Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007733.1 Hibiscus syriacus cultivar Beakdansim tig00109987_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: 1979160
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 9
Found at i:1298342 original size:19 final size:19
Alignment explanation
Indices: 1298318--1298356 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1298308 TTAAACGGGA
1298318 AACGGACGATTGAGCCGAT
1 AACGGACGATTGAGCCGAT
1298337 AACGGACGATTGAGCCGAT
1 AACGGACGATTGAGCCGAT
1298356 A
1 A
1298357 GCGGGACGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.21, G:0.31, T:0.15
Consensus pattern (19 bp):
AACGGACGATTGAGCCGAT
Found at i:1300517 original size:20 final size:21
Alignment explanation
Indices: 1300492--1300538 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
1300482 CACTAATTTT
*
1300492 AAAAAGTGCATTT-AAAATAA
1 AAAAAGTACATTTAAAAATAA
*
1300512 AAAAAGTATATTTAAAAAATAA
1 AAAAAGTACATTT-AAAAATAA
1300534 AAAAA
1 AAAAA
1300539 TCAAAACACT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 11 0.48
22 12 0.52
ACGTcount: A:0.68, C:0.02, G:0.06, T:0.23
Consensus pattern (21 bp):
AAAAAGTACATTTAAAAATAA
Found at i:1304262 original size:36 final size:37
Alignment explanation
Indices: 1304200--1304278 Score: 119
Period size: 36 Copynumber: 2.2 Consensus size: 37
1304190 ACTTAATGTT
1304200 AAGTTTTGAACATGATACTAAAATGAAACAA-AATCTA
1 AAGTTTTGAACATGATACTAAAATGAAACAAGAAT-TA
*
1304237 AAGTTTTTAACATG-TACTAAAATGAAACAAGAATTA
1 AAGTTTTGAACATGATACTAAAATGAAACAAGAATTA
1304273 AA-TTTT
1 AAGTTTT
1304279 AGGAATGGTT
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
35 4 0.10
36 20 0.50
37 16 0.40
ACGTcount: A:0.49, C:0.09, G:0.10, T:0.32
Consensus pattern (37 bp):
AAGTTTTGAACATGATACTAAAATGAAACAAGAATTA
Found at i:1314528 original size:20 final size:19
Alignment explanation
Indices: 1314503--1314562 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 19
1314493 TTTTGGTGCA
*
1314503 GAGGGAATCGATACCCCCAT
1 GAGGGAATCGATACCCCC-C
* *
1314523 GAGGGAACCGATTCCCCCC
1 GAGGGAATCGATACCCCCC
1314542 GCAGGGGAATCGATACCCCCC
1 G-A-GGGAATCGATACCCCCC
1314563 TGGGGTTCTG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
19 1 0.03
20 17 0.52
21 15 0.45
ACGTcount: A:0.25, C:0.37, G:0.27, T:0.12
Consensus pattern (19 bp):
GAGGGAATCGATACCCCCC
Found at i:1316811 original size:25 final size:25
Alignment explanation
Indices: 1316777--1316826 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
1316767 TTAAAGAGTT
1316777 TTAAAAGGGAGAAGTGTTAGAGTAA
1 TTAAAAGGGAGAAGTGTTAGAGTAA
*
1316802 TTAAAGGGGAGAAGTGTTAGAGTAA
1 TTAAAAGGGAGAAGTGTTAGAGTAA
1316827 GGGGGAGTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.42, C:0.00, G:0.34, T:0.24
Consensus pattern (25 bp):
TTAAAAGGGAGAAGTGTTAGAGTAA
Found at i:1316833 original size:21 final size:22
Alignment explanation
Indices: 1316778--1316833 Score: 60
Period size: 25 Copynumber: 2.5 Consensus size: 22
1316768 TAAAGAGTTT
*
1316778 TAAAAGGGAGAAGTGTTAGAGTAA
1 TAAAGGGGAGAAGTGTTAGAG--A
1316802 TTAAAGGGGAGAAGTGTTAGAG-
1 -TAAAGGGGAGAAGTGTTAGAGA
*
1316824 TAAGGGGGAG
1 TAAAGGGGAG
1316834 TAATTTCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 9 0.31
25 20 0.69
ACGTcount: A:0.39, C:0.00, G:0.41, T:0.20
Consensus pattern (22 bp):
TAAAGGGGAGAAGTGTTAGAGA
Found at i:1319800 original size:33 final size:33
Alignment explanation
Indices: 1319753--1319834 Score: 128
Period size: 33 Copynumber: 2.5 Consensus size: 33
1319743 CACTTCCAAT
* * *
1319753 GTTTTAATCATCTTCTATTGGTGCACCTTCAGG
1 GTTTCAATCATCTTCAATTGGTGCACCTCCAGG
*
1319786 GTTTCAATCATCTTCAATTGGTGCATCTCCAGG
1 GTTTCAATCATCTTCAATTGGTGCACCTCCAGG
1319819 GTTTCAATCATCTTCA
1 GTTTCAATCATCTTCA
1319835 GCTAGCAGAG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.21, C:0.23, G:0.16, T:0.40
Consensus pattern (33 bp):
GTTTCAATCATCTTCAATTGGTGCACCTCCAGG
Found at i:1320261 original size:25 final size:24
Alignment explanation
Indices: 1320189--1320274 Score: 110
Period size: 25 Copynumber: 3.8 Consensus size: 24
1320179 GCTTAGTGGT
1320189 TTTTTTGTATATGGCTT-T-G-CA
1 TTTTTTGTATATGGCTTATGGTCA
*
1320210 TTTTTTGTATATGGC-T-CGGTCA
1 TTTTTTGTATATGGCTTATGGTCA
*
1320232 TTTTTTGTATATGCCTTAGTGGTCA
1 TTTTTTGTATATGGCTTA-TGGTCA
1320257 TTTTTTGTATATGGCTTA
1 TTTTTTGTATATGGCTTA
1320275 CTAGATTAGT
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
20 1 0.02
21 16 0.29
22 16 0.29
23 1 0.02
25 22 0.39
ACGTcount: A:0.15, C:0.10, G:0.20, T:0.55
Consensus pattern (24 bp):
TTTTTTGTATATGGCTTATGGTCA
Found at i:1328935 original size:8 final size:8
Alignment explanation
Indices: 1328922--1328962 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
1328912 CTCATTTTCA
1328922 GAGAATTT
1 GAGAATTT
1328930 GAGAATTT
1 GAGAATTT
*
1328938 -AGAGTTT
1 GAGAATTT
*
1328945 GGGAATTT
1 GAGAATTT
1328953 GAGAATTT
1 GAGAATTT
1328961 GA
1 GA
1328963 AAGATTATGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:1329261 original size:128 final size:128
Alignment explanation
Indices: 1329033--1329914 Score: 1619
Period size: 128 Copynumber: 6.9 Consensus size: 128
1329023 TAATCGGAGT
*
1329033 ACTATTCACATGAAGGCGCGTTCCCGGGGGCACGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1329098 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
1329161 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1329226 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
1329289 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1329354 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
1329417 ACTATTCACATGAAGGCGCGTTCCCGGGGG-GCGCCTTCCATTATTTCATCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
*
1329481 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTGCCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
1329544 ACTATTCACATGAAGGCGCGTT-CC-GGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
*
1329607 CATTACCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *** *
1329670 TC-AGGGGACATAAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTA
1 ACTA-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTA
1329734 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
65 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *
1329798 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCTATTATTTCATCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
*
1329863 CATTTCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
1329915 AATCAGGTAA
Statistics
Matches: 729, Mismatches: 20, Indels: 10
0.96 0.03 0.01
Matches are distributed among these distances:
125 5 0.01
126 111 0.15
127 119 0.16
128 493 0.68
129 1 0.00
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (128 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:1329770 original size:381 final size:384
Alignment explanation
Indices: 1329033--1329914 Score: 1628
Period size: 381 Copynumber: 2.3 Consensus size: 384
1329023 TAATCGGAGT
* *
1329033 ACTATTCACATGAAGGCGCGTTCCCGGGGGCACGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
1329098 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
1329163 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
131 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
*
1329228 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTA
196 TTACCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTA
** *
1329293 TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATT
261 GGCACATAAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATT
1329358 GCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
326 GCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
1329417 ACTATTCACATGAAGGCGCGTTCCCGGGGG-GCGCCTTCCATTATTTCATCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
*
1329481 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTGCCTATTATTTCAC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
1329546 TATTCACATGAAGGCGCGTT-CC-GGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
131 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
*
1329609 TTACCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTC-A
196 TTACCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTA
*
1329673 GGGGACATAAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCAT
261 -GGCACATAAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCAT
1329738 TGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
325 TGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
1329798 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCTATTATTTCATCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
*
1329863 CATTTCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
1329915 AATCAGGTAA
Statistics
Matches: 484, Mismatches: 12, Indels: 6
0.96 0.02 0.01
Matches are distributed among these distances:
380 1 0.00
381 252 0.52
382 85 0.18
383 116 0.24
384 30 0.06
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (384 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
TTACCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTA
GGCACATAAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATT
GCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:1330353 original size:34 final size:34
Alignment explanation
Indices: 1330315--1330414 Score: 130
Period size: 33 Copynumber: 3.0 Consensus size: 34
1330305 AAATTTAATG
*
1330315 TTAAATTTTGAATACTATAATTTATATTTTAAAT
1 TTAAATTTTGAATAATATAATTTATATTTTAAAT
* * * *
1330349 TTAAA-TTTGAATAATATTATTTTTATTTTTATT
1 TTAAATTTTGAATAATATAATTTATATTTTAAAT
* *
1330382 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTTGAATAATATAATTTATATTTTAAA
1330415 AACATTTATC
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (34 bp):
TTAAATTTTGAATAATATAATTTATATTTTAAAT
Found at i:1330964 original size:21 final size:21
Alignment explanation
Indices: 1330940--1331021 Score: 121
Period size: 21 Copynumber: 3.9 Consensus size: 21
1330930 ATAAAACCCT
*
1330940 GCGGGCTAGGCATGTAACCTG
1 GCGGGCTAGGAATGTAACCTG
*
1330961 GCGGGCTAGGCATGTAACCTG
1 GCGGGCTAGGAATGTAACCTG
1330982 GCGGGCTAGGAATGTAACCCT-
1 GCGGGCTAGGAATGTAA-CCTG
*
1331003 GCGGGCTCGGAATGTAACC
1 GCGGGCTAGGAATGTAACC
1331022 ATGCGGAGAT
Statistics
Matches: 58, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
20 2 0.03
21 53 0.91
22 3 0.05
ACGTcount: A:0.21, C:0.24, G:0.37, T:0.18
Consensus pattern (21 bp):
GCGGGCTAGGAATGTAACCTG
Found at i:1331057 original size:21 final size:21
Alignment explanation
Indices: 1331031--1331078 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1331021 CATGCGGAGA
*
1331031 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
1331052 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
1331073 GGGCAT
1 TGGCAT
1331079 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:1332855 original size:34 final size:34
Alignment explanation
Indices: 1332829--1332898 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
1332819 TTATTTTAAT
*
1332829 AAAA-AATAA-TATTTACATAAAATATTAATATAA
1 AAAATAATAACTATTTA-AAAAAATATTAATATAA
* *
1332862 AAAATAATAACTATTTAAAAAAATACTAACATAA
1 AAAATAATAACTATTTAAAAAAATATTAATATAA
1332896 AAA
1 AAA
1332899 TAAATTTCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 4 0.12
34 22 0.69
35 6 0.19
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.29
Consensus pattern (34 bp):
AAAATAATAACTATTTAAAAAAATATTAATATAA
Found at i:1332859 original size:19 final size:18
Alignment explanation
Indices: 1332814--1332886 Score: 59
Period size: 19 Copynumber: 4.3 Consensus size: 18
1332804 TAATAATTAT
1332814 AAATATT-AT-TTTAATA
1 AAATATTAATATTTAATA
*
1332830 AAA-AATAATATTTACATA
1 AAATATTAATATTTA-ATA
1332848 AAATATTAATA--TAA-A
1 AAATATTAATATTTAATA
* *
1332863 AAATAATAACTATTTAAAA
1 AAATATTAA-TATTTAATA
1332882 AAATA
1 AAATA
1332887 CTAACATAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
15 11 0.24
16 8 0.17
17 6 0.13
18 9 0.20
19 12 0.26
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (18 bp):
AAATATTAATATTTAATA
Found at i:1332880 original size:18 final size:18
Alignment explanation
Indices: 1332823--1332886 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
1332813 TAAATATTAT
1332823 TTTAATAAAA-AATAATA
1 TTTAATAAAATAATAATA
*
1332840 TTTACATAAAATATTAATA
1 TTTA-ATAAAATAATAATA
1332859 --TAA-AAAATAATAACTA
1 TTTAATAAAATAATAA-TA
*
1332875 TTTAAAAAAATA
1 TTTAATAAAATA
1332887 CTAACATAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
15 9 0.23
16 3 0.08
17 6 0.15
18 9 0.23
19 12 0.31
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (18 bp):
TTTAATAAAATAATAATA
Found at i:1334524 original size:28 final size:28
Alignment explanation
Indices: 1334487--1334545 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
1334477 TAGATATATG
1334487 TCATGATGATGTTAACATGATTGTTTCA
1 TCATGATGATGTTAACATGATTGTTTCA
* *
1334515 TCATGATGATGTTAACGTGATTGTTTTA
1 TCATGATGATGTTAACATGATTGTTTCA
1334543 TCA
1 TCA
1334546 AAACAACGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.27, C:0.10, G:0.19, T:0.44
Consensus pattern (28 bp):
TCATGATGATGTTAACATGATTGTTTCA
Found at i:1335040 original size:29 final size:29
Alignment explanation
Indices: 1335006--1335077 Score: 99
Period size: 29 Copynumber: 2.5 Consensus size: 29
1334996 GTGACCAAAA
1335006 AGGTCGCCATGCACGCCCAACGACCAAGG
1 AGGTCGCCATGCACGCCCAACGACCAAGG
* ****
1335035 AGGTCGCCATGCACTCGGGGCGACCAAGG
1 AGGTCGCCATGCACGCCCAACGACCAAGG
1335064 AGGTCGCCATGCAC
1 AGGTCGCCATGCAC
1335078 TCGGGGCGAC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.24, C:0.35, G:0.32, T:0.10
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCAACGACCAAGG
Found at i:1335078 original size:29 final size:29
Alignment explanation
Indices: 1335026--1335094 Score: 138
Period size: 29 Copynumber: 2.4 Consensus size: 29
1335016 GCACGCCCAA
1335026 CGACCAAGGAGGTCGCCATGCACTCGGGG
1 CGACCAAGGAGGTCGCCATGCACTCGGGG
1335055 CGACCAAGGAGGTCGCCATGCACTCGGGG
1 CGACCAAGGAGGTCGCCATGCACTCGGGG
1335084 CGACCAAGGAG
1 CGACCAAGGAG
1335095 CGGGAGCTAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.23, C:0.30, G:0.38, T:0.09
Consensus pattern (29 bp):
CGACCAAGGAGGTCGCCATGCACTCGGGG
Found at i:1335151 original size:27 final size:27
Alignment explanation
Indices: 1335109--1335161 Score: 90
Period size: 28 Copynumber: 2.0 Consensus size: 27
1335099 AGCTACGTGT
1335109 GCATGGGGGGAGAGATCGGTGCATGCAC
1 GCATGGGGGGAGAGATC-GTGCATGCAC
1335137 GCATGGGGGG-GAGATCGTGCATGCA
1 GCATGGGGGGAGAGATCGTGCATGCA
1335162 TGGGGAGATC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 9 0.36
27 6 0.24
28 10 0.40
ACGTcount: A:0.21, C:0.17, G:0.47, T:0.15
Consensus pattern (27 bp):
GCATGGGGGGAGAGATCGTGCATGCAC
Found at i:1335168 original size:19 final size:19
Alignment explanation
Indices: 1335144--1335190 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
1335134 CACGCATGGG
1335144 GGGGAGATCGTGCATGCAT-
1 GGGGAGATCGTGCATGC-TC
1335163 GGGGAGATCGTGCATGCTC
1 GGGGAGATCGTGCATGCTC
1335182 GGGGAGATC
1 GGGGAGATC
1335191 AGTTGTGTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 1 0.04
19 26 0.96
ACGTcount: A:0.19, C:0.17, G:0.45, T:0.19
Consensus pattern (19 bp):
GGGGAGATCGTGCATGCTC
Found at i:1335249 original size:14 final size:14
Alignment explanation
Indices: 1335230--1335258 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1335220 GAGTCCCGGC
1335230 GACCAAGCTGTGTG
1 GACCAAGCTGTGTG
1335244 GACCAAGCTGTGTG
1 GACCAAGCTGTGTG
1335258 G
1 G
1335259 GGGGTCCTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.21, G:0.38, T:0.21
Consensus pattern (14 bp):
GACCAAGCTGTGTG
Found at i:1335306 original size:17 final size:17
Alignment explanation
Indices: 1335281--1335314 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1335271 GCCCAAACTT
*
1335281 TAACTCTATCCCTCATC
1 TAACCCTATCCCTCATC
*
1335298 TAACCCTATCTCTCATC
1 TAACCCTATCCCTCATC
1335315 ATGCATCCAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.41, G:0.00, T:0.35
Consensus pattern (17 bp):
TAACCCTATCCCTCATC
Found at i:1335838 original size:21 final size:21
Alignment explanation
Indices: 1335813--1335856 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1335803 AATCTAGTTA
1335813 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
1335834 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
1335855 AT
1 AT
1335857 ATATTATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:1336360 original size:17 final size:17
Alignment explanation
Indices: 1336338--1336399 Score: 61
Period size: 17 Copynumber: 3.4 Consensus size: 17
1336328 GAGATAATTA
1336338 TGTTTAAAAAAATATTG
1 TGTTTAAAAAAATATTG
* *
1336355 TGTTTAAAAATATTTAGTG
1 TGTTTAAAAA-A-ATATTG
*
1336374 TTGTTTTAAAAAAATATTT
1 -TG-TTTAAAAAAATATTG
1336393 TGTTTAA
1 TGTTTAA
1336400 TTTATATTGT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
17 15 0.42
18 3 0.08
19 7 0.19
20 3 0.08
21 8 0.22
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.48
Consensus pattern (17 bp):
TGTTTAAAAAAATATTG
Found at i:1336403 original size:22 final size:23
Alignment explanation
Indices: 1336360--1336403 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
1336350 TATTGTGTTT
**
1336360 AAAAATATTTAGTGTTGTTTTAA
1 AAAAATATTTAGTGTTAATTTAA
*
1336383 AAAAATATTTTGT-TTAATTTA
1 AAAAATATTTAGTGTTAATTTA
1336404 TATTGTATGT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (23 bp):
AAAAATATTTAGTGTTAATTTAA
Found at i:1336662 original size:26 final size:26
Alignment explanation
Indices: 1336633--1336688 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
1336623 AAATCATATT
*
1336633 ATTA-ATAAATCATTAAATATCAAATC
1 ATTAGATAAAT-AATAAATATCAAATC
* * *
1336659 ATTAGATTAATAATAATTATTAAATC
1 ATTAGATAAATAATAAATATCAAATC
1336685 ATTA
1 ATTA
1336689 TTAATAATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 20 0.80
27 5 0.20
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (26 bp):
ATTAGATAAATAATAAATATCAAATC
Found at i:1339729 original size:17 final size:18
Alignment explanation
Indices: 1339703--1339737 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
1339693 AATGATTAGT
1339703 AATTATTAATAATAATGA
1 AATTATTAATAATAATGA
1339721 AATTA-TAATAATAATGA
1 AATTATTAATAATAATGA
1339738 TTTACTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (18 bp):
AATTATTAATAATAATGA
Found at i:1340005 original size:42 final size:42
Alignment explanation
Indices: 1339930--1340106 Score: 115
Period size: 42 Copynumber: 4.3 Consensus size: 42
1339920 GATAATAATC
*
1339930 ATTATAATGATTAATAATGAATTTAATATTAATGATTTGATG
1 ATTATAATGATTAATAATGAATTTAATAATAATGATTTGATG
*
1339972 ATTAGTAATGA-TAATAAT-AATCATT-ATAATAATGATTTGATA
1 ATTA-TAATGATTAATAATGAAT--TTAATAATAATGATTTGATG
* * * ** *
1340014 ATAATCATTA-TAATAATG-ATTTAGCAATAATCA-TT-AT-
1 ATTATAATGATTAATAATGAATTTAATAATAATGATTTGATG
* *
1340051 A--ATCATGATTTAATAATG-ATTTAAATATTTAATGATTTGATG
1 ATTATAATGA-TTAATAATGAATTT-AATA-ATAATGATTTGATG
1340093 ATTTAGTAATGATT
1 A-TTA-TAATGATT
1340107 TGATAATAAC
Statistics
Matches: 105, Mismatches: 14, Indels: 29
0.71 0.09 0.20
Matches are distributed among these distances:
35 6 0.06
37 13 0.12
38 4 0.04
39 9 0.09
40 9 0.09
41 18 0.17
42 30 0.29
43 8 0.08
45 3 0.03
46 5 0.05
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.44
Consensus pattern (42 bp):
ATTATAATGATTAATAATGAATTTAATAATAATGATTTGATG
Found at i:1340020 original size:26 final size:25
Alignment explanation
Indices: 1339977--1340162 Score: 147
Period size: 26 Copynumber: 7.5 Consensus size: 25
1339967 TGATGATTAG
*
1339977 TAATGA-TAATAATAATCATTATAA
1 TAATGATTTATAATAATCATTATAA
1340001 TAATGATTTGATAATAATCATTATAA
1 TAATGATTT-ATAATAATCATTATAA
*
1340027 TAATGATTTAGCAATAATCATTATAA
1 TAATGATTTA-TAATAATCATTATAA
* *
1340053 TCATGA-TT-TAATAATGATT-T-A
1 TAATGATTTATAATAATCATTATAA
* * * *
1340074 -AAT-ATTTAATGATTTGATGATT-TAG
1 TAATGATTT-AT-A-ATAATCATTATAA
* *
1340099 TAATGATTTGATAATAACCATTATGA
1 TAATGATTT-ATAATAATCATTATAA
1340125 TAATGATTTAATAATAATCATTATAA
1 TAATGATTT-ATAATAATCATTATAA
*
1340151 TAATCA-TTATAA
1 TAATGATTTATAA
1340163 CAATGTTTTA
Statistics
Matches: 130, Mismatches: 20, Indels: 24
0.75 0.11 0.14
Matches are distributed among these distances:
19 1 0.01
20 4 0.03
21 1 0.01
22 2 0.02
23 10 0.08
24 18 0.14
25 11 0.08
26 77 0.59
27 6 0.05
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (25 bp):
TAATGATTTATAATAATCATTATAA
Found at i:1340112 original size:98 final size:97
Alignment explanation
Indices: 1340001--1340188 Score: 270
Period size: 98 Copynumber: 1.9 Consensus size: 97
1339991 ATCATTATAA
* * * * *
1340001 TAATGATTTGATAATAATCATTATAATAATGATTTAGCAATAATCATTATAATCATGATT-TAAT
1 TAATGATTTGATAATAACCATTATAATAATGATTTAACAATAATCATTATAATAATCATTATAAC
*
1340065 AATGATTTAAATATTTAATGATTTGATGATTTAG
66 AATG-TTTAAAT-TATAATGATTTGATGATTTAG
* *
1340099 TAATGATTTGATAATAACCATTATGATAATGATTTAATAATAATCATTATAATAATCATTATAAC
1 TAATGATTTGATAATAACCATTATAATAATGATTTAACAATAATCATTATAATAATCATTATAAC
*
1340164 AATGTTTTAATTATAATGATTTGAT
66 AATGTTTAAATTATAATGATTTGAT
1340189 AGTAATGACT
Statistics
Matches: 80, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
97 13 0.16
98 60 0.75
99 7 0.09
ACGTcount: A:0.43, C:0.05, G:0.09, T:0.44
Consensus pattern (97 bp):
TAATGATTTGATAATAACCATTATAATAATGATTTAACAATAATCATTATAATAATCATTATAAC
AATGTTTAAATTATAATGATTTGATGATTTAG
Found at i:1340185 original size:124 final size:120
Alignment explanation
Indices: 1339921--1340166 Score: 334
Period size: 124 Copynumber: 2.0 Consensus size: 120
1339911 AAATGATTTG
* *
1339921 ATAATAATCATTATAATGA-TTAATAATGAATTTAATATTAATGATTTGATGATTAGTAATGATA
1 ATAATCATTATTATAATGATTTAATAATGAATTTAATATTAATGATTTGATGATTAGTAATGATA
* * * *
1339985 ATAATAATCATTATAATAATGATTTGATAATAATCATTATAATAATGATTTAGCA
66 ATAATAACCATTATAATAATGATTTAATAATAATCATTATAATAATCATTTAACA
* *
1340040 ATAATCATTATAATCATGATTTAATAATG-ATTTAAATATTTAATGATTTGATGATTTAGTAATG
1 ATAATCATTATTATAATGATTTAATAATGAATTT-AATA-TTAATGATTTGATGA-TTAGTAATG
* *
1340104 ATTTGATAATAACCATTATGATAATGATTTAATAATAATCATTATAATAATCATTATAACA
63 A--TAATAATAACCATTATAATAATGATTTAATAATAATCATTATAATAATCATT-TAACA
1340165 AT
1 AT
1340167 GTTTTAATTA
Statistics
Matches: 110, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
119 19 0.17
120 13 0.12
121 15 0.14
122 10 0.09
124 47 0.43
125 6 0.05
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.42
Consensus pattern (120 bp):
ATAATCATTATTATAATGATTTAATAATGAATTTAATATTAATGATTTGATGATTAGTAATGATA
ATAATAACCATTATAATAATGATTTAATAATAATCATTATAATAATCATTTAACA
Found at i:1340243 original size:60 final size:59
Alignment explanation
Indices: 1340177--1340514 Score: 311
Period size: 60 Copynumber: 5.6 Consensus size: 59
1340167 GTTTTAATTA
1340177 TAATGATTTGATAGTAATGACTTAGTAATGATTAGTAATAATGAAATTATTATTAATATT
1 TAATGATTTGATAGTAATGA-TTAGTAATGATTAGTAATAATGAAATTATTATTAATATT
* *
1340237 TAATGATTTGATATTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTT
1 TAATGATTTGATAGTAATGA-TTAGTAATGATTAGTAATAATGAAATTATTATTAATATT
* * * * *
1340297 TAATGATTTGATAGTAATGATTAGTAAT-AAT-GAAATTAT--TATTAATATTTAATGATT
1 TAATGATTTGATAGTAATGATTAGTAATGATTAGTAATAATGAAATTATTA-TTAAT-ATT
* ** *
1340354 TGAT-ATTAATGATTTAGTAATGATTAGTAAT-A--A-TAA-AATTGTTATTAATATTTAATGAT
1 TAATGATT--TGA--TAGTAATGATTAGTAATGATTAGTAATAA-TGAAATTATTA-TTAAT-AT
1340413 T
59 T
* * * *
1340414 TGATAGTAATAAT-TTAGTAATGATTAGTAATGATTAGTAATAATGAAATTGTTATTAATATT
1 T-A-A-TGAT-TTGATAGTAATGATTAGTAATGATTAGTAATAATGAAATTATTATTAATATT
*
1340476 TAATGATTTGATAGTAATGATTTAGTAATGATTAATAAT
1 TAATGATTTGATAGTAATGA-TTAGTAATGATTAGTAAT
1340515 GATTTAGTAA
Statistics
Matches: 232, Mismatches: 24, Indels: 44
0.77 0.08 0.15
Matches are distributed among these distances:
55 6 0.03
56 8 0.03
57 12 0.05
58 9 0.04
59 20 0.09
60 148 0.64
61 2 0.01
62 5 0.02
63 8 0.03
64 12 0.05
65 2 0.01
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.45
Consensus pattern (59 bp):
TAATGATTTGATAGTAATGATTAGTAATGATTAGTAATAATGAAATTATTATTAATATT
Found at i:1340315 original size:109 final size:109
Alignment explanation
Indices: 1340199--1340805 Score: 533
Period size: 109 Copynumber: 5.4 Consensus size: 109
1340189 AGTAATGACT
1340199 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTA
* *
1340264 ATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
66 ATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGA
1340308 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTA
*
1340373 ATGATTAGTAATAATAAAATTGTTATTAATATTTAATGATTTGA
66 ATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGA
* * * * * ** * *
1340417 TAGTAATAATTTAGTAATGATTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGA
1 TAGTAATGA-TTAGTAAT-AAT-GAAATTATTATTAAT-ATTTAA-TGAT-TTGATA-TTAATGA
* * * *
1340482 TTTGATAGTAATGATTTAGTAATGATTAATAATGATTTAGTAATGATTAGTAAT-AATT-A
59 -TT--TAGTAATGA-TTAGTAAT-AATAA-AATTA-TTATTAAT-ATT--TAATGATTTGA
* * * * * * *
1340541 -AATTATTATTAATATTTAATG-AATTGA-TATTAATGATTTAGTAATGA-TTAATAATAATGAA
1 TAGTAATGATTAGTA-ATAATGAAATT-ATTATTAAT-A-TT--TAATGATTTGATATTAATG-A
* * * * * *
1340602 ATT-GT--T-ATTAATATTTAAT-GATTTGA-TAGTAATGATTTAGTAATGA-TT--
59 TTTAGTAATGATTAGTA-ATAATAAAATT-ATTATTAAT-A-TT--TAATGATTTGA
*
1340650 TAGTAACGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTA
* *
1340715 ATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
66 ATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGA
* *
1340759 TAGTAATGATTGGTAATAATGAAATTATTCTTAATATTTAATGATTT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTT
1340806 AGTAATGATT
Statistics
Matches: 403, Mismatches: 55, Indels: 80
0.75 0.10 0.15
Matches are distributed among these distances:
106 15 0.04
107 14 0.03
108 4 0.01
109 180 0.45
110 55 0.14
111 4 0.01
112 19 0.05
113 6 0.01
114 4 0.01
115 5 0.01
116 9 0.02
117 3 0.01
119 15 0.04
120 25 0.06
121 7 0.02
122 12 0.03
123 15 0.04
124 4 0.01
125 3 0.01
126 4 0.01
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (109 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTA
ATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGA
Found at i:1340377 original size:169 final size:176
Alignment explanation
Indices: 1340177--1340763 Score: 542
Period size: 169 Copynumber: 3.4 Consensus size: 176
1340167 GTTTTAATTA
*
1340177 TAATGATTTGATAGTAATGACTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATG
1 TAATGATTTGATAGTAATGACTTAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATG
*
1340242 ATTTGATA-T-TAA-T-G-AT-TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAAT
66 ATTTGATAGTATAATTAGAATATTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAAT
1340301 GATTTGATAGTAATGA-TTAGTAATAATGAAATTATTATTAATATT
131 GATTTGATAGTAATGATTTAGTAATAATGAAATTATTATTAATATT
* * *
1340346 TAATGATTTGATATTAATGATTTAGTAATGATTAGTAATAATAAAATTGTTATTAATATTTAATG
1 TAATGATTTGATAGTAATGACTTAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATG
*
1340411 ATTTGATAGTAATAATTTAGTAATGATTAGTAATGATTAGTAATAATGAAATTGTTATTAATATT
66 ATTTGATAGT-ATAA-TTAG-AAT-ATTAGTAATGATTAGTAATAATGAAATTATTATTAATATT
* * * * *
1340476 TAATGATTTGATAGTAATGATTTAGTAATGAT-TAATAATGATT--TA-G
127 TAATGATTTGATAGTAATGATTTAGTAATAATGAAATTATTATTAATATT
* * * *
1340522 TAATGA--T--TAGTAAT-AATTA--AATTATTATTAATATTTAATGAATTGA-TATTAATGATT
1 TAATGATTTGATAGTAATGACTTAGTAATGATTAGTAATA-ATAA--AATT-ATTATTAAT-A-T
* * * * *
1340579 TAGTAATGA-TTAATA--ATAA-T-GAA-ATT-GT--T-ATTAATATTTAATG-ATTTGA-TAGT
60 T--TAATGATTTGATAGTATAATTAGAATATTAGTAATGATTAGTA-ATAATGAAATT-ATTATT
*
1340632 AATGATTTAGTAATGA-TT--TAGTAACGA-TTAGTAATAATGAAATTATTATTAATATT
121 AAT-A-TT--TAATGATTTGATAGTAATGATTTAGTAATAATGAAATTATTATTAATATT
* * * *
1340688 TAATGATTTGATATTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATG
1 TAATGATTTGATAGTAATGACTTAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATG
1340753 ATTTGATAGTA
66 ATTTGATAGTA
1340764 ATGATTGGTA
Statistics
Matches: 341, Mismatches: 37, Indels: 80
0.74 0.08 0.17
Matches are distributed among these distances:
162 25 0.07
163 23 0.07
164 2 0.01
165 6 0.02
166 21 0.06
167 5 0.01
168 5 0.01
169 84 0.25
170 22 0.06
171 8 0.02
172 26 0.08
173 13 0.04
174 4 0.01
175 6 0.02
176 12 0.04
177 4 0.01
179 65 0.19
180 10 0.03
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.45
Consensus pattern (176 bp):
TAATGATTTGATAGTAATGACTTAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATG
ATTTGATAGTATAATTAGAATATTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAAT
GATTTGATAGTAATGATTTAGTAATAATGAAATTATTATTAATATT
Found at i:1340410 original size:131 final size:127
Alignment explanation
Indices: 1340275--1340769 Score: 475
Period size: 130 Copynumber: 3.7 Consensus size: 127
1340265 TGATTAGTAA
1340275 TAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTATT
1 TAATG-AATTATTATTAATTTTTAATGA-TT--TAGTAATGATTAGTAATAATGAAATTATTATT
* *
1340340 AATATTTAATGATTTGATATTAATGATTTAGTAATGATTAGTAATAATAAAATTGTTATTAATAT
62 AATATTTAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATAAAATTATTATTAATAT
1340405 T
127 T
* * * *
1340406 TAATGATTTGATAGTAATAATTTAGTAATGA-TTAGTAATGATTAGTAATAATGAAATTGTTATT
1 TAATGAATT-AT--TATTAATTT-TTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATT
* * * * *
1340470 AATATTTAATGATTTGATAGTAATGATTTAGTAATGATTAATAATGATTTAGTAATGATTAGTAA
62 AATATTTAATGATTTGATAGTAATGATTTAGTAATGATTAGTAAT-A-ATA-AAATTATTATTAA
1340535 TAATT
124 T-ATT
* * * *
1340540 AAATTATTATTAATATTTAATGAATTGATATTAATGATTTAGTAATGATTAATAATAATGAAATT
1 TAATGA--A-T--TA-TT-ATTAATT--T-TTAATGATTTAGTAATGATTAGTAATAATGAAATT
*
1340605 GTTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGATTTAGTAACGATTAGTAATAAT
56 ATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGA-TTAGT----A--A-TAAT-A-
1340670 GAAATTATTATTAATATT
111 -AAATTATTATTAATATT
* *
1340688 TAATG-ATT-TGA-T-A---TTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATT
1 TAATGAATTATTATTAATTTTTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATA
1340746 TTTAATGATTTGATAGTAATGATT
66 TTTAATGATTTGATAGTAATGATT
1340770 GGTAATAATG
Statistics
Matches: 306, Mismatches: 30, Indels: 56
0.78 0.08 0.14
Matches are distributed among these distances:
130 77 0.25
131 74 0.24
132 3 0.01
133 18 0.06
134 13 0.04
137 3 0.01
138 6 0.02
139 3 0.01
140 9 0.03
141 69 0.23
142 5 0.02
144 1 0.00
145 1 0.00
146 1 0.00
147 1 0.00
148 9 0.03
149 13 0.04
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (127 bp):
TAATGAATTATTATTAATTTTTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATA
TTTAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATAAAATTATTATTAATATT
Found at i:1340503 original size:11 final size:11
Alignment explanation
Indices: 1340487--1340666 Score: 82
Period size: 11 Copynumber: 16.6 Consensus size: 11
1340477 AATGATTTGA
1340487 TAGTAATGATT
1 TAGTAATGATT
1340498 TAGTAATGA-T
1 TAGTAATGATT
*
1340508 TAATAATGATT
1 TAGTAATGATT
1340519 TAGTAATGA-T
1 TAGTAATGATT
*
1340529 TAGTAAT-AAT
1 TAGTAATGATT
*
1340539 TA--AATTA-T
1 TAGTAATGATT
*
1340547 TATTAAT-ATT
1 TAGTAATGATT
*
1340557 TAATGAATTGA--
1 TAGT-AA-TGATT
*
1340568 TATTAATGATT
1 TAGTAATGATT
1340579 TAGTAATGATT
1 TAGTAATGATT
*
1340590 AATAATAATGAAATTGT
1 --TAGTAATG--A-T-T
*
1340607 TATTAAT-A-T
1 TAGTAATGATT
1340616 T--TAATGATTT
1 TAGTAATGA-TT
1340626 GATAGTAATGATT
1 --TAGTAATGATT
1340639 TAGTAATGATT
1 TAGTAATGATT
*
1340650 TAGTAACGA-T
1 TAGTAATGATT
1340660 TAGTAAT
1 TAGTAAT
1340667 AATGAAATTA
Statistics
Matches: 136, Mismatches: 9, Indels: 49
0.70 0.05 0.25
Matches are distributed among these distances:
7 4 0.03
8 7 0.05
9 8 0.06
10 37 0.27
11 52 0.38
12 3 0.02
13 10 0.07
14 6 0.04
15 7 0.05
16 1 0.01
17 1 0.01
ACGTcount: A:0.42, C:0.01, G:0.13, T:0.44
Consensus pattern (11 bp):
TAGTAATGATT
Found at i:1340515 original size:21 final size:21
Alignment explanation
Indices: 1340490--1340595 Score: 105
Period size: 21 Copynumber: 5.2 Consensus size: 21
1340480 GATTTGATAG
1340490 TAATGATTTAGTAATGATTAA
1 TAATGATTTAGTAATGATTAA
*
1340511 TAATGATTTAGTAATGATTAG
1 TAATGATTTAGTAATGATTAA
* * *
1340532 TAAT-AATTA--AATTATTAT
1 TAATGATTTAGTAATGATTAA
* *
1340550 TAAT-ATTTAATGAATTGA-TAT
1 TAATGATTTAGT-AA-TGATTAA
1340571 TAATGATTTAGTAATGATTAA
1 TAATGATTTAGTAATGATTAA
1340592 TAAT
1 TAAT
1340596 AATGAAATTG
Statistics
Matches: 71, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
18 15 0.21
20 7 0.10
21 41 0.58
22 8 0.11
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.45
Consensus pattern (21 bp):
TAATGATTTAGTAATGATTAA
Found at i:1340546 original size:211 final size:212
Alignment explanation
Indices: 1340308--1340726 Score: 750
Period size: 211 Copynumber: 2.0 Consensus size: 212
1340298 AATGATTTGA
*
1340308 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGAATTGATATTAATGATTTAGTA
*
1340373 ATGATTAGTAATAATAAAATTGTTATTAATATTTAATGATTTGATAGTAATAATTTAGTAATGA-
66 ATGATTAATAATAATAAAATTGTTATTAATATTTAATGATTTGATAGTAATAATTTAGTAATGAT
* *
1340437 TTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTTAGT
131 TTAGTAACGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGT
1340502 AATGATTAATAATGATT
196 AATGATTAATAATGATT
*
1340519 TAGTAATGATTAGTAATAATTAAATTATTATTAATATTTAATGAATTGATATTAATGATTTAGTA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGAATTGATATTAATGATTTAGTA
* *
1340584 ATGATTAATAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGAT
66 ATGATTAATAATAATAAAATTGTTATTAATATTTAATGATTTGATAGTAATAATTTAGTAATGAT
*
1340649 TTAGTAACGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGT
131 TTAGTAACGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGT
*
1340714 AATGATTAGTAAT
196 AATGATTAATAAT
1340727 AATGAAATTA
Statistics
Matches: 198, Mismatches: 9, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
211 124 0.63
212 74 0.37
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (212 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGAATTGATATTAATGATTTAGTA
ATGATTAATAATAATAAAATTGTTATTAATATTTAATGATTTGATAGTAATAATTTAGTAATGAT
TTAGTAACGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGT
AATGATTAATAATGATT
Found at i:1340581 original size:60 final size:60
Alignment explanation
Indices: 1340511--1340769 Score: 356
Period size: 60 Copynumber: 4.1 Consensus size: 60
1340501 TAATGATTAA
* * *
1340511 TAATGATTTAGTAATGATTAGTAATAATTAAATTATTATTAATATTTAATGAATTGATAT
1 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAG
* *
1340571 TAATGATTTAGTAATGATTAATAATAATGAAATTGTTATTAATATTTAATGATTTGATAG
1 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAG
1340631 TAATGATTTAGTAATGATTTAGTAACGATTAGTAATAATGAAATTATTATTAATATTTAATGATT
1 TAATGATTTAG---T-A---A-T---GATTAGTAATAATGAAATTATTATTAATATTTAATGATT
*
1340696 TGATAT
55 TGATAG
*
1340702 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAG
1 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAG
1340762 TAATGATT
1 TAATGATT
1340770 GGTAATAATG
Statistics
Matches: 178, Mismatches: 10, Indels: 22
0.85 0.05 0.10
Matches are distributed among these distances:
60 117 0.66
63 2 0.01
64 2 0.01
67 2 0.01
68 2 0.01
71 53 0.30
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.46
Consensus pattern (60 bp):
TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAG
Found at i:1340646 original size:25 final size:24
Alignment explanation
Indices: 1340617--1340720 Score: 67
Period size: 22 Copynumber: 4.3 Consensus size: 24
1340607 TATTAATATT
1340617 TAATGATTTGATAGTAATGATTTAG
1 TAATGATTT-ATAGTAATGATTTAG
* *
1340642 TAATGA-TT-TAGTAACGATTAGTAA
1 TAATGATTTATAGTAATGATT--TAG
* *
1340666 TAATGAAATTATTATTAAT-A-TT--
1 TAATG-ATTTA-TAGTAATGATTTAG
*
1340688 TAATGATTTGATATTAATGATTTAG
1 TAATGATTT-ATAGTAATGATTTAG
1340713 TAATGATT
1 TAATGATT
1340721 AGTAATAATG
Statistics
Matches: 63, Mismatches: 5, Indels: 22
0.70 0.06 0.24
Matches are distributed among these distances:
21 10 0.16
22 17 0.27
23 2 0.03
24 10 0.16
25 15 0.24
26 3 0.05
27 1 0.02
28 5 0.08
ACGTcount: A:0.39, C:0.01, G:0.14, T:0.45
Consensus pattern (24 bp):
TAATGATTTATAGTAATGATTTAG
Found at i:1340689 original size:49 final size:47
Alignment explanation
Indices: 1340642--1340815 Score: 154
Period size: 49 Copynumber: 3.4 Consensus size: 47
1340632 AATGATTTAG
*
1340642 TAATGATTTAGTAACGATTAGTAATAATGAAATTATTATTAATATTT
1 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTT
*
1340689 AATGATTTGATATTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAAT-TTT
1 --T-A-ATG--ATT--T-A----GTAATGATTAGTAATAATGAAATTATTATTAATATTT
* *
1340748 TAATGATTTGATAGTAATGATTGGTAATAATGAAATTATTCTTAATA-TT
1 TAATGA-TT--TAGTAATGATTAGTAATAATGAAATTATTATTAATATTT
1340797 TAATGATTTAGTAATGATT
1 TAATGATTTAGTAATGATT
1340816 TGATAGTAAT
Statistics
Matches: 106, Mismatches: 6, Indels: 29
0.75 0.04 0.21
Matches are distributed among these distances:
46 11 0.10
48 2 0.02
49 40 0.38
50 1 0.01
51 2 0.02
53 5 0.05
54 4 0.04
55 3 0.03
56 2 0.02
57 1 0.01
59 3 0.03
60 32 0.30
ACGTcount: A:0.40, C:0.01, G:0.13, T:0.46
Consensus pattern (47 bp):
TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTT
Found at i:1340754 original size:46 final size:46
Alignment explanation
Indices: 1340701--1340815 Score: 176
Period size: 49 Copynumber: 2.4 Consensus size: 46
1340691 TGATTTGATA
*
1340701 TTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTT
1 TTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATAT
* *
1340747 TTAATGATTTGATAGTAATGATTGGTAATAATGAAATTATTCTTAATAT
1 TTAATGA-TT--TAGTAATGATTAGTAATAATGAAATTATTATTAATAT
1340796 TTAATGATTTAGTAATGATT
1 TTAATGATTTAGTAATGATT
1340816 TGATAGTAAT
Statistics
Matches: 63, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
46 18 0.29
47 2 0.03
48 2 0.03
49 41 0.65
ACGTcount: A:0.39, C:0.01, G:0.13, T:0.47
Consensus pattern (46 bp):
TTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATAT
Found at i:1340775 original size:141 final size:139
Alignment explanation
Indices: 1340431--1340775 Score: 537
Period size: 131 Copynumber: 2.5 Consensus size: 139
1340421 AATAATTTAG
1340431 TAATGA-TTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATG
1 TAATGATTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATG
*
1340495 ATTTAGTAATGATTAATAATGATTTAGTAATGATTAGTAATAATTAAATTATTATTAATATTTAA
66 A-TT-GTAATGATTAATAATGATTTAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAA
*
1340560 TGAATTGATAT
129 TGATTTGATAT
*
1340571 TAATGATTTAGTAATGATTAATAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATG
1 TAATGATTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATG
* *
1340636 ATT-T-A-G-----TAATGATTTAGTAACGATTAGTAATAATGAAATTATTATTAATATTTAATG
66 ATTGTAATGATTAATAATGATTTAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATG
1340693 ATTTGATAT
131 ATTTGATAT
* *
1340702 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATG
1 TAATGATTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATG
1340767 ATTGGTAAT
66 ATT-GTAAT
1340776 AATGAAATTA
Statistics
Matches: 193, Mismatches: 7, Indels: 15
0.90 0.03 0.07
Matches are distributed among these distances:
131 122 0.63
133 1 0.01
134 1 0.01
136 1 0.01
137 1 0.01
138 1 0.01
140 8 0.04
141 58 0.30
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.45
Consensus pattern (139 bp):
TAATGATTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATG
ATTGTAATGATTAATAATGATTTAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATG
ATTTGATAT
Found at i:1340802 original size:131 final size:130
Alignment explanation
Indices: 1340308--1340781 Score: 512
Period size: 131 Copynumber: 3.5 Consensus size: 130
1340298 AATGATTTGA
* * *
1340308 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTA
1 TAGTAATGATTAATAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAATA
** * * * *
1340373 ATG-ATTAGT-A-A-TAATAA-AATTGTTATTAATATTTAATGATTTGATAGTAATAAT-TTAGT
66 ATGAATTAGTAACATTAATAATAA-TGAAATTATTA-TTAAT-ATTTAAT-G-AAT--TGATATT
1340432 AATGA-T
124 AATGATT
* *
1340438 TAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTTAGTA
1 TAGTAATGATTAATAATAATGAAATTATTATTAATATTTAATGATTTGATAGT-A--A--T-G--
* * * *
1340503 ATGATTAATAATGATTTAGTAATGATTAGTAATAATTAAATTATTATTAATATTTAATGAATTGA
58 AT--TTAATAATGAATTAGTAA-CATTAATAATAATGAAATTATTATTAATATTTAATGAATTGA
1340568 TATTAATGATT
120 TATTAATGATT
* *
1340579 TAGTAATGATTAATAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTTAGTA
1 TAGTAATGATTAATAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAATA
* * *
1340644 ATGATTTAGTAACGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGAT
66 ATGAATTAGTAAC-ATTAATAATAATGAAATTATTATTAATATTTAATGAATTGATATTAATGAT
1340709 T
130 T
* *
1340710 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTGGTAA
1 TAGTAATGATTAATAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATT--TAA
1340775 TAATGAA
64 TAATGAA
1340782 ATTATTCTTA
Statistics
Matches: 301, Mismatches: 22, Indels: 39
0.83 0.06 0.11
Matches are distributed among these distances:
130 51 0.17
131 125 0.42
133 11 0.04
135 2 0.01
136 2 0.01
138 3 0.01
139 1 0.00
140 17 0.06
141 61 0.20
142 2 0.01
143 6 0.02
144 6 0.02
145 12 0.04
146 2 0.01
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (130 bp):
TAGTAATGATTAATAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAATA
ATGAATTAGTAACATTAATAATAATGAAATTATTATTAATATTTAATGAATTGATATTAATGATT
Found at i:1343057 original size:15 final size:14
Alignment explanation
Indices: 1343034--1343064 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
1343024 TACAACACTA
1343034 AACTTTAATATAAT
1 AACTTTAATATAAT
1343048 AACTTATAATATAAT
1 AACTT-TAATATAAT
1343063 AA
1 AA
1343065 ACTAATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AACTTTAATATAAT
Found at i:1343425 original size:22 final size:21
Alignment explanation
Indices: 1343387--1343427 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1343377 TTTATGTATA
*
1343387 ATATAACTTAAACTAACAATC
1 ATATAACCTAAACTAACAATC
*
1343408 ATATAACCCTAAATTAACAA
1 ATATAA-CCTAAACTAACAA
1343428 ACTAATTAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.54, C:0.20, G:0.00, T:0.27
Consensus pattern (21 bp):
ATATAACCTAAACTAACAATC
Found at i:1343566 original size:13 final size:13
Alignment explanation
Indices: 1343527--1343573 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
1343517 CTCACAAGAG
1343527 CCTTATCTCCCTTT
1 CCTT-TCTCCCTTT
* *
1343541 CTTCTTCTTCCTTT
1 CCT-TTCTCCCTTT
1343555 CCTTTCTCCCTTT
1 CCTTTCTCCCTTT
1343568 -CTTTCT
1 CCTTTCT
1343574 TTCTCGGCTG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 6 0.21
13 9 0.32
14 12 0.43
15 1 0.04
ACGTcount: A:0.02, C:0.40, G:0.00, T:0.57
Consensus pattern (13 bp):
CCTTTCTCCCTTT
Found at i:1343600 original size:29 final size:27
Alignment explanation
Indices: 1343568--1343632 Score: 87
Period size: 26 Copynumber: 2.4 Consensus size: 27
1343558 TTCTCCCTTT
*
1343568 CTTTCTTTCTCGGCTGCAATTTCTTCTCC
1 CTTTCTTTCT--GCTGCAATCTCTTCTCC
1343597 CTTTC-TTCTGCTGCAATCTCTTCTCC
1 CTTTCTTTCTGCTGCAATCTCTTCTCC
*
1343623 ATTTCTTTCT
1 CTTTCTTTCT
1343633 TTTATGTTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 20 0.61
27 4 0.12
28 4 0.12
29 5 0.15
ACGTcount: A:0.08, C:0.34, G:0.08, T:0.51
Consensus pattern (27 bp):
CTTTCTTTCTGCTGCAATCTCTTCTCC
Found at i:1343722 original size:33 final size:33
Alignment explanation
Indices: 1343675--1343741 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
1343665 ATAATTTAGG
*
1343675 TGTCACCGACTGCCTTAATTATTTCACCAATAA
1 TGTCACCGACTGCCTCAATTATTTCACCAATAA
**
1343708 TGTCACCGGTTGCCTCAATTATTTCACCAATAA
1 TGTCACCGACTGCCTCAATTATTTCACCAATAA
1343741 T
1 T
1343742 TGTGCAATTG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.28, C:0.27, G:0.10, T:0.34
Consensus pattern (33 bp):
TGTCACCGACTGCCTCAATTATTTCACCAATAA
Found at i:1343893 original size:18 final size:19
Alignment explanation
Indices: 1343861--1343899 Score: 71
Period size: 18 Copynumber: 2.1 Consensus size: 19
1343851 AGGCATGCAG
1343861 CGGGAGCAGGAGGGGAGCA
1 CGGGAGCAGGAGGGGAGCA
1343880 CGGGAGCA-GAGGGGAGCA
1 CGGGAGCAGGAGGGGAGCA
1343898 CG
1 CG
1343900 TGAAGCTTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.26, C:0.18, G:0.56, T:0.00
Consensus pattern (19 bp):
CGGGAGCAGGAGGGGAGCA
Found at i:1343991 original size:29 final size:29
Alignment explanation
Indices: 1343915--1343996 Score: 110
Period size: 29 Copynumber: 2.8 Consensus size: 29
1343905 CTTGGTCTCC
* ***
1343915 GGGACTGCTTGGCGACCTACAAGGTCGCT
1 GGGAGTGCTTGGCGACCTTGTAGGTCGCT
* *
1343944 GGGAGTGCATGGCGACCTTGTAGGTTGCT
1 GGGAGTGCTTGGCGACCTTGTAGGTCGCT
1343973 GGGAGTGCTTGGCGACCTTGTAGG
1 GGGAGTGCTTGGCGACCTTGTAGG
1343997 GGTGTTGGGG
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.15, C:0.21, G:0.40, T:0.24
Consensus pattern (29 bp):
GGGAGTGCTTGGCGACCTTGTAGGTCGCT
Found at i:1344020 original size:31 final size:29
Alignment explanation
Indices: 1343941--1344021 Score: 108
Period size: 29 Copynumber: 2.7 Consensus size: 29
1343931 CTACAAGGTC
*
1343941 GCTGGGAGTGCATGGCGACCTTGTAGGTT
1 GCTGGGAGTGCATGGCGACCTTGTAGGGT
*
1343970 GCTGGGAGTGCTTGGCGACCTTGTAGGGGT
1 GCTGGGAGTGCATGGCGACCTTGTA-GGGT
* *
1344000 GTTGGGGAATGCATGGCGACCT
1 GCT-GGGAGTGCATGGCGACCT
1344022 GTTGGGAACG
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
29 24 0.53
30 5 0.11
31 16 0.36
ACGTcount: A:0.14, C:0.17, G:0.43, T:0.26
Consensus pattern (29 bp):
GCTGGGAGTGCATGGCGACCTTGTAGGGT
Found at i:1348793 original size:6 final size:6
Alignment explanation
Indices: 1348784--1348808 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1348774 GGGATGATAA
1348784 ACGGGG ACGGGG ACGGGG ACGGGG A
1 ACGGGG ACGGGG ACGGGG ACGGGG A
1348809 AAACCCATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.16, G:0.64, T:0.00
Consensus pattern (6 bp):
ACGGGG
Found at i:1348888 original size:13 final size:13
Alignment explanation
Indices: 1348872--1348915 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
1348862 GCCCCGATTA
*
1348872 CCCGATTATCCGC
1 CCCGATTACCCGC
1348885 CCCGATTACCCGC
1 CCCGATTACCCGC
*
1348898 CCCGA-TACCCGA
1 CCCGATTACCCGC
1348910 CCCGAT
1 CCCGAT
1348916 AAATATTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 11 0.39
13 17 0.61
ACGTcount: A:0.18, C:0.50, G:0.16, T:0.16
Consensus pattern (13 bp):
CCCGATTACCCGC
Found at i:1348908 original size:12 final size:12
Alignment explanation
Indices: 1348881--1348916 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
1348871 ACCCGATTAT
1348881 CCGCCCCGATTAC
1 CCGCCCCGA-TAC
1348894 CCGCCCCGATAC
1 CCGCCCCGATAC
*
1348906 CCGACCCGATA
1 CCGCCCCGATA
1348917 AATATTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 13 0.59
13 9 0.41
ACGTcount: A:0.19, C:0.53, G:0.17, T:0.11
Consensus pattern (12 bp):
CCGCCCCGATAC
Found at i:1349046 original size:12 final size:12
Alignment explanation
Indices: 1349029--1349066 Score: 76
Period size: 12 Copynumber: 3.2 Consensus size: 12
1349019 ACCCGATTCT
1349029 CGGCCCAATACC
1 CGGCCCAATACC
1349041 CGGCCCAATACC
1 CGGCCCAATACC
1349053 CGGCCCAATACC
1 CGGCCCAATACC
1349065 CG
1 CG
1349067 TTTAAATAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.24, C:0.50, G:0.18, T:0.08
Consensus pattern (12 bp):
CGGCCCAATACC
Found at i:1351078 original size:25 final size:25
Alignment explanation
Indices: 1351050--1351103 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
1351040 TGTGAAGAAG
* *
1351050 CTTTTGCTTGTTTCTGGTATTTGTT
1 CTTTTACTTGTTTCTGGTACTTGTT
1351075 CTTTTACTTGTTTCTGGTACTTGTT
1 CTTTTACTTGTTTCTGGTACTTGTT
1351100 CTTT
1 CTTT
1351104 GCACTCGTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.06, C:0.15, G:0.17, T:0.63
Consensus pattern (25 bp):
CTTTTACTTGTTTCTGGTACTTGTT
Found at i:1354853 original size:21 final size:20
Alignment explanation
Indices: 1354811--1354871 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
1354801 AAACTTGGTA
*
1354811 TTTCTTAATGATTTTT-TAAT
1 TTTCTTTATG-TTTTTATAAT
1354831 TTTCTTTATGTTCTTTATAAT
1 TTTCTTTATGTT-TTTATAAT
**
1354852 TTTAATTAT-TTTTTATAAT
1 TTTCTTTATGTTTTTATAAT
1354871 T
1 T
1354872 AAAAAATTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
19 11 0.31
20 14 0.39
21 11 0.31
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.67
Consensus pattern (20 bp):
TTTCTTTATGTTTTTATAAT
Found at i:1354866 original size:19 final size:20
Alignment explanation
Indices: 1354822--1354871 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
1354812 TTCTTAATGA
**
1354822 TTTTT-TAATTTTCTTTATG
1 TTTTTATAATTTTAATTATG
1354841 TTCTTTATAATTTTAATTAT-
1 TT-TTTATAATTTTAATTATG
1354861 TTTTTATAATT
1 TTTTTATAATT
1354872 AAAAAATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 11 0.41
20 5 0.19
21 11 0.41
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.70
Consensus pattern (20 bp):
TTTTTATAATTTTAATTATG
Found at i:1355597 original size:16 final size:16
Alignment explanation
Indices: 1355576--1355612 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
1355566 ATATAAATTA
*
1355576 AATAAAGATATTTAAT
1 AATAAAGATATTAAAT
1355592 AATAAAGATATTAAAT
1 AATAAAGATATTAAAT
1355608 AATAA
1 AATAA
1355613 GGAGATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.32
Consensus pattern (16 bp):
AATAAAGATATTAAAT
Found at i:1360241 original size:35 final size:35
Alignment explanation
Indices: 1360196--1360266 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
1360186 GTGAACAATA
1360196 AATATAGTTAACCAATAATTTTATTAATCACTCTC
1 AATATAGTTAACCAATAATTTTATTAATCACTCTC
1360231 AATATAGTTAACCAATAATTTTATTAATCACTCTC
1 AATATAGTTAACCAATAATTTTATTAATCACTCTC
1360266 A
1 A
1360267 TTTGTTTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.41, C:0.17, G:0.03, T:0.39
Consensus pattern (35 bp):
AATATAGTTAACCAATAATTTTATTAATCACTCTC
Found at i:1360470 original size:15 final size:16
Alignment explanation
Indices: 1360426--1360472 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
1360416 AAAATTAAAT
*
1360426 TTGAAAGTTAGAGTGA
1 TTGAAAGTTAGAGTAA
1360442 TT-AAA-TTAGGAGTAA
1 TTGAAAGTTA-GAGTAA
1360457 TTGAAAGTTA-AGTAA
1 TTGAAAGTTAGAGTAA
1360472 T
1 T
1360473 AAAATTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
14 3 0.11
15 16 0.59
16 5 0.19
17 3 0.11
ACGTcount: A:0.43, C:0.00, G:0.23, T:0.34
Consensus pattern (16 bp):
TTGAAAGTTAGAGTAA
Found at i:1360837 original size:55 final size:55
Alignment explanation
Indices: 1360734--1360844 Score: 179
Period size: 55 Copynumber: 2.0 Consensus size: 55
1360724 AGAGTGGGAC
* *
1360734 AATTCTGTTGTTTGTGTAGGTCCCTGTGGTGGATCGGTAACCTTAAAAAAGGCAA
1 AATTATGTTGTTTGTGTAGGTCCCTGTGGTGGATCAGTAACCTTAAAAAAGGCAA
* *
1360789 AATTATGTTGTTTGTGTGGGTCCCTGTGGTGG-TCAGTGACCTTAAAAAAGGCAA
1 AATTATGTTGTTTGTGTAGGTCCCTGTGGTGGATCAGTAACCTTAAAAAAGGCAA
1360843 AA
1 AA
1360845 CTGAATGGAC
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
54 22 0.42
55 30 0.58
ACGTcount: A:0.26, C:0.14, G:0.28, T:0.32
Consensus pattern (55 bp):
AATTATGTTGTTTGTGTAGGTCCCTGTGGTGGATCAGTAACCTTAAAAAAGGCAA
Found at i:1372707 original size:3 final size:3
Alignment explanation
Indices: 1372701--1372774 Score: 148
Period size: 3 Copynumber: 24.7 Consensus size: 3
1372691 CTACAACATT
1372701 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1372749 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
1372775 ATATTCAAAA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 71 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:1377419 original size:20 final size:20
Alignment explanation
Indices: 1377394--1377432 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1377384 TAAATTAAAT
*
1377394 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
1377414 ATTAGATAGAATCAGTTTT
1 ATTAGATAGAATCAGTTTT
1377433 TATTCTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.05, G:0.18, T:0.41
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:1377470 original size:19 final size:20
Alignment explanation
Indices: 1377446--1377483 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1377436 TCTATTAGTT
*
1377446 ATTAGATAGGATC-ATTTTA
1 ATTAGATAGAATCAATTTTA
1377465 ATTAGATAGAATCAATTTT
1 ATTAGATAGAATCAATTTT
1377484 TTATTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.39, C:0.05, G:0.13, T:0.42
Consensus pattern (20 bp):
ATTAGATAGAATCAATTTTA
Found at i:1377485 original size:52 final size:51
Alignment explanation
Indices: 1377393--1377541 Score: 246
Period size: 52 Copynumber: 2.9 Consensus size: 51
1377383 CTAAATTAAA
1377393 TATTAGATAGGATCAGTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
1 TATTAGATAGGATCAGTTTTAATTAGATAGAATCA-TTTTTATTCTATTAGT
*
1377445 TATTAGATAGGATCA-TTTTAATTAGATAGAATCAATTTTTTATTTTATTAGT
1 TATTAGATAGGATCAGTTTTAATTAGATAGAATC-A-TTTTTATTCTATTAGT
*
1377497 TATTAGATAGGATCATTTTTAATTAGATAGAATCATTTTTATTCT
1 TATTAGATAGGATCAGTTTTAATTAGATAGAATCATTTTTATTCT
1377542 TTTGCTAATT
Statistics
Matches: 92, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
51 27 0.29
52 47 0.51
53 18 0.20
ACGTcount: A:0.34, C:0.05, G:0.13, T:0.48
Consensus pattern (51 bp):
TATTAGATAGGATCAGTTTTAATTAGATAGAATCATTTTTATTCTATTAGT
Found at i:1377523 original size:20 final size:20
Alignment explanation
Indices: 1377498--1377537 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1377488 TTTATTAGTT
*
1377498 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCATTTTTA
1377518 ATTAGATAGAATCATTTTTA
1 ATTAGATAGAATCATTTTTA
1377538 TTCTTTTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCATTTTTA
Found at i:1382131 original size:20 final size:20
Alignment explanation
Indices: 1382106--1382144 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1382096 TAAATTAAAT
*
1382106 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
1382126 ATTAGATAGAATCAGTTTT
1 ATTAGATAGAATCAGTTTT
1382145 TATTCTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.05, G:0.18, T:0.41
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:1382190 original size:19 final size:20
Alignment explanation
Indices: 1382158--1382195 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
1382148 TCTATTAGTT
1382158 ATTAGATATGATCA-TTTTA
1 ATTAGATATGATCAGTTTTA
1382177 ATTAGATA-GAATCAGTTTT
1 ATTAGATATG-ATCAGTTTT
1382196 TTATTCTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 1 0.06
19 12 0.71
20 4 0.24
ACGTcount: A:0.37, C:0.05, G:0.13, T:0.45
Consensus pattern (20 bp):
ATTAGATATGATCAGTTTTA
Found at i:1382197 original size:52 final size:52
Alignment explanation
Indices: 1382105--1382254 Score: 266
Period size: 52 Copynumber: 2.9 Consensus size: 52
1382095 CTAAATTAAA
1382105 TATTAGATAGGATCAGTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
1 TATTAGATAGGATCAGTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
*
1382157 TATTAGATATGATCA-TTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
1 TATTAGATAGGATCAGTTTTAATTAGATAGAATCAG-TTTTTATTCTATTAGT
*
1382209 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCT
1 TATTAGATAGGATCAGTTTTAATTAGATAGAATCAGTTTTTATTCT
1382255 GTTGCTAATT
Statistics
Matches: 94, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
51 20 0.21
52 54 0.57
53 20 0.21
ACGTcount: A:0.33, C:0.06, G:0.13, T:0.48
Consensus pattern (52 bp):
TATTAGATAGGATCAGTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
Found at i:1382235 original size:20 final size:21
Alignment explanation
Indices: 1382210--1382250 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
1382200 TCTATTAGTT
*
1382210 ATTAGATAGGATCA-TTTTTA
1 ATTAGATAGAATCAGTTTTTA
1382230 ATTAGATAGAATCAGTTTTTA
1 ATTAGATAGAATCAGTTTTTA
1382251 TTCTGTTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.44
Consensus pattern (21 bp):
ATTAGATAGAATCAGTTTTTA
Found at i:1387036 original size:25 final size:25
Alignment explanation
Indices: 1387008--1387063 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
1386998 CCACCATGCT
1387008 TATTTTCCCAAAATCGTTTGAGCTA
1 TATTTTCCCAAAATCGTTTGAGCTA
* * *
1387033 TATTTTCCCAGAATTGTTTGAGTTA
1 TATTTTCCCAAAATCGTTTGAGCTA
*
1387058 CATTTT
1 TATTTT
1387064 ATGGATCAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.25, C:0.16, G:0.12, T:0.46
Consensus pattern (25 bp):
TATTTTCCCAAAATCGTTTGAGCTA
Found at i:1387127 original size:28 final size:28
Alignment explanation
Indices: 1387083--1387139 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
1387073 CTCTTCGTTT
*
1387083 ATATTATATCGATGAGTCAGTCCTTGAA
1 ATATTATATCGATGAGTCAATCCTTGAA
*
1387111 ATATTATATCG-TCGAGTCAATGCTTGAA
1 ATATTATATCGAT-GAGTCAATCCTTGAA
1387139 A
1 A
1387140 GTAACGGCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 1 0.04
28 25 0.96
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (28 bp):
ATATTATATCGATGAGTCAATCCTTGAA
Found at i:1389691 original size:73 final size:73
Alignment explanation
Indices: 1389569--1389800 Score: 383
Period size: 73 Copynumber: 3.2 Consensus size: 73
1389559 AAAAATGCGC
* *
1389569 GAGTGTTTGTCTATATGCGGCCTAACGGTCTTGATTCTTCAGATCTAAAAATGCGCGCGAGCGAC
1 GAGTGTGTGTCTATATGCGGCCTAACGGTCTTGATTCTTCAGATTTAAAAATGCGCGCGAGCGAC
1389634 ATTGAAGT
66 ATTGAAGT
* * *
1389642 GAGTGTTTGTCTTTATGCGGCCTAACGGTCTTGATTCTTCAGATTTAAAAATGCGCGCGAGCAAC
1 GAGTGTGTGTCTATATGCGGCCTAACGGTCTTGATTCTTCAGATTTAAAAATGCGCGCGAGCGAC
1389707 ATTGAAGT
66 ATTGAAGT
* * *
1389715 GAGGGTGTGTCTATATGCGGTCTAACGGTCTTGATTCTTCAGATTTAAAATTGCGCGCGAGCGAC
1 GAGTGTGTGTCTATATGCGGCCTAACGGTCTTGATTCTTCAGATTTAAAAATGCGCGCGAGCGAC
1389780 ATTGAAGT
66 ATTGAAGT
*
1389788 GAGCGTGTGTCTA
1 GAGTGTGTGTCTA
1389801 CGTGCGCGGT
Statistics
Matches: 149, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
73 149 1.00
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (73 bp):
GAGTGTGTGTCTATATGCGGCCTAACGGTCTTGATTCTTCAGATTTAAAAATGCGCGCGAGCGAC
ATTGAAGT
Found at i:1389974 original size:93 final size:92
Alignment explanation
Indices: 1389816--1390142 Score: 268
Period size: 93 Copynumber: 3.5 Consensus size: 92
1389806 GCGGTTTTTT
* * * * * *
1389816 TTTTCTGTCTATATGCAGCCTAACGGTCTTGA-TTCTTCCTAAATGGAATATCGCAG-GCTGTAT
1 TTTT-TGTCAATATACAGCGTAACGGTCTTGATTTC-TCCTAAA-GGAA-ATCACAGAACTGCAT
* ** *
1389879 TTAAGTGAGTGTGCATCTGCAAGTGTGCGCG
62 TTAAGTAAGTGTGCATCCACAAGTGTGCACG
* *
1389910 TTTTTGTTAATATACGGCGTAACGGTCTTGATTTCTCCTAAAGGAAATCACATGAACTGCATTTA
1 TTTTTGTCAATATACAGCGTAACGGTCTTGATTTCTCCTAAAGGAAATCACA-GAACTGCATTTA
* * *
1389975 TGTAAGTGTGTATCCACAAGTGTGCATG
65 AGTAAGTGTGCATCCACAAGTGTGCACG
* * * * *
1390003 TTTTTGTCAGTATACAGTGTAACGGTCTTGATTCCTCCTAAA-TAGAATCACACAGACTGCATTT
1 TTTTTGTCAATATACAGCGTAACGGTCTTGATTTCTCCTAAAGGA-AATCACAGA-ACTGCATTT
* * * * * * *
1390067 AAGT--TTGTGCGTCTAAAAGTTTTCACA
64 AAGTAAGTGTGCATCCACAAGTGTGCACG
* ** * *
1390094 TTTTGGTCAATATACAGCGTAATAGTCTTGATTCCTCCTAAAGGCAATC
1 TTTTTGTCAATATACAGCGTAACGGTCTTGATTTCTCCTAAAGGAAATC
1390143 GCGTGAGCGC
Statistics
Matches: 188, Mismatches: 39, Indels: 15
0.78 0.16 0.06
Matches are distributed among these distances:
91 60 0.32
92 7 0.04
93 114 0.61
94 7 0.04
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.35
Consensus pattern (92 bp):
TTTTTGTCAATATACAGCGTAACGGTCTTGATTTCTCCTAAAGGAAATCACAGAACTGCATTTAA
GTAAGTGTGCATCCACAAGTGTGCACG
Found at i:1395850 original size:150 final size:152
Alignment explanation
Indices: 1395265--1395878 Score: 642
Period size: 153 Copynumber: 4.0 Consensus size: 152
1395255 CCAAGTCAAC
* *
1395265 CAAACCCAAGGATGGTGACAATGCTACCAAAGCCAAGGATCATGCCCGTAAAAGTGGTAGTAGAC
1 CAAACCCAAGGA-GGCGACAATGCTACCAAAGCCAAGGATCATACCCGTAAAAGTGGTAGTAGAC
** * * * * *
1395330 CAGTTGTTGTTGCTTTAGAAGTGAGCAGTAAACCCAAAACTGAGGTCAGTGTCGTCACGCCCAAG
65 CAGTTGACGTTGCTTCAAAAGTGAGCAGCAAACCCAAAACTGAGGACAGTGTCGACACGCCCAAG
*
1395395 TCAACCAAACCCAAGGGCGACGA
130 TCAACCAAACCCAAGGACGACGA
* * *
1395418 CAAACCCAAGGATGGTGACAATGCTACCAAAGGCAAGGATCATACCCGCAAAAGTGGTAGTAGAC
1 CAAACCCAAGGA-GGCGACAATGCTACCAAAGCCAAGGATCATACCCGTAAAAGTGGTAGTAGAC
** * * * ** * *
1395483 CAGTTGTTGTTGCTTTAGAAGTGAGCAGCGAACCCAAAACTGAGGAGGGTGTCGACAGGCCTAAG
65 CAGTTGACGTTGCTTCAAAAGTGAGCAGCAAACCCAAAACTGAGGACAGTGTCGACACGCCCAAG
* *
1395548 TCAACCAAACCCAAGGCCGATGA
130 TCAACCAAACCCAAGGACGACGA
* * * * * * *
1395571 CAAACCGAAGGATGGCAACAATGTTATCGAAGCCAACGATCATACCCCTAAAAGTGGTAGTAGAC
1 CAAACCCAAGGA-GGCGACAATGCTACCAAAGCCAAGGATCATACCCGTAAAAGTGGTAGTAGAC
* * ** * ** *
1395636 CAGTTGACGATGCTTCAAAAGTGGGCAGCAAGTCCAAAACTGAGGACGGTGTCGTTACGGCCAAG
65 CAGTTGACGTTGCTTCAAAAGTGAGCAGCAAACCCAAAACTGAGGACAGTGTCGACACGCCCAAG
* * * *
1395701 CCAACCAAACCGAAGGATGACAA
130 TCAACCAAACCCAAGGACGACGA
* * * * * *
1395724 CAAACCCAA-G-CGCGACAATGTTACCAAAGCCAAGGATCATACCAC-TAACACTGTTAGTGGAC
1 CAAACCCAAGGAGGCGACAATGCTACCAAAGCCAAGGATCATACC-CGTAAAAGTGGTAGTAGAC
* * * * *
1395786 CAGTTGACGTTGCTTCAAAAGTGGGCAGCAAATCCAAAAATGAGGACAGTGTTGACACTCCCAAG
65 CAGTTGACGTTGCTTCAAAAGTGAGCAGCAAACCCAAAACTGAGGACAGTGTCGACACGCCCAAG
* * * *
1395851 TCTACTAAACCCGAGGACGA-GC
130 TCAACCAAACCCAAGGACGACGA
1395873 CAAACC
1 CAAACC
1395879 AAGACACTAC
Statistics
Matches: 389, Mismatches: 71, Indels: 6
0.83 0.15 0.01
Matches are distributed among these distances:
149 6 0.02
150 111 0.29
151 1 0.00
152 1 0.00
153 270 0.69
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.17
Consensus pattern (152 bp):
CAAACCCAAGGAGGCGACAATGCTACCAAAGCCAAGGATCATACCCGTAAAAGTGGTAGTAGACC
AGTTGACGTTGCTTCAAAAGTGAGCAGCAAACCCAAAACTGAGGACAGTGTCGACACGCCCAAGT
CAACCAAACCCAAGGACGACGA
Found at i:1396908 original size:21 final size:21
Alignment explanation
Indices: 1396883--1396924 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1396873 TAGTGCTCAA
1396883 GTATTTGAACTATGCTTTCTT
1 GTATTTGAACTATGCTTTCTT
* *
1396904 GTATTTGAATTATGTTTTCTT
1 GTATTTGAACTATGCTTTCTT
1396925 ATGTTAATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.10, G:0.14, T:0.57
Consensus pattern (21 bp):
GTATTTGAACTATGCTTTCTT
Found at i:1397709 original size:14 final size:14
Alignment explanation
Indices: 1397690--1397740 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
1397680 AGACTTCTAC
1397690 AATAATTAATAAAA
1 AATAATTAATAAAA
* *
1397704 AATAATTAA-ATTAC
1 AATAATTAATA-AAA
*
1397718 AATAATTAATAAAG
1 AATAATTAATAAAA
*
1397732 CATAATTAA
1 AATAATTAA
1397741 ATTCACTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
13 1 0.03
14 28 0.93
15 1 0.03
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (14 bp):
AATAATTAATAAAA
Found at i:1397718 original size:28 final size:28
Alignment explanation
Indices: 1397687--1397743 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
1397677 TGAAGACTTC
1397687 TACAATAATTAATAAAAAATAATTAAAT
1 TACAATAATTAATAAAAAATAATTAAAT
**
1397715 TACAATAATTAATAAAGCATAATTAAAT
1 TACAATAATTAATAAAAAATAATTAAAT
1397743 T
1 T
1397744 CACTTTTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (28 bp):
TACAATAATTAATAAAAAATAATTAAAT
Found at i:1400109 original size:18 final size:18
Alignment explanation
Indices: 1400086--1400143 Score: 80
Period size: 18 Copynumber: 3.2 Consensus size: 18
1400076 TTTTATTAAT
*
1400086 ATTTATGAATGATGTGGC
1 ATTTATGTATGATGTGGC
*
1400104 ATTTATGTATGATGTGGA
1 ATTTATGTATGATGTGGC
* *
1400122 ATTTATGTATAATGTGAC
1 ATTTATGTATGATGTGGC
1400140 ATTT
1 ATTT
1400144 TTCCTTTTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.29, C:0.03, G:0.22, T:0.45
Consensus pattern (18 bp):
ATTTATGTATGATGTGGC
Found at i:1402172 original size:23 final size:23
Alignment explanation
Indices: 1402146--1402189 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
1402136 ATTTGAAATA
*
1402146 TTAAGACCTAATAA-ATTTTAACC
1 TTAA-ACCCAATAATATTTTAACC
*
1402169 TTAAACCCATTAATATTTTAA
1 TTAAACCCAATAATATTTTAA
1402190 AACTCAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.43, C:0.16, G:0.02, T:0.39
Consensus pattern (23 bp):
TTAAACCCAATAATATTTTAACC
Found at i:1411537 original size:37 final size:34
Alignment explanation
Indices: 1411454--1411537 Score: 96
Period size: 35 Copynumber: 2.3 Consensus size: 34
1411444 ATTAAACATT
*
1411454 TTTTATATTTTTAATTTTGTAAAAAAATTATAAAA
1 TTTTATA-ATTTAATTTTGTAAAAAAATTATAAAA
* *
1411489 TATTATGAATTTAATTTTTTAAAGAAAATATATAAATA
1 TTTTAT-AATTTAATTTTGTAAA-AAAAT-TATAAA-A
1411527 TTTTATAATTT
1 TTTTATAATTT
1411538 GTAATATTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
35 18 0.44
36 6 0.15
37 11 0.27
38 6 0.15
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (34 bp):
TTTTATAATTTAATTTTGTAAAAAAATTATAAAA
Found at i:1413509 original size:21 final size:21
Alignment explanation
Indices: 1413466--1413572 Score: 180
Period size: 21 Copynumber: 5.1 Consensus size: 21
1413456 TTTTCCCAAT
** *
1413466 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTTGGAAAA
1413486 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
1413507 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
1413528 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
1413549 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
1413570 TCG
1 TCG
1413573 GAACGTGGTA
Statistics
Matches: 83, Mismatches: 3, Indels: 1
0.95 0.03 0.01
Matches are distributed among these distances:
20 12 0.14
21 71 0.86
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAATTTGGAAAA
Found at i:1413611 original size:41 final size:41
Alignment explanation
Indices: 1413566--1413703 Score: 116
Period size: 41 Copynumber: 3.4 Consensus size: 41
1413556 GCGAATTTGG
* * * *
1413566 AAAATCGGAACGTGGTACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTATCACAACGCGATAATAC
* * * *
1413607 AAAATCGCAACGCGATACTGACTTTCACAACTCGATACT-T
1 AAAATCGCAACGCGATACTGACTATCACAACGCGATAATAC
** * * * * *
1413647 AATTTCGCAACTCAATACTGACTTTCGCAACGAGATAATAC
1 AAAATCGCAACGCGATACTGACTATCACAACGCGATAATAC
* *
1413688 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
1413704 TTTCAAAGCG
Statistics
Matches: 73, Mismatches: 23, Indels: 2
0.74 0.23 0.02
Matches are distributed among these distances:
40 31 0.42
41 42 0.58
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTATCACAACGCGATAATAC
Found at i:1413642 original size:20 final size:20
Alignment explanation
Indices: 1413611--1413677 Score: 89
Period size: 20 Copynumber: 3.4 Consensus size: 20
1413601 TAATACAAAA
*
1413611 TCGCAACGCGATACTGACTT
1 TCGCAACTCGATACTGACTT
* * *
1413631 TCACAACTCGATACTTAATT
1 TCGCAACTCGATACTGACTT
*
1413651 TCGCAACTCAATACTGACTT
1 TCGCAACTCGATACTGACTT
1413671 TCGCAAC
1 TCGCAAC
1413678 GAGATAATAC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.30, C:0.30, G:0.12, T:0.28
Consensus pattern (20 bp):
TCGCAACTCGATACTGACTT
Found at i:1413898 original size:22 final size:22
Alignment explanation
Indices: 1413870--1413913 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1413860 CACTCTCTCA
*
1413870 CCCATCTCCGATGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
1413892 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1413914 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1414234 original size:20 final size:20
Alignment explanation
Indices: 1414176--1414225 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1414166 TTTATTCTCT
* **
1414176 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCACTTTCG
1414196 CGTTGCGATTGTCACTTTCG
1 CGTTGCGATTGTCACTTTCG
*
1414216 TGTTGCGATT
1 CGTTGCGATT
1414226 TTCATTTTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.16, C:0.20, G:0.26, T:0.38
Consensus pattern (20 bp):
CGTTGCGATTGTCACTTTCG
Found at i:1414421 original size:25 final size:24
Alignment explanation
Indices: 1414365--1414421 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
1414355 TTATGTTTAT
*
1414365 TATGTTTTTGGTATATCTTCACAG
1 TATGTTTTTGGTATATCTTAACAG
*
1414389 TGTAGTTTTTGGTATATC-TAACTTAG
1 TAT-GTTTTTGGTATATCTTAAC--AG
1414415 TATGTTT
1 TATGTTT
1414422 ATTGTTTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
24 5 0.19
25 18 0.67
26 4 0.15
ACGTcount: A:0.21, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TATGTTTTTGGTATATCTTAACAG
Found at i:1415571 original size:18 final size:18
Alignment explanation
Indices: 1415550--1415597 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
1415540 TCCACTTCGG
1415550 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
1415568 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1415586 GAGCCATCACCT
1 GAGCCATCACCT
1415598 GATCGACCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1416188 original size:20 final size:20
Alignment explanation
Indices: 1416138--1416204 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
1416128 TAGTTTACTT
* *
1416138 TCGCAACACGAAAATGATTA
1 TCGCAACGCGAAAATGACTA
*
1416158 TCGCAACGCGAAAATGGCTA
1 TCGCAACGCGAAAATGACTA
* **
1416178 TCGCAATGCG-AAATGAAAA
1 TCGCAACGCGAAAATGACTA
1416197 TCGCAACG
1 TCGCAACG
1416205 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 13 0.33
20 26 0.67
ACGTcount: A:0.40, C:0.22, G:0.21, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:1416199 original size:19 final size:19
Alignment explanation
Indices: 1416177--1416273 Score: 97
Period size: 19 Copynumber: 5.6 Consensus size: 19
1416167 GAAAATGGCT
1416177 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1416196 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
1416210 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1416229 ATCGCAA--C--AA-CAAA
1 ATCGCAATGCGAAATGAAA
*
1416243 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1416262 ATCGCAATGCGA
1 ATCGCAATGCGA
1416274 TTTGTGTTTC
Statistics
Matches: 63, Mismatches: 5, Indels: 20
0.72 0.06 0.23
Matches are distributed among these distances:
14 20 0.32
15 3 0.05
16 3 0.05
17 3 0.05
18 3 0.05
19 31 0.49
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1416212 original size:14 final size:14
Alignment explanation
Indices: 1416193--1416251 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
1416183 ATGCGAAATG
1416193 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1416207 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
*
1416226 AAAATCGCAACAAC
1 AAAATCGCAACGAC
1416240 AAAATCGCAACG
1 AAAATCGCAACG
1416252 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
14 21 0.58
15 1 0.03
16 2 0.06
17 1 0.03
18 1 0.03
19 10 0.28
ACGTcount: A:0.51, C:0.24, G:0.15, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1416219 original size:33 final size:33
Alignment explanation
Indices: 1416177--1416268 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
1416167 GAAAATGGCT
*
1416177 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACAACAAA
1416210 ATCGCAATGCGAAATGAAAATCGCAACAACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACAACAAA
*
1416243 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
1416269 TGCGATTTGT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.49, C:0.22, G:0.17, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACAACAAA
Found at i:1416345 original size:20 final size:20
Alignment explanation
Indices: 1416299--1416385 Score: 104
Period size: 20 Copynumber: 4.4 Consensus size: 20
1416289 GCGATTTTGC
**
1416299 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATAGTCATTTCCG
* *
1416318 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
1416338 CGTTGCGATAGTCATTTCCA
1 CGTTGCGATAGTCATTTCCG
* *
1416358 CGTTGCGATGGTCATTTTCG
1 CGTTGCGATAGTCATTTCCG
1416378 CGTTGCGA
1 CGTTGCGA
1416386 AAGTAAGTTT
Statistics
Matches: 57, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
19 13 0.23
20 44 0.77
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:1416410 original size:19 final size:20
Alignment explanation
Indices: 1416373--1416410 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1416363 CGATGGTCAT
1416373 TTTCGCGTTGCGAAAGTAAG
1 TTTCGCGTTGCGAAAGTAAG
*
1416393 TTTCGTGTTGCG-AAGTAA
1 TTTCGCGTTGCGAAAGTAA
1416411 ACTATTCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.24, C:0.13, G:0.29, T:0.34
Consensus pattern (20 bp):
TTTCGCGTTGCGAAAGTAAG
Found at i:1416826 original size:44 final size:44
Alignment explanation
Indices: 1416745--1416853 Score: 114
Period size: 44 Copynumber: 2.5 Consensus size: 44
1416735 GACTCACCTG
* * * *
1416745 TCATTCCTCAAGAGT-CC-CCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCTCCCCCAACCGTTCAAGAGGCCACTA
* *
1416787 TCATCCCTCAAGAGTCCCTCCCCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCTCCCCCAACCGTTCAAGAGGCCACTA
** *
1416831 TCATCATTGAAGAGGTCCCTCCC
1 TCATCCCTCAAGA-GTCCCTCCC
1416854 ACCATTCCAG
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
42 14 0.25
43 2 0.04
44 30 0.55
45 9 0.16
ACGTcount: A:0.22, C:0.40, G:0.16, T:0.22
Consensus pattern (44 bp):
TCATCCCTCAAGAGTCCCTCCCCCAACCGTTCAAGAGGCCACTA
Found at i:1418276 original size:14 final size:14
Alignment explanation
Indices: 1418242--1418280 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1418232 TTGATTATTT
1418242 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
1418256 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
1418270 TGTTGATTTGT
1 AATTGATTTGT
1418281 TTAATTGGTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:1418476 original size:20 final size:20
Alignment explanation
Indices: 1418451--1418526 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
1418441 TCGCATTGCG
*
1418451 ATTTTCTAGTTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
* ***
1418471 ATTTTCGCGTTGCGATTTTTC
1 ATTTTCGAGTTGCGA-TAGCC
*
1418492 A-TTTCGAATTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
*
1418511 ATTTTCGCGTTGCGAT
1 ATTTTCGAGTTGCGAT
1418527 TTCCCCGTTG
Statistics
Matches: 42, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
19 3 0.07
20 36 0.86
21 3 0.07
ACGTcount: A:0.17, C:0.20, G:0.21, T:0.42
Consensus pattern (20 bp):
ATTTTCGAGTTGCGATAGCC
Found at i:1418484 original size:34 final size:34
Alignment explanation
Indices: 1418439--1418542 Score: 109
Period size: 40 Copynumber: 2.9 Consensus size: 34
1418429 GCGATTTTCA
*
1418439 TTTCGCATTGCGATTTTCTAGTTGCGATAGCCAT
1 TTTCGCGTTGCGATTTTCTAGTTGCGATAGCCAT
*
1418473 TTTCGCGTTGCGATTTTTCATTTCGAATTGCGATAGCCAT
1 TTTCGCGTTGCGA-TTTTC---T--AGTTGCGATAGCCAT
* **
1418513 TTTCGCGTTGCGATTTCCCCGTTGCGATAG
1 TTTCGCGTTGCGATTTTCTAGTTGCGATAG
1418543 TCAAATGAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
34 21 0.36
35 5 0.09
38 1 0.02
39 4 0.07
40 27 0.47
ACGTcount: A:0.15, C:0.22, G:0.22, T:0.40
Consensus pattern (34 bp):
TTTCGCGTTGCGATTTTCTAGTTGCGATAGCCAT
Found at i:1418763 original size:20 final size:20
Alignment explanation
Indices: 1418738--1418829 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
1418728 TTGAAGATGA
1418738 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
***
1418758 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
* **
1418778 TTGCGATTTTGTATTATCTCG
1 TTGCGATTTT-CAGAATCTCG
** * * *
1418799 TTGCGATAGTCAGTATCGCA
1 TTGCGATTTTCAGAATCTCG
1418819 TTGCGATTTTC
1 TTGCGATTTTC
1418830 CAAATTCGCA
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
20 39 0.72
21 15 0.28
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Found at i:1418858 original size:20 final size:21
Alignment explanation
Indices: 1418814--1418865 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
1418804 ATAGTCAGTA
*
1418814 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
1418835 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
1418855 TCGCATTGCGA
1 TCGCATTGCGA
1418866 ATTAGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:1419671 original size:24 final size:24
Alignment explanation
Indices: 1419644--1419697 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1419634 GTATTCGAAA
*
1419644 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
1419668 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
1419692 TTTGAT
1 TTTGAT
1419698 GATGTTTAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:1419889 original size:12 final size:12
Alignment explanation
Indices: 1419872--1419896 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1419862 ATATAATCCT
1419872 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1419884 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1419896 G
1 G
1419897 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1422166 original size:19 final size:19
Alignment explanation
Indices: 1422138--1422267 Score: 74
Period size: 19 Copynumber: 7.6 Consensus size: 19
1422128 GAAATTACTA
*
1422138 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
**
1422157 TCGCATTGCGA--TTC-CC
1 TCGCATTGCGATTTTCATT
1422173 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1422190 TCGCATTGCGA-----AAT
1 TCGCATTGCGATTTTCATT
*
1422204 TCGCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
1422223 TCGTATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
* *
1422239 TCG--TTACGATTTTTATT
1 TCGCATTGCGATTTTCATT
1422256 TCGCATTGCGAT
1 TCGCATTGCGAT
1422268 AGTCAGTTTT
Statistics
Matches: 81, Mismatches: 15, Indels: 30
0.64 0.12 0.24
Matches are distributed among these distances:
14 23 0.28
16 12 0.15
17 13 0.16
19 33 0.41
ACGTcount: A:0.16, C:0.22, G:0.18, T:0.43
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1422186 original size:33 final size:32
Alignment explanation
Indices: 1422144--1422267 Score: 169
Period size: 33 Copynumber: 3.8 Consensus size: 32
1422134 ACTATCGCAA
1422144 TGCGATTTTCATTTCGCATTGCGATTCCCTCGT
1 TGCGATTTTCATTTCGCATTGCGATT-CCTCGT
*
1422177 TGCGATTTTCATTTCGCATTGCGAAATT-CGCGT
1 TGCGATTTTCATTTCGCATTGCG--ATTCCTCGT
*
1422210 TGCGATTTTCATTTCGTATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTC-CTCGT
* *
1422243 TACGATTTTTATTTCGCATTGCGAT
1 TGCGATTTTCATTTCGCATTGCGAT
1422268 AGTCAGTTTT
Statistics
Matches: 81, Mismatches: 6, Indels: 8
0.85 0.06 0.08
Matches are distributed among these distances:
31 3 0.04
33 75 0.93
35 3 0.04
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.44
Consensus pattern (32 bp):
TGCGATTTTCATTTCGCATTGCGATTCCTCGT
Found at i:1422384 original size:14 final size:14
Alignment explanation
Indices: 1422365--1422401 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1422355 CATCAATTAA
1422365 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1422379 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1422393 ACAAATCAA
1 ACAAATCAA
1422402 TTAACAATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1423817 original size:21 final size:21
Alignment explanation
Indices: 1423751--1423817 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1423741 GTGAATCTGG
*
1423751 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
1423771 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
1423793 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
1423814 CTCT
1 CTCT
1423818 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:1423836 original size:42 final size:41
Alignment explanation
Indices: 1423751--1423873 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
1423741 GTGAATCTGG
* * * *
1423751 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
1423793 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
1423835 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
1423874 CGAGTCAGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:1426025 original size:33 final size:34
Alignment explanation
Indices: 1425971--1426036 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 34
1425961 ACGAGATAAT
*
1425971 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCACAACGCGGAAATGACTATCGCAACGA
*
1426005 GAGAATCACAATGC-GAAATGACTATCGCAACG
1 GAGAATCACAACGCGGAAATGACTATCGCAACG
1426037 CGAAATGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 18 0.60
34 12 0.40
ACGTcount: A:0.39, C:0.23, G:0.24, T:0.14
Consensus pattern (34 bp):
GAGAATCACAACGCGGAAATGACTATCGCAACGA
Found at i:1426055 original size:52 final size:53
Alignment explanation
Indices: 1425975--1426077 Score: 163
Period size: 52 Copynumber: 2.0 Consensus size: 53
1425965 GATAATGAGA
** *
1425975 ATCGCAACGCGGAAATGACTATCGCAACGAGAGAATCACAATGCGAAATGACT
1 ATCGCAACGCGGAAATGAAAATCGCAACGAGAGAATCACAACGCGAAATGACT
*
1426028 ATCGCAACGC-GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGA
1 ATCGCAACGCGGAAATGAAAATCGCAACGAGAGAATCACAACGCGAAATGA
1426078 AAATCGAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
52 36 0.78
53 10 0.22
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.13
Consensus pattern (53 bp):
ATCGCAACGCGGAAATGAAAATCGCAACGAGAGAATCACAACGCGAAATGACT
Found at i:1426091 original size:19 final size:19
Alignment explanation
Indices: 1425947--1426083 Score: 96
Period size: 19 Copynumber: 7.6 Consensus size: 19
1425937 CTTTTGGTTA
*
1425947 AAATGAAAATCGCAACGAG
1 AAATGAAAATCGCAACGCG
*
1425966 ATAATGAGAATCGCAACGCGG
1 A-AATGAAAATCGCAACGC-G
**
1425987 AAATGACTATCGCAA--CG
1 AAATGAAAATCGCAACGCG
* * *
1426004 --A-GAGAATCACAATGCG
1 AAATGAAAATCGCAACGCG
**
1426020 AAATGACTATCGCAACGCG
1 AAATGAAAATCGCAACGCG
1426039 AAATGAAAATCGCAA--CG
1 AAATGAAAATCGCAACGCG
*
1426056 --A-GAGAATCGCAACGCG
1 AAATGAAAATCGCAACGCG
1426072 AAATGAAAATCG
1 AAATGAAAATCG
1426084 AAATGCGATT
Statistics
Matches: 91, Mismatches: 15, Indels: 24
0.70 0.12 0.18
Matches are distributed among these distances:
14 18 0.20
15 2 0.02
16 4 0.04
17 3 0.03
18 3 0.03
19 32 0.35
20 27 0.30
21 2 0.02
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.13
Consensus pattern (19 bp):
AAATGAAAATCGCAACGCG
Found at i:1426109 original size:19 final size:19
Alignment explanation
Indices: 1426087--1426131 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
1426077 AAAATCGAAA
**
1426087 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTCGCGT
1426106 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
1426125 TGCGATT
1 TGCGATT
1426132 CTCTCGTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.47
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:1426707 original size:20 final size:20
Alignment explanation
Indices: 1426682--1426732 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1426672 GCTATGTAAA
1426682 TCGCATTGCGATAGTAAG-AT
1 TCGCATTGCGAT-GTAAGTAT
* * *
1426702 TCGCATTACGATTTACGTAT
1 TCGCATTGCGATGTAAGTAT
1426722 TCGCATTGCGA
1 TCGCATTGCGA
1426733 ATTATGAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 3 0.12
20 23 0.88
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (20 bp):
TCGCATTGCGATGTAAGTAT
Found at i:1426765 original size:20 final size:20
Alignment explanation
Indices: 1426740--1426795 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
1426730 CGAATTATGA
1426740 AAATCGCAACGCGAATACGT
1 AAATCGCAACGCGAATACGT
1426760 AAATCGCAACGCGAATACGT
1 AAATCGCAACGCGAATACGT
*
1426780 AAATCGCAATGCGAAT
1 AAATCGCAACGCGAAT
1426796 TAGGAAAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.41, C:0.23, G:0.20, T:0.16
Consensus pattern (20 bp):
AAATCGCAACGCGAATACGT
Found at i:1426917 original size:21 final size:22
Alignment explanation
Indices: 1426869--1426917 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
1426859 ACTTATTCGT
1426869 ATTGCG-AATTGGGAAAATCGC
1 ATTGCGAAATTGGGAAAATCGC
**
1426890 AACGCGAAATT-GGAAAATCGC
1 ATTGCGAAATTGGGAAAATCGC
1426911 ATTGCGA
1 ATTGCGA
1426918 TAGTCATAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.37, C:0.16, G:0.27, T:0.20
Consensus pattern (22 bp):
ATTGCGAAATTGGGAAAATCGC
Found at i:1426970 original size:143 final size:143
Alignment explanation
Indices: 1426700--1426961 Score: 318
Period size: 143 Copynumber: 1.8 Consensus size: 143
1426690 CGATAGTAAG
* * *
1426700 ATTCGCATTACGATTTACGTATTCGCATTGCGAATTATGAAAATCGCAACGCGAATACGTAAATC
1 ATTCGCATTACGAGTTACGTATTCGCATTGCGAATTAGGAAAATCGCAACGCGAATACGAAAATC
* *
1426765 GCAACGCGAATACGTAAATCGCAATGCGAATTAGGAAAATTGTATTGCGATAGTCAGTATCGCAT
66 GCAACGCGAATACGTAAATCGCAATGCGAATTAGGAAAACTGTATTGCGATAATCAGTATCGCAT
1426830 TGCGATTTTCCAA
131 TGCGATTTTCCAA
* * * * **
1426843 ATTCGCATTGCGAGTTACTTATTCGTATTGCGAATTGGGAAAATCGCAACGCGAAATTGGAAAAT
1 ATTCGCATTACGAGTTACGTATTCGCATTGCGAATTAGGAAAATCGCAACGCG-AATACGAAAAT
** *
1426908 CGCATTGCG-ATA-GTCATAATCGCATTGCGAATCT-GG-AAACTG-ATTTGCGATAAT
65 CGCAACGCGAATACGT-A-AATCGCAATGCGAAT-TAGGAAAACTGTA-TTGCGATAAT
1426962 GGAGATCGCG
Statistics
Matches: 100, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
142 3 0.03
143 65 0.65
144 31 0.31
145 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (143 bp):
ATTCGCATTACGAGTTACGTATTCGCATTGCGAATTAGGAAAATCGCAACGCGAATACGAAAATC
GCAACGCGAATACGTAAATCGCAATGCGAATTAGGAAAACTGTATTGCGATAATCAGTATCGCAT
TGCGATTTTCCAA
Found at i:1427286 original size:51 final size:51
Alignment explanation
Indices: 1427189--1427288 Score: 123
Period size: 51 Copynumber: 2.0 Consensus size: 51
1427179 GATAAAATTT
** * *
1427189 AATAAAAAATTATATTTTATTAAAATTTGTCATCTCGACGTGACGAGTTTG
1 AATAAAAAATTATATTTTATTAAAATTCATCATCTCGAAGTAACGAGTTTG
*
1427240 AATAAAAATATT-TTTTTTATTAAAATTCATCA-CTTCGAAGTAACGAGTT
1 AATAAAAA-ATTATATTTTATTAAAATTCATCATC-TCGAAGTAACGAGTT
1427289 GTACAAACAC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
50 1 0.02
51 38 0.90
52 3 0.07
ACGTcount: A:0.39, C:0.10, G:0.11, T:0.40
Consensus pattern (51 bp):
AATAAAAAATTATATTTTATTAAAATTCATCATCTCGAAGTAACGAGTTTG
Done.