATAAAATTGAAA
2788022 AA
1 AA
2788024 AAATTATTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.60, C:0.09, G:0.02, T:0.29
Consensus pattern (22 bp):
AATTCAAATCATAAAATTGAAA
Found at i:2788141 original size:39 final size:39
Alignment explanation
Indices: 2788098--2788186 Score: 103
Period size: 39 Copynumber: 2.3 Consensus size: 39
2788088 TTTAAAAAAT
2788098 AATTTAGAATGTTAAT-GT-GAAATAATTTAAGAAATTTA-A
1 AATTTAGAATGTT-ATGGTAGAAA-AATTTAAGAAA-TTAGA
* * *
2788137 AATTTAGAATATTATGGTAGCAAAATTTAAGAAATTAGG
1 AATTTAGAATGTTATGGTAGAAAAATTTAAGAAATTAGA
2788176 AATTTAGAATG
1 AATTTAGAATG
2788187 CTAGAGTGAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
38 5 0.12
39 35 0.81
40 3 0.07
ACGTcount: A:0.47, C:0.01, G:0.16, T:0.36
Consensus pattern (39 bp):
AATTTAGAATGTTATGGTAGAAAAATTTAAGAAATTAGA
Found at i:2794818 original size:23 final size:22
Alignment explanation
Indices: 2794792--2794856 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
2794782 CCTTGGAGAG
*
2794792 AAGAAAAAAAGAAAAGAGAAGTT
1 AAGAAAAAAAGAAAAGAGAA-AT
*
2794815 AAG-AAAAGAGAAAA-AGAAAT
1 AAGAAAAAAAGAAAAGAGAAAT
* *
2794835 GAGAAGATAAAGAAAAGAGAAA
1 AAGAA-AAAAAGAAAAGAGAAA
2794857 ATGAGATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
20 3 0.09
21 5 0.15
22 18 0.53
23 8 0.24
ACGTcount: A:0.71, C:0.00, G:0.23, T:0.06
Consensus pattern (22 bp):
AAGAAAAAAAGAAAAGAGAAAT
Found at i:2794828 original size:28 final size:29
Alignment explanation
Indices: 2794792--2794857 Score: 98
Period size: 28 Copynumber: 2.3 Consensus size: 29
2794782 CCTTGGAGAG
* *
2794792 AAGAAAAAAAGAAAAGAGAAG-TTAAGAA
1 AAGAGAAAAAGAAAAGAGAAGATAAAGAA
*
2794820 AAGAGAAAAAGAAATGAGAAGATAAAGAA
1 AAGAGAAAAAGAAAAGAGAAGATAAAGAA
2794849 AAGAGAAAA
1 AAGAGAAAA
2794858 TGAGATAAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 19 0.56
29 15 0.44
ACGTcount: A:0.71, C:0.00, G:0.23, T:0.06
Consensus pattern (29 bp):
AAGAGAAAAAGAAAAGAGAAGATAAAGAA
Found at i:2794873 original size:29 final size:29
Alignment explanation
Indices: 2794792--2794876 Score: 86
Period size: 29 Copynumber: 3.0 Consensus size: 29
2794782 CCTTGGAGAG
* *
2794792 AAGAAAAAAAGAAA-AGAGAAG-TTAAGAA
1 AAGAGAAAAAGAAATA-AGAAGATAAAGAA
*
2794820 AAGAGAAAAAGAAATGAGAAGATAAAGAA
1 AAGAGAAAAAGAAATAAGAAGATAAAGAA
* *
2794849 AAGAGAAAATGAGATAAAGAA-ATAAAGA
1 AAGAGAAAAAGAAAT-AAGAAGATAAAGA
2794877 TAACTTTTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
28 18 0.38
29 26 0.54
30 4 0.08
ACGTcount: A:0.69, C:0.00, G:0.22, T:0.08
Consensus pattern (29 bp):
AAGAGAAAAAGAAATAAGAAGATAAAGAA
Found at i:2799709 original size:60 final size:60
Alignment explanation
Indices: 2799627--2799768 Score: 221
Period size: 60 Copynumber: 2.4 Consensus size: 60
2799617 TGAGTTCTTC
* * * * *
2799627 GACTATTAAAAATTATAAAATAATCTCTCGATTATAGGGTACTGTTTTATTGAGTCCCTT
1 GACTATTAGAAGTTATAAAATAATCTCTCGACTATAGGGTAATGCTTTATTGAGTCCCTT
* *
2799687 GACTATTAGAAGTTACAAAATAATCTTTCGACTATAGGGTAATGCTTTATTGAGTCCCTT
1 GACTATTAGAAGTTATAAAATAATCTCTCGACTATAGGGTAATGCTTTATTGAGTCCCTT
2799747 GACTATTAGAAGTTATAAAATA
1 GACTATTAGAAGTTATAAAATA
2799769 GTCACCTTAC
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 74 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (60 bp):
GACTATTAGAAGTTATAAAATAATCTCTCGACTATAGGGTAATGCTTTATTGAGTCCCTT
Found at i:2801912 original size:2 final size:2
Alignment explanation
Indices: 2801905--2801933 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2801895 TAGTCCTTTC
2801905 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2801934 CTGAATTGGA
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2807522 original size:2 final size:2
Alignment explanation
Indices: 2807515--2807563 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
2807505 ATATTAACAT
2807515 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
2807557 TA CA TA T
1 TA TA TA T
2807564 TAAAATATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2814477 original size:20 final size:20
Alignment explanation
Indices: 2814410--2814485 Score: 64
Period size: 20 Copynumber: 3.6 Consensus size: 20
2814400 CCCAGAGGGT
*
2814410 ATCGATTCCC-CTGTGGGCGGA
1 ATCGATTCCCTC-ATGGG-GGA
*
2814431 ATCGATTCCCCTTCAAAGGGGGA
1 ATCGATT-CCC-TC-ATGGGGGA
* *
2814454 ATCGGTTCCCTCATGGGGGT
1 ATCGATTCCCTCATGGGGGA
2814474 ATCGATTCCCTC
1 ATCGATTCCCTC
2814486 TGCACCAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
20 17 0.38
21 9 0.20
22 6 0.13
23 9 0.20
24 4 0.09
ACGTcount: A:0.17, C:0.29, G:0.28, T:0.26
Consensus pattern (20 bp):
ATCGATTCCCTCATGGGGGA
Found at i:2821259 original size:21 final size:22
Alignment explanation
Indices: 2821233--2821277 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
2821223 GAATGAAAAT
2821233 AGGGAATCG-GTACCCTGCTAC
1 AGGGAATCGAGTACCCTGCTAC
* *
2821254 AGGGAATCGATTCCCCTGCTAC
1 AGGGAATCGAGTACCCTGCTAC
2821276 AG
1 AG
2821278 TATTGCTACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.24, C:0.29, G:0.27, T:0.20
Consensus pattern (22 bp):
AGGGAATCGAGTACCCTGCTAC
Found at i:2821861 original size:24 final size:23
Alignment explanation
Indices: 2821837--2821922 Score: 72
Period size: 23 Copynumber: 3.7 Consensus size: 23
2821827 TCTTATAAAT
*
2821837 TTGCACCGAAGTGCCACATAGAA
1 TTGCACCGAAGTGCCACGTAGAA
* *
2821860 TTTGTC-CCAAAG-GACCGCGTAGAGA
1 -TTG-CACCGAAGTG-CCACGTAGA-A
2821885 -TGCACCGAAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
2821907 TTGCACCGTAA-TGCCA
1 TTGCACCG-AAGTGCCA
2821923 TATAATATGT
Statistics
Matches: 50, Mismatches: 5, Indels: 15
0.71 0.07 0.21
Matches are distributed among these distances:
22 2 0.04
23 28 0.56
24 18 0.36
25 2 0.04
ACGTcount: A:0.30, C:0.27, G:0.24, T:0.19
Consensus pattern (23 bp):
TTGCACCGAAGTGCCACGTAGAA
Found at i:2836638 original size:42 final size:42
Alignment explanation
Indices: 2836579--2836662 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
2836569 TCCATTTCTT
2836579 CCATTCGCGGTGTCTAACGTTCATTTTTGGGATTCTGAACTA
1 CCATTCGCGGTGTCTAACGTTCATTTTTGGGATTCTGAACTA
2836621 CCATTCGCGGTGTCTAACGTTCATTTTTGGGATTCTGAACTA
1 CCATTCGCGGTGTCTAACGTTCATTTTTGGGATTCTGAACTA
2836663 TTATACTACG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.38
Consensus pattern (42 bp):
CCATTCGCGGTGTCTAACGTTCATTTTTGGGATTCTGAACTA
Found at i:2845453 original size:31 final size:30
Alignment explanation
Indices: 2845407--2845492 Score: 93
Period size: 31 Copynumber: 2.8 Consensus size: 30
2845397 TTCGATAATA
* *
2845407 TAATAATTATTTTATAGTA-TTTAGGTAAATT
1 TAATAA-TATTTTATAATATTTTA-ATAAATT
*
2845438 TATTAATAATTTTATAATATTTTAATAAATT
1 TAATAAT-ATTTTATAATATTTTAATAAATT
*
2845469 TAATAAGTATTTTATAATTTTTTA
1 TAATAA-TATTTTATAATATTTTA
2845493 TATTTTATTG
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
30 1 0.02
31 41 0.87
32 5 0.11
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (30 bp):
TAATAATATTTTATAATATTTTAATAAATT
Found at i:2845455 original size:11 final size:10
Alignment explanation
Indices: 2845436--2845494 Score: 57
Period size: 10 Copynumber: 5.6 Consensus size: 10
2845426 TTTAGGTAAA
2845436 TTTATTAATAAT
1 TTTA-TAAT-AT
2845448 TTTATAATAT
1 TTTATAATAT
2845458 TTTAATAA-AT
1 TTT-ATAATAT
*
2845468 TTAATAAGTAT
1 TTTATAA-TAT
*
2845479 TTTATAATTT
1 TTTATAATAT
2845489 TTTATA
1 TTTATA
2845495 TTTTATTGAC
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
9 4 0.10
10 17 0.41
11 16 0.39
12 4 0.10
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (10 bp):
TTTATAATAT
Found at i:2845944 original size:15 final size:15
Alignment explanation
Indices: 2845924--2845953 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2845914 AAAAAATATA
*
2845924 TTATTTGTTTTTTAT
1 TTATTTATTTTTTAT
2845939 TTATTTATTTTTTAT
1 TTATTTATTTTTTAT
2845954 AAAGGGACTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (15 bp):
TTATTTATTTTTTAT
Found at i:2846258 original size:31 final size:31
Alignment explanation
Indices: 2846217--2846302 Score: 95
Period size: 31 Copynumber: 2.7 Consensus size: 31
2846207 CAATAAAATA
* *
2846217 TAAAAAATTATAAAATACTTATTAAATTTA-T
1 TAAAATATTATAAAATA-TTATTAAATTTACC
*
2846248 TAAAATATTATAAAATTATTAATAAATTTACC
1 TAAAATATTATAAAA-TATTATTAAATTTACC
*
2846280 T-AAATACTATAAAATAATTATTA
1 TAAAATATTATAAAAT-ATTATTA
2846303 TATTATCGAA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
30 1 0.02
31 43 0.91
32 3 0.06
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (31 bp):
TAAAATATTATAAAATATTATTAAATTTACC
Found at i:2847753 original size:10 final size:10
Alignment explanation
Indices: 2847735--2847779 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
2847725 TTTATTTTAA
*
2847735 AATTCTTATG
1 AATTTTTATG
2847745 AATTTTTATG
1 AATTTTTATG
*
2847755 TATTTTTAT-
1 AATTTTTATG
2847764 -ATTTTT-TG
1 AATTTTTATG
2847772 AATTTTTA
1 AATTTTTA
2847780 AAATCAAGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
7 1 0.03
8 6 0.20
9 6 0.20
10 17 0.57
ACGTcount: A:0.27, C:0.02, G:0.07, T:0.64
Consensus pattern (10 bp):
AATTTTTATG
Found at i:2847776 original size:17 final size:18
Alignment explanation
Indices: 2847746--2847779 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2847736 ATTCTTATGA
*
2847746 ATTTTTATGTATTTTTAT
1 ATTTTTATGAATTTTTAT
2847764 ATTTTT-TGAATTTTTA
1 ATTTTTATGAATTTTTA
2847780 AAATCAAGAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (18 bp):
ATTTTTATGAATTTTTAT
Found at i:2848059 original size:31 final size:30
Alignment explanation
Indices: 2847989--2848061 Score: 76
Period size: 31 Copynumber: 2.4 Consensus size: 30
2847979 ACATTCAAGT
* *
2847989 AATTTTGAAAATTTTATTTAAAATAATAAAA
1 AATTTT-AAAATTATATTTAAAATAACAAAA
**
2848020 AAACTTAAAATTATATTTAAAA-AACCCAAAA
1 AATTTTAAAATTATATTTAAAATAA--CAAAA
2848051 AATTTTAAAAT
1 AATTTTAAAAT
2848062 CTTAAAAAGA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
29 2 0.06
30 15 0.44
31 17 0.50
ACGTcount: A:0.58, C:0.05, G:0.01, T:0.36
Consensus pattern (30 bp):
AATTTTAAAATTATATTTAAAATAACAAAA
Found at i:2850407 original size:21 final size:22
Alignment explanation
Indices: 2850353--2850404 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 22
2850343 CTCAACGTAT
*
2850353 AATTATAAATTAGTTAAAAATTA
1 AATT-TAAATTAGTTAAAAATAA
*
2850376 AATTTAAATTA-TTTAAAATAA
1 AATTTAAATTAGTTAAAAATAA
2850397 AATATTAA
1 AAT-TTAA
2850405 TTACATTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 11 0.42
22 11 0.42
23 4 0.15
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
AATTTAAATTAGTTAAAAATAA
Found at i:2850994 original size:18 final size:18
Alignment explanation
Indices: 2850961--2850995 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2850951 CTTGATTTTT
* *
2850961 TTAAATTTTTTTAAATAA
1 TTAAATTTTATAAAATAA
2850979 TTAAATTTTATAAAATA
1 TTAAATTTTATAAAATA
2850996 TATATTTGAA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTAAATTTTATAAAATAA
Found at i:2854560 original size:15 final size:15
Alignment explanation
Indices: 2854540--2854571 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2854530 ATACAAAAAT
*
2854540 AAAAATAGAAGATAA
1 AAAAATAAAAGATAA
2854555 AAAAATAAAAGATAA
1 AAAAATAAAAGATAA
2854570 AA
1 AA
2854572 TGAAATATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.78, C:0.00, G:0.09, T:0.12
Consensus pattern (15 bp):
AAAAATAAAAGATAA
Found at i:2854623 original size:29 final size:29
Alignment explanation
Indices: 2854576--2854687 Score: 95
Period size: 29 Copynumber: 3.7 Consensus size: 29
2854566 ATAAAATGAA
*
2854576 ATATAAAATAATAATATATATAACAT-ATAAT
1 ATATATAATAA-AA-ATATATAA-ATAATAAT
2854607 -TATAGTAATAAAAATATATAAATAATAAT
1 ATATA-TAATAAAAATATATAAATAATAAT
*
2854636 ATATATAA-AAAGAATATATATATATATATAT
1 ATATATAATAAA-AATATATAAATA-ATA-AT
* *
2854667 ATATATATATATATATATATA
1 ATATATA-ATAAAAATATATA
2854688 TCGATAGAAT
Statistics
Matches: 69, Mismatches: 4, Indels: 15
0.78 0.05 0.17
Matches are distributed among these distances:
28 5 0.07
29 27 0.39
30 13 0.19
31 14 0.20
32 8 0.12
33 2 0.03
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (29 bp):
ATATATAATAAAAATATATAAATAATAAT
Found at i:2854623 original size:31 final size:30
Alignment explanation
Indices: 2854576--2854688 Score: 90
Period size: 31 Copynumber: 3.7 Consensus size: 30
2854566 ATAAAATGAA
* *
2854576 ATATAAAATAATAATATATATAACATATAAT
1 ATATATAATAAAAATATATATAACA-ATAAT
*
2854607 -TATAGTAATAAAAATATATA-AATAATAAT
1 ATATA-TAATAAAAATATATATAACAATAAT
*
2854636 ATATATAA-AAAGAATATATATATA-TATATAT
1 ATATATAATAAA-AATATATATA-ACAATA-AT
* *
2854667 ATATATATATATATATATATAT
1 ATATATA-ATAAAAATATATAT
2854689 CGATAGAATA
Statistics
Matches: 68, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
28 3 0.04
29 16 0.24
30 15 0.22
31 23 0.34
32 9 0.13
33 2 0.03
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (30 bp):
ATATATAATAAAAATATATATAACAATAAT
Found at i:2854630 original size:14 final size:14
Alignment explanation
Indices: 2854471--2854683 Score: 67
Period size: 14 Copynumber: 14.4 Consensus size: 14
2854461 ACAAAAACAA
2854471 ATATAAA-AAATATAT
1 ATATAAATAAA-A-AT
2854486 ATATAAAT-AAAAT
1 ATATAAATAAAAAT
* *
2854499 ACATAAAATAAAGAAG
1 ATAT-AAATAAA-AAT
*
2854515 ATAATAACAATAACAAT
1 AT-AT-A-AATAAAAAT
* *
2854532 ACAAAAATAAAAAT
1 ATATAAATAAAAAT
* * *
2854546 AGA-AGATAAAAAA
1 ATATAAATAAAAAT
* *
2854559 ATAAAAGATAAAATGAA
1 ATATAA-ATAAAA--AT
2854576 ATATAAAATAATAATAT
1 ATAT-AAATAA-AA-AT
* *
2854593 ATATAACATATAATT
1 ATATAA-ATAAAAAT
2854608 ATAGT-AATAAAAAT
1 ATA-TAAATAAAAAT
2854622 ATATAAATAATAATAT
1 ATATAAATAA-AA-AT
*
2854638 ATATAAA-AAGAAT
1 ATATAAATAAAAAT
* * *
2854651 ATATATATATATAT
1 ATATAAATAAAAAT
* * *
2854665 ATATATATATATAT
1 ATATAAATAAAAAT
2854679 ATATA
1 ATATA
2854684 TATATCGATA
Statistics
Matches: 155, Mismatches: 25, Indels: 37
0.71 0.12 0.17
Matches are distributed among these distances:
13 24 0.15
14 53 0.34
15 27 0.17
16 18 0.12
17 24 0.15
18 9 0.06
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (14 bp):
ATATAAATAAAAAT
Found at i:2854639 original size:2 final size:2
Alignment explanation
Indices: 2854620--2854688 Score: 81
Period size: 2 Copynumber: 36.0 Consensus size: 2
2854610 AGTAATAAAA
* * * *
2854620 AT AT AT AA AT A- AT A- AT AT AT AT AA AA AG A- 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
2854659 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
2854689 CGATAGAATA
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
1 3 0.05
2 57 0.95
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (2 bp):
AT
Found at i:2854709 original size:9 final size:9
Alignment explanation
Indices: 2854695--2854725 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
2854685 ATATCGATAG
*
2854695 AATATAGAA
1 AATATAAAA
2854704 AATATAAAA
1 AATATAAAA
2854713 AATATAAAA
1 AATATAAAA
2854722 AATA
1 AATA
2854726 GCCAAATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (9 bp):
AATATAAAA
Found at i:2868039 original size:16 final size:16
Alignment explanation
Indices: 2868018--2868083 Score: 57
Period size: 16 Copynumber: 4.1 Consensus size: 16
2868008 AGATAAAATG
2868018 AAATATATAAAATAAT
1 AAATATATAAAATAAT
*
2868034 AAATATATATAA-AAT
1 AAATATATAAAATAAT
*
2868049 ATAAT-TATAGTAATAA-
1 A-AATATATA-AAATAAT
*
2868065 AAATATATTTAAATAAT
1 AAATATA-TAAAATAAT
2868082 AA
1 AA
2868084 TGATATATGA
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
15 11 0.27
16 25 0.61
17 5 0.12
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (16 bp):
AAATATATAAAATAAT
Found at i:2868050 original size:9 final size:9
Alignment explanation
Indices: 2868018--2868051 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
2868008 AGATAAAATG
2868018 AAATATATA
1 AAATATATA
2868027 AAATA-ATA
1 AAATATATA
2868035 AATATATATA
1 AA-ATATATA
2868045 AAATATA
1 AAATATA
2868052 ATTATAGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 5 0.22
9 13 0.57
10 5 0.22
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
AAATATATA
Found at i:2868081 original size:19 final size:19
Alignment explanation
Indices: 2868029--2868083 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
2868019 AATATATAAA
2868029 ATAA-TAAATATATATAAAAT
1 ATAATTAAATA-ATA-AAAAT
*
2868049 ATAATTATAGTAATAAAAAT
1 ATAATTA-AATAATAAAAAT
*
2868069 ATATTTAAATAATAA
1 ATAATTAAATAATAA
2868084 TGATATATGA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 7 0.23
20 15 0.50
21 5 0.17
22 3 0.10
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (19 bp):
ATAATTAAATAATAAAAAT
Found at i:2868174 original size:2 final size:2
Alignment explanation
Indices: 2868167--2868195 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2868157 AAGATAATTA
2868167 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
2868196 ATAAGAATAA
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:2872498 original size:10 final size:10
Alignment explanation
Indices: 2872469--2872502 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
2872459 CTTGGGATAG
2872469 TAAGAAAGCT
1 TAAGAAAGCT
2872479 TAAGTAAAGCT
1 TAAG-AAAGCT
*
2872490 TAAGGAAGCT
1 TAAGAAAGCT
2872500 TAA
1 TAA
2872503 AACTCTAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.47, C:0.09, G:0.21, T:0.24
Consensus pattern (10 bp):
TAAGAAAGCT
Found at i:2875168 original size:27 final size:27
Alignment explanation
Indices: 2875110--2875182 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 27
2875100 TAGAGCTTGG
* * * * *
2875110 GGGTATTTTAGGCCATTTCACATTTTAG
1 GGGTATTTTA-GTCATTTCAAAGTTCAA
2875138 GGGTATTTTAGTCATTTCAAAGTTCAA
1 GGGTATTTTAGTCATTTCAAAGTTCAA
* *
2875165 GGGTATTTCAGTCCTTTC
1 GGGTATTTTAGTCATTTC
2875183 CTTTCGTCTA
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
27 28 0.74
28 10 0.26
ACGTcount: A:0.22, C:0.15, G:0.21, T:0.42
Consensus pattern (27 bp):
GGGTATTTTAGTCATTTCAAAGTTCAA
Found at i:2878816 original size:32 final size:32
Alignment explanation
Indices: 2878695--2878825 Score: 101
Period size: 32 Copynumber: 4.1 Consensus size: 32
2878685 AACCAACCTA
* * * *
2878695 AAGG-AATATCTTGGGGCCTGATAGCCTACCC
1 AAGGAAATACCTTGGAGCCTCAAAGCCTACCC
*
2878726 AAGGGAGA-ACCTTAGG-GCCT-AAGAGCCTACCC
1 AA-GGAAATACCTT-GGAGCCTCAA-AGCCTACCC
*
2878758 AAGGAAATACCTTGGAGCCTTAAAGCCTACCC
1 AAGGAAATACCTTGGAGCCTCAAAGCCTACCC
* * * *
2878790 AAGGAAATGA-TTTGGGGCCTCGAAGCCTATCC
1 AAGGAAAT-ACCTTGGAGCCTCAAAGCCTACCC
2878822 AAGG
1 AAGG
2878826 TCACCTTTGG
Statistics
Matches: 83, Mismatches: 9, Indels: 15
0.78 0.08 0.14
Matches are distributed among these distances:
31 9 0.11
32 68 0.82
33 6 0.07
ACGTcount: A:0.31, C:0.25, G:0.26, T:0.18
Consensus pattern (32 bp):
AAGGAAATACCTTGGAGCCTCAAAGCCTACCC
Found at i:2880550 original size:2 final size:2
Alignment explanation
Indices: 2880543--2880578 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2880533 TTCCCTTTTA
2880543 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
2880579 TGAAGTCTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2891629 original size:8 final size:8
Alignment explanation
Indices: 2891616--2891641 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
2891606 AAATTATGGG
2891616 AGACCAAA
1 AGACCAAA
2891624 AGACCAAA
1 AGACCAAA
2891632 AGACCAAA
1 AGACCAAA
2891640 AG
1 AG
2891642 CCTTACCTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.62, C:0.23, G:0.15, T:0.00
Consensus pattern (8 bp):
AGACCAAA
Found at i:2898582 original size:12 final size:13
Alignment explanation
Indices: 2898537--2898581 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
2898527 GTAATCCCCA
2898537 ACCCGATTACCCG
1 ACCCGATTACCCG
* *
2898550 TCCCGATTATCCG
1 ACCCGATTACCCG
*
2898563 GCCCGA-TACCCG
1 ACCCGATTACCCG
2898575 ACCCGAT
1 ACCCGAT
2898582 AAATATTAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.20, C:0.44, G:0.18, T:0.18
Consensus pattern (13 bp):
ACCCGATTACCCG
Found at i:2903729 original size:8 final size:7
Alignment explanation
Indices: 2903725--2903765 Score: 57
Period size: 8 Copynumber: 5.7 Consensus size: 7
2903715 AAAAAAAGGA
2903725 AAAAAAG
1 AAAAAAG
2903732 AGAAAAAG
1 A-AAAAAG
2903740 AACAAAAG
1 AA-AAAAG
2903748 AAAAAAG
1 AAAAAAG
2903755 -AAAAAG
1 AAAAAAG
2903761 AAAAA
1 AAAAA
2903766 TAAGGCGGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
6 6 0.19
7 11 0.35
8 14 0.45
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:2903746 original size:9 final size:8
Alignment explanation
Indices: 2903715--2903759 Score: 56
Period size: 8 Copynumber: 5.6 Consensus size: 8
2903705 CCTAAATTGA
2903715 AAAAAAAGG
1 AAAAAAA-G
2903724 AAAAAAAG
1 AAAAAAAG
*
2903732 AGAAAAAG
1 AAAAAAAG
*
2903740 AACAAAAG
1 AAAAAAAG
2903748 -AAAAAAG
1 AAAAAAAG
2903755 AAAAA
1 AAAAA
2903760 GAAAAATAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
7 6 0.19
8 18 0.58
9 7 0.23
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:2903746 original size:16 final size:15
Alignment explanation
Indices: 2903716--2903759 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 15
2903706 CTAAATTGAA
2903716 AAAAAAGGAAAAAAAG
1 AAAAAA-GAAAAAAAG
*
2903732 AGAAAAAGAACAAAAG
1 A-AAAAAGAAAAAAAG
2903748 AAAAAAGAAAAA
1 AAAAAAGAAAAA
2903760 GAAAAATAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 10 0.40
16 10 0.40
17 5 0.20
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAAAAAG
Found at i:2906865 original size:27 final size:26
Alignment explanation
Indices: 2906818--2906899 Score: 69
Period size: 27 Copynumber: 3.1 Consensus size: 26
2906808 CATACGTCTA
* *
2906818 TTATTTTA-TAAATTTTAATTATTTGAT
1 TTATTTTATTACATTAT-ATTATTT-AT
*
2906845 TTATTTTATTACATTATATTATATAT
1 TTATTTTATTACATTATATTATTTAT
* *
2906871 TTATATGTTTTTACTTTAT-TTATTTAT
1 TTAT-T-TTATTACATTATATTATTTAT
2906898 TT
1 TT
2906900 CTAATTTCAT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
26 6 0.13
27 24 0.52
28 16 0.35
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (26 bp):
TTATTTTATTACATTATATTATTTAT
Found at i:2906938 original size:27 final size:27
Alignment explanation
Indices: 2906908--2906963 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
2906898 TTCTAATTTC
*
2906908 ATTTTTCCTATT-TTTATTATTCTCTTT
1 ATTTTTACTATTATTT-TTATTCTCTTT
*
2906935 ATTTTTACTATTATTTTTATTTTCTTT
1 ATTTTTACTATTATTTTTATTCTCTTT
2906962 AT
1 AT
2906964 GTTCATTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 23 0.88
28 3 0.12
ACGTcount: A:0.18, C:0.11, G:0.00, T:0.71
Consensus pattern (27 bp):
ATTTTTACTATTATTTTTATTCTCTTT
Found at i:2906939 original size:18 final size:18
Alignment explanation
Indices: 2906916--2906957 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2906906 TCATTTTTCC
* *
2906916 TATTTTTATTATTCTCTT
1 TATTTTTACTATTATCTT
*
2906934 TATTTTTACTATTATTTT
1 TATTTTTACTATTATCTT
2906952 TATTTT
1 TATTTT
2906958 CTTTATGTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (18 bp):
TATTTTTACTATTATCTT
Found at i:2907077 original size:17 final size:17
Alignment explanation
Indices: 2907050--2907093 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
2907040 TTTATTTATT
2907050 TATTTTT-CTTTCT-TTC
1 TATTTTTACTTT-TGTTC
2907066 TATTTTTACTTTTGTTC
1 TATTTTTACTTTTGTTC
2907083 T-TTTTTA-TTTT
1 TATTTTTACTTTT
2907094 TCTTTATCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 4 0.15
16 14 0.54
17 8 0.31
ACGTcount: A:0.09, C:0.11, G:0.02, T:0.77
Consensus pattern (17 bp):
TATTTTTACTTTTGTTC
Found at i:2907078 original size:22 final size:23
Alignment explanation
Indices: 2907048--2907104 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 23
2907038 TATTTATTTA
*
2907048 TTTATTTTTCTTTC-TTTCTATT
1 TTTACTTTTCTTTCTTTTCTATT
* *
2907070 TTTACTTTT-GTTCTTTTTTATT
1 TTTACTTTTCTTTCTTTTCTATT
2907092 TTT-CTTTATCTTT
1 TTTACTTT-TCTTT
2907105 TTTATCTTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
21 7 0.25
22 19 0.68
23 2 0.07
ACGTcount: A:0.09, C:0.12, G:0.02, T:0.77
Consensus pattern (23 bp):
TTTACTTTTCTTTCTTTTCTATT
Found at i:2907129 original size:9 final size:9
Alignment explanation
Indices: 2907025--2907161 Score: 52
Period size: 9 Copynumber: 14.7 Consensus size: 9
2907015 GATTATCCCC
2907025 ATTTTCTTT
1 ATTTTCTTT
* *
2907034 AATTTATTT
1 ATTTTCTTT
*
2907043 A-TTTATTT
1 ATTTTCTTT
2907051 ATTTTTCTTT
1 A-TTTTCTTT
*
2907061 -CTTTCTATT
1 ATTTTCT-TT
*
2907070 -TTTACTTTT
1 ATTTTC-TTT
* *
2907079 GTTCTTTTTT
1 ATT-TTCTTT
2907089 ATTTTTCTTT
1 A-TTTTCTTT
2907099 ATCTTT-TTT
1 AT-TTTCTTT
*
2907108 ATCTTCATGTT
1 ATTTTC-T-TT
2907119 ATTTTCTTT
1 ATTTTCTTT
2907128 A-TTTCATGTGT
1 ATTTTC-T-T-T
2907139 -TTTTCTTT
1 ATTTTCTTT
*
2907147 ATTTTATTT
1 ATTTTCTTT
2907156 ATTTTC
1 ATTTTC
2907162 ACTTTTTATC
Statistics
Matches: 98, Mismatches: 14, Indels: 32
0.68 0.10 0.22
Matches are distributed among these distances:
8 20 0.20
9 38 0.39
10 25 0.26
11 15 0.15
ACGTcount: A:0.14, C:0.10, G:0.03, T:0.73
Consensus pattern (9 bp):
ATTTTCTTT
Found at i:2907135 original size:19 final size:19
Alignment explanation
Indices: 2907105--2907161 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 19
2907095 CTTTATCTTT
2907105 TTTATCTTCATGTTATTTTC
1 TTTAT-TTCATGTTATTTTC
2907125 TTTATTTCATGTGT-TTTTC
1 TTTATTTCATGT-TATTTTC
*
2907144 TTTATTTTAT-TTATTTTC
1 TTTATTTCATGTTATTTTC
2907162 ACTTTTTATC
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
17 1 0.03
18 6 0.18
19 21 0.62
20 6 0.18
ACGTcount: A:0.14, C:0.11, G:0.05, T:0.70
Consensus pattern (19 bp):
TTTATTTCATGTTATTTTC
Found at i:2908330 original size:2 final size:2
Alignment explanation
Indices: 2908325--2908359 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2908315 AAAATTAAAT
2908325 TA TA TA TA TA 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 TA TA TA TA TA T
2908360 TTTTTTTAAA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2908790 original size:3 final size:3
Alignment explanation
Indices: 2908782--2908848 Score: 125
Period size: 3 Copynumber: 22.3 Consensus size: 3
2908772 TTACCCTATG
2908782 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
2908830 AAT AAT AAC AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT A
2908849 GTAGTAGTAG
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2909107 original size:23 final size:22
Alignment explanation
Indices: 2909063--2909107 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
2909053 TTCAGATTTC
* * *
2909063 TTTTTTTAAAAAATTGATAATA
1 TTTTTTTAAAAAAATAAAAATA
2909085 TTTTATTTAAAAAAATAAAAATA
1 TTTT-TTTAAAAAAATAAAAATA
2909108 AATGTGACAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
TTTTTTTAAAAAAATAAAAATA
Found at i:2909963 original size:27 final size:29
Alignment explanation
Indices: 2909933--2909987 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
2909923 TAACTTAAAA
*
2909933 TATTCAAA-ATATATAGATATT-TTTTAC
1 TATTCAAACATAAATAGATATTATTTTAC
*
2909960 TATTCAAACTTAAATAGATATTATTTTA
1 TATTCAAACATAAATAGATATTATTTTA
2909988 ATTTGAGATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 8 0.33
28 11 0.46
29 5 0.21
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (29 bp):
TATTCAAACATAAATAGATATTATTTTAC
Found at i:2917437 original size:29 final size:29
Alignment explanation
Indices: 2917369--2917477 Score: 86
Period size: 29 Copynumber: 3.8 Consensus size: 29
2917359 AATTTTTGTT
* **
2917369 TTTATATTTTAAAATATATTATTTAATTA
1 TTTATATTATAAAATATATTATTTAACAA
* *
2917398 TTAAAATTATAAAATATATTAGTTTAACAA
1 TTTATATTATAAAATATATTA-TTTAACAA
2917428 TTTATA-TATAATAA-ATA--A-TTATA-AA
1 TTTATATTATAA-AATATATTATTTA-ACAA
*
2917453 TATATTATTATAAAATATATTATTT
1 TTTA-TATTATAAAATATATTATTT
2917478 TAATTATTTA
Statistics
Matches: 63, Mismatches: 8, Indels: 17
0.72 0.09 0.19
Matches are distributed among these distances:
25 8 0.13
26 5 0.08
27 9 0.14
29 27 0.43
30 14 0.22
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.50
Consensus pattern (29 bp):
TTTATATTATAAAATATATTATTTAACAA
Found at i:2917471 original size:21 final size:22
Alignment explanation
Indices: 2917451--2917502 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
2917441 AATAATTATA
2917451 AATATATT-ATTA-TAAAATAT
1 AATATATTAATTATTAAAATAT
* *
2917471 ATTATTTTAATTATTTAAAATATT
1 AATATATTAATTA-TTAAAATA-T
2917495 AATATATT
1 AATATATT
2917503 CGGATCAGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
20 6 0.25
21 4 0.17
23 7 0.29
24 7 0.29
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
AATATATTAATTATTAAAATAT
Found at i:2917502 original size:29 final size:28
Alignment explanation
Indices: 2917378--2917502 Score: 83
Period size: 29 Copynumber: 4.4 Consensus size: 28
2917368 TTTTATATTT
*
2917378 TAAAATATATTA-TTTAATTATTAAAATTA
1 TAAAATATATTATTTTAATTATTTAAA--A
* ** *
2917407 TAAAATATATTAGTTTAACAATTT-ATA
1 TAAAATATATTATTTTAATTATTTAAAA
* * * * * **
2917434 TATAATAAATAATTATAAATATATTATTA
1 TAAAATATATTATTTTAATTAT-TTAAAA
2917463 TAAAATATATTATTTTAATTATTTAAAA
1 TAAAATATATTATTTTAATTATTTAAAA
*
2917491 TATTAATATATT
1 TA-AAATATATT
2917503 CGGATCAGAT
Statistics
Matches: 72, Mismatches: 20, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
27 16 0.22
28 8 0.11
29 40 0.56
30 8 0.11
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (28 bp):
TAAAATATATTATTTTAATTATTTAAAA
Found at i:2920330 original size:24 final size:22
Alignment explanation
Indices: 2920275--2920521 Score: 245
Period size: 22 Copynumber: 11.0 Consensus size: 22
2920265 ATATATGTAG
2920275 TTTTG-AAAA-ATAT-ATATAA
1 TTTTGAAAAATATATAATATAA
2920294 TTTTGAAAAATATATAATATAA
1 TTTTGAAAAATATATAATATAA
2920316 TTTTGAAAAATATATAATATAA
1 TTTTGAAAAATATATAATATAA
** * *
2920338 TTTTTCAAAATATATTATGTAA
1 TTTTGAAAAATATATAATATAA
*
2920360 TTTTTGAAAATATATGTAATATATAA
1 -TTTTGAAAA-ATATAT-A-ATATAA
*
2920386 TTTTGAAAAATATATAATATAGT
1 TTTTGAAAAATATATAATATA-A
*
2920409 TTTTG-AAAATATATTATATAA
1 TTTTGAAAAATATATAATATAA
2920430 TTTTTGAAAATATATATAATATATAA
1 -TTTTGAAAA-ATATAT-A-ATATAA
* **
2920456 TTTTGGAAAATATATAATATTTT
1 TTTTGAAAAATATATAATA-TAA
*
2920479 TTTTG--AAATATATTATATAA
1 TTTTGAAAAATATATAATATAA
2920499 TTTTTGAAAAAATATATAATATA
1 -TTTTG-AAAAATATATAATATA
2920522 TATATATATT
Statistics
Matches: 189, Mismatches: 21, Indels: 31
0.78 0.09 0.13
Matches are distributed among these distances:
19 5 0.03
20 5 0.03
21 20 0.11
22 73 0.39
23 23 0.12
24 35 0.19
25 17 0.09
26 11 0.06
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (22 bp):
TTTTGAAAAATATATAATATAA
Found at i:2920395 original size:70 final size:70
Alignment explanation
Indices: 2920275--2920523 Score: 359
Period size: 70 Copynumber: 3.7 Consensus size: 70
2920265 ATATATGTAG
*
2920275 TTTTGAAAA-ATA-TATATAA-TTTTGAAAA-ATATAT-A-ATATAATTTTGAAAAATATATAAT
1 TTTTCAAAATATATTATATAATTTTTGAAAATATATATAATATATAATTTTGAAAAATATATAAT
2920334 ATAAT
66 ATAAT
* *
2920339 TTTTCAAAATATATTATGTAATTTTTGAAAATATATGTAATATATAATTTTGAAAAATATATAAT
1 TTTTCAAAATATATTATATAATTTTTGAAAATATATATAATATATAATTTTGAAAAATATATAAT
*
2920404 ATAGT
66 ATAAT
* *
2920409 TTTTGAAAATATATTATATAATTTTTGAAAATATATATAATATATAATTTTGGAAAATATATAAT
1 TTTTCAAAATATATTATATAATTTTTGAAAATATATATAATATATAATTTTGAAAAATATATAAT
*
2920474 AT-TT
66 ATAAT
** *
2920478 TTTTTGAAATATATTATATAATTTTTGAAAAAATATATAATATATA
1 TTTTCAAAATATATTATATAATTTTTGAAAATATATATAATATATA
2920524 TATATATTTT
Statistics
Matches: 167, Mismatches: 12, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
64 8 0.05
65 3 0.02
66 6 0.04
67 9 0.05
68 5 0.03
69 45 0.27
70 91 0.54
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (70 bp):
TTTTCAAAATATATTATATAATTTTTGAAAATATATATAATATATAATTTTGAAAAATATATAAT
ATAAT
Found at i:2920618 original size:26 final size:27
Alignment explanation
Indices: 2920578--2920633 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 27
2920568 TTTTGAAAAC
2920578 ATAGTGTTTGAAAATATA-ATATATTAT
1 ATAGTGTTTGAAAATATATATATATT-T
*
2920605 ATAGT-TTTTAAAATATATATATATTT
1 ATAGTGTTTGAAAATATATATATATTT
2920631 ATA
1 ATA
2920634 CAATATATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 15 0.56
27 12 0.44
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (27 bp):
ATAGTGTTTGAAAATATATATATATTT
Found at i:2920638 original size:19 final size:20
Alignment explanation
Indices: 2920595--2920641 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
2920585 TTGAAAATAT
*
2920595 AATATATTATATAGTTTTTAA
1 AATATA-TATATAGTTTATAA
*
2920616 AATATATATATA-TTTATAC
1 AATATATATATAGTTTATAA
2920635 AATATAT
1 AATATAT
2920642 TACTTTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 12 0.50
20 6 0.25
21 6 0.25
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (20 bp):
AATATATATATAGTTTATAA
Found at i:2920680 original size:21 final size:21
Alignment explanation
Indices: 2920653--2920707 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
2920643 ACTTTTTATT
2920653 TTATTTTTATTTTTATTTTTA
1 TTATTTTTATTTTTATTTTTA
* *
2920674 TTCTTTTTATTTTTATTTTTT
1 TTATTTTTATTTTTATTTTTA
*
2920695 TTATTTTCATTTT
1 TTATTTTTATTTT
2920708 GGTTTAGGTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.15, C:0.04, G:0.00, T:0.82
Consensus pattern (21 bp):
TTATTTTTATTTTTATTTTTA
Found at i:2920701 original size:6 final size:6
Alignment explanation
Indices: 2920645--2920693 Score: 64
Period size: 6 Copynumber: 7.8 Consensus size: 6
2920635 AATATATTAC
2920645 TTTTTA -TTTTA TTTTTA TTTTTA TTTTTA TTCTTTTTA TTTTTA TTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA ---TTTTTA TTTTTA TTTTT
2920694 TTTATTTTCA
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
5 5 0.13
6 28 0.72
9 6 0.15
ACGTcount: A:0.14, C:0.02, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:2920706 original size:15 final size:15
Alignment explanation
Indices: 2920645--2920707 Score: 81
Period size: 15 Copynumber: 4.1 Consensus size: 15
2920635 AATATATTAC
*
2920645 TTTTTATTTTATTTTT
1 TTTTTATTTT-TATTT
*
2920661 ATTTTTATTTTTATTC
1 -TTTTTATTTTTATTT
2920677 TTTTTATTTTTATTT
1 TTTTTATTTTTATTT
*
2920692 TTTTTATTTTCATTT
1 TTTTTATTTTTATTT
2920707 T
1 T
2920708 GGTTTAGGTC
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
15 29 0.69
16 3 0.07
17 10 0.24
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTATTTTTATTT
Found at i:2923554 original size:20 final size:20
Alignment explanation
Indices: 2923511--2923558 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
2923501 TCTAAATCCT
* *
2923511 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATTCCATTTTGC
2923531 TTTTCAAAA-TCCATTTTAGC
1 TTTTCAAAATTCCATTTT-GC
2923551 TTTT-AAAA
1 TTTTCAAAA
2923559 GAAAATCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.50
Consensus pattern (20 bp):
TTTTCAAAATTCCATTTTGC
Found at i:2924895 original size:21 final size:21
Alignment explanation
Indices: 2924845--2924900 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
2924835 GTGCTTGATA
2924845 GTATCGATACTACTGTTCACG
1 GTATCGATACTACTGTTCACG
* **
2924866 ATATCGATACTACTGTTCGTG
1 GTATCGATACTACTGTTCACG
*
2924887 GTATAGATACTACT
1 GTATCGATACTACT
2924901 ATAGCAGTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.36
Consensus pattern (21 bp):
GTATCGATACTACTGTTCACG
Found at i:2928817 original size:14 final size:14
Alignment explanation
Indices: 2928798--2928824 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2928788 GGGAGAATGG
2928798 GAGAGAGAAAAGTA
1 GAGAGAGAAAAGTA
2928812 GAGAGAGAAAAGT
1 GAGAGAGAAAAGT
2928825 TAAAAGGGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.37, T:0.07
Consensus pattern (14 bp):
GAGAGAGAAAAGTA
Found at i:2929024 original size:17 final size:19
Alignment explanation
Indices: 2929002--2929036 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
2928992 GCTTTTGTTC
2929002 AGTTTG-AGAGGG-AATCT
1 AGTTTGAAGAGGGCAATCT
2929019 AGTTTGAAGAGGGCAATC
1 AGTTTGAAGAGGGCAATC
2929037 GAGATGTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 6 0.38
19 4 0.25
ACGTcount: A:0.31, C:0.09, G:0.34, T:0.26
Consensus pattern (19 bp):
AGTTTGAAGAGGGCAATCT
Found at i:2941644 original size:32 final size:32
Alignment explanation
Indices: 2941608--2941680 Score: 137
Period size: 32 Copynumber: 2.3 Consensus size: 32
2941598 ATTTAGATGA
2941608 ATTAATGTTCGAGTAAATTTTCAATAATTTTC
1 ATTAATGTTCGAGTAAATTTTCAATAATTTTC
*
2941640 ATTAATGTTGGAGTAAATTTTCAATAATTTTC
1 ATTAATGTTCGAGTAAATTTTCAATAATTTTC
2941672 ATTAATGTT
1 ATTAATGTT
2941681 TTAAAAATAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.34, C:0.07, G:0.11, T:0.48
Consensus pattern (32 bp):
ATTAATGTTCGAGTAAATTTTCAATAATTTTC
Found at i:2944495 original size:13 final size:13
Alignment explanation
Indices: 2944477--2944503 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2944467 CATAGTTAAA
2944477 CAGTCTACATATG
1 CAGTCTACATATG
2944490 CAGTCTACATATG
1 CAGTCTACATATG
2944503 C
1 C
2944504 GCATCTGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.30
Consensus pattern (13 bp):
CAGTCTACATATG
Found at i:2953495 original size:29 final size:30
Alignment explanation
Indices: 2953426--2953484 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
2953416 TTACAAACAT
*
2953426 GACTAAAATA-ATAAAAACATAAAGTTAAAG
1 GACTAAAATAGA-AAAAACAGAAAGTTAAAG
2953456 GACTAAAATAGAAAAAACAGAAAGTTAAA
1 GACTAAAATAGAAAAAACAGAAAGTTAAA
2953485 TGGATGAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.64, C:0.07, G:0.12, T:0.17
Consensus pattern (30 bp):
GACTAAAATAGAAAAAACAGAAAGTTAAAG
Found at i:2954821 original size:21 final size:20
Alignment explanation
Indices: 2954767--2954821 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
2954757 TGGATTTAGT
2954767 GGATTTGGTGATTTTAAATG
1 GGATTTGGTGATTTTAAATG
*
2954787 GGATTTAGTGATTTTAAATG
1 GGATTTGGTGATTTTAAATG
*
2954807 GTATTTGGTTGATTT
1 GGATTTGG-TGATTT
2954822 GACAGGTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
20 25 0.81
21 6 0.19
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.49
Consensus pattern (20 bp):
GGATTTGGTGATTTTAAATG
Found at i:2955026 original size:3 final size:3
Alignment explanation
Indices: 2955004--2955068 Score: 69
Period size: 3 Copynumber: 21.7 Consensus size: 3
2954994 TGCCAACATG
* * * * *
2955004 TAA TAA TAT TAA TAA GTAA TAA TAA TAA TAT TAA TAT TAA TCA TGA
1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2955050 TAA TAA TAA TAA T-A TAA TA
1 TAA TAA TAA TAA TAA TAA TA
2955069 TATTTTTTTG
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
2 2 0.04
3 46 0.90
4 3 0.06
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:2957456 original size:15 final size:13
Alignment explanation
Indices: 2957414--2957456 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
2957404 AGAAGATTAG
2957414 AACATAATAAGCC
1 AACATAATAAGCC
*
2957427 AACATAATAATCC
1 AACATAATAAGCC
2957440 AACATATGATAAGCC
1 AACATA--ATAAGCC
2957455 AA
1 AA
2957457 AAATATCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 18 0.69
15 8 0.31
ACGTcount: A:0.53, C:0.21, G:0.07, T:0.19
Consensus pattern (13 bp):
AACATAATAAGCC
Found at i:2957545 original size:18 final size:18
Alignment explanation
Indices: 2957522--2957580 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
2957512 GCATATACAA
**
2957522 AAATAACCAAAATATTTG
1 AAATAACCAAAATATCCG
2957540 AAATAACCAAAATATCCG
1 AAATAACCAAAATATCCG
* * *
2957558 AAGTAACCAAAACATCCA
1 AAATAACCAAAATATCCG
2957576 AAATA
1 AAATA
2957581 TGAAATCCTA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.58, C:0.19, G:0.05, T:0.19
Consensus pattern (18 bp):
AAATAACCAAAATATCCG
Found at i:2959415 original size:20 final size:20
Alignment explanation
Indices: 2959370--2959419 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
2959360 TGAAGAACAA
2959370 TATCGATACTGATTGAAGTAG
1 TATCGATACTGATTGAAG-AG
*
2959391 TATCGATACTGATGTGGAG-G
1 TATCGATACTGAT-TGAAGAG
2959411 TATCGATAC
1 TATCGATAC
2959420 CAAGGACAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 10 0.37
21 13 0.48
22 4 0.15
ACGTcount: A:0.30, C:0.12, G:0.26, T:0.32
Consensus pattern (20 bp):
TATCGATACTGATTGAAGAG
Found at i:2960212 original size:24 final size:24
Alignment explanation
Indices: 2960175--2960247 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
2960165 GAGTCGAGGG
*
2960175 TTCTACGCGATCCTTCGGGACAAA
1 TTCTACGCGGTCCTTCGGGACAAA
* **
2960199 TTCTACGTGGTCCTTTTGGACAAA
1 TTCTACGCGGTCCTTCGGGACAAA
* *
2960223 TTCTACACGGTCATTCGGGACAAA
1 TTCTACGCGGTCCTTCGGGACAAA
2960247 T
1 T
2960248 CTATGTGGCA
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.30
Consensus pattern (24 bp):
TTCTACGCGGTCCTTCGGGACAAA
Found at i:2960529 original size:14 final size:14
Alignment explanation
Indices: 2960491--2960527 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
2960481 TTTTTCCGAC
*
2960491 TTAAATGTTTTCCA
1 TTAAATGTTTTACA
2960505 TTAAATG-TTTACA
1 TTAAATGTTTTACA
2960518 -TAAATGTTTT
1 TTAAATGTTTT
2960528 TAGTATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
12 6 0.29
13 8 0.38
14 7 0.33
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.51
Consensus pattern (14 bp):
TTAAATGTTTTACA
Found at i:2978639 original size:23 final size:23
Alignment explanation
Indices: 2978589--2978663 Score: 62
Period size: 24 Copynumber: 3.2 Consensus size: 23
2978579 CTACGCGGTC
* * **
2978589 CTTCGGGACAAATTATATGTAGTC
1 CTTCGGGACAAA-TCTATGTGGAA
2978613 CTTCGGGACAAATCTATGTGGAA
1 CTTCGGGACAAATCTATGTGGAA
* *
2978636 CTTCGGTG-CATATTCTACGTGGAA
1 CTTCGG-GACA-AATCTATGTGGAA
2978660 CTTC
1 CTTC
2978664 AGTTCAAATT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
23 15 0.35
24 28 0.65
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (23 bp):
CTTCGGGACAAATCTATGTGGAA
Found at i:2985978 original size:26 final size:25
Alignment explanation
Indices: 2985930--2985978 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
2985920 ATTTATATAC
* *
2985930 TTTTTAATAAAATTTATATATAATT
1 TTTTTAATAAAATTTAAAGATAATT
*
2985955 TTTTTTATAAAATTTAAAAGATAA
1 TTTTTAATAAAATTT-AAAGATAA
2985979 ATTGGTAGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (25 bp):
TTTTTAATAAAATTTAAAGATAATT
Found at i:2992041 original size:17 final size:18
Alignment explanation
Indices: 2992009--2992042 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2991999 ATTGGCATAC
2992009 AACAATGACTACATCATT
1 AACAATGACTACATCATT
*
2992027 AACAATGTC-ACATCAT
1 AACAATGACTACATCAT
2992043 CAGTATATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.44, C:0.24, G:0.06, T:0.26
Consensus pattern (18 bp):
AACAATGACTACATCATT
Found at i:2998066 original size:20 final size:19
Alignment explanation
Indices: 2998041--2998097 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 19
2998031 GTTGGAATCC
2998041 AAAGTTTCAAA-TCTATAAGG
1 AAAGTTTCAAACTCT-T-AGG
*
2998061 AAAGTTTCGAAACTCTTATG
1 AAAGTTTC-AAACTCTTAGG
2998081 AAAGTTTCAAAACTCTT
1 AAAGTTTC-AAACTCTT
2998098 GTAAAGTGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 26 0.79
21 4 0.12
22 3 0.09
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.33
Consensus pattern (19 bp):
AAAGTTTCAAACTCTTAGG
Found at i:2998111 original size:19 final size:20
Alignment explanation
Indices: 2998060--2998113 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 20
2998050 AATCTATAAG
* *
2998060 GAAAGTTTCGAAACTCTTAT
1 GAAAGTGTCAAAACTCTTAT
* *
2998080 GAAAGTTTCAAAACTCTTGT
1 GAAAGTGTCAAAACTCTTAT
*
2998100 -AAAGTGTGAAAACT
1 GAAAGTGTCAAAACT
2998114 TCAAAGTCTC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (20 bp):
GAAAGTGTCAAAACTCTTAT
Found at i:2999196 original size:74 final size:73
Alignment explanation
Indices: 2999055--2999192 Score: 161
Period size: 74 Copynumber: 1.9 Consensus size: 73
2999045 CTAATTGAAT
* * * * ***
2999055 ATAAATTTGTAATAATATATTCATATTTGAATTGAATATAAATTCATAAATACTATATTTTATTT
1 ATAAATTTATAATAATATATTCATATTTCAATCGAATATAAATTCATAAATAATATATCACATTT
2999120 AATAAAAC
66 AATAAAAC
* * **
2999128 ATAAATTTATAAATAATGTATTCCTATTTCAATCGAATATAAATTTGT-AATAATATATCACATT
1 ATAAATTTAT-AATAATATATTCATATTTCAATCGAATATAAATTCATAAATAATATATCACATT
2999192 T
65 T
2999193 TAATTGAATA
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
73 22 0.42
74 31 0.58
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.43
Consensus pattern (73 bp):
ATAAATTTATAATAATATATTCATATTTCAATCGAATATAAATTCATAAATAATATATCACATTT
AATAAAAC
Found at i:2999205 original size:36 final size:38
Alignment explanation
Indices: 2999046--2999205 Score: 143
Period size: 36 Copynumber: 4.3 Consensus size: 38
2999036 TATTGTATTC
* *
2999046 TAATTGAATATAAATTTGT-AATAATATATTCATATTT
1 TAATTGAATATAAATTTATAAATAATATATTCACATTT
* * * **
2999083 GAATTGAATATAAATTCATAAATACTATATT-TTA-TT
1 TAATTGAATATAAATTTATAAATAATATATTCACATTT
** * *
2999119 TAATAAAACATAAATTTATAAATAATGTATTC-CTATTT
1 TAATTGAATATAAATTTATAAATAATATATTCAC-ATTT
* * *
2999157 CAATCGAATATAAATTTGT-AATAATATA-TCACATTT
1 TAATTGAATATAAATTTATAAATAATATATTCACATTT
2999193 TAATTGAATATAA
1 TAATTGAATATAA
2999206 TTCCTTAAAT
Statistics
Matches: 97, Mismatches: 21, Indels: 11
0.75 0.16 0.09
Matches are distributed among these distances:
36 43 0.44
37 28 0.29
38 26 0.27
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.43
Consensus pattern (38 bp):
TAATTGAATATAAATTTATAAATAATATATTCACATTT
Found at i:3001354 original size:21 final size:22
Alignment explanation
Indices: 3001312--3001355 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
3001302 AGATGAATAT
* *
3001312 TCTAGATCATTTTGAGGATGAA
1 TCTAGATCAATTTGAAGATGAA
*
3001334 TCTAGA-CAATTTGAAGCTGAA
1 TCTAGATCAATTTGAAGATGAA
3001355 T
1 T
3001356 TTGGCATTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.34
Consensus pattern (22 bp):
TCTAGATCAATTTGAAGATGAA
Found at i:3006698 original size:17 final size:18
Alignment explanation
Indices: 3006671--3006706 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
3006661 TAGTAATAAA
3006671 AAAATAACCTCACAAAAC
1 AAAATAACCTCACAAAAC
*
3006689 AAAA-AACCTCACCAAAC
1 AAAATAACCTCACAAAAC
3006706 A
1 A
3006707 CTCCAAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.61, C:0.31, G:0.00, T:0.08
Consensus pattern (18 bp):
AAAATAACCTCACAAAAC
Found at i:3010910 original size:21 final size:20
Alignment explanation
Indices: 3010864--3010913 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
3010854 AAAAACATAG
*
3010864 AAGGGATCGATCATTTATGTC
1 AAGGGATCGATCATTT-TCTC
*
3010885 GAGGGATCGATCATTTTCTCC
1 AAGGGATCGATCATTTTCT-C
3010906 AAGGGATC
1 AAGGGATC
3010914 AATCCTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 2 0.08
21 23 0.92
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (20 bp):
AAGGGATCGATCATTTTCTC
Found at i:3017852 original size:2 final size:2
Alignment explanation
Indices: 3017845--3017875 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3017835 TGAAGGGAGG
3017845 TA TA TA 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 TA TA TA T
3017876 GTGTGTGTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3018405 original size:30 final size:30
Alignment explanation
Indices: 3018338--3018407 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
3018328 GATGATTGCT
* * *
3018338 ACAGTGACCACCATAGCTCTCCAGGAGCAT
1 ACAGCGACCTCCATAGCTCTCCAGGAGCAC
** *
3018368 ATGGCGACCTCCATAGGTCTCCAGGAGCAC
1 ACAGCGACCTCCATAGCTCTCCAGGAGCAC
3018398 ACAGCGACCT
1 ACAGCGACCT
3018408 ATGGAGCTAC
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.27, C:0.34, G:0.23, T:0.16
Consensus pattern (30 bp):
ACAGCGACCTCCATAGCTCTCCAGGAGCAC
Found at i:3019347 original size:34 final size:34
Alignment explanation
Indices: 3019302--3019368 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 34
3019292 AATAGGAATT
*
3019302 ATAACTTCTCTC-GATCAACCAAGGAGAAAACAATG
1 ATAACTTCTCTCTGAT-AA-AAAGGAGAAAACAATG
3019337 ATAA-TTCTCTCTTGATAAAAAGGAGAAAACAA
1 ATAACTTCTCTC-TGATAAAAAGGAGAAAACAA
3019369 CTCTCAAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 20 0.69
35 6 0.21
36 3 0.10
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.22
Consensus pattern (34 bp):
ATAACTTCTCTCTGATAAAAAGGAGAAAACAATG
Found at i:3025271 original size:2 final size:2
Alignment explanation
Indices: 3025264--3025288 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3025254 CGTTCCTAGG
3025264 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
3025289 GCAAAGCCAA
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:3026808 original size:23 final size:23
Alignment explanation
Indices: 3026779--3026883 Score: 147
Period size: 23 Copynumber: 4.5 Consensus size: 23
3026769 ACATTTATGC
3026779 TCGTTTACGTTCATTTATTGTGT
1 TCGTTTACGTTCATTTATTGTGT
* * *
3026802 TCGTTTATGTTCGTTCATTTGTGT
1 TCGTTTACGTTCATTTA-TTGTGT
* *
3026826 TTGTTTACGTTCGTTTATTGTGT
1 TCGTTTACGTTCATTTATTGTGT
3026849 TCGTTTACGTTCATTTATTGTGT
1 TCGTTTACGTTCATTTATTGTGT
*
3026872 TCGTTTATGTTC
1 TCGTTTACGTTC
3026884 GTTACATCCG
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
23 52 0.72
24 20 0.28
ACGTcount: A:0.10, C:0.12, G:0.19, T:0.58
Consensus pattern (23 bp):
TCGTTTACGTTCATTTATTGTGT
Found at i:3026843 original size:47 final size:46
Alignment explanation
Indices: 3026779--3026886 Score: 153
Period size: 47 Copynumber: 2.3 Consensus size: 46
3026769 ACATTTATGC
* * *
3026779 TCGTTTACGTTCATTTATTGTGTTCGTTTATGTTCGTTCATTTGTGT
1 TCGTTTACGTTCGTTTATTGTGTTCGTTTACGTTCATTCA-TTGTGT
* *
3026826 TTGTTTACGTTCGTTTATTGTGTTCGTTTACGTTCATTTATTGTGT
1 TCGTTTACGTTCGTTTATTGTGTTCGTTTACGTTCATTCATTGTGT
*
3026872 TCGTTTATGTTCGTT
1 TCGTTTACGTTCGTT
3026887 ACATCCGTTC
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
46 19 0.35
47 35 0.65
ACGTcount: A:0.10, C:0.12, G:0.19, T:0.58
Consensus pattern (46 bp):
TCGTTTACGTTCGTTTATTGTGTTCGTTTACGTTCATTCATTGTGT
Found at i:3027405 original size:39 final size:39
Alignment explanation
Indices: 3027346--3027429 Score: 159
Period size: 39 Copynumber: 2.2 Consensus size: 39
3027336 GTATACAAGT
*
3027346 TAAAGTAAATTTGGTAGCCTTTGAGCATGTTTGATATAG
1 TAAATTAAATTTGGTAGCCTTTGAGCATGTTTGATATAG
3027385 TAAATTAAATTTGGTAGCCTTTGAGCATGTTTGATATAG
1 TAAATTAAATTTGGTAGCCTTTGAGCATGTTTGATATAG
3027424 TAAATT
1 TAAATT
3027430 GACCATTTGG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.32, C:0.07, G:0.20, T:0.40
Consensus pattern (39 bp):
TAAATTAAATTTGGTAGCCTTTGAGCATGTTTGATATAG
Found at i:3031656 original size:2 final size:2
Alignment explanation
Indices: 3031649--3031677 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3031639 TATGCTATGT
3031649 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3031678 TTTAAGTTTA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3041772 original size:23 final size:22
Alignment explanation
Indices: 3041723--3041793 Score: 72
Period size: 23 Copynumber: 3.1 Consensus size: 22
3041713 AAAAGTTTAA
*
3041723 AATACTTATTTAATT-TTAAAAT
1 AATA-TTATTTATTTATTAAAAT
*
3041745 CATATTATTTATTTATATAAAAT
1 AATATTATTTATTTAT-TAAAAT
* *
3041768 AATATTAATTATTTATTTGAAAT
1 AATATTATTTATTTA-TTAAAAT
3041791 AAT
1 AAT
3041794 GTTTTATTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
21 9 0.22
22 4 0.10
23 27 0.66
24 1 0.02
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (22 bp):
AATATTATTTATTTATTAAAAT
Found at i:3042826 original size:11 final size:11
Alignment explanation
Indices: 3042812--3042843 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
3042802 CAAAACACGT
3042812 AAAAAATAATA
1 AAAAAATAATA
3042823 AAAAAATAATA
1 AAAAAATAATA
3042834 ATAAAAATAA
1 A-AAAAATAA
3042844 ACAAAATGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.60
12 8 0.40
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (11 bp):
AAAAAATAATA
Found at i:3043064 original size:39 final size:37
Alignment explanation
Indices: 3042973--3043090 Score: 95
Period size: 39 Copynumber: 3.1 Consensus size: 37
3042963 TAAAACAAAT
*
3042973 AAAAATAATAAATAT-ATA-ATACTAAGTAAA-ACAAGTAA
1 AAAAATAA-AAATATAATATATA-TAAATAAATA-AA-TAA
*
3043011 AAAAATAAAGATATACATGATAT-TAAGA-AAA-AAATAA
1 AAAAATAAAAATATA-AT-ATATATAA-ATAAATAAATAA
3043048 AATAAAGTAAAAATATAATATATATAAATAAATAAATAA
1 AA-AAA-TAAAAATATAATATATATAAATAAATAAATAA
3043087 AAAA
1 AAAA
3043091 TAGAATATTA
Statistics
Matches: 67, Mismatches: 3, Indels: 20
0.74 0.03 0.22
Matches are distributed among these distances:
37 15 0.22
38 23 0.34
39 26 0.39
40 1 0.01
41 2 0.03
ACGTcount: A:0.69, C:0.03, G:0.05, T:0.24
Consensus pattern (37 bp):
AAAAATAAAAATATAATATATATAAATAAATAAATAA
Found at i:3043109 original size:41 final size:39
Alignment explanation
Indices: 3043067--3043157 Score: 112
Period size: 39 Copynumber: 2.3 Consensus size: 39
3043057 AAAATATAAT
*
3043067 ATATATAAATAAATAA-ATAAAAAATAGAATATTAAGAAA
1 ATATATATATAAA-AACATAAAAAATAGAATATTAAGAAA
* * *
3043106 ATATATATATAAAAACGTATAAAATATAATATTAAGAAA
1 ATATATATATAAAAACATAAAAAATAGAATATTAAGAAA
* *
3043145 AAAAATATATAAA
1 ATATATATATAAA
3043158 CATAGCAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
38 2 0.04
39 43 0.96
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.27
Consensus pattern (39 bp):
ATATATATATAAAAACATAAAAAATAGAATATTAAGAAA
Done.