Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007950.1 Hibiscus syriacus cultivar Beakdansim tig00110372_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: 1941792
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 10
Found at i:337425 original size:33 final size:33
Alignment explanation
Indices: 337361--337426 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
337351 AAATAATTTG
*
337361 ATGATAATGATAGAGATAATGATAATAATATAT
1 ATGATAATGATAGAGAAAATGATAATAATATAT
* * *
337394 ATGATAATGCTA-AGAAAATAGATGATGATATAT
1 ATGATAATGATAGAGAAAAT-GATAATAATATAT
337427 GTACATGAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 6 0.21
33 22 0.79
ACGTcount: A:0.50, C:0.02, G:0.17, T:0.32
Consensus pattern (33 bp):
ATGATAATGATAGAGAAAATGATAATAATATAT
Found at i:342132 original size:147 final size:147
Alignment explanation
Indices: 341898--342198 Score: 487
Period size: 147 Copynumber: 2.0 Consensus size: 147
341888 GAGTCGAGGG
* * * * * *
341898 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATTTATGAGGTCTTTGAGGCACATA
1 TCTACGCGGTCCTTCGGGA-ATATATATATTCTGTGGAACATGTATGAAGTCTTTAAGACACATA
* *
341963 CTTGGTCCTTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTAT
65 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTAT
*
342028 ATGGCACTACGGTGCAAT
130 AGGGCACTACGGTGCAAT
*
342046 TCTACGCGGTCCTTCGGG-ATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACATA
1 TCTACGCGGTCCTTCGGGAATATATATATTCTGTGGAACATGTATGAAGTCTT-TAAGACACATA
342110 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTAT
65 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTAT
342175 AGGGCACTACGGTGCAAT
130 AGGGCACTACGGTGCAAT
342193 TCTACG
1 TCTACG
342199 TGGCACTTCG
Statistics
Matches: 142, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
146 29 0.20
147 95 0.67
148 18 0.13
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.36
Consensus pattern (147 bp):
TCTACGCGGTCCTTCGGGAATATATATATTCTGTGGAACATGTATGAAGTCTTTAAGACACATAC
TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTATA
GGGCACTACGGTGCAAT
Found at i:342210 original size:23 final size:23
Alignment explanation
Indices: 342170--342221 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
342160 TATGGACATT
342170 ATTATA-G-GGCACTACGGTGCA
1 ATTATACGTGGCACTACGGTGCA
* *
342191 ATTCTACGTGGCACTTCGGTGCA
1 ATTATACGTGGCACTACGGTGCA
342214 ATTATACG
1 ATTATACG
342222 AGCTGTGGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 5 0.19
22 1 0.04
23 20 0.77
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (23 bp):
ATTATACGTGGCACTACGGTGCA
Found at i:344214 original size:24 final size:20
Alignment explanation
Indices: 344186--344244 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 20
344176 ACATGGGTAG
*
344186 TGCATCGATGCACATGTTAAGGGA
1 TGCATCGATGCAC-T-TT-A-GAA
* *
344210 TGCATTGATACACTTTAGAA
1 TGCATCGATGCACTTTAGAA
344230 TGCATCGATGCACTT
1 TGCATCGATGCACTT
344245 CAAGGGGGAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
20 15 0.50
21 1 0.03
22 2 0.07
23 1 0.03
24 11 0.37
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.31
Consensus pattern (20 bp):
TGCATCGATGCACTTTAGAA
Found at i:345044 original size:2 final size:2
Alignment explanation
Indices: 345037--345068 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
345027 AATAGAAGTA
345037 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
345069 GTTTATAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:345829 original size:23 final size:23
Alignment explanation
Indices: 345795--345862 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
345785 AATCTTATAT
*
345795 GGCACTACGGTGCATTTCTACGC
1 GGCACTATGGTGCATTTCTACGC
* * *
345818 GGCACTATGGTGCAATTCTATGT
1 GGCACTATGGTGCATTTCTACGC
*
345841 GGCACT-TCGGTGCATTTATACG
1 GGCACTAT-GGTGCATTTCTACG
345863 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
22 1 0.03
23 36 0.97
ACGTcount: A:0.19, C:0.24, G:0.26, T:0.31
Consensus pattern (23 bp):
GGCACTATGGTGCATTTCTACGC
Found at i:347238 original size:18 final size:18
Alignment explanation
Indices: 347215--347270 Score: 112
Period size: 18 Copynumber: 3.1 Consensus size: 18
347205 TCCTCCTCAT
347215 TTCCTCCATCTTTTCTTC
1 TTCCTCCATCTTTTCTTC
347233 TTCCTCCATCTTTTCTTC
1 TTCCTCCATCTTTTCTTC
347251 TTCCTCCATCTTTTCTTC
1 TTCCTCCATCTTTTCTTC
347269 TT
1 TT
347271 TATATTTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.05, C:0.38, G:0.00, T:0.57
Consensus pattern (18 bp):
TTCCTCCATCTTTTCTTC
Found at i:347492 original size:33 final size:33
Alignment explanation
Indices: 347455--347521 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
347445 CCATCTTAAG
347455 TTCACCCCTCAACACCTCAACTTCTTTCACCAC
1 TTCACCCCTCAACACCTCAACTTCTTTCACCAC
*
347488 TTCACCCCTCAATACCTCAACTTCTTTCACCAC
1 TTCACCCCTCAACACCTCAACTTCTTTCACCAC
347521 T
1 T
347522 CCATCTATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.24, C:0.46, G:0.00, T:0.30
Consensus pattern (33 bp):
TTCACCCCTCAACACCTCAACTTCTTTCACCAC
Found at i:347579 original size:21 final size:21
Alignment explanation
Indices: 347554--347597 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
347544 CCCCTTATGC
347554 CTCTCAAGTGTCTCTTCGACT
1 CTCTCAAGTGTCTCTTCGACT
*
347575 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTGTCTCTTCGACT
347596 CT
1 CT
347598 TGATTGTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.34, G:0.11, T:0.41
Consensus pattern (21 bp):
CTCTCAAGTGTCTCTTCGACT
Found at i:349717 original size:182 final size:182
Alignment explanation
Indices: 349410--349802 Score: 633
Period size: 182 Copynumber: 2.2 Consensus size: 182
349400 TACGCATACT
* * * *
349410 TATTAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTGTCATTTCGAGACTG
1 TATTAAAGTATCGACACTTTCAATATATTCGGTAGCGCTATACCGGTTTTGTCATTTAGAGACCG
* * *
349475 GTTTTGTCATATTTGTACCTGTTATATCTTTATGGATCGATACATTTTTATAAAGTATCGACACT
66 ATTTTGTCATATTTGTACCTGTTATATCGTTATGGATCGATACATTGTTATAAAGTATCGACACT
*
349540 TTATAAGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTTTCGATACTTA
131 TTATAAGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
* * *
349592 TATTAAAGTATCGACACTTTCAATATATTCGGTCGCTCTATACCGGTTTTGTCCTTTAGAGACCG
1 TATTAAAGTATCGACACTTTCAATATATTCGGTAGCGCTATACCGGTTTTGTCATTTAGAGACCG
* * * *
349657 ATTTTGTCATATTTTTACTTGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCGATACT
66 ATTTTGTCATATTTGTACCTGTTATATCGTTATGGATCGATACATTGTTATAAAGTATCGACACT
* *
349722 TTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAATGTGTCGATACTTA
131 TTATAAGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
349774 TATTAAAGTATCGACACTTTCAATATATT
1 TATTAAAGTATCGACACTTTCAATATATT
349803 AAAGTATCGA
Statistics
Matches: 194, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
182 194 1.00
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (182 bp):
TATTAAAGTATCGACACTTTCAATATATTCGGTAGCGCTATACCGGTTTTGTCATTTAGAGACCG
ATTTTGTCATATTTGTACCTGTTATATCGTTATGGATCGATACATTGTTATAAAGTATCGACACT
TTATAAGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
Found at i:349792 original size:20 final size:20
Alignment explanation
Indices: 349764--349817 Score: 54
Period size: 25 Copynumber: 2.5 Consensus size: 20
349754 TCACAATGTG
*
349764 TCGATACTTATATTAAAGTA
1 TCGACACTTATATTAAAGTA
349784 TCGACACTTTCAATATATTAAAGTA
1 TCGACAC--T---TATATTAAAGTA
349809 TCGACACTT
1 TCGACACTT
349818 TCAATATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 10
0.72 0.03 0.26
Matches are distributed among these distances:
20 7 0.25
22 1 0.04
23 1 0.04
25 19 0.68
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (20 bp):
TCGACACTTATATTAAAGTA
Found at i:349801 original size:25 final size:25
Alignment explanation
Indices: 349772--349827 Score: 112
Period size: 25 Copynumber: 2.2 Consensus size: 25
349762 TGTCGATACT
349772 TATATTAAAGTATCGACACTTTCAA
1 TATATTAAAGTATCGACACTTTCAA
349797 TATATTAAAGTATCGACACTTTCAA
1 TATATTAAAGTATCGACACTTTCAA
349822 TATATT
1 TATATT
349828 CGGTCGCTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.39
Consensus pattern (25 bp):
TATATTAAAGTATCGACACTTTCAA
Found at i:349945 original size:207 final size:207
Alignment explanation
Indices: 349590--350008 Score: 757
Period size: 207 Copynumber: 2.0 Consensus size: 207
349580 TTTCGATACT
*
349590 TATATTAAAGTATCGACACTTTCAATATATTCGGTCGCTCTATACCGGTTTTGTCCTTTAGAGAC
1 TATATTAAAGTATCGACACTTTCAATATATTCGGTCGCTCTATACCGGTTATGTCCTTTAGAGAC
*
349655 CGATTTTGTCATATTTTTACTTGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCGATA
66 CGATTTTGTCATATTTTTACTTGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCAATA
* *
349720 CTTTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAATGTGTCGATACTTATATTAAAGTAT
131 CTTTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTCATATTAAAGTAT
349785 CGACACTTTCAA
196 CGACACTTTCAA
349797 TATATTAAAGTATCGACACTTTCAATATATTCGGTCGCTCTATACCGGTTATGTCCTTTAGAGAC
1 TATATTAAAGTATCGACACTTTCAATATATTCGGTCGCTCTATACCGGTTATGTCCTTTAGAGAC
* * *
349862 CGGTTTTGTCATATTTTTACTTGTTATATTGTTGTGGATCGATACATTGTTATAAAGTATTAATA
66 CGATTTTGTCATATTTTTACTTGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCAATA
* *
349927 CTTTATAGGCGCTAAAACTTCTTCTCTTTTAAATTCACAAAGTGTTGATACTCATATTAAAGTAT
131 CTTTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTCATATTAAAGTAT
349992 CGACACTTTCAA
196 CGACACTTTCAA
350004 TATAT
1 TATAT
350009 CTGGTACCGC
Statistics
Matches: 203, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
207 203 1.00
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (207 bp):
TATATTAAAGTATCGACACTTTCAATATATTCGGTCGCTCTATACCGGTTATGTCCTTTAGAGAC
CGATTTTGTCATATTTTTACTTGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCAATA
CTTTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTCATATTAAAGTAT
CGACACTTTCAA
Found at i:360623 original size:21 final size:21
Alignment explanation
Indices: 360597--360640 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
360587 AAATTCCCTT
360597 TCCATGAGATCTTTCTGCACA
1 TCCATGAGATCTTTCTGCACA
360618 TCCATGAGATCTTTCTGCACA
1 TCCATGAGATCTTTCTGCACA
360639 TC
1 TC
360641 GGACAGCCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.30, G:0.14, T:0.34
Consensus pattern (21 bp):
TCCATGAGATCTTTCTGCACA
Found at i:366749 original size:35 final size:35
Alignment explanation
Indices: 366702--366787 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
366692 AAAACAGTCA
* * *
366702 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
* * * *
366737 TCAATTTTATTCTAAACCCTAAATTCTAAAATACT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
*
366772 TCAATTAAATTCTAAA
1 TCAATTTAATTCTAAA
366788 ATACTTCAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.41, C:0.21, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
Found at i:366781 original size:21 final size:21
Alignment explanation
Indices: 366756--366798 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
366746 TTCTAAACCC
366756 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
366777 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
366798 T
1 T
366799 TAAGGTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTCTAAAATACTTCAAT
Found at i:366945 original size:16 final size:18
Alignment explanation
Indices: 366913--366946 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
366903 TATTAATGTA
366913 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
366931 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
366947 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:374480 original size:21 final size:21
Alignment explanation
Indices: 374456--374495 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
374446 CTATTCAGTA
374456 TAAAAAA-TATTTATTATATAC
1 TAAAAAATTATTTA-TATATAC
374477 TAAAAAATTATTTATATAT
1 TAAAAAATTATTTATATAT
374496 GAACTCAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (21 bp):
TAAAAAATTATTTATATATAC
Found at i:375455 original size:161 final size:161
Alignment explanation
Indices: 375190--375508 Score: 611
Period size: 161 Copynumber: 2.0 Consensus size: 161
375180 AACTTAACAT
*
375190 TAATATACGATCATTTTCTTAATTAAATAAATAGTATACAAATTAAAATATAAACTAATACTAAA
1 TAATATACGATCATTCTCTTAATTAAATAAATAGTATACAAATTAAAATATAAACTAATACTAAA
*
375255 TAAATAAATAAATAAAATATTCGCAATAATTAACATAACACAATAATAAAACTAATGCAAATTAA
66 TAAATAAATAAATAAAATATTCGCAATAATTAACATAACACAATAATAAAACTAATACAAATTAA
*
375320 ATAAATTGTTACCGTATCGACAAAATGAGTC
131 ATAAATTGTTACCATATCGACAAAATGAGTC
375351 TAATATACGATCATTCTCTTAATTAAATAAATAGTATACAAATTAAAATATAAACTAATACTAAA
1 TAATATACGATCATTCTCTTAATTAAATAAATAGTATACAAATTAAAATATAAACTAATACTAAA
375416 TAAATAAATAAATAAAATATTCGCAATAATTAACATAACACAATAATAAAACTAATACAAATTAA
66 TAAATAAATAAATAAAATATTCGCAATAATTAACATAACACAATAATAAAACTAATACAAATTAA
375481 ATAAATTGTTACCATATCGACAAAATGA
131 ATAAATTGTTACCATATCGACAAAATGA
375509 CTCGTGATAT
Statistics
Matches: 155, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
161 155 1.00
ACGTcount: A:0.54, C:0.11, G:0.05, T:0.30
Consensus pattern (161 bp):
TAATATACGATCATTCTCTTAATTAAATAAATAGTATACAAATTAAAATATAAACTAATACTAAA
TAAATAAATAAATAAAATATTCGCAATAATTAACATAACACAATAATAAAACTAATACAAATTAA
ATAAATTGTTACCATATCGACAAAATGAGTC
Found at i:377299 original size:13 final size:13
Alignment explanation
Indices: 377281--377307 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
377271 GAAATAGATG
377281 CGTATTATAAATT
1 CGTATTATAAATT
377294 CGTATTATAAATT
1 CGTATTATAAATT
377307 C
1 C
377308 CATATAAACA
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:0.11, G:0.07, T:0.44
Consensus pattern (13 bp):
CGTATTATAAATT
Found at i:377689 original size:43 final size:44
Alignment explanation
Indices: 377566--377734 Score: 243
Period size: 44 Copynumber: 3.9 Consensus size: 44
377556 CTTGTTTCGA
**
377566 TTTTGGATTTAGGTAAAGTATGTGCTAAAGTTTCATTTCATTGT
1 TTTTGGATTTAGGTTGAGTATGTGCTAAAGTTTCATTTCATTGT
* *
377610 TTTCGGATTTAGGTTGAGTAAGTGCTAAAGTTTCATTTCATTGT
1 TTTTGGATTTAGGTTGAGTATGTGCTAAAGTTTCATTTCATTGT
* * * *
377654 TTTTGGATCTACG-TGAGTATGCGCTAAAGTGTCATTTCATTGT
1 TTTTGGATTTAGGTTGAGTATGTGCTAAAGTTTCATTTCATTGT
*
377697 TTTTGGATTTAGGTTGAGTATGTGCTAAATTTTC-TTTC
1 TTTTGGATTTAGGTTGAGTATGTGCTAAAGTTTCATTTC
377735 TCGTACTTCA
Statistics
Matches: 109, Mismatches: 15, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
43 42 0.39
44 67 0.61
ACGTcount: A:0.22, C:0.09, G:0.22, T:0.47
Consensus pattern (44 bp):
TTTTGGATTTAGGTTGAGTATGTGCTAAAGTTTCATTTCATTGT
Found at i:384030 original size:2 final size:2
Alignment explanation
Indices: 384023--384052 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
384013 TTAATAATTC
384023 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
384053 TTTCATCACG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:384344 original size:36 final size:35
Alignment explanation
Indices: 384291--384360 Score: 122
Period size: 36 Copynumber: 2.0 Consensus size: 35
384281 TATCCTTCAA
384291 ATAAAAATAATTTATAATAATATTAATTATCAATT
1 ATAAAAATAATTTATAATAATATTAATTATCAATT
*
384326 ATAAAAATGATTTTATAATAATATTAATTATCAAT
1 ATAAAAAT-AATTTATAATAATATTAATTATCAAT
384361 GCAATCTTAC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 8 0.24
36 25 0.76
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (35 bp):
ATAAAAATAATTTATAATAATATTAATTATCAATT
Found at i:386601 original size:15 final size:15
Alignment explanation
Indices: 386578--386732 Score: 125
Period size: 15 Copynumber: 10.4 Consensus size: 15
386568 CACAACAGAA
*
386578 CAGATAACAGTAGAC
1 CAGATAACAATAGAC
*
386593 CAAATAACAATAGAC
1 CAGATAACAATAGAC
*
386608 CAGATAACAATAGAA
1 CAGATAACAATAGAC
* * *
386623 CATATAACAGT-GAT
1 CAGATAACAATAGAC
* * * *
386637 CGGATAACAACAAAA
1 CAGATAACAATAGAC
* *
386652 TAGATAACAGTAGAC
1 CAGATAACAATAGAC
* *
386667 CAAATAACAATATAC
1 CAGATAACAATAGAC
*
386682 CAGATAACAAT-GAAA
1 CAGATAACAATAG-AC
386697 CAGATAACAATAGAC
1 CAGATAACAATAGAC
* * *
386712 CAAATAATAGTAGAC
1 CAGATAACAATAGAC
386727 CAGATA
1 CAGATA
386733 GAAGTAGACG
Statistics
Matches: 106, Mismatches: 31, Indels: 6
0.74 0.22 0.04
Matches are distributed among these distances:
14 9 0.08
15 96 0.91
16 1 0.01
ACGTcount: A:0.54, C:0.17, G:0.13, T:0.16
Consensus pattern (15 bp):
CAGATAACAATAGAC
Found at i:386738 original size:15 final size:15
Alignment explanation
Indices: 386697--386748 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
386687 AACAATGAAA
* *
386697 CAGATAACAATAGAC
1 CAGATAATAGTAGAC
*
386712 CAAATAATAGTAGAC
1 CAGATAATAGTAGAC
386727 CAGATAGA-AGTAGAC
1 CAGATA-ATAGTAGAC
*
386742 GAGATAA
1 CAGATAA
386749 CTTGAGCATT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
14 1 0.03
15 29 0.94
16 1 0.03
ACGTcount: A:0.52, C:0.13, G:0.19, T:0.15
Consensus pattern (15 bp):
CAGATAATAGTAGAC
Found at i:386749 original size:45 final size:45
Alignment explanation
Indices: 386581--386732 Score: 146
Period size: 45 Copynumber: 3.4 Consensus size: 45
386571 AACAGAACAG
* * * * *
386581 ATAACAGTAGACCAAATAACAAT-AGACCAGATAACAATAGAACAT
1 ATAACAATAGACCAGATAACAATGA-AACAGATAACAATAGACCAA
* * * ** * *
386626 ATAACAGT-GATCGGATAACAACAAAATAGATAACAGTAGACCAA
1 ATAACAATAGACCAGATAACAATGAAACAGATAACAATAGACCAA
*
386670 ATAACAATATACCAGATAACAATGAAACAGATAACAATAGACCAA
1 ATAACAATAGACCAGATAACAATGAAACAGATAACAATAGACCAA
* *
386715 ATAATAGTAGACCAGATA
1 ATAACAATAGACCAGATA
386733 GAAGTAGACG
Statistics
Matches: 85, Mismatches: 20, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
44 32 0.38
45 53 0.62
ACGTcount: A:0.55, C:0.16, G:0.12, T:0.16
Consensus pattern (45 bp):
ATAACAATAGACCAGATAACAATGAAACAGATAACAATAGACCAA
Found at i:388388 original size:17 final size:18
Alignment explanation
Indices: 388366--388399 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
388356 TATTTAATGT
388366 AATATTT-ATATTTTTAC
1 AATATTTAATATTTTTAC
388383 AATATTTAATATTTTTA
1 AATATTTAATATTTTTA
388400 ATAGTAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (18 bp):
AATATTTAATATTTTTAC
Found at i:388674 original size:2 final size:2
Alignment explanation
Indices: 388667--388691 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
388657 TTAAATGAGG
388667 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
388692 CGTTCATGTT
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:391704 original size:8 final size:8
Alignment explanation
Indices: 391691--391716 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
391681 ATAGTGATTG
391691 AATTATTT
1 AATTATTT
391699 AATTATTT
1 AATTATTT
391707 AATTATTT
1 AATTATTT
391715 AA
1 AA
391717 ATGATATTAA
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:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (8 bp):
AATTATTT
Found at i:395648 original size:75 final size:78
Alignment explanation
Indices: 395535--395684 Score: 216
Period size: 76 Copynumber: 2.0 Consensus size: 78
395525 CTAAAATACC
* * *
395535 TAAAAAATAATAATATAATATTCTAAATCCTAATTAAAATACT-AACACATATTTAAACTAAAAT
1 TAAAAAATAATAATATAATATTCTAAAACCTAAATAAAATACTAAAAACATATTTAAACTAAAAT
395599 ACAAAGATAATGA
66 ACAAAGATAATGA
* * * *
395612 TAAAATATAA-AA-ATAATATTGTAAAACTTAAATAAAATACTAAAAACCTATTTAAACTAAAAT
1 TAAAAAATAATAATATAATATTCTAAAACCTAAATAAAATACTAAAAACATATTTAAACTAAAAT
395675 ACAAAGATAA
66 ACAAAGATAA
395685 AATATAATGT
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
75 25 0.38
76 31 0.48
77 9 0.14
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29
Consensus pattern (78 bp):
TAAAAAATAATAATATAATATTCTAAAACCTAAATAAAATACTAAAAACATATTTAAACTAAAAT
ACAAAGATAATGA
Found at i:397527 original size:14 final size:14
Alignment explanation
Indices: 397491--397530 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
397481 GTTCAGAAAA
*
397491 AATAAAATTAATCAG
1 AATAAAATAAAT-AG
397506 AATAAAATAAATAG
1 AATAAAATAAATAG
*
397520 AATGAAATAAA
1 AATAAAATAAA
397531 GTTCGCTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.68, C:0.03, G:0.07, T:0.23
Consensus pattern (14 bp):
AATAAAATAAATAG
Found at i:397569 original size:20 final size:19
Alignment explanation
Indices: 397537--397577 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
397527 TAAAGTTCGC
*
397537 TAAAAAAATAAAACGAAAA
1 TAAAAAAATAAAACAAAAA
397556 TAAAAAAATAAAAACAAAAA
1 TAAAAAAAT-AAAACAAAAA
397576 TA
1 TA
397578 TAACGAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.80, C:0.05, G:0.02, T:0.12
Consensus pattern (19 bp):
TAAAAAAATAAAACAAAAA
Found at i:403277 original size:23 final size:23
Alignment explanation
Indices: 403227--403277 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
403217 AAGTTGTGGT
* *
403227 TAAAATAAAAAATAAGAATTAAA
1 TAAAAGAAAAAATAAGAAATAAA
*
403250 TAAAAGAAAAAATAATTAAATAAA
1 TAAAAGAAAAAATAA-GAAATAAA
403274 -AAAA
1 TAAAA
403278 TTAAAGAGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 18 0.75
24 6 0.25
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (23 bp):
TAAAAGAAAAAATAAGAAATAAA
Found at i:403752 original size:12 final size:12
Alignment explanation
Indices: 403737--403766 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
403727 AAAAGTATAC
403737 GAAAAATAGAGA
1 GAAAAATAGAGA
*
403749 GAAAACTAGAGA
1 GAAAAATAGAGA
403761 GAAAAA
1 GAAAAA
403767 GAAGATTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.67, C:0.03, G:0.23, T:0.07
Consensus pattern (12 bp):
GAAAAATAGAGA
Found at i:403982 original size:76 final size:75
Alignment explanation
Indices: 403872--404019 Score: 235
Period size: 76 Copynumber: 2.0 Consensus size: 75
403862 TCTTAAATCC
403872 TAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAGATAAAAT-ATAAAAATAAT
1 TAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAA-ATAAAATGATAAAAATAAT
403936 ATCCTAAAACT
65 ATCCTAAAACT
* * * *
403947 TAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAATATAATGTTTAAAATATT
1 TAATTAAAATACT-AAAACCTATTTAAACTAAAATACAAAGATAAAATAAAATGATAAAAATAAT
404012 ATCCTAAA
65 ATCCTAAA
404020 TTTGAGTTTA
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
75 19 0.28
76 48 0.72
ACGTcount: A:0.58, C:0.10, G:0.03, T:0.29
Consensus pattern (75 bp):
TAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAATAAAATGATAAAAATAATA
TCCTAAAACT
Found at i:423289 original size:14 final size:14
Alignment explanation
Indices: 423270--423298 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
423260 TTTACTGTTC
423270 ATAAATATGTTTTT
1 ATAAATATGTTTTT
423284 ATAAATATGTTTTT
1 ATAAATATGTTTTT
423298 A
1 A
423299 CCTTAAAATT
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:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (14 bp):
ATAAATATGTTTTT
Found at i:427919 original size:23 final size:23
Alignment explanation
Indices: 427901--427961 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
427891 CTCATATAAA
*
427901 TACACCGAAGTGCCACATAGAAT
1 TACACCGTAGTGCCACATAGAAT
* *
427924 TACACCGTAGTGCCGCGTAGAAT
1 TACACCGTAGTGCCACATAGAAT
427947 TACACCGTAGTGCCA
1 TACACCGTAGTGCCA
427962 TATAATAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.31, C:0.28, G:0.21, T:0.20
Consensus pattern (23 bp):
TACACCGTAGTGCCACATAGAAT
Found at i:428102 original size:103 final size:103
Alignment explanation
Indices: 427977--428194 Score: 384
Period size: 103 Copynumber: 2.1 Consensus size: 103
427967 TAATGTCCAT
*
427977 AAGGACCACATATCATTCCTTAAGAATCATATACATATA-CTAGAGATCAAGTATGTGTCTCACC
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAG-GATCAAGTATGTGTCTCACC
428041 AGACTTCACACATGTTCCAAAAAATACATATATGTCCCG
65 AGACTTCACACATGTTCCAAAAAATACATATATGTCCCG
*
428080 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
* *
428145 TACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAAAATACATATATGTCCCG
428183 AAGGACCACATA
1 AAGGACCACATA
428195 GACCCTCGAC
Statistics
Matches: 110, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
103 107 0.97
104 3 0.03
ACGTcount: A:0.38, C:0.24, G:0.12, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAAAATACATATATGTCCCG
Found at i:429733 original size:3 final size:3
Alignment explanation
Indices: 429725--429770 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
429715 ATATTAATTA
*
429725 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
429771 AATATATTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:430212 original size:19 final size:19
Alignment explanation
Indices: 430188--430225 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
430178 CCCGAACCTG
*
430188 AAAAAAAAAAGAAGACAGA
1 AAAAAAAAAAGAACACAGA
430207 AAAAAAAAAAGAACACAGA
1 AAAAAAAAAAGAACACAGA
430226 GCCGGAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.79, C:0.08, G:0.13, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAGAACACAGA
Found at i:442601 original size:12 final size:12
Alignment explanation
Indices: 442584--442623 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
442574 TATTATGCTT
442584 GAAAAAAAAAGA
1 GAAAAAAAAAGA
442596 GAAAAAGAAAA-A
1 GAAAAA-AAAAGA
442608 GAAAAAAAAAG-
1 GAAAAAAAAAGA
442619 GAAAA
1 GAAAA
442624 GAGGGGGGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 9 0.35
12 13 0.50
13 4 0.15
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.00
Consensus pattern (12 bp):
GAAAAAAAAAGA
Found at i:443846 original size:82 final size:82
Alignment explanation
Indices: 443746--444322 Score: 1028
Period size: 82 Copynumber: 7.0 Consensus size: 82
443736 TGTGATATCC
443746 CAGTCCAATCGTTGAATTTGGAAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGT
1 CAGTCCAATCGTTGAATTTGGAAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGT
443811 TATCTGATCTGATTTGG
66 TATCTGATCTGATTTGG
443828 CAGTCCAATCGTTGAATTTGGAAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGT
1 CAGTCCAATCGTTGAATTTGGAAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGT
443893 TATCTGATCTGATTTGG
66 TATCTGATCTGATTTGG
443910 CAGTCCAATCGTTGAATTTGGAAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGT
1 CAGTCCAATCGTTGAATTTGGAAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGT
443975 TATCTGATCTGATTTGG
66 TATCTGATCTGATTTGG
443992 CAGTCCAATCGTTGAATTTGGAAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGT
1 CAGTCCAATCGTTGAATTTGGAAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGT
*
444057 TATCTGATCTGGTTTGG
66 TATCTGATCTGATTTGG
* * * *
444074 CAGAACCAATCATTGAATTTGGAAGATGAATTTGCTAATAGCATCTTCTGGAATTGTTCTTTAAG
1 CAG-TCCAATCGTTGAATTTGGAAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAG
444139 TTATCTGATCTGATTTGG
65 TTATCTGATCTGATTTGG
* *
444157 CAGAACCAATCATTGAATTTGGAAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAG
1 CAG-TCCAATCGTTGAATTTGGAAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAG
444222 TTATCTGATCTGATTTGG
65 TTATCTGATCTGATTTGG
* *
444240 CAGAACCAATCATTGAATTTGGAAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAG
1 CAG-TCCAATCGTTGAATTTGGAAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAG
* *
444305 TTATTTGATCTGGTTTGG
65 TTATCTGATCTGATTTGG
444323 TAAGAACTAC
Statistics
Matches: 484, Mismatches: 10, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
82 248 0.51
83 236 0.49
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (82 bp):
CAGTCCAATCGTTGAATTTGGAAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGT
TATCTGATCTGATTTGG
Found at i:445246 original size:114 final size:114
Alignment explanation
Indices: 445046--445943 Score: 1575
Period size: 114 Copynumber: 7.9 Consensus size: 114
445036 ATTCAAATCT
445046 ATCAAATTGATGGATTAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 ATCAAATTGATGGATTAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
445111 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
*
445160 ATCAAATTGATGGATTAGATTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 ATCAAATTGATGGATTAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
445225 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
445274 ATCAAATTGATGGATTAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 ATCAAATTGATGGATTAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
445339 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
445388 ATCAAATTGATGGATTAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 ATCAAATTGATGGATTAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
445453 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
*
445502 ATCAAATTGATGGATTAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATATGAAGAAGGA
1 ATCAAATTGATGGATTAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
445567 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
445616 ATCAAATTGATGGATTAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 ATCAAATTGATGGATTAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
445681 AGAAGAAGTTCATAATGGGAAGAATTTGTTCAACCTTTTACCTGAATTC
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
* * *
445730 ATCAAATTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTAAAGAAGGA
1 ATCAAATTGATGGATTAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * * * *
445795 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTAAATTC
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
* * * * * *
445844 ATC-ATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGA
1 ATCAAATTGATGGATTAGCTTTTCCAGAGAAG-GTTCATAATGAGAAGAA--C-TCATCTGAAGA
* *
445907 AGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAA
62 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA
445944 TAACTCTATC
Statistics
Matches: 757, Mismatches: 23, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
112 2 0.00
113 35 0.05
114 673 0.89
115 1 0.00
116 46 0.06
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (114 bp):
ATCAAATTGATGGATTAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
Found at i:446183 original size:3 final size:3
Alignment explanation
Indices: 446175--446246 Score: 110
Period size: 3 Copynumber: 24.3 Consensus size: 3
446165 ATATTAATTA
*
446175 ATT ATT ATT ATT ATT ATA ATT ATT ATT A-T ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
446222 ATT ATC ATT ATT ATC ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
446247 AATATTTAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
2 2 0.03
3 60 0.97
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:446679 original size:17 final size:17
Alignment explanation
Indices: 446657--446692 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
446647 ACCCGAACCT
*
446657 GAAAAAAAAAGAAGACA
1 GAAAAAAAAAGAACACA
446674 GAAAAAAAAAGAACACA
1 GAAAAAAAAAGAACACA
446691 GA
1 GA
446693 GCCGGAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.75, C:0.08, G:0.17, T:0.00
Consensus pattern (17 bp):
GAAAAAAAAAGAACACA
Found at i:449968 original size:16 final size:16
Alignment explanation
Indices: 449947--449984 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
449937 TAATGCCCAT
449947 GCTATATGATACGAGA
1 GCTATATGATACGAGA
449963 GCTATATGATACGAGA
1 GCTATATGATACGAGA
449979 GCTATA
1 GCTATA
449985 GGTATAGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.26
Consensus pattern (16 bp):
GCTATATGATACGAGA
Found at i:450054 original size:22 final size:21
Alignment explanation
Indices: 450021--450072 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
450011 GGGTATACGC
* * *
450021 GGTCCTTCGGACATATATAGT
1 GGTCATTCGGACAAATACAGT
*
450042 GGTCATTCAGGACAAATACATT
1 GGTCATTC-GGACAAATACAGT
450064 GGTCATTCG
1 GGTCATTCG
450073 AGATAATTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 8 0.31
22 18 0.69
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (21 bp):
GGTCATTCGGACAAATACAGT
Found at i:452412 original size:2 final size:2
Alignment explanation
Indices: 452405--452444 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
452395 TGAATTCAAG
452405 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
452445 TTAAATACAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:452688 original size:17 final size:17
Alignment explanation
Indices: 452666--452699 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
452656 TCATAAATTT
452666 AAAATATATTTTAAATA
1 AAAATATATTTTAAATA
452683 AAAATATATTTTAAATA
1 AAAATATATTTTAAATA
452700 TAATTTAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAAATATATTTTAAATA
Found at i:452693 original size:28 final size:29
Alignment explanation
Indices: 452662--452722 Score: 88
Period size: 28 Copynumber: 2.1 Consensus size: 29
452652 AAATTCATAA
*
452662 ATTTAAAATATATTTTAA-ATAAAAATAT
1 ATTTAAAATATAATTTAAGATAAAAATAT
* *
452690 ATTTTAAATATAATTTAAGATAAGAATAT
1 ATTTAAAATATAATTTAAGATAAAAATAT
452719 ATTT
1 ATTT
452723 TTAATGTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 16 0.55
29 13 0.45
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.44
Consensus pattern (29 bp):
ATTTAAAATATAATTTAAGATAAAAATAT
Found at i:456123 original size:97 final size:97
Alignment explanation
Indices: 455957--456151 Score: 390
Period size: 97 Copynumber: 2.0 Consensus size: 97
455947 TAAAGATAAC
455957 ACTCTCAACCTTTCGATATTTGATTATTCACACTTCTGATATCTATGATGTTCGAACTTGATTCT
1 ACTCTCAACCTTTCGATATTTGATTATTCACACTTCTGATATCTATGATGTTCGAACTTGATTCT
456022 TCAAAGAATAATAACAATTCATTTACTAACAG
66 TCAAAGAATAATAACAATTCATTTACTAACAG
456054 ACTCTCAACCTTTCGATATTTGATTATTCACACTTCTGATATCTATGATGTTCGAACTTGATTCT
1 ACTCTCAACCTTTCGATATTTGATTATTCACACTTCTGATATCTATGATGTTCGAACTTGATTCT
456119 TCAAAGAATAATAACAATTCATTTACTAACAG
66 TCAAAGAATAATAACAATTCATTTACTAACAG
456151 A
1 A
456152 GGTTACTTTG
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
97 98 1.00
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.38
Consensus pattern (97 bp):
ACTCTCAACCTTTCGATATTTGATTATTCACACTTCTGATATCTATGATGTTCGAACTTGATTCT
TCAAAGAATAATAACAATTCATTTACTAACAG
Found at i:461478 original size:3 final size:3
Alignment explanation
Indices: 461470--461510 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
461460 TACAGGGTTT
461470 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
461511 GCAGCCATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:464405 original size:15 final size:16
Alignment explanation
Indices: 464378--464414 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
464368 TTTCAAGCGA
464378 ATGAAGTTTTCCACTGG
1 ATGAAGTTTTCCA-TGG
464395 -TGAAG-TTTCCATGG
1 ATGAAGTTTTCCATGG
464409 ATGAAG
1 ATGAAG
464415 CACAAAAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 3 0.16
15 11 0.58
16 5 0.26
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.32
Consensus pattern (16 bp):
ATGAAGTTTTCCATGG
Found at i:468664 original size:20 final size:20
Alignment explanation
Indices: 468618--468668 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
468608 GTTAAAATAA
468618 AGAGAGAGAGAGAGAAAATG
1 AGAGAGAGAGAGAGAAAATG
* *
468638 AGTGAGAGAGAGAG-AAACG
1 AGAGAGAGAGAGAGAAAATG
468657 TAGAGAGAGAGA
1 -AGAGAGAGAGA
468669 ATTTTAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 4 0.15
20 23 0.85
ACGTcount: A:0.51, C:0.02, G:0.41, T:0.06
Consensus pattern (20 bp):
AGAGAGAGAGAGAGAAAATG
Found at i:481546 original size:26 final size:26
Alignment explanation
Indices: 481517--481574 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
481507 TTATTAATTA
*
481517 TGCATGATATTTATTCACACTGATTT
1 TGCATGATATTTACTCACACTGATTT
** *
481543 TGCATGATATTTACTCATGCTGGTTT
1 TGCATGATATTTACTCACACTGATTT
481569 TGCATG
1 TGCATG
481575 TAATACTCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.22, C:0.16, G:0.17, T:0.45
Consensus pattern (26 bp):
TGCATGATATTTACTCACACTGATTT
Found at i:481873 original size:26 final size:26
Alignment explanation
Indices: 481801--481878 Score: 84
Period size: 26 Copynumber: 3.0 Consensus size: 26
481791 TGTACACCAT
** * *
481801 ATATTTACTCGTATTGATTATGCATG
1 ATATTTACTCACACTGATTTTGCATG
*
481827 ATATTTATTCACACTGATTTTGCATG
1 ATATTTACTCACACTGATTTTGCATG
** *
481853 ATATTTACTCATGCTGGTTTTGCATG
1 ATATTTACTCACACTGATTTTGCATG
481879 TACTACTCAA
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.24, C:0.14, G:0.15, T:0.46
Consensus pattern (26 bp):
ATATTTACTCACACTGATTTTGCATG
Found at i:496580 original size:16 final size:15
Alignment explanation
Indices: 496554--496584 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
496544 ATGTATGACC
496554 GGTCATCCCGGGATG
1 GGTCATCCCGGGATG
496569 GGTCAGTCCCGGGATG
1 GGTCA-TCCCGGGATG
496585 CCGGCCGGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.13, C:0.26, G:0.42, T:0.19
Consensus pattern (15 bp):
GGTCATCCCGGGATG
Found at i:496745 original size:4 final size:4
Alignment explanation
Indices: 496732--496784 Score: 63
Period size: 4 Copynumber: 13.0 Consensus size: 4
496722 GACCTGAAAC
* *
496732 AAAT -AAT AAAT AAAT AAAT GAAAAT AAAT AAAT AAAT AGAT AAAT TAAT
1 AAAT AAAT AAAT AAAT AAAT --AAAT AAAT AAAT AAAT AAAT AAAT AAAT
496781 AAAT
1 AAAT
496785 TAATTAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
3 3 0.07
4 35 0.83
6 4 0.10
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:496789 original size:12 final size:12
Alignment explanation
Indices: 496736--496791 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 12
496726 TGAAACAAAT
*
496736 AATAAATAAATA
1 AATAAATTAATA
*
496748 AATGAA--AATA
1 AATAAATTAATA
*
496758 AATAAATAAATA
1 AATAAATTAATA
*
496770 GATAAATTAATA
1 AATAAATTAATA
*
496782 AATTAATTAA
1 AATAAATTAA
496792 AAACATTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
10 9 0.25
12 27 0.75
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.29
Consensus pattern (12 bp):
AATAAATTAATA
Found at i:496882 original size:73 final size:72
Alignment explanation
Indices: 496802--496989 Score: 234
Period size: 73 Copynumber: 2.5 Consensus size: 72
496792 AAACATTTTT
* *
496802 AAAACTATACAATATATGTTTTAAAAAAATAATTTTCAAAACCACATAACATA-TATTTTAAAAA
1 AAAACTATATAATATAT-TTTT-AAAAACTAATTTTCAAAACCACATAACATACTATTTTAAAAA
496866 AAAAATTTC
64 AAAAATTTC
* * * * *
496875 AAAACTATATAATATATTTTTAAAAACTAATTTTCAAAACTATATAATATACTTTTTTTAAAAAC
1 AAAACTATATAATATATTTTTAAAAACTAATTTTCAAAACCACATAACATAC-TATTTTAAAAAA
* *
496940 TAATTTTC
65 AAAATTTC
496948 AAAACTATATAATATTTATATTTTAAAAACTAATTTTCAAAA
1 AAAACTATATAATA--TAT-TTTTAAAAACTAATTTTCAAAA
496990 TTATATAATA
Statistics
Matches: 101, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
71 26 0.26
72 4 0.04
73 46 0.46
75 3 0.03
76 22 0.22
ACGTcount: A:0.51, C:0.10, G:0.01, T:0.39
Consensus pattern (72 bp):
AAAACTATATAATATATTTTTAAAAACTAATTTTCAAAACCACATAACATACTATTTTAAAAAAA
AAATTTC
Found at i:496910 original size:35 final size:35
Alignment explanation
Indices: 496788--497104 Score: 279
Period size: 38 Copynumber: 8.9 Consensus size: 35
496778 AATAAATTAA
* *
496788 TTAAAAAC--ATTTTTAAAACTATACAATATATGTT
1 TTAAAAACTAATTTTCAAAACTATATAATATAT-TT
* * * *
496822 TTAAAAAAATAATTTTCAAAACCACATAACATATATT
1 TT-AAAAACTAATTTTCAAAACTATATAATATAT-TT
** *
496859 TTAAAAAAAAAATTTCAAAACTATATAATATATTT
1 TTAAAAACTAATTTTCAAAACTATATAATATATTT
496894 TTAAAAACTAATTTTCAAAACTATATAATATACTTTTT
1 TTAAAAACTAATTTTCAAAACTATATAATATA---TTT
496932 TTAAAAACTAATTTTCAAAACTATATAATATTTATATT
1 TTAAAAACTAATTTTCAAAACTATATAATA--TAT-TT
* *
496970 TTAAAAACTAATTTTCAAAATTATATAATATATAT
1 TTAAAAACTAATTTTCAAAACTATATAATATATTT
* * **
497005 TTAGAAACTAATTTTCAAAATTATAT-ATACGTTT
1 TTAAAAACTAATTTTCAAAACTATATAATATATTT
* * * *
497039 TTCAAAA-T-GTTTTTAAAAGCTATATATTATATATAT
1 TTAAAAACTAATTTTCAAAA-CTATATA--ATATATTT
* *
497075 TTAGAAAA--AGTTTTCAAAACAATATAATAT
1 TTA-AAAACTAATTTTCAAAACTATATAATAT
497105 GTATTTTCAA
Statistics
Matches: 236, Mismatches: 32, Indels: 30
0.79 0.11 0.10
Matches are distributed among these distances:
32 8 0.03
33 6 0.03
34 16 0.07
35 62 0.26
36 42 0.18
37 36 0.15
38 64 0.27
40 2 0.01
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.41
Consensus pattern (35 bp):
TTAAAAACTAATTTTCAAAACTATATAATATATTT
Found at i:496913 original size:13 final size:13
Alignment explanation
Indices: 496892--496989 Score: 51
Period size: 13 Copynumber: 7.6 Consensus size: 13
496882 TATAATATAT
496892 TTTTAAAAACTAA
1 TTTTAAAAACTAA
*
496905 TTTTCAAAACT-A
1 TTTTAAAAACTAA
* * **
496917 -TATAATATACTTT
1 TTTTAA-AAACTAA
496930 TTTTAAAAACTAA
1 TTTTAAAAACTAA
*
496943 TTTTCAAAACT-A
1 TTTTAAAAACTAA
* * **
496955 -TATAATATTTATA
1 TTTTAAAAACTA-A
496968 TTTTAAAAACTAA
1 TTTTAAAAACTAA
496981 TTTTCAAAA
1 TTTT-AAAA
496990 TTATATAATA
Statistics
Matches: 59, Mismatches: 19, Indels: 13
0.65 0.21 0.14
Matches are distributed among these distances:
11 8 0.14
12 6 0.10
13 30 0.51
14 15 0.25
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTTAAAAACTAA
Found at i:496995 original size:38 final size:36
Alignment explanation
Indices: 496930--497152 Score: 174
Period size: 36 Copynumber: 6.2 Consensus size: 36
496920 AATATACTTT
496930 TTTTAAAAACTAATTTTCAAAACTATATAATATTTATA
1 TTTTAAAAACTAATTTTCAAAACTATATAATA--TATA
*
496968 TTTTAAAAACTAATTTTCAAAATTATATAATATATA
1 TTTTAAAAACTAATTTTCAAAACTATATAATATATA
* * **
497004 -TTTAGAAACTAATTTTCAAAATTATAT-ATACGT-
1 TTTTAAAAACTAATTTTCAAAACTATATAATATATA
* * * *
497037 TTTTCAAAA-T-GTTTTTAAAAGCTATATATTATATA
1 TTTTAAAAACTAATTTTCAAAA-CTATATAATATATA
* * *
497072 TATTTAGAAAA--AGTTTTCAAAACAATATAATATGTA
1 T-TTTA-AAAACTAATTTTCAAAACTATATAATATATA
** * * *
497108 TTTTCAAAAA-TGTTTTTAAAAATTATATATTATATA
1 TTTT-AAAAACTAATTTTCAAAACTATATAATATATA
*
497144 TTTTCAAAA
1 TTTTAAAAA
497153 TATTTTAAAA
Statistics
Matches: 151, Mismatches: 25, Indels: 21
0.77 0.13 0.11
Matches are distributed among these distances:
32 8 0.05
33 6 0.04
34 13 0.09
35 38 0.25
36 42 0.28
37 13 0.09
38 31 0.21
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (36 bp):
TTTTAAAAACTAATTTTCAAAACTATATAATATATA
Found at i:497142 original size:70 final size:70
Alignment explanation
Indices: 496871--497146 Score: 240
Period size: 73 Copynumber: 3.9 Consensus size: 70
496861 AAAAAAAAAA
* ** * * * *
496871 TTTCAAAACTATATAATA--TATTTTTAAAAACTAATTTTCAAAACTATATAATATACTTTTTTT
1 TTTCAAAACTATATAATATGTATTTTCAAAAA-TGTTTTTAAAAATTATAT-AT-TA-TATATTT
*
496934 AAAAACTAAT
62 AGAAAC-AAT
* * ** * *
496944 TTTCAAAACTATATAATATTTATATTTTAAAAACTAATTTTCAAAATTATATAATATATATTTAG
1 TTTCAAAACTATATAATATGTAT-TTTCAAAAA-TGTTTTTAAAAATTATATATTATATATTTAG
497009 AAACTAAT
64 AAAC-AAT
* * **
497017 TTTCAAAATTATAT-ATACGT-TTTTC-AAAATGTTTTTAAAAGCTATATATTATATATATTTAG
1 TTTCAAAACTATATAATATGTATTTTCAAAAATGTTTTTAAAAATTATATA-T-TATATATTTAG
497079 AAA-AAGT
64 AAACAA-T
*
497086 TTTCAAAACAATATAATATGTATTTTCAAAAATGTTTTTAAAAATTATATATTATATATTT
1 TTTCAAAACTATATAATATGTATTTTCAAAAATGTTTTTAAAAATTATATATTATATATTT
497147 TCAAAATATT
Statistics
Matches: 174, Mismatches: 20, Indels: 21
0.81 0.09 0.10
Matches are distributed among these distances:
68 16 0.09
69 17 0.10
70 31 0.18
71 7 0.04
72 25 0.14
73 45 0.26
74 2 0.01
75 4 0.02
76 27 0.16
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (70 bp):
TTTCAAAACTATATAATATGTATTTTCAAAAATGTTTTTAAAAATTATATATTATATATTTAGAA
ACAAT
Found at i:498045 original size:164 final size:163
Alignment explanation
Indices: 497834--498879 Score: 1156
Period size: 164 Copynumber: 6.3 Consensus size: 163
497824 TTGAATATAA
*
497834 TCGAACTCGAAGGTCTT--TAGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGC
1 TCGAACTCGAAGGTCTTGGTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGC
* *** *
497897 CCTCGAAGCTGAGTGTAATCGAACTTGGGGGTCTTTGGCAGATAGCTCTTCTCGACTTAAGCTAT
66 CCTTGAAGCTGAGTGTAATCGAACTCAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTAT
497962 ACTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
131 ACTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
* * * * *
497995 TCGAACTCGAAGGTCTTGGTGGGCAGATAGCCCTTCTGGCCTTGAGCTATGCTGTAAATGATATG
1 TCGAACTCGAAGGTCTTGGT-GGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
* * *
498060 CCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTAGTTGGCAGATAACCCTTCTTGACTTAA
65 CCCTTGAAGCTGAGTGTAATCGAACTCAAGGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAA
* * *
498125 GTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAG
126 GCTATACTGCAAATGATGTGCCTT-GGAGCTGAGCGTAG
* *
498164 TCGAACTCGAGGGTCTT--TGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTG-
1 TCGAACTCGAAGGTCTTGGTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGC
* * * * * *
498226 CCTTGGAGCTGAGCGTAGTCGAACTCGAA-GGTCTTGGTGGACAGATAGCCCTTCTGGCCTTGAG
66 CCTTGAAGCTGAGTGTAATCGAACTC-AAGGGTCTT--TGG-CAGATAGCCCTTCTCGACTTAAG
* * * * * *
498290 CTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAA
127 CTATACTGCAAATGATGTG-CCTTGGAGCTGAGCGTAG
* * * * * *
498328 TCGAACT-TAAGGGTCTTTAGTTGGCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATG
1 TCGAACTCGAA-GGTC-TT-GGTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATG
* * *
498392 TG-CCTTCGAAGCTGAATGTAGTCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAG
63 TGCCCTT-GAAGCTGAGTGTAATCGAACTCAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAG
*
498456 CTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
127 CTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
* * * * * * * * *
498493 TCGAACTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATG
1 TCGAACTCGAAGGTC-TTGGTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
* *
498558 CCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTAGTTGGCAGATAACCCTTCTCGACTTAA
65 CCCTTGAAGCTGAGTGTAATCGAACTCAAGGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAA
* * *
498623 GTTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAG
126 GCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
* * * * * * * *
498661 TCAAACTCAAAGGTCTTTTGTTAGCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGT
1 TCGAACTCGAAGGTC--TTGGTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
* * * * *
498726 G-CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGCAGATAGCCCTTCTCAACTTAAGCT
64 GCCCTTGAAGCTGAGTGTAATCGAACTCAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCT
* *
498790 ATTCTACAAATGATGTGCCTTGGAGCTGAGCGTAG
129 ATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
* * * *
498825 TCGAACTCGAAGGTCTTGGTGGACAGATAGCCCTTCTGGCCTTGAGCTAAGCTGC
1 TCGAACTCGAAGGTCTTGGTGG-CAGATAGCCCTTCTCGACTTAAGCTATGCTGC
498880 CAATAGTTTG
Statistics
Matches: 752, Mismatches: 105, Indels: 54
0.83 0.12 0.06
Matches are distributed among these distances:
161 18 0.02
162 5 0.01
163 31 0.04
164 260 0.35
165 65 0.09
166 81 0.11
167 4 0.01
168 194 0.26
169 94 0.12
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (163 bp):
TCGAACTCGAAGGTCTTGGTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGC
CCTTGAAGCTGAGTGTAATCGAACTCAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTAT
ACTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
Found at i:498180 original size:249 final size:248
Alignment explanation
Indices: 497769--498831 Score: 1500
Period size: 249 Copynumber: 4.3 Consensus size: 248
497759 ACAGTTTTAT
* * * * * * * *
497769 TGACAAATAGCCCTTCTTGCCTTGAGCTATTCTGTAAGCTTGATTTG-CCTCT-AAGTTGAATAT
1 TGACAGATAGCCCTTCTGGCCTTGAGCTATGCTGTAA--ATGATATGCCCT-TGAAGCTGAGTGT
* * * *
497832 AATCGAACTCGAA-GGTCTTTA----GCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGA
63 AATCGAACT-TAAGGGTCTTTAGTTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGA
* * * * * *
497892 TGTGCCCTCGAAGCTGAGTGTAATCGAACTTGGGGGTCTTTGGCAGATAGCTCTTCTCGACTTAA
127 TGTGCCTTCGAAGCTGAATGTAGTCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAA
*
497957 GCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTGG
192 GCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTGG
*
498014 TGGGCAGATAGCCCTTCTGGCCTTGAGCTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAA
1 T-GACAGATAGCCCTTCTGGCCTTGAGCTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAA
*
498079 TCGAACTTAAGGGTCTTTAGTTGGCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGT
65 TCGAACTTAAGGGTCTTTAGTTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATGT
*
498144 GCCTTCGAAGCTGAACGTAGTCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCT
130 GCCTTCGAAGCTGAATGTAGTCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCT
* *
498209 ATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTGG
195 ATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTGG
498263 TGGACAGATAGCCCTTCTGGCCTTGAGCTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAA
1 T-GACAGATAGCCCTTCTGGCCTTGAGCTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAA
*
498328 TCGAACTTAAGGGTCTTTAGTTGGCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGT
65 TCGAACTTAAGGGTCTTTAGTTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATGT
498393 GCCTTCGAAGCTGAATGTAGTCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCT
130 GCCTTCGAAGCTGAATGTAGTCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCT
*
498458 ATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGG
195 ATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTC-TTGG
* * *
498513 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAAT
1 TGACAGATAGCCCTTCTGGCCTTGAGCTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAAT
*
498578 CGAACTTAAGGGTCTTTAGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG
66 CGAACTTAAGGGTCTTTAGTTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATGTG
* * * * * * *
498643 CCTT-GGAGCTGAGTGTAGTCAAACTCAAAGGTCTTTTGTTAGCAGATAACCCTTCTTGACTTAA
131 CCTTCGAAGCTGAATGTAGTCGAACTCGAGGGTC-TTTG---GCAGATAGCCCTTCTCGACTTAA
*
498707 GTTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTT--
192 GCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTGG
* *** * * ** * * * *
498762 TGGCAGATAGCCCTTCTCAACTTAAGCTATTCTACAAATGATGTG-CCTTGGAGCTGAGCGTAGT
1 TGACAGATAGCCCTTCTGGCCTTGAGCTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAAT
498826 CGAACT
66 CGAACT
498832 CGAAGGTCTT
Statistics
Matches: 752, Mismatches: 53, Indels: 23
0.91 0.06 0.03
Matches are distributed among these distances:
244 9 0.01
245 29 0.04
246 32 0.04
248 46 0.06
249 557 0.74
250 5 0.01
251 2 0.00
252 72 0.10
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.30
Consensus pattern (248 bp):
TGACAGATAGCCCTTCTGGCCTTGAGCTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAAT
CGAACTTAAGGGTCTTTAGTTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATGTG
CCTTCGAAGCTGAATGTAGTCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTA
TACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTGG
Found at i:502915 original size:16 final size:17
Alignment explanation
Indices: 502888--502919 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
502878 TGCAAACGAT
502888 GAACACAAAATAAAAGA
1 GAACACAAAATAAAAGA
502905 GAACA-AAAATAAAAG
1 GAACACAAAATAAAAG
502920 GGTTAGCGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.72, C:0.09, G:0.12, T:0.06
Consensus pattern (17 bp):
GAACACAAAATAAAAGA
Found at i:505328 original size:16 final size:15
Alignment explanation
Indices: 505302--505332 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
505292 ATGTATGACC
505302 GGTCATCCCGGGATG
1 GGTCATCCCGGGATG
505317 GGTCAGTCCCGGGATG
1 GGTCA-TCCCGGGATG
505333 CCGGCCGGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.13, C:0.26, G:0.42, T:0.19
Consensus pattern (15 bp):
GGTCATCCCGGGATG
Found at i:505493 original size:4 final size:4
Alignment explanation
Indices: 505480--505543 Score: 64
Period size: 4 Copynumber: 17.0 Consensus size: 4
505470 GACCTGAAAC
* *
505480 AAAT -AAT AAAT AAAT AAAT GAA- AAA- AAAT -AAT AAAT AAAT TAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* *
505524 AAAT AGAT AAAT TAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT
505544 TAATTAAAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
3 11 0.22
4 38 0.78
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (4 bp):
AAAT
Found at i:505514 original size:21 final size:24
Alignment explanation
Indices: 505474--505543 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
505464 ATCCTGGACC
505474 TGAAACAAATAATAAATAAATAAA
1 TGAAACAAATAATAAATAAATAAA
505498 TGAAA-AAA-AAT-AATAAATAAA
1 TGAAACAAATAATAAATAAATAAA
* * *
505519 T-TAATAAATAGATAAATTAATAAA
1 TGAAACAAATA-ATAAATAAATAAA
505543 T
1 T
505544 TAATTAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
20 2 0.05
21 14 0.35
22 4 0.10
23 5 0.12
24 15 0.38
ACGTcount: A:0.69, C:0.01, G:0.04, T:0.26
Consensus pattern (24 bp):
TGAAACAAATAATAAATAAATAAA
Found at i:505603 original size:38 final size:36
Alignment explanation
Indices: 505555--505794 Score: 268
Period size: 38 Copynumber: 6.5 Consensus size: 36
505545 AATTAAAAAC
* * *
505555 ATTTTTAAAACTATACAATATATGTTTTAAAAAAAATA
1 ATTTTCAAAACTATATAATATAT-TTTT-AAAAAACTA
* * * *
505593 ATTTTCAAAACCACATAACATATATTTTAAAAAAAAAATA
1 ATTTTCAAAACTATAT-A-ATATATTTT--TAAAAAACTA
505633 ATTTTCAAAACTATATAATATATTTTT-AAAAACTA
1 ATTTTCAAAACTATATAATATATTTTTAAAAAACTA
*
505668 ATTTTCAAAACTATATAATATACTTTTTTAAAAACTA
1 ATTTTCAAAACTATATAATATA-TTTTTAAAAAACTA
*
505705 ATTTTCAAAACTATATAATATATATATTTTAAAAACTA
1 ATTTTCAAAACTATATAATATAT-T-TTTAAAAAACTA
* * *
505743 ATTTTCAAAATTATATAATATATATTT-AGAAACTA
1 ATTTTCAAAACTATATAATATATTTTTAAAAAACTA
*
505778 ATTTTCAAAATTATATA
1 ATTTTCAAAACTATATA
505795 TACGTTTTTC
Statistics
Matches: 182, Mismatches: 12, Indels: 19
0.85 0.06 0.09
Matches are distributed among these distances:
35 53 0.29
36 9 0.05
37 31 0.17
38 55 0.30
39 5 0.03
40 29 0.16
ACGTcount: A:0.50, C:0.08, G:0.01, T:0.40
Consensus pattern (36 bp):
ATTTTCAAAACTATATAATATATTTTTAAAAAACTA
Found at i:505627 original size:40 final size:39
Alignment explanation
Indices: 505583--505664 Score: 128
Period size: 40 Copynumber: 2.1 Consensus size: 39
505573 TATATGTTTT
505583 AAAAAAAATAATTTTCAAAACCACATAACATATATTTTAA
1 AAAAAAAATAATTTTCAAAACCACATAACATAT-TTTTAA
* * *
505623 AAAAAAAATAATTTTCAAAACTATATAATATATTTTTAA
1 AAAAAAAATAATTTTCAAAACCACATAACATATTTTTAA
505662 AAA
1 AAA
505665 CTAATTTTCA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
39 9 0.23
40 30 0.77
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.33
Consensus pattern (39 bp):
AAAAAAAATAATTTTCAAAACCACATAACATATTTTTAA
Found at i:505628 original size:75 final size:72
Alignment explanation
Indices: 505549--505752 Score: 221
Period size: 75 Copynumber: 2.7 Consensus size: 72
505539 TAAATTAATT
* * *
505549 AAAAACATTTTTAAAACTATACAATATATGTTTTAAAAAAAATAATTTTCAAAACCACATAACAT
1 AAAAAAATTTTTAAAACTATATAATATAT-TTTT--AAAAACTAATTTTCAAAACCACATAACAT
505614 A-TATTTTAAA
63 ACTATTTT-AA
* * *
505624 AAAAAAATAATTTTCAAAACTATATAATATATTTTTAAAAACTAATTTTCAAAACTATATAATAT
1 AAAAAAAT--TTTT-AAAACTATATAATATATTTTTAAAAACTAATTTTCAAAACCACATAACAT
*
505689 ACTTTTTTAA
63 ACTATTTTAA
** *
505699 AAACTAATTTTCAAAACTATATAATATATATATTTTAAAAACTAATTTTCAAAA
1 AAAAAAATTTTTAAAACTATAT-A-ATATAT-TTTTAAAAACTAATTTTCAAAA
505753 TTATATAATA
Statistics
Matches: 112, Mismatches: 10, Indels: 14
0.82 0.07 0.10
Matches are distributed among these distances:
72 10 0.09
73 4 0.04
74 6 0.05
75 63 0.56
76 5 0.04
77 8 0.07
78 16 0.14
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.38
Consensus pattern (72 bp):
AAAAAAATTTTTAAAACTATATAATATATTTTTAAAAACTAATTTTCAAAACCACATAACATACT
ATTTTAA
Found at i:505677 original size:13 final size:13
Alignment explanation
Indices: 505656--505752 Score: 53
Period size: 13 Copynumber: 7.6 Consensus size: 13
505646 TATAATATAT
505656 TTTTAAAAACTAA
1 TTTTAAAAACTAA
*
505669 TTTTCAAAACT-A
1 TTTTAAAAACTAA
* * *
505681 -TATAATATACT-T
1 TTTTAA-AAACTAA
505693 TTTTAAAAACTAA
1 TTTTAAAAACTAA
*
505706 TTTTCAAAACT-A
1 TTTTAAAAACTAA
* *
505718 -TATAATATA-TATA
1 TTTTAA-AAACTA-A
505731 TTTTAAAAACTAA
1 TTTTAAAAACTAA
505744 TTTTCAAAA
1 TTTT-AAAA
505753 TTATATAATA
Statistics
Matches: 61, Mismatches: 14, Indels: 17
0.66 0.15 0.18
Matches are distributed among these distances:
11 7 0.11
12 12 0.20
13 32 0.52
14 10 0.16
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.42
Consensus pattern (13 bp):
TTTTAAAAACTAA
Found at i:505908 original size:70 final size:69
Alignment explanation
Indices: 505632--505909 Score: 244
Period size: 72 Copynumber: 3.9 Consensus size: 69
505622 AAAAAAAAAT
* * * * * *
505632 AATTTTCAAAACTATATAATA--TATTTTTAAAAACTAATTTTCAAAACTATATAATATACTTTT
1 AATTTTCAAAACTATATAATATGTATTTTCAAAAA-T-GTTTTTAAAATTATATATTATA--TAT
*
505695 TTAAAAAC
62 TTAGAAAC
* * * * *
505703 TAATTTTCAAAACTATATAATATATATATTTTAAAAACTAATTTTCAAAATTATATAATATATAT
1 -AATTTTCAAAACTATATAATATGTAT-TTTCAAAAA-T-GTTTTTAAAATTATATATTATATAT
505768 TTAGAAAC
62 TTAGAAAC
* * *
505776 TAATTTTCAAAATTATAT-ATACGT-TTTTC-AAAATGTTTTTAAAAGCTATATATTATATATAT
1 -AATTTTCAAAACTATATAATATGTATTTTCAAAAATGTTTTTAAAA-TTATATA-T-TATATAT
505838 TTAGAAA-
62 TTAGAAAC
*
505845 AAGTTTTCAAAACAATATAATATGTATTTTCAAAAATGTTTTTGAAAATTATATATTATATATTT
1 AA-TTTTCAAAACTATATAATATGTATTTTCAAAAATGTTTTT-AAAATTATATATTATATATTT
505910 TCAAAATATT
Statistics
Matches: 180, Mismatches: 15, Indels: 24
0.82 0.07 0.11
Matches are distributed among these distances:
67 8 0.04
68 9 0.05
69 17 0.09
70 31 0.17
71 7 0.04
72 42 0.23
73 30 0.17
74 3 0.02
75 33 0.18
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (69 bp):
AATTTTCAAAACTATATAATATGTATTTTCAAAAATGTTTTTAAAATTATATATTATATATTTAG
AAAC
Found at i:505909 original size:36 final size:35
Alignment explanation
Indices: 505634--505915 Score: 143
Period size: 35 Copynumber: 7.9 Consensus size: 35
505624 AAAAAAATAA
* * *
505634 TTTTCAAAACTATATA--ATATATTTTTAAAAACTAA
1 TTTTTAAAACTATATATTATATATTTTCAAAAA-T-G
* * * *
505669 TTTTCAAAACTATATAATATACT-TTTTTAAAAACTAA
1 TTTTTAAAACTATATATTATA-TATTTTCAAAAA-T-G
* *
505706 TTTTCAAAACTATATAATATATATATTTT-AAAAACTAA
1 TTTTTAAAACTATAT-AT-TATATATTTTCAAAAA-T-G
* * * * *
505744 TTTTCAAAATTATATAATATATA-TTT-AGAAACTAA
1 TTTTTAAAACTATATATTATATATTTTCA-AAAAT-G
* * **
505779 TTTTCAAAATTATATA-TACGT-TTTTC-AAAATG
1 TTTTTAAAACTATATATTATATATTTTCAAAAATG
*
505811 TTTTTAAAAGCTATATATTATATATATTT-AGAAAAAG
1 TTTTTAAAA-CTATATATTATATAT-TTTCA-AAAATG
* * * *
505848 TTTTCAAAACAATATAATATGTATTTTCAAAAATG
1 TTTTTAAAACTATATATTATATATTTTCAAAAATG
*
505883 TTTTTGAAAATTATATATTATATATTTTCAAAA
1 TTTTT-AAAACTATATATTATATATTTTCAAAA
505916 TATTTAAAAA
Statistics
Matches: 207, Mismatches: 23, Indels: 33
0.79 0.09 0.13
Matches are distributed among these distances:
32 8 0.04
33 10 0.05
34 9 0.04
35 52 0.25
36 48 0.23
37 46 0.22
38 26 0.13
39 8 0.04
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (35 bp):
TTTTTAAAACTATATATTATATATTTTCAAAAATG
Found at i:512228 original size:18 final size:19
Alignment explanation
Indices: 512205--512242 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
512195 TAAAGTAGAA
512205 ATCTAA-TTTAATAAAATT
1 ATCTAATTTTAATAAAATT
*
512223 ATCTAATTTTAATCAAATT
1 ATCTAATTTTAATAAAATT
512242 A
1 A
512243 GGATTCTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (19 bp):
ATCTAATTTTAATAAAATT
Found at i:530377 original size:31 final size:31
Alignment explanation
Indices: 530339--530408 Score: 131
Period size: 31 Copynumber: 2.3 Consensus size: 31
530329 ACAAGGTGTG
530339 GGACAAATTTGGCAAAGGATTTTTGGTTACA
1 GGACAAATTTGGCAAAGGATTTTTGGTTACA
*
530370 GGACAAATTTGGCAAAGGTTTTTTGGTTACA
1 GGACAAATTTGGCAAAGGATTTTTGGTTACA
530401 GGACAAAT
1 GGACAAAT
530409 AGGTTCAAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.33, C:0.10, G:0.26, T:0.31
Consensus pattern (31 bp):
GGACAAATTTGGCAAAGGATTTTTGGTTACA
Found at i:540545 original size:65 final size:65
Alignment explanation
Indices: 540412--540571 Score: 202
Period size: 65 Copynumber: 2.5 Consensus size: 65
540402 TGCACTAAGA
* *
540412 GTGCATCGATGCATAAAATGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAGCCAGAGTGCATCGATACATAGCTG
* * *
540476 GTGCATCGATGCATCAAATACATTCGATGTTTTCATAAA-A-CTCTGAGTGCATCGATACATAG-
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCA-AAATAGC-CAGAGTGCATCGATACATAGC
*
540538 TAT
64 T-G
*
540541 GTGCATCGATGCATGAAATGCATTCGATGTT
1 GTGCATCGATGCATAAAATGCATTCGATGTT
540572 CAATTTATTC
Statistics
Matches: 84, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
64 29 0.35
65 52 0.62
66 3 0.04
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAGCCAGAGTGCATCGATACATAGCTG
Found at i:545221 original size:3 final size:3
Alignment explanation
Indices: 545215--545297 Score: 105
Period size: 3 Copynumber: 27.0 Consensus size: 3
545205 TTACCCATTT
* *
545215 TTA TTA TTA TTA TTA TTA TTA TTA -TA TTTA TAA TAA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
*
545260 TTA TTA TTA TTA TTA TTA TATA TTA TTTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA T-TA TTA -TTA TTA TTA TTA
545298 CAAAACTCAA
Statistics
Matches: 72, Mismatches: 4, Indels: 8
0.86 0.05 0.10
Matches are distributed among these distances:
2 2 0.03
3 62 0.86
4 8 0.11
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:558127 original size:30 final size:28
Alignment explanation
Indices: 558089--558151 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 28
558079 GCTTGAAGAG
558089 AAAAAG-AAAAGAAAAAAAAGGAAAGAGAA
1 AAAAAGAAAAAGAAAAAAAA-G-AAGAGAA
558118 AAAAGAGAAAAAAGAAAAAAAAGAAGAGAA
1 AAAA-AG-AAAAAGAAAAAAAAGAAGAGAA
558148 AAAA
1 AAAA
558152 TGGGGTCAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
29 4 0.13
30 13 0.42
31 1 0.03
32 13 0.42
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (28 bp):
AAAAAGAAAAAGAAAAAAAAGAAGAGAA
Found at i:558142 original size:9 final size:9
Alignment explanation
Indices: 558089--558142 Score: 56
Period size: 9 Copynumber: 5.9 Consensus size: 9
558079 GCTTGAAGAG
558089 AAAAAGAAA
1 AAAAAGAAA
558098 AGAAAA-AAA
1 A-AAAAGAAA
* *
558107 AGGAAAGAGA
1 A-AAAAGAAA
*
558117 AAAAAGAGA
1 AAAAAGAAA
558126 AAAAAGAAA
1 AAAAAGAAA
558135 AAAAAGAA
1 AAAAAGAA
558143 GAGAAAAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
9 32 0.82
10 7 0.18
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:559445 original size:92 final size:92
Alignment explanation
Indices: 559283--559753 Score: 896
Period size: 92 Copynumber: 5.2 Consensus size: 92
559273 AGAAGACCCA
*
559283 ATAGTATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAGT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAGT
559348 TATTGAATTTGGAAGAGGAATGTGCTC
66 TATTGAATTTGGAAGAGGAATGTGCTC
559375 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAGT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAGT
559440 TATTGAATTTGGAAGAGGAATGTGCTC
66 TATTGAATTTGGAAGAGGAATGTGCTC
559467 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAGT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAGT
559532 TATTGAATTTGGAAGAGGAATGTGCTC
66 TATTGAATTTGGAAGAGGAATGTGCTC
559559 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAGT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAGT
559624 TATTGAATTTGGAAGAGGAATGTGCTC
66 TATTGAATTTGGAAGAGGAATGTGCTC
*
559651 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATATGAACCACAGAACCAGT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAGT
559716 TA-TGAATTTGGAAGAGGAA--TG-TC
66 TATTGAATTTGGAAGAGGAATGTGCTC
559739 ATAGCATCTTCTGGA
1 ATAGCATCTTCTGGA
559754 CTTTGAGTTA
Statistics
Matches: 377, Mismatches: 2, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
88 17 0.05
89 2 0.01
91 17 0.05
92 341 0.90
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.35
Consensus pattern (92 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAGT
TATTGAATTTGGAAGAGGAATGTGCTC
Found at i:560874 original size:112 final size:113
Alignment explanation
Indices: 560498--561153 Score: 722
Period size: 113 Copynumber: 5.8 Consensus size: 113
560488 GCAAAGATTC
* * * *
560498 AAATCCATCAATTGATGGATCAGCATTACCAGATAGAGTTCATAATGAGAAGAACTCATCATCTG
1 AAATTCATCATTTGATGGATCAGCATTTCCAGGTAGAGTTCATAATGAGAAGAA--C-TCATCTG
*
560563 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG-TT
63 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTGCTT
* * * *** * *
560613 AAATTCATTATTTTATGGATCAGCATTACCAAAAAGAGTTCATAATAAGAAGAACTCATCTAAAG
1 AAATTCATCATTTGATGGATCAGCATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAG
* * *
560678 AA-AAAG-AGAAATTCATAATGAGAAGAA-TTG-TTCA-CTTTTGCTT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTGCTT
* * * *
560721 GAATTCATCACTTGATGGATCAGCTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAA
1 AAATTCATCATTTGATGGATCAGCATTTCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAA
*
560785 GAA-GAAGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTGTTT
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTGCTT
* * * ** *
560833 GAATTCATCATTTGATAGATTAAAATTTCTAGGTAGAGTTCATAATGAGAAGAACTCATCATTTG
1 AAATTCATCATTTGATGGATCAGCATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATC---TG
* * * *
560898 AAGAAGGAAGAAGAAATTCATAATGAGAATAATTTGTTCAACCTTTTGCTC
63 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTGCTT
* * * * * * *
560949 AAATCCATCACTTGATGGGTCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGAAG
1 AAATTCATCATTTGATGGATCAGCATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAG
* *
561014 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAAACTTTTG-TT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTGCTT
* * * * * *
561061 CAAATTCATTATTTGATGGATCAACATTTCCAGAG-AAAGTTCATAATAAGAAGAACTTATTTGA
1 -AAATTCATCATTTGATGGATCAGCATTTCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGA
* *
561125 AG-AGGAAGAAGAAGTTCAAAATAAGAAGA
64 AGAAGGAAGAAGAAGTTCATAATGAGAAGA
561154 GCTTATTCAA
Statistics
Matches: 454, Mismatches: 74, Indels: 29
0.82 0.13 0.05
Matches are distributed among these distances:
107 6 0.01
108 62 0.14
109 23 0.05
110 23 0.05
111 7 0.02
112 95 0.21
113 97 0.21
115 54 0.12
116 87 0.19
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (113 bp):
AAATTCATCATTTGATGGATCAGCATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTGCTT
Found at i:561039 original size:24 final size:23
Alignment explanation
Indices: 560996--561040 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
560986 GTTCATAATG
*
560996 AGAAGAATTCATCTGAAGAAGGA
1 AGAAGAATTCATATGAAGAAGGA
561019 AGAAGAAGTTCATAATG-AGAAG
1 AGAAGAA-TTCAT-ATGAAGAAG
561041 AACTTGTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 7 0.37
24 10 0.53
25 2 0.11
ACGTcount: A:0.49, C:0.07, G:0.27, T:0.18
Consensus pattern (23 bp):
AGAAGAATTCATATGAAGAAGGA
Found at i:561378 original size:3 final size:3
Alignment explanation
Indices: 561370--561440 Score: 64
Period size: 3 Copynumber: 25.0 Consensus size: 3
561360 GGCAGCTGAT
561370 TTA TTA TTA TTA -TA TTA -TA TT- TATA TTA TTA TTA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA
* *
561412 TTA -TA TTA -TA ATA TTA TTAA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA
561441 CAAAACCCAA
Statistics
Matches: 57, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
2 11 0.19
3 42 0.74
4 4 0.07
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:561387 original size:11 final size:11
Alignment explanation
Indices: 561371--561440 Score: 73
Period size: 10 Copynumber: 7.0 Consensus size: 11
561361 GCAGCTGATT
561371 TATTATTATTA
1 TATTATTATTA
561382 TATTA-TATT-
1 TATTATTATTA
561391 TA-TATTA-T-
1 TATTATTATTA
561399 TATTATTATTA
1 TATTATTATTA
561410 TATTA-TATTA
1 TATTATTATTA
*
561420 TAATATTATTA
1 TATTATTATTA
*
561431 -ATTAATATTA
1 TATTATTATTA
561441 CAAAACCCAA
Statistics
Matches: 51, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
8 5 0.10
9 9 0.18
10 22 0.43
11 15 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TATTATTATTA
Found at i:561398 original size:22 final size:22
Alignment explanation
Indices: 561371--561440 Score: 92
Period size: 22 Copynumber: 3.2 Consensus size: 22
561361 GCAGCTGATT
561371 TATTATTATTA-TATTATATTTA
1 TATTATTATTATTATTATA-TTA
561393 TATTATTATTATTATTATATTA
1 TATTATTATTATTATTATATTA
*
561415 TATTA-TAATATTATTA-ATTAA
1 TATTATTATTATTATTATATT-A
561436 TATTA
1 TATTA
561441 CAAAACCCAA
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
20 3 0.07
21 16 0.36
22 19 0.42
23 7 0.16
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TATTATTATTATTATTATATTA
Found at i:561410 original size:28 final size:30
Alignment explanation
Indices: 561370--561440 Score: 110
Period size: 28 Copynumber: 2.4 Consensus size: 30
561360 GGCAGCTGAT
561370 TTATTATTATTATATTATATT-T-ATATTA
1 TTATTATTATTATATTATATTATAATATTA
561398 TTATTATTATTATATTATATTATAATATTA
1 TTATTATTATTATATTATATTATAATATTA
*
561428 TTAATTAATATTA
1 TT-ATTATTATTA
561441 CAAAACCCAA
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
28 21 0.54
29 1 0.03
30 8 0.21
31 9 0.23
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (30 bp):
TTATTATTATTATATTATATTATAATATTA
Found at i:563033 original size:117 final size:123
Alignment explanation
Indices: 562804--563044 Score: 293
Period size: 117 Copynumber: 2.0 Consensus size: 123
562794 TGTAGTTATA
*
562804 TAAATATATATAATAAATAATAATTTATATTTTTTTTACATAAATTATTTTAATATTTATTTTTC
1 TAAATATATATAATAAATAATAATTTATATTTTTTTTACATAAATTATATTAATATTTA--TTTC
* * * *
562869 AATATCGAAGAAAAGGGCAGTCTTAATACAACTAGATGTCCTATTCTGGTATTT-TAAAAT
64 AATATCGAAGAAAAGAGCAGTCTTAATAC-ACTAGAAGTCATATTCTGATATTTCTAAAAT
*
562929 TAAATATCATA-AA-AAATAATAATTTA-ATTTTTTTTA-AT-TATTATATTAATATTTA-TT-A
1 TAAATAT-ATATAATAAATAATAATTTATATTTTTTTTACATAAATTATATTAATATTTATTTCA
* *
562987 ATATCGAAGAAAAGAGCTGTCTTAAGGTAC-CTAGAAGTCATTTTCTGATATTTCTAAA
65 ATATCGAAGAAAAGAGCAGTCTTAA--TACACTAGAAGTCATATTCTGATATTTCTAAA
563045 TAAATAATAT
Statistics
Matches: 104, Mismatches: 8, Indels: 15
0.82 0.06 0.12
Matches are distributed among these distances:
117 43 0.41
118 6 0.06
119 3 0.03
121 15 0.14
122 2 0.02
123 10 0.10
124 13 0.12
125 9 0.09
126 3 0.03
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.43
Consensus pattern (123 bp):
TAAATATATATAATAAATAATAATTTATATTTTTTTTACATAAATTATATTAATATTTATTTCAA
TATCGAAGAAAAGAGCAGTCTTAATACACTAGAAGTCATATTCTGATATTTCTAAAAT
Found at i:574658 original size:21 final size:19
Alignment explanation
Indices: 574634--574674 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
574624 GTCATGCAAC
574634 TAATAATAGTTGCATAATGCA
1 TAATAATAGTT-CAT-ATGCA
*
574655 TAATAATGGTTCATATGCA
1 TAATAATAGTTCATATGCA
574674 T
1 T
574675 TGTAAGTTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 3 0.16
21 10 0.53
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.37
Consensus pattern (19 bp):
TAATAATAGTTCATATGCA
Found at i:577817 original size:20 final size:21
Alignment explanation
Indices: 577780--577821 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
577770 GTCATGCAAC
577780 TAATAATAGTTGCATAATGCA
1 TAATAATAGTTGCATAATGCA
*
577801 TAATAATGGTT-CATAATGCA
1 TAATAATAGTTGCATAATGCA
577821 T
1 T
577822 TGTAAGTTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (21 bp):
TAATAATAGTTGCATAATGCA
Found at i:578807 original size:9 final size:9
Alignment explanation
Indices: 578793--578824 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
578783 AATTAGAATT
578793 GACAAGGAA
1 GACAAGGAA
578802 GACAAGGAA
1 GACAAGGAA
578811 GACAAGGAA
1 GACAAGGAA
578820 GACAA
1 GACAA
578825 TTTTAGAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.56, C:0.12, G:0.31, T:0.00
Consensus pattern (9 bp):
GACAAGGAA
Found at i:579232 original size:23 final size:22
Alignment explanation
Indices: 579174--579233 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 22
579164 TTAATTATGT
579174 CTTTGTGACATG-TTTCTCTGC
1 CTTTGTGACATGTTTTCTCTGC
** * *
579195 CTTAATGGCACGTTTATCTCTGC
1 CTTTGTGACATGTTT-TCTCTGC
579218 CTTTGTGACATGTTTT
1 CTTTGTGACATGTTTT
579234 TCTTTGTATT
Statistics
Matches: 29, Mismatches: 8, Indels: 3
0.73 0.20 0.08
Matches are distributed among these distances:
21 8 0.28
22 3 0.10
23 18 0.62
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (22 bp):
CTTTGTGACATGTTTTCTCTGC
Found at i:580207 original size:104 final size:103
Alignment explanation
Indices: 580040--580227 Score: 252
Period size: 104 Copynumber: 1.8 Consensus size: 103
580030 TTATTAGTAT
* * * *
580040 AAATTGTGATGATTTTTTTACACTAAAAATATATTTTGTGACCATCAATATTATTACACTAA-GT
1 AAATTGTGATAATTTTTTGACACTAAAAATATATTTTGTGACCAGCAATATTATCACACTAAGGT
580104 ATTTTTAGTGACCAAATGTTTAATACTATTATCAATAG
66 ATTTTTAGTGACCAAATGTTTAATACTATTATCAATAG
* * * * *
580142 AAATTGTGATAAATTTATTTGACACTGAAAGTATATTTTGTGACTAGCAATGTTATCACATTAAG
1 AAATTGTGAT-AATTT-TTTGACACTAAAAATATATTTTGTGACCAGCAATATTATCACACTAAG
*
580207 TGTTTTTTTAGTGACCAAATG
64 -GTATTTTTAGTGACCAAATG
580228 CTCGACACTA
Statistics
Matches: 72, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
102 10 0.14
103 4 0.06
104 39 0.54
106 19 0.26
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.41
Consensus pattern (103 bp):
AAATTGTGATAATTTTTTGACACTAAAAATATATTTTGTGACCAGCAATATTATCACACTAAGGT
ATTTTTAGTGACCAAATGTTTAATACTATTATCAATAG
Found at i:580862 original size:12 final size:12
Alignment explanation
Indices: 580845--580893 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
580835 GAATTAATTT
*
580845 TATATATTTTAA
1 TATATATTATAA
580857 TATATA-TAT-A
1 TATATATTATAA
580867 TATATATTATTAA
1 TATATATTA-TAA
580880 T-TATTATTATAA
1 TATA-TATTATAA
580892 TA
1 TA
580894 ATTTAATTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
10 7 0.23
11 4 0.13
12 13 0.42
13 7 0.23
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TATATATTATAA
Found at i:580890 original size:20 final size:21
Alignment explanation
Indices: 580844--580900 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
580834 GGAATTAATT
580844 TTATATATTTTAATATATATA
1 TTATATATTTTAATATATATA
580865 TATATATATTATTAAT-TAT-TA
1 T-TATATATT-TTAATATATATA
*
580886 TTATAATAATTTAAT
1 TTAT-ATATTTTAAT
580901 TAAATGCTCT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
20 8 0.25
21 8 0.25
22 11 0.34
23 5 0.16
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTATATATTTTAATATATATA
Found at i:582075 original size:38 final size:38
Alignment explanation
Indices: 582019--582151 Score: 113
Period size: 42 Copynumber: 3.3 Consensus size: 38
582009 TTCACTTCAA
* ** *
582019 TAGTGATAAAAATTATTATCGTCATAAATCACCAAGAC
1 TAGTGACAAAAACAATTATCGTCAAAAATCACCAAGAC
* *
582057 TAGTGACAAAAACAATTATCGTCACAAATCATCAACTAAGAT
1 TAGTGACAAAAACAATTATCGTCA-AAA--ATC-ACCAAGAC
* * *
582099 TAATGACAAAAACAATTATCATCACAAATAATCAACTAAGAC
1 TAGTGACAAAAACAATTATCGT--CAAA-AATC-ACCAAGAC
582141 TAGTGACAAAA
1 TAGTGACAAAA
582152 TATTTTCATC
Statistics
Matches: 78, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
38 21 0.27
39 2 0.03
41 3 0.04
42 47 0.60
43 2 0.03
44 3 0.04
ACGTcount: A:0.50, C:0.17, G:0.09, T:0.24
Consensus pattern (38 bp):
TAGTGACAAAAACAATTATCGTCAAAAATCACCAAGAC
Found at i:582117 original size:42 final size:42
Alignment explanation
Indices: 582052--582151 Score: 155
Period size: 42 Copynumber: 2.4 Consensus size: 42
582042 ATAAATCACC
* * *
582052 AAGACTAGTGACAAAAACAATTATCGTCACAAATCATCAACT
1 AAGACTAATGACAAAAACAATTATCATCACAAATAATCAACT
*
582094 AAGATTAATGACAAAAACAATTATCATCACAAATAATCAACT
1 AAGACTAATGACAAAAACAATTATCATCACAAATAATCAACT
*
582136 AAGACTAGTGACAAAA
1 AAGACTAATGACAAAA
582152 TATTTTCATC
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.52, C:0.18, G:0.09, T:0.21
Consensus pattern (42 bp):
AAGACTAATGACAAAAACAATTATCATCACAAATAATCAACT
Found at i:583307 original size:34 final size:36
Alignment explanation
Indices: 583246--583315 Score: 117
Period size: 34 Copynumber: 2.0 Consensus size: 36
583236 ATGTGCAGGG
583246 GGAACAGATTCCCCCCTGGGGGGGTATCGATTCCCCA
1 GGAACAGATT-CCCCCTGGGGGGGTATCGATTCCCCA
583283 GGAACAGATT-CCCCT-GGGGGGTATCGATTCCCC
1 GGAACAGATTCCCCCTGGGGGGGTATCGATTCCCC
583316 CCTAAATGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
34 18 0.55
35 5 0.15
37 10 0.30
ACGTcount: A:0.19, C:0.31, G:0.30, T:0.20
Consensus pattern (36 bp):
GGAACAGATTCCCCCTGGGGGGGTATCGATTCCCCA
Found at i:583745 original size:22 final size:21
Alignment explanation
Indices: 583720--583792 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 21
583710 TTATATGAAA
583720 TGATATATGAATATGCAATACG
1 TGATATATGAATATG-AATACG
* * **
583742 TGATACATGTGATATGATATGAAA
1 TGATATATG-AATATGA-AT-ACG
*
583766 TGACATATGAATATGTAATACG
1 TGATATATGAATATG-AATACG
583788 TGATA
1 TGATA
583793 CATGTGATAT
Statistics
Matches: 37, Mismatches: 10, Indels: 8
0.67 0.18 0.15
Matches are distributed among these distances:
22 14 0.38
23 14 0.38
24 9 0.24
ACGTcount: A:0.41, C:0.07, G:0.19, T:0.33
Consensus pattern (21 bp):
TGATATATGAATATGAATACG
Found at i:583757 original size:23 final size:22
Alignment explanation
Indices: 583730--583804 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 22
583720 TGATATATGA
583730 ATATGCAATACGTGATACATGTG
1 ATATG-AATACGTGATACATGTG
* ** *
583753 ATATG-ATATGAAATGACATATG
1 ATATGAATACGTGAT-ACATGTG
583775 AATATGTAATACGTGATACATGTG
1 -ATATG-AATACGTGATACATGTG
583799 ATATGA
1 ATATGA
583805 TATGAAATAC
Statistics
Matches: 40, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
21 6 0.15
22 7 0.17
23 15 0.38
24 6 0.15
25 6 0.15
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (22 bp):
ATATGAATACGTGATACATGTG
Found at i:583774 original size:46 final size:46
Alignment explanation
Indices: 583704--583816 Score: 187
Period size: 46 Copynumber: 2.5 Consensus size: 46
583694 GAGATAAGCT
*
583704 ATGTGAT-T-ATATGAAATGATATATGAATATGCAATACGTGATAC
1 ATGTGATATGATATGAAATGACATATGAATATGCAATACGTGATAC
*
583748 ATGTGATATGATATGAAATGACATATGAATATGTAATACGTGATAC
1 ATGTGATATGATATGAAATGACATATGAATATGCAATACGTGATAC
583794 ATGTGATATGATATGAAAT-ACAT
1 ATGTGATATGATATGAAATGACAT
583817 GGTTACACAT
Statistics
Matches: 65, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
44 7 0.11
45 5 0.08
46 53 0.82
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.34
Consensus pattern (46 bp):
ATGTGATATGATATGAAATGACATATGAATATGCAATACGTGATAC
Found at i:584021 original size:38 final size:38
Alignment explanation
Indices: 583965--584060 Score: 147
Period size: 38 Copynumber: 2.5 Consensus size: 38
583955 TATAAGACAT
* *
583965 ATGATAGGTCCTACGGGACACAGATTACATCCTTCGGG
1 ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
* *
584003 ATGACAGGTCCTTCGGGACACAGATGACATCTTTCGGG
1 ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
*
584041 ATGATAGGTCCTTTGGGACA
1 ATGATAGGTCCTTCGGGACA
584061 TTTATACGAG
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 52 1.00
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (38 bp):
ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
Found at i:584250 original size:20 final size:21
Alignment explanation
Indices: 584214--584255 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
584204 TGACATGATG
*
584214 TATATATATGTCATATTGAAA
1 TATATACATGTCATATTGAAA
584235 TATATACATG-CATATTGAAA
1 TATATACATGTCATATTGAAA
584255 T
1 T
584256 GTTATGATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (21 bp):
TATATACATGTCATATTGAAA
Found at i:584289 original size:54 final size:54
Alignment explanation
Indices: 584225--584338 Score: 219
Period size: 54 Copynumber: 2.1 Consensus size: 54
584215 ATATATATGT
584225 CATATTGAAATATATACATGCATATTGAAATGTTATGATTAAATGGTAAGAATA
1 CATATTGAAATATATACATGCATATTGAAATGTTATGATTAAATGGTAAGAATA
*
584279 CATATTGAAATATATACATGCATATTGAAATGTTATGATTAAATGGTAAGAATG
1 CATATTGAAATATATACATGCATATTGAAATGTTATGATTAAATGGTAAGAATA
584333 CATATT
1 CATATT
584339 CATGAAATCT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 59 1.00
ACGTcount: A:0.43, C:0.06, G:0.15, T:0.36
Consensus pattern (54 bp):
CATATTGAAATATATACATGCATATTGAAATGTTATGATTAAATGGTAAGAATA
Found at i:585996 original size:2 final size:2
Alignment explanation
Indices: 585989--586023 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
585979 TATCATTGGA
585989 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
586024 ATAATAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:589505 original size:35 final size:37
Alignment explanation
Indices: 589440--589510 Score: 128
Period size: 35 Copynumber: 2.0 Consensus size: 37
589430 TATGTGCAGG
589440 GGGAACAGATTCCCCCCTGGGGGGGTATCGATTCCCT
1 GGGAACAGATTCCCCCCTGGGGGGGTATCGATTCCCT
589477 GGGAACAGATT-CCCCCT-GGGGGGTATCGATTCCC
1 GGGAACAGATTCCCCCCTGGGGGGGTATCGATTCCC
589511 CCCTAAATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
35 17 0.50
36 6 0.18
37 11 0.32
ACGTcount: A:0.17, C:0.30, G:0.32, T:0.21
Consensus pattern (37 bp):
GGGAACAGATTCCCCCCTGGGGGGGTATCGATTCCCT
Found at i:589940 original size:22 final size:21
Alignment explanation
Indices: 589915--589987 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 21
589905 TTATATGAAA
589915 TGATATATGAATATGCAATACG
1 TGATATATGAATATG-AATACG
* * **
589937 TGATACATGTGATATGATATGAAA
1 TGATATATG-AATATGA-AT-ACG
*
589961 TGACATATGAATATGTAATACG
1 TGATATATGAATATG-AATACG
589983 TGATA
1 TGATA
589988 CATGTGATAT
Statistics
Matches: 37, Mismatches: 10, Indels: 8
0.67 0.18 0.15
Matches are distributed among these distances:
22 14 0.38
23 14 0.38
24 9 0.24
ACGTcount: A:0.41, C:0.07, G:0.19, T:0.33
Consensus pattern (21 bp):
TGATATATGAATATGAATACG
Found at i:589952 original size:23 final size:22
Alignment explanation
Indices: 589925--589999 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 22
589915 TGATATATGA
589925 ATATGCAATACGTGATACATGTG
1 ATATG-AATACGTGATACATGTG
* ** *
589948 ATATG-ATATGAAATGACATATG
1 ATATGAATACGTGAT-ACATGTG
589970 AATATGTAATACGTGATACATGTG
1 -ATATG-AATACGTGATACATGTG
589994 ATATGA
1 ATATGA
590000 TATGAAATAC
Statistics
Matches: 40, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
21 6 0.15
22 7 0.17
23 15 0.38
24 6 0.15
25 6 0.15
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (22 bp):
ATATGAATACGTGATACATGTG
Found at i:589969 original size:46 final size:46
Alignment explanation
Indices: 589899--590011 Score: 187
Period size: 46 Copynumber: 2.5 Consensus size: 46
589889 GAGATAAGCT
*
589899 ATGTGAT-T-ATATGAAATGATATATGAATATGCAATACGTGATAC
1 ATGTGATATGATATGAAATGACATATGAATATGCAATACGTGATAC
*
589943 ATGTGATATGATATGAAATGACATATGAATATGTAATACGTGATAC
1 ATGTGATATGATATGAAATGACATATGAATATGCAATACGTGATAC
589989 ATGTGATATGATATGAAAT-ACAT
1 ATGTGATATGATATGAAATGACAT
590012 GGTTACACAT
Statistics
Matches: 65, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
44 7 0.11
45 5 0.08
46 53 0.82
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.34
Consensus pattern (46 bp):
ATGTGATATGATATGAAATGACATATGAATATGCAATACGTGATAC
Found at i:590216 original size:38 final size:38
Alignment explanation
Indices: 590160--590255 Score: 147
Period size: 38 Copynumber: 2.5 Consensus size: 38
590150 TATAAGACAT
* *
590160 ATGATAGGTCCTACGGGACACAGATTACATCCTTCGGG
1 ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
* *
590198 ATGACAGGTCCTTCGGGACACAGATGACATCTTTCGGG
1 ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
*
590236 ATGATAGGTCCTTTGGGACA
1 ATGATAGGTCCTTCGGGACA
590256 TTTATACGAG
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 52 1.00
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (38 bp):
ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
Found at i:590445 original size:20 final size:20
Alignment explanation
Indices: 590409--590504 Score: 73
Period size: 20 Copynumber: 5.0 Consensus size: 20
590399 TGACATGATG
*
590409 TATATATATGTCATATTGAAA
1 TATATACATG-CATATTGAAA
590430 TATATACATGCATATTGAAA
1 TATATACATGCATATTGAAA
*
590450 TGT-T--ATG---ATT-AAA
1 TATATACATGCATATTGAAA
* *
590463 TGGTA-AGAATGCATATTGAAA
1 T-ATATA-CATGCATATTGAAA
590484 TATATACATGCATATTGAAA
1 TATATACATGCATATTGAAA
590504 T
1 T
590505 GTTATGATTA
Statistics
Matches: 61, Mismatches: 4, Indels: 21
0.71 0.05 0.24
Matches are distributed among these distances:
13 4 0.07
14 5 0.08
17 6 0.10
19 1 0.02
20 31 0.51
21 14 0.23
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.38
Consensus pattern (20 bp):
TATATACATGCATATTGAAA
Found at i:590484 original size:54 final size:54
Alignment explanation
Indices: 590420--590533 Score: 228
Period size: 54 Copynumber: 2.1 Consensus size: 54
590410 ATATATATGT
590420 CATATTGAAATATATACATGCATATTGAAATGTTATGATTAAATGGTAAGAATG
1 CATATTGAAATATATACATGCATATTGAAATGTTATGATTAAATGGTAAGAATG
590474 CATATTGAAATATATACATGCATATTGAAATGTTATGATTAAATGGTAAGAATG
1 CATATTGAAATATATACATGCATATTGAAATGTTATGATTAAATGGTAAGAATG
590528 CATATT
1 CATATT
590534 CATGAAATCT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 60 1.00
ACGTcount: A:0.42, C:0.06, G:0.16, T:0.36
Consensus pattern (54 bp):
CATATTGAAATATATACATGCATATTGAAATGTTATGATTAAATGGTAAGAATG
Found at i:604788 original size:14 final size:14
Alignment explanation
Indices: 604769--604797 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
604759 AAGTTTTAGG
604769 TTCGAGTTCGAGTT
1 TTCGAGTTCGAGTT
604783 TTCGAGTTCGAGTT
1 TTCGAGTTCGAGTT
604797 T
1 T
604798 GAGGCTTAAA
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:0.14, C:0.14, G:0.28, T:0.45
Consensus pattern (14 bp):
TTCGAGTTCGAGTT
Found at i:615192 original size:126 final size:126
Alignment explanation
Indices: 614967--615232 Score: 532
Period size: 126 Copynumber: 2.1 Consensus size: 126
614957 ACATAGATAG
614967 ACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCCCGAGGGACATGAATGACATAAT
1 ACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCCCGAGGGACATGAATGACATAAT
615032 AGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTC
66 AGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTC
615093 ACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCCCGAGGGACATGAATGACATAAT
1 ACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCCCGAGGGACATGAATGACATAAT
615158 AGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTC
66 AGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTC
615219 ACGTGAATAGTGAA
1 ACGTGAATAGTGAA
615233 CCGATTATAG
Statistics
Matches: 140, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
126 140 1.00
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.22
Consensus pattern (126 bp):
ACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCCCGAGGGACATGAATGACATAAT
AGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTC
Found at i:615313 original size:8 final size:8
Alignment explanation
Indices: 615300--615340 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
615290 TCACAATCTT
615300 TCAAATTC
1 TCAAATTC
615308 TCAAATTC
1 TCAAATTC
* *
615316 CCAAACTC
1 TCAAATTC
615324 T-AAATTC
1 TCAAATTC
615331 TCAAATTC
1 TCAAATTC
615339 TC
1 TC
615341 TGAAAATGAG
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:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:618362 original size:12 final size:13
Alignment explanation
Indices: 618329--618366 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
618319 AAATACATAA
618329 ATATATTTAATAT
1 ATATATTTAATAT
*
618342 ATTTATTTAATAT
1 ATATATTTAATAT
618355 A-ATATTTAATAT
1 ATATATTTAATAT
618367 TATTAGTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
ATATATTTAATAT
Found at i:625672 original size:34 final size:34
Alignment explanation
Indices: 625628--625694 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 34
625618 AATAGGAATT
*
625628 ACAACTTCTCTC-GATCTAACAAGGAGAAAACAATA
1 ACAACTTCTCTCTGA--TAAAAAGGAGAAAACAATA
625663 ACAA-TTCTCTCTTGATAAAAAGGAGAAAACAA
1 ACAACTTCTCTC-TGATAAAAAGGAGAAAACAA
625695 CTCTCAAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 23 0.79
35 4 0.14
36 2 0.07
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.21
Consensus pattern (34 bp):
ACAACTTCTCTCTGATAAAAAGGAGAAAACAATA
Found at i:632609 original size:15 final size:15
Alignment explanation
Indices: 632589--632618 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
632579 ATCTTTCTTT
632589 ATTATGCTTTCATCA
1 ATTATGCTTTCATCA
*
632604 ATTATGCTTTTATCA
1 ATTATGCTTTCATCA
632619 GCTTTCACTC
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:0.27, C:0.17, G:0.07, T:0.50
Consensus pattern (15 bp):
ATTATGCTTTCATCA
Done.