Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold376
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: 580560
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.32
Warning! 34811 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:316385 original size:45 final size:45
Alignment explanation
Indices: 316314--316444 Score: 133
Period size: 45 Copynumber: 2.9 Consensus size: 45
316304 CTATAGTCTA
* * *
316314 AAATGAGTAATATCATAGCTGGAAGATGTTATGACATCATGATA-
1 AAATGAGTAAGACCATAGCTGAAAGATGTTATGACATCATGATAT
* *
316358 AGGATGAGTAAGACCATAGCTGAAAGATACTCTA-G-CATCATGATAT
1 A-AATGAGTAAGACCATAGCTGAAAGAT-GT-TATGACATCATGATAT
* * * *
316404 AAATGAGTAAGGCCATAACTGAAATACGTTATGACATCATG
1 AAATGAGTAAGACCATAGCTGAAAGATGTTATGACATCATG
316445 GTAAACAGGA
Statistics
Matches: 70, Mismatches: 11, Indels: 11
0.76 0.12 0.12
Matches are distributed among these distances:
43 2 0.03
44 3 0.04
45 60 0.86
46 3 0.04
47 2 0.03
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.26
Consensus pattern (45 bp):
AAATGAGTAAGACCATAGCTGAAAGATGTTATGACATCATGATAT
Found at i:317685 original size:13 final size:13
Alignment explanation
Indices: 317655--317688 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
317645 GTTCCCAAGT
*
317655 TATGTTTT-AATC
1 TATGTTTTAAATA
317667 TATGTTTTAAATA
1 TATGTTTTAAATA
317680 TATGTTTTA
1 TATGTTTTA
317689 TGCGTGCCCC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.29, C:0.03, G:0.09, T:0.59
Consensus pattern (13 bp):
TATGTTTTAAATA
Found at i:324530 original size:137 final size:138
Alignment explanation
Indices: 324281--324549 Score: 371
Period size: 137 Copynumber: 2.0 Consensus size: 138
324271 GAGCTATAAT
* * * *
324281 ATGGGCCTGATCACACAAGTTGTCGGTCAGAATGTAAGCTACACGATGCTACTCACACAAGCTGT
1 ATGGGCCTGATCACACAAGTTGTCAGTCAAAACGTAAGCTACACGATGCTACTCACACAAGCTAT
* * * * * * *
324346 CGAGTATCCGTAACTAATGCTAGACCTCATCCATCGGTAGGACATTCAAGACCAACACCCGAAAC
66 CAAGTATCCGCAACAAATGCTAGAACTCAGCCACCGGTAGGAAATTCAAGACCAACACCCGAAAC
324411 ATAGTAAC
131 ATAGTAAC
* * *
324419 ATGGGTCTGCTCACAGAAGTTGTCAGTCAAAACGT-AGCTACACGATGCTACTCACACAAGCTAT
1 ATGGGCCTGATCACACAAGTTGTCAGTCAAAACGTAAGCTACACGATGCTACTCACACAAGCTAT
* *
324483 CAAGTATCCGCAACAAATG-TCAGAACTCAGCCACCGGTAGGAAATTCAAGGCCAGCACCCGAAA
66 CAAGTATCCGCAACAAATGCT-AGAACTCAGCCACCGGTAGGAAATTCAAGACCAACACCCGAAA
324547 CAT
130 CAT
324550 GGAAACCCTA
Statistics
Matches: 114, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
136 1 0.01
137 84 0.74
138 29 0.25
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (138 bp):
ATGGGCCTGATCACACAAGTTGTCAGTCAAAACGTAAGCTACACGATGCTACTCACACAAGCTAT
CAAGTATCCGCAACAAATGCTAGAACTCAGCCACCGGTAGGAAATTCAAGACCAACACCCGAAAC
ATAGTAAC
Found at i:324722 original size:17 final size:17
Alignment explanation
Indices: 324700--324735 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
324690 ATAGAATCAC
324700 ATACTAACATTCAACTA
1 ATACTAACATTCAACTA
324717 ATACTAACATTCAACTA
1 ATACTAACATTCAACTA
324734 AT
1 AT
324736 CAGCATTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (17 bp):
ATACTAACATTCAACTA
Found at i:332957 original size:16 final size:16
Alignment explanation
Indices: 332927--332962 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
332917 TTTTTAACAT
332927 AAATTAAACTAAATTCA
1 AAATTAAACTAAATT-A
332944 AAATTAAA-TAAATTA
1 AAATTAAACTAAATTA
332959 AAAT
1 AAAT
332963 AATTAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.26
16 6 0.32
17 8 0.42
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.31
Consensus pattern (16 bp):
AAATTAAACTAAATTA
Found at i:334587 original size:27 final size:27
Alignment explanation
Indices: 334557--334860 Score: 373
Period size: 27 Copynumber: 11.3 Consensus size: 27
334547 ATTCGTGGGC
* * *
334557 AAATGACCGGAATACCTTCGAAGGGTA
1 AAATGACTGAAATACCCTCGAAGGGTA
*
334584 AAATGA-TCGAAATACCCTCAAAGGGTA
1 AAATGACT-GAAATACCCTCGAAGGGTA
* *
334611 AAATGACTGAAATACTCTCGATGGGTA
1 AAATGACTGAAATACCCTCGAAGGGTA
*
334638 AAATGACCGAAATACCCTCGAAGGGTA
1 AAATGACTGAAATACCCTCGAAGGGTA
* *
334665 AAATGACTAAAATACCCTCGAAAGGTA
1 AAATGACTGAAATACCCTCGAAGGGTA
* **
334692 AAATGACTGAAATACCCTCAAAATGTA
1 AAATGACTGAAATACCCTCGAAGGGTA
*
334719 AAATGGCTGAAATACCCTCGAAGGGTA
1 AAATGACTGAAATACCCTCGAAGGGTA
*
334746 AAATGA-TCGAAATACCC-CAAAGGGTA
1 AAATGACT-GAAATACCCTCGAAGGGTA
* *
334772 AAATGATTGAAATACCCCCGAAGGGTA
1 AAATGACTGAAATACCCTCGAAGGGTA
* *
334799 AAATGATTGAAATACCCCCGAAGGGTA
1 AAATGACTGAAATACCCTCGAAGGGTA
* *
334826 AAATGACTGAAATACCC-CCATAGGTTA
1 AAATGACTGAAATACCCTCGA-AGGGTA
334853 AAATGACT
1 AAATGACT
334861 ATTATACCCC
Statistics
Matches: 245, Mismatches: 26, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
26 26 0.11
27 218 0.89
28 1 0.00
ACGTcount: A:0.42, C:0.19, G:0.20, T:0.19
Consensus pattern (27 bp):
AAATGACTGAAATACCCTCGAAGGGTA
Found at i:334885 original size:134 final size:134
Alignment explanation
Indices: 334581--334845 Score: 372
Period size: 134 Copynumber: 2.0 Consensus size: 134
334571 CCTTCGAAGG
* * * *
334581 GTAAAATGA-TCGAAATACCCTCAAAGGGTAAAATGA-CTGAAATACTCTCGATGGGTAAAATGA
1 GTAAAATGACT-GAAATACCCTCGAAGGGTAAAATGATC-GAAATAC-CCCAAAGGGTAAAATGA
* *
334644 CCGAAATACCCTCGAAGGGTAAAATGACTAAAATACCCTCGAAAGGTAAAATGACTGAAATACCC
63 CCGAAATACCCCCGAAGGGTAAAATGACTAAAATACCCCCGAAAGGTAAAATGACTGAAATACCC
*
334709 TCAAAAT
128 CCAAAAT
* **
334716 GTAAAATGGCTGAAATACCCTCGAAGGGTAAAATGATCGAAATACCCCAAAGGGTAAAATGATTG
1 GTAAAATGACTGAAATACCCTCGAAGGGTAAAATGATCGAAATACCCCAAAGGGTAAAATGACCG
* * *
334781 AAATACCCCCGAAGGGTAAAATGATTGAAATACCCCCGAAGGGTAAAATGACTGAAATACCCCCA
66 AAATACCCCCGAAGGGTAAAATGACTAAAATACCCCCGAAAGGTAAAATGACTGAAATACCCCCA
334846 TAGGTTAAAA
Statistics
Matches: 115, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
134 74 0.64
135 39 0.34
136 2 0.02
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.19
Consensus pattern (134 bp):
GTAAAATGACTGAAATACCCTCGAAGGGTAAAATGATCGAAATACCCCAAAGGGTAAAATGACCG
AAATACCCCCGAAGGGTAAAATGACTAAAATACCCCCGAAAGGTAAAATGACTGAAATACCCCCA
AAAT
Found at i:335253 original size:28 final size:28
Alignment explanation
Indices: 335213--335267 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
335203 ACTGTACAGA
* *
335213 TTACTGTATTGGGCTAAGGCCCGCACTG
1 TTACTGTATTGGGATAAGGCCCACACTG
*
335241 TTACTGTTTTGGGATAAGGCCCACACT
1 TTACTGTATTGGGATAAGGCCCACACT
335268 ATACTGTCAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.20, C:0.24, G:0.25, T:0.31
Consensus pattern (28 bp):
TTACTGTATTGGGATAAGGCCCACACTG
Found at i:342107 original size:41 final size:42
Alignment explanation
Indices: 342062--342152 Score: 112
Period size: 44 Copynumber: 2.1 Consensus size: 42
342052 TTTTATCTAA
* * * *
342062 GAAAAAAG-TTTAAAAAGATGAGAATATAATATTGGGTTGTT
1 GAAAAAAGATTCAAAAAGAGGAGAAGATAATATTAGGTTGTT
*
342103 GAAAAAAAGAATTCAAAAAGAGGAGAAGATAATCTTAGGTTGTT
1 G-AAAAAAG-ATTCAAAAAGAGGAGAAGATAATATTAGGTTGTT
342147 GAAAAA
1 GAAAAA
342153 GGAATTTAAG
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
41 1 0.02
42 7 0.17
43 5 0.12
44 29 0.69
ACGTcount: A:0.51, C:0.02, G:0.22, T:0.25
Consensus pattern (42 bp):
GAAAAAAGATTCAAAAAGAGGAGAAGATAATATTAGGTTGTT
Found at i:347240 original size:42 final size:43
Alignment explanation
Indices: 347155--347263 Score: 184
Period size: 43 Copynumber: 2.6 Consensus size: 43
347145 TATCCTAGAA
*
347155 AAAAAAGAATTTAAAAAGAGGAGATGATAATCTTGGGATGTTG
1 AAAAAAGAATTTAAAAAGAGGAGACGATAATCTTGGGATGTTG
* *
347198 AAAAAATAATTTAAAAAGAGGAGACGATAATCTT-GGCTGTTG
1 AAAAAAGAATTTAAAAAGAGGAGACGATAATCTTGGGATGTTG
347240 AAAAAAGAATTTAAAAAGAGGAGA
1 AAAAAAGAATTTAAAAAGAGGAGA
347264 AAATAAACAT
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
42 30 0.48
43 32 0.52
ACGTcount: A:0.50, C:0.04, G:0.23, T:0.23
Consensus pattern (43 bp):
AAAAAAGAATTTAAAAAGAGGAGACGATAATCTTGGGATGTTG
Found at i:357096 original size:20 final size:20
Alignment explanation
Indices: 357059--357096 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
357049 TGTTTAGATG
*
357059 AGTTTATTTTATATCTATAA
1 AGTTTATTTTACATCTATAA
357079 AGTTATATTTTACA-CTAT
1 AGTT-TATTTTACATCTAT
357097 TTTTGCATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.34, C:0.08, G:0.05, T:0.53
Consensus pattern (20 bp):
AGTTTATTTTACATCTATAA
Found at i:357531 original size:29 final size:28
Alignment explanation
Indices: 357499--357554 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
357489 TCAGGTTACA
* * *
357499 TTTTAGTTACTTATGTTTGAAATGTTATG
1 TTTTAGTCACTTACG-TTAAAATGTTATG
357528 TTTTAGTCACTTACGTTAAAATGTTAT
1 TTTTAGTCACTTACGTTAAAATGTTAT
357555 AACATTTTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 11 0.46
29 13 0.54
ACGTcount: A:0.27, C:0.07, G:0.14, T:0.52
Consensus pattern (28 bp):
TTTTAGTCACTTACGTTAAAATGTTATG
Found at i:357983 original size:16 final size:14
Alignment explanation
Indices: 357964--358004 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 14
357954 AATGTAAAAT
357964 AAAGAAATAAAAGTTA
1 AAAGAAATAAAAG--A
357980 AAAGAAATAAAAGA
1 AAAGAAATAAAAGA
*
357994 AAAAAAATAAA
1 AAAGAAATAAA
358005 TTACTCAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 11 0.46
16 13 0.54
ACGTcount: A:0.78, C:0.00, G:0.10, T:0.12
Consensus pattern (14 bp):
AAAGAAATAAAAGA
Found at i:361765 original size:27 final size:27
Alignment explanation
Indices: 361725--361894 Score: 198
Period size: 27 Copynumber: 6.3 Consensus size: 27
361715 GTGTGGTCAA
* *
361725 TAAAATGACCGAAATACCCTTGTAGGG
1 TAAAATGACCGAAATACCCCTATAGGG
* ** *
361752 TAAAATGACTGAAATACCCCCGTTGGG
1 TAAAATGACCGAAATACCCCTATAGGG
*
361779 TAAAATGACCGAAATACCCCCATAGGG
1 TAAAATGACCGAAATACCCCTATAGGG
* * * *
361806 TAAAATTACTGAAATAACCCTATAAGG
1 TAAAATGACCGAAATACCCCTATAGGG
* *
361833 TAAAATGACTGAAATATCCCC-ATTGGG
1 TAAAATGACCGAAATA-CCCCTATAGGG
*
361860 TAAAATAACCGAAATACCCCTATAGGG
1 TAAAATGACCGAAATACCCCTATAGGG
361887 TAAAATGA
1 TAAAATGA
361895 TTCTTATACC
Statistics
Matches: 121, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
26 4 0.03
27 114 0.94
28 3 0.02
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (27 bp):
TAAAATGACCGAAATACCCCTATAGGG
Found at i:361908 original size:81 final size:81
Alignment explanation
Indices: 361725--361894 Score: 236
Period size: 81 Copynumber: 2.1 Consensus size: 81
361715 GTGTGGTCAA
* * * *
361725 TAAAATGAC-CGAAAT-ACCCTTGTAGGGTAAAATGACTGAAATACCCCCGTTGGGTAAAATGAC
1 TAAAATGACTC-AAATAACCC-TATAAGGTAAAATGACTGAAATACCCCCATTGGGTAAAATAAC
361788 CGAAATACCCCCATAGGG
64 CGAAATACCCCCATAGGG
* * *
361806 TAAAATTACTGAAATAACCCTATAAGGTAAAATGACTGAAATATCCCCATTGGGTAAAATAACCG
1 TAAAATGACTCAAATAACCCTATAAGGTAAAATGACTGAAATACCCCCATTGGGTAAAATAACCG
*
361871 AAATACCCCTATAGGG
66 AAATACCCCCATAGGG
361887 TAAAATGA
1 TAAAATGA
361895 TTCTTATACC
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
81 74 0.95
82 4 0.05
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (81 bp):
TAAAATGACTCAAATAACCCTATAAGGTAAAATGACTGAAATACCCCCATTGGGTAAAATAACCG
AAATACCCCCATAGGG
Found at i:362217 original size:58 final size:58
Alignment explanation
Indices: 362127--362255 Score: 188
Period size: 58 Copynumber: 2.2 Consensus size: 58
362117 TGTGATATTA
**
362127 GTGTGTTGACTGGGTCGGTCGATTTTATCCCCACCTGGTGTGTTAGTGGTA-GGAAGTG
1 GTGTGTTGGTTGGGTCGGTCGATTTTATCCCCACCTGGTGTGTTAGTGGTACGG-AGTG
* * *
362185 GTGTGTTGGTTGGGTGGGTCGATTTTATCCCCACCTGGTGTGTTGGTGGTACGGAGTT
1 GTGTGTTGGTTGGGTCGGTCGATTTTATCCCCACCTGGTGTGTTAGTGGTACGGAGTG
*
362243 ATGTGTTGGTTGG
1 GTGTGTTGGTTGG
362256 ATTGGGATAG
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
58 62 0.97
59 2 0.03
ACGTcount: A:0.11, C:0.13, G:0.39, T:0.37
Consensus pattern (58 bp):
GTGTGTTGGTTGGGTCGGTCGATTTTATCCCCACCTGGTGTGTTAGTGGTACGGAGTG
Found at i:368532 original size:17 final size:16
Alignment explanation
Indices: 368494--368532 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
368484 GTCGATTTAC
368494 TCTTCTAATTTTTCCCT
1 TCTT-TAATTTTTCCCT
*
368511 GCTTTAATTTTTCCCTT
1 TCTTTAATTTTTCCC-T
368528 TCTTT
1 TCTTT
368533 TTCTAGTTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.10, C:0.26, G:0.03, T:0.62
Consensus pattern (16 bp):
TCTTTAATTTTTCCCT
Found at i:369342 original size:27 final size:26
Alignment explanation
Indices: 369312--369484 Score: 202
Period size: 27 Copynumber: 6.4 Consensus size: 26
369302 GTGAGATCAA
*
369312 TAAAATGACCGAAATACCCTCGTAGGG
1 TAAAATGACTGAAATACCC-CGTAGGG
*
369339 TAAAATAACTGAAATACCCTCGTAGGG
1 TAAAATGACTGAAATACCC-CGTAGGG
*
369366 TAAAATGATTGAAATACCCCCGTAGGG
1 TAAAATGACTGAAATA-CCCCGTAGGG
*
369393 TAAAATGACTAAAATACCCCGATAGGG
1 TAAAATGACTGAAATACCCCG-TAGGG
* ** *
369420 TAAAATGACCGAAATACCCCCAAATGG
1 TAAAATGACTGAAATA-CCCCGTAGGG
* *
369447 TAAAATGACTGAAATACCACCATAGGT
1 TAAAATGACTGAAATACC-CCGTAGGG
369474 TAAAATGACTG
1 TAAAATGACTG
369485 TTGTACTGCT
Statistics
Matches: 127, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
26 7 0.06
27 113 0.89
28 7 0.06
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (26 bp):
TAAAATGACTGAAATACCCCGTAGGG
Found at i:369380 original size:54 final size:53
Alignment explanation
Indices: 369312--369482 Score: 225
Period size: 54 Copynumber: 3.2 Consensus size: 53
369302 GTGAGATCAA
* *
369312 TAAAATGACCGAAATACCCTCGTAGGGTAAAATAACTGAAATACCCTCGTAGGG
1 TAAAATGACCGAAATACCCCCGTAGGGTAAAATGACTGAAATACCC-CGTAGGG
** *
369366 TAAAATGATTGAAATACCCCCGTAGGGTAAAATGACTAAAATACCCCGATAGGG
1 TAAAATGACCGAAATACCCCCGTAGGGTAAAATGACTGAAATACCCCG-TAGGG
** * * *
369420 TAAAATGACCGAAATACCCCCAAATGGTAAAATGACTGAAATACCACCATAGGT
1 TAAAATGACCGAAATACCCCCGTAGGGTAAAATGACTGAAATACC-CCGTAGGG
369474 TAAAATGAC
1 TAAAATGAC
369483 TGTTGTACTG
Statistics
Matches: 102, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
53 2 0.02
54 98 0.96
55 2 0.02
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (53 bp):
TAAAATGACCGAAATACCCCCGTAGGGTAAAATGACTGAAATACCCCGTAGGG
Found at i:369938 original size:19 final size:19
Alignment explanation
Indices: 369914--369955 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
369904 GGGGATTACA
369914 CACTGAGCTTTCGTAAACG
1 CACTGAGCTTTCGTAAACG
369933 CACTGAGCTTTCGTAAACG
1 CACTGAGCTTTCGTAAACG
369952 CACT
1 CACT
369956 TTTTCCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (19 bp):
CACTGAGCTTTCGTAAACG
Found at i:370811 original size:40 final size:40
Alignment explanation
Indices: 370757--370847 Score: 110
Period size: 40 Copynumber: 2.3 Consensus size: 40
370747 CATTTGAATA
* * * **
370757 AAAAACGCTGCTATAAATCGAGCATTAGCGGTGCTTTTTG
1 AAAAATGCCGCTATAAATCGACCATTAGCGGCACTTTTTG
** *
370797 AAAAATGCCGCTATAGGTCGACCATTAGTGGCACTTTTTG
1 AAAAATGCCGCTATAAATCGACCATTAGCGGCACTTTTTG
370837 AAAAATGCCGC
1 AAAAATGCCGC
370848 AAAAAAATAA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (40 bp):
AAAAATGCCGCTATAAATCGACCATTAGCGGCACTTTTTG
Found at i:375900 original size:348 final size:348
Alignment explanation
Indices: 375262--375948 Score: 1176
Period size: 348 Copynumber: 2.0 Consensus size: 348
375252 AACCCGAGCC
* *
375262 ATTTAACTCCTAATATTCCAGTACTTATTACTTCTCCGAATTAAGAGTATGATTTTGTCAACTGA
1 ATTTAACTCCTAAAATTCCAGTACTTATTACTTCTCCGAATTAAGAGTATGATTTTGTCAACTCA
* *
375327 CAAAGTCAGATAAACATTAAGTCAAAAAAGACGTCGTTTGATTTAGTGTGGTTAGACGTACAGTT
66 CAAAGTCAGATAAACACTAAGTCAAAAAAGACATCGTTTGATTTAGTGTGGTTAGACGTACAGTT
* * * *
375392 GGAATTCCGAAAGGAACGTTTCTAATCGGTTTTCTGTGAACACATTGGCGTGCCAAGTGGAGATT
131 GGAATTCCGAAAGGAACATTTCTAATCAGTTTTCTGTGAACACATTGGCATGCCAAGTGGAGACT
* * *
375457 GCTGTTTGGTTCCGTCAAGGGAACTAGTAACCGGATTTAAATGTCCCACGCGGTTGAGGGCATTG
196 ACTGTTTGGTTCCGTCAAGGGAACTAGTAACCAGATTTAAATGTCCCACGCGGTTAAGGGCATTG
*
375522 GTTCGAGCTAGGCTCTTCTAGAACGCAAAGCTGCTGGAGTTCTAAATCACGAACGTTTCGTGGTT
261 GTTCGAGCTAGGCTCTTCTAGAACGCAAAGCTGCCGGAGTTCTAAATCACGAACGTTTCGTGGTT
375587 GTTCGATCGGTAAGAATTAGGTA
326 GTTCGATCGGTAAGAATTAGGTA
* *
375610 ATTTAACTCCTAAAATTCCAGTACTTATTACTTCTCTGGATTAAGAGTATGATTTTGTCAACTCA
1 ATTTAACTCCTAAAATTCCAGTACTTATTACTTCTCCGAATTAAGAGTATGATTTTGTCAACTCA
* * *
375675 TAAAGTCAGATCAACACTAAGTCAAAAAATACATCGTTTGATTTAGTGTGGTTAGACGTACAGTT
66 CAAAGTCAGATAAACACTAAGTCAAAAAAGACATCGTTTGATTTAGTGTGGTTAGACGTACAGTT
* *
375740 GGAATTCTGAAAGGAACATTTCTAATCATTTTTCTGTGAACACATTGGCATGCCAAGTGGAGACT
131 GGAATTCCGAAAGGAACATTTCTAATCAGTTTTCTGTGAACACATTGGCATGCCAAGTGGAGACT
*
375805 ACTGTTTGGTTCCGTCAAGGGAAGTAGTAACCAGATTTAAATGTCCCACGCGGTTAAGGGCATTG
196 ACTGTTTGGTTCCGTCAAGGGAACTAGTAACCAGATTTAAATGTCCCACGCGGTTAAGGGCATTG
* *
375870 GTTCGAGCTAGGCTCTTCTAGAATGCAAAGCTGCCGGAGTTCTAAATCACGAATGTTTCGTGGTT
261 GTTCGAGCTAGGCTCTTCTAGAACGCAAAGCTGCCGGAGTTCTAAATCACGAACGTTTCGTGGTT
375935 GTTCGATCGGTAAG
326 GTTCGATCGGTAAG
375949 GGTTAGTTAT
Statistics
Matches: 317, Mismatches: 22, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
348 317 1.00
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (348 bp):
ATTTAACTCCTAAAATTCCAGTACTTATTACTTCTCCGAATTAAGAGTATGATTTTGTCAACTCA
CAAAGTCAGATAAACACTAAGTCAAAAAAGACATCGTTTGATTTAGTGTGGTTAGACGTACAGTT
GGAATTCCGAAAGGAACATTTCTAATCAGTTTTCTGTGAACACATTGGCATGCCAAGTGGAGACT
ACTGTTTGGTTCCGTCAAGGGAACTAGTAACCAGATTTAAATGTCCCACGCGGTTAAGGGCATTG
GTTCGAGCTAGGCTCTTCTAGAACGCAAAGCTGCCGGAGTTCTAAATCACGAACGTTTCGTGGTT
GTTCGATCGGTAAGAATTAGGTA
Found at i:402049 original size:41 final size:40
Alignment explanation
Indices: 402004--402116 Score: 100
Period size: 42 Copynumber: 2.7 Consensus size: 40
401994 TTGAAGCGCA
* *
402004 GCTAATGTTTGGTCTTTTAGCGGCGTTTTTAAATAAGCACC
1 GCTAATGTTAGGT-TTTTAGCGGCGTTTTTAAAGAAGCACC
* * ** ** *
402045 GCTAAAGTTAAGATTTTTAGCAACGTTTTTTTGAGAAGCGCC
1 GCTAATGTT-AGGTTTTTAGCGGCG-TTTTTAAAGAAGCACC
*
402087 GCTAATGTTAGGGGTTTTAGCGGCGTTTTT
1 GCTAATGTTA-GGTTTTTAGCGGCGTTTTT
402117 GTTGAAGCAC
Statistics
Matches: 55, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
41 23 0.42
42 32 0.58
ACGTcount: A:0.22, C:0.14, G:0.25, T:0.39
Consensus pattern (40 bp):
GCTAATGTTAGGTTTTTAGCGGCGTTTTTAAAGAAGCACC
Found at i:402107 original size:83 final size:82
Alignment explanation
Indices: 401917--402116 Score: 206
Period size: 82 Copynumber: 2.4 Consensus size: 82
401907 TTTAAGTATT
** * * * * * *
401917 CGCCGCTAATGGTCGGGGGTTTTAGTGGCGTTTTTAATCAATCGCCTCTAACGTTAAGGTATTTA
1 CGCCGCTAAT-GTTAGGGGTTTTAGCGGCGTTTTTAATCAAGCACCGCTAAAGTTAAGATATTTA
**
401982 GCGGCATTTTCTTTGAAG
65 GCAACATTTTCTTTGAAG
* * ** *
402000 CGCAGCTAATGTTTGGTCTTTTAGCGGCGTTTTTAAAT-AAGCACCGCTAAAGTTAAGATTTTTA
1 CGCCGCTAATGTTAGGGGTTTTAGCGGCGTTTTT-AATCAAGCACCGCTAAAGTTAAGATATTTA
*
402064 GCAACGTTTT-TTTGAGAAG
65 GCAACATTTTCTTT--GAAG
402083 CGCCGCTAATGTTAGGGGTTTTAGCGGCGTTTTT
1 CGCCGCTAATGTTAGGGGTTTTAGCGGCGTTTTT
402117 GTTGAAGCAC
Statistics
Matches: 95, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
81 3 0.03
82 46 0.48
83 46 0.48
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.37
Consensus pattern (82 bp):
CGCCGCTAATGTTAGGGGTTTTAGCGGCGTTTTTAATCAAGCACCGCTAAAGTTAAGATATTTAG
CAACATTTTCTTTGAAG
Found at i:403117 original size:7 final size:7
Alignment explanation
Indices: 403105--403152 Score: 60
Period size: 7 Copynumber: 6.7 Consensus size: 7
403095 GATATAAGGT
403105 TTAGGGG
1 TTAGGGG
403112 TTAGGGG
1 TTAGGGG
*
403119 TTAGGGAT
1 TTAGGG-G
403127 TTAGGGG
1 TTAGGGG
**
403134 TTAGAAG
1 TTAGGGG
403141 TTAGGGG
1 TTAGGGG
403148 TTAGG
1 TTAGG
403153 AATTTAGGGG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
7 28 0.82
8 6 0.18
ACGTcount: A:0.21, C:0.00, G:0.48, T:0.31
Consensus pattern (7 bp):
TTAGGGG
Found at i:403125 original size:29 final size:29
Alignment explanation
Indices: 403087--403152 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 29
403077 ATGATTATTA
* * **
403087 GGGTTTGGGATATAAGGTTTAGGGGTTAG
1 GGGTTAGGGATATAAGGGTTAGAAGTTAG
* *
403116 GGGTTAGGGATTTAGGGGTTAGAAGTTAG
1 GGGTTAGGGATATAAGGGTTAGAAGTTAG
403145 GGGTTAGG
1 GGGTTAGG
403153 AATTTAGGGG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.21, C:0.00, G:0.47, T:0.32
Consensus pattern (29 bp):
GGGTTAGGGATATAAGGGTTAGAAGTTAG
Found at i:403129 original size:22 final size:22
Alignment explanation
Indices: 403104--403206 Score: 91
Period size: 22 Copynumber: 4.6 Consensus size: 22
403094 GGATATAAGG
403104 TTTAGGGGTTAGGGGTTAGGGA
1 TTTAGGGGTTAGGGGTTAGGGA
**
403126 TTTAGGGGTTAGAAGTTAGGG-
1 TTTAGGGGTTAGGGGTTAGGGA
* ** * *
403147 GTTAGGAATTTAGGGGCTAAGAGA
1 TTTAGG-GGTTAGGGG-TTAGGGA
* *
403171 TTTAAGGGTTAGGGGTTAGGAA
1 TTTAGGGGTTAGGGGTTAGGGA
*
403193 TTTAGGGTTTAGGG
1 TTTAGGGGTTAGGG
403207 TGTCAATTAA
Statistics
Matches: 60, Mismatches: 18, Indels: 6
0.71 0.21 0.07
Matches are distributed among these distances:
21 5 0.08
22 40 0.67
23 11 0.18
24 4 0.07
ACGTcount: A:0.24, C:0.01, G:0.43, T:0.32
Consensus pattern (22 bp):
TTTAGGGGTTAGGGGTTAGGGA
Found at i:403199 original size:15 final size:15
Alignment explanation
Indices: 403112--403183 Score: 83
Period size: 15 Copynumber: 4.8 Consensus size: 15
403102 GGTTTAGGGG
*
403112 TTAGGGGTTAGGGAT
1 TTAGGGGTTAGGAAT
*
403127 TTAGGGGTTA-GAAG
1 TTAGGGGTTAGGAAT
403141 TTAGGGGTTAGGAAT
1 TTAGGGGTTAGGAAT
* *
403156 TTAGGGGCTAAGAGAT
1 TTAGGGGTTAGGA-AT
*
403172 TTAAGGGTTAGG
1 TTAGGGGTTAGG
403184 GGTTAGGAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
14 12 0.26
15 24 0.51
16 11 0.23
ACGTcount: A:0.26, C:0.01, G:0.42, T:0.31
Consensus pattern (15 bp):
TTAGGGGTTAGGAAT
Found at i:404355 original size:24 final size:24
Alignment explanation
Indices: 404321--404366 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
404311 CGAAAAAGCT
404321 ATTTTCTCCCCAAAAATTCCCCCCA
1 ATTTTCTCCCCAAAAA-TCCCCCCA
404346 ATTTT-TCCCCAAAAATCCCCC
1 ATTTTCTCCCCAAAAATCCCCC
404367 AAATCTAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 6 0.29
24 10 0.48
25 5 0.24
ACGTcount: A:0.28, C:0.43, G:0.00, T:0.28
Consensus pattern (24 bp):
ATTTTCTCCCCAAAAATCCCCCCA
Found at i:404790 original size:12 final size:12
Alignment explanation
Indices: 404773--404797 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
404763 AGTTTGAAAC
404773 TGTTCATAATTT
1 TGTTCATAATTT
404785 TGTTCATAATTT
1 TGTTCATAATTT
404797 T
1 T
404798 CACTATCCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.08, T:0.60
Consensus pattern (12 bp):
TGTTCATAATTT
Found at i:404852 original size:17 final size:17
Alignment explanation
Indices: 404826--404864 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
404816 ATAGAAAACG
404826 ATAA-AATGTTATTA-GA
1 ATAATAATGTTA-TACGA
404842 ATAATAATGTTATACGA
1 ATAATAATGTTATACGA
404859 ATAATA
1 ATAATA
404865 TTATGAAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.51, C:0.03, G:0.10, T:0.36
Consensus pattern (17 bp):
ATAATAATGTTATACGA
Found at i:405205 original size:25 final size:26
Alignment explanation
Indices: 405171--405227 Score: 89
Period size: 25 Copynumber: 2.2 Consensus size: 26
405161 CTCGTTGCAT
*
405171 AATAATTCTTACTCTAT-GCGTATCA
1 AATAATTCTTACTCTATAGCGTATAA
*
405196 AATAATTCTTACTCTATAGCTTATAA
1 AATAATTCTTACTCTATAGCGTATAA
405222 AATAAT
1 AATAAT
405228 ATAAATCTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 17 0.59
26 12 0.41
ACGTcount: A:0.39, C:0.16, G:0.05, T:0.40
Consensus pattern (26 bp):
AATAATTCTTACTCTATAGCGTATAA
Found at i:405513 original size:9 final size:9
Alignment explanation
Indices: 405496--405532 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
405486 TGAGTTTTCA
405496 AATTCGAAT
1 AATTCGAAT
*
405505 AACTCGAAT
1 AATTCGAAT
405514 AATTCGAAT
1 AATTCGAAT
405523 AATTCGAAT
1 AATTCGAAT
405532 A
1 A
405533 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:407900 original size:69 final size:69
Alignment explanation
Indices: 407825--407984 Score: 214
Period size: 69 Copynumber: 2.3 Consensus size: 69
407815 ATGAGAAAAT
* * *
407825 ATTAACATCTATATTTTCAATAATAAATTTTATAATTTTAGAAATAATTGAAAATGTTA-TGTTC
1 ATTAACATCTATATTTTCAATAATAAATTTTACAATTTGAAAAATAATTGAAAATGTTAGT-TTC
407889 TAAAG
65 TAAAG
* ** *
407894 GTTAACATCTATATTTGGAATAATAAATTTTACAATTTGAAAAATAATTGTAAATGTTAGTTTCT
1 ATTAACATCTATATTTTCAATAATAAATTTTACAATTTGAAAAATAATTGAAAATGTTAGTTTCT
*
407959 AAAT
66 AAAG
* *
407963 ATTAACACCTATATTTTTAATA
1 ATTAACATCTATATTTTCAATA
407985 TATCACCCCA
Statistics
Matches: 78, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
69 77 0.99
70 1 0.01
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.43
Consensus pattern (69 bp):
ATTAACATCTATATTTTCAATAATAAATTTTACAATTTGAAAAATAATTGAAAATGTTAGTTTCT
AAAG
Found at i:408114 original size:16 final size:16
Alignment explanation
Indices: 408112--408262 Score: 185
Period size: 16 Copynumber: 9.0 Consensus size: 16
408102 ATACACAACT
408112 TACATAACTTACATAA
1 TACATAACTTACATAA
* *
408128 TACTTAACTTCCATAA
1 TACATAACTTACATAA
408144 TACATAACTTACATAA
1 TACATAACTTACATAA
*
408160 TACACAACTTACATAA
1 TACATAACTTACATAA
*
408176 CTTACGTAATACTTAACATAA
1 --TACAT-A-ACTT-ACATAA
*
408197 CTTACATAACTTGCATAA
1 --TACATAACTTACATAA
408215 TACATAACTTACATAA
1 TACATAACTTACATAA
*
408231 TACACAACTTACATAA
1 TACATAACTTACATAA
408247 TACATAACTTACATAA
1 TACATAACTTACATAA
408263 CTCATTTATA
Statistics
Matches: 118, Mismatches: 12, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
16 88 0.75
18 8 0.07
19 5 0.04
20 5 0.04
21 12 0.10
ACGTcount: A:0.46, C:0.21, G:0.01, T:0.31
Consensus pattern (16 bp):
TACATAACTTACATAA
Found at i:408122 original size:25 final size:26
Alignment explanation
Indices: 408093--408264 Score: 141
Period size: 25 Copynumber: 6.8 Consensus size: 26
408083 AAAGTGATAT
*
408093 ACTTACATAA-TACACAACTTACATA
1 ACTTACATAACTACATAACTTACATA
* *
408118 ACTTACATAA-TACTTAACTTCCATA
1 ACTTACATAACTACATAACTTACATA
*
408143 A--TACATAACTTACATAA--TACACA
1 ACTTACATAAC-TACATAACTTACATA
*
408166 ACTTACATAACTTACGTAATACTTAACATA
1 ACTTACATAAC-TACAT-A-ACTT-ACATA
*
408196 ACTTACATAACTTGCATAA--TACATA
1 ACTTACATAAC-TACATAACTTACATA
*
408221 ACTTACATAA-TACACAACTTACATA
1 ACTTACATAACTACATAACTTACATA
408246 A--TACATAACTTACATAACT
1 ACTTACATAAC-TACATAACT
408265 CATTTATACT
Statistics
Matches: 121, Mismatches: 13, Indels: 26
0.76 0.08 0.16
Matches are distributed among these distances:
23 24 0.20
25 72 0.60
26 2 0.02
27 1 0.01
28 1 0.01
29 2 0.02
30 19 0.16
ACGTcount: A:0.46, C:0.22, G:0.01, T:0.31
Consensus pattern (26 bp):
ACTTACATAACTACATAACTTACATA
Found at i:413610 original size:66 final size:66
Alignment explanation
Indices: 413520--413673 Score: 229
Period size: 66 Copynumber: 2.3 Consensus size: 66
413510 TAAAACGGAG
* *
413520 GCAGCATCGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCAGCTACAACTTAAAGCAG
1 GCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAG-TATAAAGAACTCCAGCTACAACTTAAAGCAG
413584 AT
65 AT
* *
413586 GCAGCAGCGAGAGAAGCTGAGGTTCAACGAAAGTATAAAGAACTCCAGCTACAACTTAAAGCTGA
1 GCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATAAAGAACTCCAGCTACAACTTAAAGCAGA
413651 T
66 T
* * *
413652 GCGGTAGCGAGAGAAGCAGAGG
1 GCAGCAGCGAGAGAAGCTGAGG
413674 CTGCAGCGAG
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
66 76 0.95
67 4 0.05
ACGTcount: A:0.40, C:0.18, G:0.27, T:0.15
Consensus pattern (66 bp):
GCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATAAAGAACTCCAGCTACAACTTAAAGCAGA
T
Found at i:414089 original size:43 final size:42
Alignment explanation
Indices: 414035--414190 Score: 224
Period size: 43 Copynumber: 3.6 Consensus size: 42
414025 TTAAAAAAAA
* *
414035 CGCCACTAAAGGTTATGGTCATTT-GCGGCGTTTGTCGGATAAG
1 CGCCGCTAAAGGTCATGGTC-TTTAGCGGCGTTTGTCGGA-AAG
* *
414078 CGTCGCTAAAGGTCATGGTCTTTAGCGACGTTTGTCGGAAAAG
1 CGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTCGG-AAAG
*
414121 CGCCGCTAAAGGTTATGGTCTTTAGCGGCGTTTGTCGGGAAAG
1 CGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTC-GGAAAG
414164 CGCCGCTAAAGGTCATGGTCTTTAGCG
1 CGCCGCTAAAGGTCATGGTCTTTAGCG
414191 TTTTTACAGG
Statistics
Matches: 102, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
42 3 0.03
43 96 0.94
44 3 0.03
ACGTcount: A:0.21, C:0.20, G:0.31, T:0.28
Consensus pattern (42 bp):
CGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTCGGAAAG
Found at i:414185 original size:86 final size:86
Alignment explanation
Indices: 414030--414190 Score: 263
Period size: 86 Copynumber: 1.9 Consensus size: 86
414020 GCGTTTTAAA
*
414030 AAAAACGCCACTAAAGGTTATGGTCATTTGCGGCGTTTGTCGGATAAGCGTCGCTAAAGGTCATG
1 AAAAACGCCACTAAAGGTTATGGTCATTTGCGGCGTTTGTCGGATAAGCGCCGCTAAAGGTCATG
414095 GTCTTTAGCGACGTTTGTCGG
66 GTCTTTAGCGACGTTTGTCGG
* *
414116 AAAAGCGCCGCTAAAGGTTATGGTC-TTTAGCGGCGTTTGTCGGGA-AAGCGCCGCTAAAGGTCA
1 AAAAACGCCACTAAAGGTTATGGTCATTT-GCGGCGTTTGTC-GGATAAGCGCCGCTAAAGGTCA
414179 TGGTCTTTAGCG
64 TGGTCTTTAGCG
414191 TTTTTACAGG
Statistics
Matches: 70, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
85 3 0.04
86 64 0.91
87 3 0.04
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.27
Consensus pattern (86 bp):
AAAAACGCCACTAAAGGTTATGGTCATTTGCGGCGTTTGTCGGATAAGCGCCGCTAAAGGTCATG
GTCTTTAGCGACGTTTGTCGG
Found at i:414319 original size:43 final size:43
Alignment explanation
Indices: 414262--414514 Score: 269
Period size: 43 Copynumber: 5.9 Consensus size: 43
414252 CGTTTTTAAA
* * * * *
414262 AAAAACGCCACTAAATG-TCATAGTCTTTAGTGGCGTTTGTGGG
1 AAAAGCGCCGCTAAA-GATCATGGTCTTTAGCGGCGTTTGTTGG
*
414305 AAAAGCGCCGCTAAAGATCATGGTCTTCAGCGGCGTTTGTTGG
1 AAAAGCGCCGCTAAAGATCATGGTCTTTAGCGGCGTTTGTTGG
* * * *
414348 AAAGGCGCCGCTAACGATCAGGGTCTTTAGCGGTGTTT-TCTGG
1 AAAAGCGCCGCTAAAGATCATGGTCTTTAGCGGCGTTTGT-TGG
* ** *
414391 AGAAGCGCAACTAAAGATCAGGGTCTTTAGCGGCGTTTGTTGG
1 AAAAGCGCCGCTAAAGATCATGGTCTTTAGCGGCGTTTGTTGG
* * **
414434 AGAAGCGCCGCTAAAGACCATGACCTTTAGCGGCGTTTG-TGG
1 AAAAGCGCCGCTAAAGATCATGGTCTTTAGCGGCGTTTGTTGG
* * *
414476 TGAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTT
1 -AAAAGCGCCGCTAAAGATCATGGTCTTTAGCGGCGTTT
414515 ATTTCTAAAA
Statistics
Matches: 176, Mismatches: 30, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
42 5 0.03
43 170 0.97
44 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.27
Consensus pattern (43 bp):
AAAAGCGCCGCTAAAGATCATGGTCTTTAGCGGCGTTTGTTGG
Found at i:414375 original size:232 final size:231
Alignment explanation
Indices: 413959--414422 Score: 662
Period size: 232 Copynumber: 2.0 Consensus size: 231
413949 CTTCTAATTT
*
413959 GTTTTTACAGGAGGGCTGAAAATATAAAAAAATATCTTTTACAAATCTGCCAAAATTAGTGGCGT
1 GTTTTTACAGGAGGGATGAAAATATAAAAAAATATCTTTTACAAATCTGCCAAAATTAGTGGCGT
* * * *
414024 TTTAAAAAAAACGCCACTAAAGGTTATGGTCATTTGCGGCGTTTGTCGGATAAGCGTCGCTAAAG
66 TTTAAAAAAAACGCCACTAAAGGTCATAGTCATTTGCGGCGTTTGTCGGAAAAGCGCCGCTAAAG
* * * * *
414089 GTCATGGTCTTTAGCGACGTTTGTCGGAAAAGCGCCGCTAAAGGTTATGGTCTTTAGCGGCGTTT
131 ATCATGGTCTTCAGCGACGTTTGTCGGAAAAGCGCCGCTAAAGATCAGGGTCTTTAGCGGCGTTT
** * *
414154 GTCGGGA-AAGCGCCGCTAAAGGTCATGGTCTTTAGC
196 -TCGGGAGAAGCGCAACTAAAGATCAGGGTCTTTAGC
* *
414190 GTTTTTACAGGAGTGATGAAAATATAAAAAAATTTCTTTTACAAATCTGCCAAAATTAGTGGCGT
1 GTTTTTACAGGAGGGATGAAAATATAAAAAAATATCTTTTACAAATCTGCCAAAATTAGTGGCG-
* * *
414255 TTTTAAAAAAAACGCCACTAAATGTCATAGTC-TTTAGTGGCGTTTGTGGGAAAAGCGCCGCTAA
65 TTTTAAAAAAAACGCCACTAAAGGTCATAGTCATTT-GCGGCGTTTGTCGGAAAAGCGCCGCTAA
* * * * *
414319 AGATCATGGTCTTCAGCGGCGTTTGTTGGAAAGGCGCCGCTAACGATCAGGGTCTTTAGCGGTGT
129 AGATCATGGTCTTCAGCGACGTTTGTCGGAAAAGCGCCGCTAAAGATCAGGGTCTTTAGCGGCGT
*
414384 TTTCTGGAGAAGCGCAACTAAAGATCAGGGTCTTTAGC
194 TTTCGGGAGAAGCGCAACTAAAGATCAGGGTCTTTAGC
414422 G
1 G
414423 GCGTTTGTTG
Statistics
Matches: 205, Mismatches: 25, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
231 69 0.34
232 136 0.66
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (231 bp):
GTTTTTACAGGAGGGATGAAAATATAAAAAAATATCTTTTACAAATCTGCCAAAATTAGTGGCGT
TTTAAAAAAAACGCCACTAAAGGTCATAGTCATTTGCGGCGTTTGTCGGAAAAGCGCCGCTAAAG
ATCATGGTCTTCAGCGACGTTTGTCGGAAAAGCGCCGCTAAAGATCAGGGTCTTTAGCGGCGTTT
TCGGGAGAAGCGCAACTAAAGATCAGGGTCTTTAGC
Found at i:416565 original size:43 final size:43
Alignment explanation
Indices: 416518--416627 Score: 123
Period size: 43 Copynumber: 2.6 Consensus size: 43
416508 AAAGTGCTGG
* * *
416518 TAAAGGTTATGTTCTTTAGCGGCGCTTGT-GATAAAAGCGTCGC
1 TAAAGGTCATGTTCTTTAGCGGCGCTAGTAGAT-AAAGCGCCGC
* * * *
416561 TAAAGATCATGTTCTTTAGCGGTGCTAGTAGGTAAAGCGCCGT
1 TAAAGGTCATGTTCTTTAGCGGCGCTAGTAGATAAAGCGCCGC
* *
416604 TAAAGGTCATTTTCTATAGCGGCG
1 TAAAGGTCATGTTCTTTAGCGGCG
416628 TTTTTTCACA
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
43 53 0.96
44 2 0.04
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (43 bp):
TAAAGGTCATGTTCTTTAGCGGCGCTAGTAGATAAAGCGCCGC
Found at i:417225 original size:23 final size:21
Alignment explanation
Indices: 417199--417240 Score: 66
Period size: 23 Copynumber: 1.9 Consensus size: 21
417189 TATTACAGAG
417199 ATTATAATTACAATAATTTAGTA
1 ATTATAATT-CAAT-ATTTAGTA
417222 ATTATAATTCAATATTTAG
1 ATTATAATTCAATATTTAG
417241 AGAGGTTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 6 0.32
22 4 0.21
23 9 0.47
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (21 bp):
ATTATAATTCAATATTTAGTA
Found at i:428124 original size:26 final size:26
Alignment explanation
Indices: 428093--428143 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
428083 CATTGAAGTT
* * *
428093 TGGTTTATCTTTTTACATGCATGAAG
1 TGGTTTATATTTATACACGCATGAAG
428119 TGGTTTATATTTATACACGCATGAA
1 TGGTTTATATTTATACACGCATGAA
428144 ATCATAAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.43
Consensus pattern (26 bp):
TGGTTTATATTTATACACGCATGAAG
Found at i:429695 original size:21 final size:21
Alignment explanation
Indices: 429652--429698 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
429642 TTAAATTTGA
* *
429652 AATTTTACAATTTAATCATCT
1 AATTTTACAATATAATCAACT
* *
429673 AATTTTACAATATCATTAACT
1 AATTTTACAATATAATCAACT
429694 AATTT
1 AATTT
429699 AAATAGTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (21 bp):
AATTTTACAATATAATCAACT
Found at i:429995 original size:42 final size:42
Alignment explanation
Indices: 429914--430089 Score: 155
Period size: 42 Copynumber: 4.3 Consensus size: 42
429904 TGCAGCTAAA
* *
429914 TCTTTAGCGACGCTTA-AAA-AAA-ACCGCTAAAGATA-ATGT
1 TCTTTAGCGGCGCTTAGAAATAAACGCCGCTAAAGA-ACATGT
* *
429953 TCTTTACCGGCGCTTAAGACA-AAACGCCGCTAAAGAACATGT
1 TCTTTAGCGGCGCTT-AGAAATAAACGCCGCTAAAGAACATGT
** * *
429995 TCTTTAGAAGCGCTTAGAAATAAACGCCACTAAAGACCATGT
1 TCTTTAGCGGCGCTTAGAAATAAACGCCGCTAAAGAACATGT
* * *** * * *
430037 TCTTTAGCGGCGTTTTGTCTTAAGCGCCACTAAAGAACATGG
1 TCTTTAGCGGCGCTTAGAAATAAACGCCGCTAAAGAACATGT
430079 TCTTTAGCGGC
1 TCTTTAGCGGC
430090 ATTTTTATCT
Statistics
Matches: 112, Mismatches: 20, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
39 13 0.12
40 1 0.01
41 10 0.09
42 88 0.79
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.26
Consensus pattern (42 bp):
TCTTTAGCGGCGCTTAGAAATAAACGCCGCTAAAGAACATGT
Found at i:430070 original size:84 final size:83
Alignment explanation
Indices: 429977--430168 Score: 222
Period size: 84 Copynumber: 2.3 Consensus size: 83
429967 TAAGACAAAA
* * * *
429977 CGCCGCTAAAGAACATGTTCTTTAGAAGCGCTTAGAAATAAACGCCACTAAAGACCATGTTCTTT
1 CGCCGCTAAAGAACATGGTCTTTAGAAGCACTTAGAAATAAACGCCACTAAAGAACATGGTCTTT
*
430042 AGCGGCGTTTTGTCTTAAG
66 AGCAGCGTTTTGT-TTAAG
* ** * ** ** * *
430061 CGCCACTAAAGAACATGGTCTTTAGCGGCATTTTTATCTAAGCGCCTCTAAAGAACATGGTCTTT
1 CGCCGCTAAAGAACATGGTCTTTAGAAGCACTTAGAAATAAACGCCACTAAAGAACATGGTCTTT
*
430126 AGCAGCTTTTTGTTTAAG
66 AGCAGCGTTTTGTTTAAG
*
430144 CGCTGCTAAAGAACATGGTCTTTAG
1 CGCCGCTAAAGAACATGGTCTTTAG
430169 CGGCGTTTTT
Statistics
Matches: 90, Mismatches: 18, Indels: 1
0.83 0.17 0.01
Matches are distributed among these distances:
83 28 0.31
84 62 0.69
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (83 bp):
CGCCGCTAAAGAACATGGTCTTTAGAAGCACTTAGAAATAAACGCCACTAAAGAACATGGTCTTT
AGCAGCGTTTTGTTTAAG
Found at i:430103 original size:42 final size:41
Alignment explanation
Indices: 430019--430180 Score: 216
Period size: 42 Copynumber: 3.9 Consensus size: 41
430009 TAGAAATAAA
* * *
430019 CGCCACTAAAGACCATGTTCTTTAGCGGCGTTTTGTCTTAAG
1 CGCCACTAAAGAACATGGTCTTTAGCGGCTTTTTGTC-TAAG
*
430061 CGCCACTAAAGAACATGGTCTTTAGCGGCATTTTTATCTAAG
1 CGCCACTAAAGAACATGGTCTTTAGCGGC-TTTTTGTCTAAG
* * *
430103 CGCCTCTAAAGAACATGGTCTTTAGCAGCTTTTTGTTTAAG
1 CGCCACTAAAGAACATGGTCTTTAGCGGCTTTTTGTCTAAG
**
430144 CGCTGCTAAAGAACATGGTCTTTAGCGGCGTTTTTGT
1 CGCCACTAAAGAACATGGTCTTTAGCGGC-TTTTTGT
430181 TTGTAAACGC
Statistics
Matches: 107, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
41 36 0.34
42 65 0.61
43 6 0.06
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.34
Consensus pattern (41 bp):
CGCCACTAAAGAACATGGTCTTTAGCGGCTTTTTGTCTAAG
Found at i:430168 original size:83 final size:84
Alignment explanation
Indices: 430019--430178 Score: 241
Period size: 83 Copynumber: 1.9 Consensus size: 84
430009 TAGAAATAAA
* * *
430019 CGCCACTAAAGACCATGTTCTTTAGCGGCGTTTTGTCTTAAGCGCCACTAAAGAACATGGTCTTT
1 CGCCACTAAAGAACATGGTCTTTAGCAGCGTTTTGTCTTAAGCGCCACTAAAGAACATGGTCTTT
430084 AGCGGCATTTTTATCTAAG
66 AGCGGCATTTTTATCTAAG
* * **
430103 CGCCTCTAAAGAACATGGTCTTTAGCAGCTTTTTGT-TTAAGCGCTGCTAAAGAACATGGTCTTT
1 CGCCACTAAAGAACATGGTCTTTAGCAGCGTTTTGTCTTAAGCGCCACTAAAGAACATGGTCTTT
*
430167 AGCGGCGTTTTT
66 AGCGGCATTTTT
430179 GTTTGTAAAC
Statistics
Matches: 68, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
83 37 0.54
84 31 0.46
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (84 bp):
CGCCACTAAAGAACATGGTCTTTAGCAGCGTTTTGTCTTAAGCGCCACTAAAGAACATGGTCTTT
AGCGGCATTTTTATCTAAG
Found at i:431113 original size:35 final size:35
Alignment explanation
Indices: 431059--431186 Score: 123
Period size: 35 Copynumber: 3.6 Consensus size: 35
431049 TAATTGACAT
* *
431059 TCGTCGGTTTATCCGACTAGTGCTGGGCTCAAATA
1 TCGTCGGTTTATCCAACTAGTGTTGGGCTCAAATA
* *
431094 TCGTTGGTTTATCCAACTAGAGTTGGGCTCACTAATTA
1 TCGTCGGTTTATCCAACTAGTGTTGGGCTCA--AA-TA
** * * *
431132 TTCGTCAATTTATCTAACTAGTGTTGGGCACACAT-
1 -TCGTCGGTTTATCCAACTAGTGTTGGGCTCAAATA
*
431167 TCGTGGGTTTATCCAACTAG
1 TCGTCGGTTTATCCAACTAG
431187 CGCTAGGCGC
Statistics
Matches: 74, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
34 16 0.22
35 27 0.36
36 1 0.01
37 3 0.04
38 2 0.03
39 25 0.34
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (35 bp):
TCGTCGGTTTATCCAACTAGTGTTGGGCTCAAATA
Found at i:431178 original size:34 final size:34
Alignment explanation
Indices: 431055--431339 Score: 216
Period size: 34 Copynumber: 8.2 Consensus size: 34
431045 TGAGTAATTG
* * * *
431055 ACATTCGTCGGTTTATCCGACTAGTGCTGGGCTC
1 ACATTCGTCGATTTATCCGACTAGCGTTGGGCAC
* * * * *
431089 AAATATCGTTGGTTTATCCAACTAGAGTTGGGCTCAC
1 ACAT-TCGTCGATTTATCCGACTAGCGTTGGG--CAC
* * ** *
431126 TAATTATTCGTCAATTTATCTAACTAGTGTTGGGCAC
1 --A-CATTCGTCGATTTATCCGACTAGCGTTGGGCAC
* * * *
431163 ACATTCGTGGGTTTATCCAACTAGCGCTAGGCGCA-
1 ACATTCGTCGATTTATCCGACTAGCG-TTGG-GCAC
* *
431198 AC-TTCCGTC-AGTTTATCTGACTAGTGTTGGGCAC
1 ACATT-CGTCGA-TTTATCCGACTAGCGTTGGGCAC
* *
431232 ACATTTGTCGATTTATCCGACTAGCGCTGGGCAC
1 ACATTCGTCGATTTATCCGACTAGCGTTGGGCAC
* *
431266 ACATTTGTCGATTTATCCGACTAGCGCTGGGCAC
1 ACATTCGTCGATTTATCCGACTAGCGTTGGGCAC
* *
431300 ACATTTGTCGATTTATCCGACTAGCGCTGGGCAC
1 ACATTCGTCGATTTATCCGACTAGCGTTGGGCAC
*
431334 AAATTC
1 ACATTC
431340 TTTCGTGGAT
Statistics
Matches: 207, Mismatches: 31, Indels: 26
0.78 0.12 0.10
Matches are distributed among these distances:
33 3 0.01
34 124 0.60
35 47 0.23
36 3 0.01
37 5 0.02
39 23 0.11
40 2 0.01
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.32
Consensus pattern (34 bp):
ACATTCGTCGATTTATCCGACTAGCGTTGGGCAC
Found at i:431221 original size:69 final size:68
Alignment explanation
Indices: 431131--431339 Score: 262
Period size: 68 Copynumber: 3.1 Consensus size: 68
431121 CTCACTAATT
* * * * * *
431131 ATTCGTCAATTTATCTAACTAGTGTTGGGCACACATTCGTGGGTTTATCCAACTAGCGCTAGGCG
1 ATTCGTCAGTTTATCTGACTAGTGTTGGGCACACATTTGTCGATTTATCCGACTAGCGCT-GG-G
431196 CA-AC
64 CACAC
431200 -TTCCGTCAGTTTATCTGACTAGTGTTGGGCACACATTTGTCGATTTATCCGACTAGCGCTGGGC
1 ATT-CGTCAGTTTATCTGACTAGTGTTGGGCACACATTTGTCGATTTATCCGACTAGCGCTGGGC
431264 ACAC
65 ACAC
* * * *
431268 ATTTGTC-GATTTATCCGACTAGCGCTGGGCACACATTTGTCGATTTATCCGACTAGCGCTGGGC
1 ATTCGTCAG-TTTATCTGACTAGTGTTGGGCACACATTTGTCGATTTATCCGACTAGCGCTGGGC
*
431332 ACAA
65 ACAC
431336 ATTC
1 ATTC
431340 TTTCGTGGAT
Statistics
Matches: 124, Mismatches: 12, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
67 4 0.03
68 67 0.54
69 53 0.43
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.31
Consensus pattern (68 bp):
ATTCGTCAGTTTATCTGACTAGTGTTGGGCACACATTTGTCGATTTATCCGACTAGCGCTGGGCA
CAC
Found at i:434752 original size:33 final size:34
Alignment explanation
Indices: 434704--434770 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 34
434694 AAGAAAAGGG
434704 GAAACCTAATCTAAAA-ATGAAAAGAAAAGAAAA
1 GAAACCTAATCTAAAACATGAAAAGAAAAGAAAA
*
434737 GAAACCTAAAT-TAAAACTATGAAAAGTAAAGAAA
1 GAAACCT-AATCTAAAAC-ATGAAAAGAAAAGAAA
434771 GATGACCAGC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 12 0.40
34 3 0.10
35 15 0.50
ACGTcount: A:0.64, C:0.09, G:0.12, T:0.15
Consensus pattern (34 bp):
GAAACCTAATCTAAAACATGAAAAGAAAAGAAAA
Found at i:448011 original size:91 final size:91
Alignment explanation
Indices: 447864--448071 Score: 317
Period size: 91 Copynumber: 2.3 Consensus size: 91
447854 TTGATTTTAG
* *
447864 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATGATTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATGATTATTAAATTAT
* * *
447929 ATTTAATATTAATTATTTTAAATTGTA
65 ATGTAATAATAATTATTTTAAATTATA
*
447956 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATGATTATTAAATTATA
448021 TGTAATAATAATTATTTTAAATTATA
66 TGTAATAATAATTATTTTAAATTATA
* * * *
448047 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
448072 GTTATAATTA
Statistics
Matches: 106, Mismatches: 10, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
91 90 0.85
92 16 0.15
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATGATTATTAAATTATA
TGTAATAATAATTATTTTAAATTATA
Found at i:448040 original size:26 final size:28
Alignment explanation
Indices: 447986--448046 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
447976 TATTATCAAG
* *
447986 AATTTTATGAAATTATATATTATTATTA
1 AATTATATGAAATAATATATTATTATTA
*
448014 AATTATATGTAATAATA-ATTATT-TTA
1 AATTATATGAAATAATATATTATTATTA
448040 AATTATA
1 AATTATA
448047 CAAATTCATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (28 bp):
AATTATATGAAATAATATATTATTATTA
Found at i:448046 original size:44 final size:43
Alignment explanation
Indices: 447904--448046 Score: 121
Period size: 44 Copynumber: 3.2 Consensus size: 43
447894 GAATTTTATG
* *
447904 AAATTATATATGATTATTAAATTATATTTAATATTAATTATTTT
1 AAATTATATATTATTATTAAATTATA-TTAATAATAATTATTTT
* ** * *
447948 AAATTGTATAAATTCATATAAGAAAATT-TATT-ATCAAGAATT-TTATG
1 AAA-T-TATATATT-AT-T-ATTAAATTATATTAAT-AATAATTATT-TT
447995 AAATTATATATTATTATTAAATTATATGTAATAATAATTATTTT
1 AAATTATATATTATTATTAAATTATAT-TAATAATAATTATTTT
448039 AAATTATA
1 AAATTATA
448047 CAAATTCATA
Statistics
Matches: 76, Mismatches: 12, Indels: 22
0.69 0.11 0.20
Matches are distributed among these distances:
42 6 0.08
43 4 0.05
44 21 0.28
45 12 0.16
46 11 0.14
47 13 0.17
48 3 0.04
49 6 0.08
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.48
Consensus pattern (43 bp):
AAATTATATATTATTATTAAATTATATTAATAATAATTATTTT
Found at i:448490 original size:16 final size:16
Alignment explanation
Indices: 448471--448522 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
448461 GATTTGCTAT
* *
448471 TACACCTCTATTCCAT
1 TACACCTCTAATCCAA
448487 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
448503 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
448519 TACA
1 TACA
448523 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.29
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:451062 original size:24 final size:25
Alignment explanation
Indices: 451023--451072 Score: 84
Period size: 24 Copynumber: 2.0 Consensus size: 25
451013 GGAAACTAAA
451023 GAAAATGAATGAATTAGGACCAAATT
1 GAAAATG-ATGAATTAGGACCAAATT
451049 GAAAATG-TGAATTAGGACCAAATT
1 GAAAATGATGAATTAGGACCAAATT
451073 AAGTGATGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 17 0.71
26 7 0.29
ACGTcount: A:0.48, C:0.08, G:0.20, T:0.24
Consensus pattern (25 bp):
GAAAATGATGAATTAGGACCAAATT
Found at i:454444 original size:145 final size:145
Alignment explanation
Indices: 454211--454968 Score: 1223
Period size: 145 Copynumber: 5.2 Consensus size: 145
454201 GTATATATTA
* * * * *
454211 TTTAGGGTTTAAGGTTAAGTATAATTAATATAAAACTCTAGATTATAAAATCATAATTGTATATA
1 TTTAGGGTTTAAGGTTACGTATAATTAATATAAAAATATACATCAT--AATCATAATTGTATATA
*
454276 GGGTTACATATTATTAATAATCTACCTTAATTATATAATTCTAATTGTACATATTATAATCTACC
64 GGGTTACATATCATTAATAATCTACCTTAATTATATAATTCTAATTGTACATATTATAATCTACC
*
454341 ATAAAATTAGTTATAGT
129 ATAAAATTAGTTATAGG
*
454358 TTTAGGGTTTAAGGTTATGTATAATTAATATAAAAATATACATCATAATCATAATTGTATATAGG
1 TTTAGGGTTTAAGGTTACGTATAATTAATATAAAAATATACATCATAATCATAATTGTATATAGG
454423 GTTACATATCATTAATAATCTACCTTAATTATATAATTCTAATTGTACATATTATAATCTACCAT
66 GTTACATATCATTAATAATCTACCTTAATTATATAATTCTAATTGTACATATTATAATCTACCAT
*
454488 AAAATTAGTTATAGT
131 AAAATTAGTTATAGG
*
454503 TTTAGGGTTTAAGGTTATGTATAATTAATATAAAAATATACATCATAATCATAATTGTATATAGG
1 TTTAGGGTTTAAGGTTACGTATAATTAATATAAAAATATACATCATAATCATAATTGTATATAGG
*
454568 GTTACATATCATTAATAATCTACCTTAATTATATAATTCTAATTGTATATATTATAATCTACCAT
66 GTTACATATCATTAATAATCTACCTTAATTATATAATTCTAATTGTACATATTATAATCTACCAT
454633 AAAATTAGTTATAGG
131 AAAATTAGTTATAGG
*
454648 TTTAGGGTTTAAGGTAACGTATAATTAATATAAAAATATACATCATAATCATAATTGTATA-ATG
1 TTTAGGGTTTAAGGTTACGTATAATTAATATAAAAATATACATCATAATCATAATTGTATATA-G
*
454712 GGTTACATATTATTAATAATCTACCTTAATTATATAATTCTAATTGTACATATTATAATCTACCA
65 GGTTACATATCATTAATAATCTACCTTAATTATATAATTCTAATTGTACATATTATAATCTACCA
454777 TAAAATTAGTTATAGG
130 TAAAATTAGTTATAGG
*
454793 TTTAGGGTTTAAGGTAACGTATAATTAATATAAAAATATACATCATAATCATAATTGTATATAGG
1 TTTAGGGTTTAAGGTTACGTATAATTAATATAAAAATATACATCATAATCATAATTGTATATAGG
** * **
454858 GTTACATATCATTAATAATCTACCTTAATTATATAATGATAATTGTATATATATTATAATCTATT
66 GTTACATATCATTAATAATCTACCTTAATTATATAATTCTAATTG--TACATATTATAATCTACC
* * *
454923 ATAAAATTAATTACATG
129 ATAAAATTAGTTATAGG
* * * *
454940 TTTAAGGTTT-AGGTTCCATATCATTAATA
1 TTTAGGGTTTAAGGTTACGTATAATTAATA
454969 AAATAATTCA
Statistics
Matches: 581, Mismatches: 26, Indels: 9
0.94 0.04 0.01
Matches are distributed among these distances:
144 1 0.00
145 485 0.83
146 16 0.03
147 79 0.14
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.41
Consensus pattern (145 bp):
TTTAGGGTTTAAGGTTACGTATAATTAATATAAAAATATACATCATAATCATAATTGTATATAGG
GTTACATATCATTAATAATCTACCTTAATTATATAATTCTAATTGTACATATTATAATCTACCAT
AAAATTAGTTATAGG
Found at i:458612 original size:19 final size:19
Alignment explanation
Indices: 458582--458659 Score: 75
Period size: 19 Copynumber: 4.1 Consensus size: 19
458572 TATACGTTTA
*
458582 TGCGCGAAGATACACTTCG
1 TGCGCCAAGATACACTTCG
*
458601 TGTGCCAAGATACACTTCG
1 TGCGCCAAGATACACTTCG
* * * *
458620 TACGACAGGATGCACTTCG
1 TGCGCCAAGATACACTTCG
* * *
458639 TGCGCCAGGATGCACCTCG
1 TGCGCCAAGATACACTTCG
458658 TG
1 TG
458660 TGCCTGTATG
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 49 1.00
ACGTcount: A:0.23, C:0.28, G:0.27, T:0.22
Consensus pattern (19 bp):
TGCGCCAAGATACACTTCG
Found at i:467871 original size:25 final size:25
Alignment explanation
Indices: 467777--467881 Score: 92
Period size: 25 Copynumber: 4.3 Consensus size: 25
467767 AGTAACTCTG
467777 AAGAGC-TATTATCAGGAAGCTC-TA
1 AAGAGCTTA-TATCAGGAAGCTCATA
* * *
467801 AATAGCCATATATCAGGAAGTTCA-A
1 AAGAG-CTTATATCAGGAAGCTCATA
** *
467826 GCGAGC-CATATCAGGAAGCTCATA
1 AAGAGCTTATATCAGGAAGCTCATA
* *
467850 AAGAGCTTATATCGGGATGCTCATA
1 AAGAGCTTATATCAGGAAGCTCATA
467875 AAGAGCT
1 AAGAGCT
467882 GCGATATGTC
Statistics
Matches: 64, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
23 14 0.22
24 10 0.16
25 38 0.59
26 2 0.03
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (25 bp):
AAGAGCTTATATCAGGAAGCTCATA
Found at i:472259 original size:63 final size:62
Alignment explanation
Indices: 472156--472302 Score: 163
Period size: 63 Copynumber: 2.3 Consensus size: 62
472146 CTGTGTGGCT
* ** * *
472156 CAAAACAGTGAGGTACACAGTCTAGACACACGCCCTTGTCTCTGGCTCGTGTATCC-CTAATTT
1 CAAAACAGTGAGTTACACAG-CTAGACACACGCCCTTGTCTCTAACTCGTGT-GCCTCTAATTC
* * *
472219 TAAAACAGTGAGTTACACAGCTTGAACACACG-CCTATGTCTTTAACTCGTGTGCCTCTAATTC
1 CAAAACAGTGAGTTACACAGCTAG-ACACACGCCCT-TGTCTCTAACTCGTGTGCCTCTAATTC
*
472282 CAAAATAGTGAGTTACACAGC
1 CAAAACAGTGAGTTACACAGC
472303 CTATCACATG
Statistics
Matches: 71, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
62 8 0.11
63 63 0.89
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (62 bp):
CAAAACAGTGAGTTACACAGCTAGACACACGCCCTTGTCTCTAACTCGTGTGCCTCTAATTC
Found at i:472890 original size:21 final size:21
Alignment explanation
Indices: 472880--472930 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
472870 AAGAAGAAAG
472880 AAAGGAAAAGAAGAAAAAGGA
1 AAAGGAAAAGAAGAAAAAGGA
*
472901 AAAGGAAAA-AACGTAAAAA-AA
1 AAAGGAAAAGAA-G-AAAAAGGA
472922 AAAGGAAAA
1 AAAGGAAAA
472931 AGGAAACAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 2 0.07
21 20 0.74
22 5 0.19
ACGTcount: A:0.75, C:0.02, G:0.22, T:0.02
Consensus pattern (21 bp):
AAAGGAAAAGAAGAAAAAGGA
Found at i:472891 original size:17 final size:15
Alignment explanation
Indices: 472869--472930 Score: 58
Period size: 15 Copynumber: 4.2 Consensus size: 15
472859 GATATTGAAG
472869 AAAGAAGAAAGAAAGGA
1 AAAGAAG-AA-AAAGGA
472886 AAAGAAGAAAAAGGA
1 AAAGAAGAAAAAGGA
* * *
472901 AAAGGA-AAAAACGT
1 AAAGAAGAAAAAGGA
472915 AAA-AA-AAAAAGGA
1 AAAGAAGAAAAAGGA
472928 AAA
1 AAA
472931 AGGAAACAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
13 10 0.26
14 9 0.23
15 11 0.28
16 2 0.05
17 7 0.18
ACGTcount: A:0.74, C:0.02, G:0.23, T:0.02
Consensus pattern (15 bp):
AAAGAAGAAAAAGGA
Found at i:472902 original size:20 final size:21
Alignment explanation
Indices: 472870--472930 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
472860 ATATTGAAGA
472870 AAGAAGAAAG-AAAGGAAAAG
1 AAGAAGAAAGAAAAGGAAAAG
472890 AAGAA-AAAGGAAAAGGAAAA-
1 AAGAAGAAA-GAAAAGGAAAAG
*
472910 AACGTAA-AAAAAAAAGGAAAA
1 AA-G-AAGAAAGAAAAGGAAAA
472931 AGGAAACAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
19 3 0.08
20 8 0.22
21 20 0.56
22 5 0.14
ACGTcount: A:0.74, C:0.02, G:0.23, T:0.02
Consensus pattern (21 bp):
AAGAAGAAAGAAAAGGAAAAG
Found at i:479511 original size:16 final size:16
Alignment explanation
Indices: 479490--479559 Score: 95
Period size: 16 Copynumber: 4.4 Consensus size: 16
479480 TTGATTTGCT
*
479490 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
* *
479506 ATTACACATCTATTCC
1 ATTACACCTCTAATCC
479522 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
*
479538 AATACACCTCTAATCC
1 ATTACACCTCTAATCC
*
479554 AATACA
1 ATTACA
479560 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.31
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:481159 original size:15 final size:15
Alignment explanation
Indices: 481135--481164 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
481125 ACTGACTTTA
*
481135 AATAATGGTTTATTT
1 AATAAAGGTTTATTT
481150 AATAAAGGTTTATTT
1 AATAAAGGTTTATTT
481165 CTGGGAGTTT
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:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (15 bp):
AATAAAGGTTTATTT
Found at i:497511 original size:125 final size:127
Alignment explanation
Indices: 497264--497514 Score: 323
Period size: 127 Copynumber: 2.0 Consensus size: 127
497254 AATCCTTCTT
* *
497264 CGCAAATGGATCAGCTCTAAAGACAATCCAACAACAAAATCAACATTTTTAAATTAATAAATCTC
1 CGCAAATGGATCAGCTCTAAAGACAATCCAACAACAAAATCAACATATTTAAACTAATAAATCTC
** *
497329 TTTCTAGGATACCCAAACCGCGATTAAAGCTTAAATCAACAATGAAACAAAAAGTACTTACA
66 TTTCTAAAATACCCAAACCGCAATTAAAGCTTAAATCAACAATGAAACAAAAAGTACTTACA
** *
497391 CGCAAATGGATCAGCATC-AAAGAGTATCCAACAACAGAATCAA-A-ATTTAAACTAATAAATCT
1 CGCAAATGGATCAGC-TCTAAAGACAATCCAACAACAAAATCAACATATTTAAACTAATAAATCT
* * * * *
497453 CTTTCTAAAATACCCCAAACCGTAATTGAAGGTTAAATCAATGAA-GAAA-AGAAAGTACTTAC
65 CTTTCTAAAATA-CCCAAACCGCAATTAAAGCTTAAATCAA-CAATGAAACAAAAAGTACTTAC
497515 GCTTTCTTCT
Statistics
Matches: 108, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
125 38 0.35
126 29 0.27
127 39 0.36
128 2 0.02
ACGTcount: A:0.46, C:0.20, G:0.11, T:0.23
Consensus pattern (127 bp):
CGCAAATGGATCAGCTCTAAAGACAATCCAACAACAAAATCAACATATTTAAACTAATAAATCTC
TTTCTAAAATACCCAAACCGCAATTAAAGCTTAAATCAACAATGAAACAAAAAGTACTTACA
Found at i:498636 original size:44 final size:44
Alignment explanation
Indices: 498548--498638 Score: 146
Period size: 44 Copynumber: 2.1 Consensus size: 44
498538 ATAGGTCAAA
* *
498548 TAATATCAAAATAACCTACACTAATCAAAGTTTAAGTGGGAAAC
1 TAATATCAAAATAACCTACACTAATCAAAGTTTAACTGAGAAAC
* *
498592 TAATATTAAAATAACCTACACTAATCAAAGTTTAACTGATAAAC
1 TAATATCAAAATAACCTACACTAATCAAAGTTTAACTGAGAAAC
498636 TAA
1 TAA
498639 AAACTGAGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.49, C:0.15, G:0.08, T:0.27
Consensus pattern (44 bp):
TAATATCAAAATAACCTACACTAATCAAAGTTTAACTGAGAAAC
Found at i:500644 original size:44 final size:44
Alignment explanation
Indices: 500517--500647 Score: 208
Period size: 44 Copynumber: 3.0 Consensus size: 44
500507 GTATGTCAAA
* * * * *
500517 TAATATTAAAATATCCTATATTAATCAAAGTTTAAGTGGAAAAC
1 TAATATTAAAATAACCTACACTAATCAGAGTTTAAGTGGGAAAC
500561 TAATATTAAAATAACCTACACTAATCAGAGTTTAAGTGGGAAAC
1 TAATATTAAAATAACCTACACTAATCAGAGTTTAAGTGGGAAAC
*
500605 TAATATTAAAATAACCTACACTAATCAGATTTTAAGTGGGAAA
1 TAATATTAAAATAACCTACACTAATCAGAGTTTAAGTGGGAAA
500648 TTAAAAATAG
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 81 1.00
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.31
Consensus pattern (44 bp):
TAATATTAAAATAACCTACACTAATCAGAGTTTAAGTGGGAAAC
Found at i:508463 original size:12 final size:12
Alignment explanation
Indices: 508446--508470 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
508436 CGTGTCTCGT
508446 ATACGGCCTACC
1 ATACGGCCTACC
508458 ATACGGCCTACC
1 ATACGGCCTACC
508470 A
1 A
508471 CACGTCCGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.40, G:0.16, T:0.16
Consensus pattern (12 bp):
ATACGGCCTACC
Found at i:526785 original size:22 final size:22
Alignment explanation
Indices: 526760--526810 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
526750 ATTATTATTT
*
526760 AAATATTGTT-TCACTATTTTAA
1 AAATATTGTTCT-ACTAATTTAA
*
526782 AAATATTGTTCTATTAATTTAA
1 AAATATTGTTCTACTAATTTAA
526804 AAATATT
1 AAATATT
526811 TTTTTTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 25 0.96
23 1 0.04
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.49
Consensus pattern (22 bp):
AAATATTGTTCTACTAATTTAA
Found at i:534710 original size:2 final size:2
Alignment explanation
Indices: 534703--534730 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
534693 ATGATAAGCC
534703 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
534731 GGCTTATCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:535268 original size:25 final size:25
Alignment explanation
Indices: 535187--535299 Score: 84
Period size: 25 Copynumber: 4.5 Consensus size: 25
535177 CAAACATGTA
* **
535187 AACGGGAAGCTCTTGTGAGCCAAAT
1 AACGGGAAGCTCATAAGAGCCAAAT
* * * * *
535212 ATCGAGAAGCTCAAAAGTGCC-ATT
1 AACGGGAAGCTCATAAGAGCCAAAT
* * *
535236 AATTGGGAAGCTCATGAGAGCTAAAT
1 AA-CGGGAAGCTCATAAGAGCCAAAT
*
535262 AACGGGAAGCTCGTAAGAGCCAAAT
1 AACGGGAAGCTCATAAGAGCCAAAT
* *
535287 ATCGGGACGCTCA
1 AACGGGAAGCTCA
535300 GCTGTGGTGT
Statistics
Matches: 63, Mismatches: 23, Indels: 4
0.70 0.26 0.04
Matches are distributed among these distances:
24 3 0.05
25 56 0.89
26 4 0.06
ACGTcount: A:0.35, C:0.19, G:0.27, T:0.19
Consensus pattern (25 bp):
AACGGGAAGCTCATAAGAGCCAAAT
Found at i:550353 original size:2 final size:2
Alignment explanation
Indices: 550316--550343 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
550306 ATGATAAGCG
550316 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
550344 CAAAATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:554133 original size:73 final size:73
Alignment explanation
Indices: 554014--554174 Score: 200
Period size: 73 Copynumber: 2.2 Consensus size: 73
554004 TTGAAGAACC
* * * ** *
554014 ATTAATCAATAAGCTCCGGATAGCCATATATCGGGAAGTTCAAGCGAACTATATCAGGAAGCTCC
1 ATTAATCAAGAAGCTCTGAATAATCATATATCGGAAAGTTCAAGCGAACTATATCAGGAAGCTCC
554079 GGAGAGAC-
66 GGAGAG-CG
* * **
554087 ATTAATCAGGAAGCTCTGAATAATCATATATCGGAAAGTTTC-AGCGAGCTATATTGGGAAGCTC
1 ATTAATCAAGAAGCTCTGAATAATCATATATCGGAAAG-TTCAAGCGAACTATATCAGGAAGCTC
554151 CGGAGAGCG
65 CGGAGAGCG
554160 ATTAATCAAGAAGCT
1 ATTAATCAAGAAGCT
554175 TATAAAGAGT
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
72 1 0.01
73 71 0.95
74 3 0.04
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.23
Consensus pattern (73 bp):
ATTAATCAAGAAGCTCTGAATAATCATATATCGGAAAGTTCAAGCGAACTATATCAGGAAGCTCC
GGAGAGCG
Found at i:554700 original size:5 final size:5
Alignment explanation
Indices: 554673--554711 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
554663 TAAATTTAGC
* *
554673 TCAAT TCAAT ACAAT TCATAT TCAAT TCAAT CCAAT TCA
1 TCAAT TCAAT TCAAT TCA-AT TCAAT TCAAT TCAAT TCA
554712 CATCTTGGGC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.41, C:0.23, G:0.00, T:0.36
Consensus pattern (5 bp):
TCAAT
Found at i:556892 original size:33 final size:33
Alignment explanation
Indices: 556855--556919 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
556845 CAAACTTACC
*
556855 CTGTGTTTATTG-TCTCGACAGACTTACTCTATT
1 CTGTGTTTACTGTTCT-GACAGACTTACTCTATT
*
556888 CTGTGTTTACTGTTCTGTCAGACTTACTCTAT
1 CTGTGTTTACTGTTCTGACAGACTTACTCTAT
556920 GTGAATGCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 26 0.90
34 3 0.10
ACGTcount: A:0.17, C:0.22, G:0.15, T:0.46
Consensus pattern (33 bp):
CTGTGTTTACTGTTCTGACAGACTTACTCTATT
Found at i:560972 original size:68 final size:68
Alignment explanation
Indices: 560849--561017 Score: 185
Period size: 68 Copynumber: 2.5 Consensus size: 68
560839 GTCTATGGGA
* * * * * * *
560849 AAACATGGCATCATATTGTGTAAGACCATAGCTGGGCTACAGTAACATATAAAGTCTGCCAGGAT
1 AAACATGACATCATATTGTGTAAGACCATAGTTGAGCTACAGCAAAATATAAAGTCAGCCAAGAT
*
560914 AGT
66 AGG
** ** * *
560917 AAACATGACATCATATTGTGTATTACCATAGTTGAGCTATGGCAAAATATGAAGTCAGTCAAGAT
1 AAACATGACATCATATTGTGTAAGACCATAGTTGAGCTACAGCAAAATATAAAGTCAGCCAAGAT
560982 AGG
66 AGG
* * *
560985 AAACATGACAACTTATAGTGTAAGACCATAGTT
1 AAACATGACATCATATTGTGTAAGACCATAGTT
561018 AGGTTACGGT
Statistics
Matches: 82, Mismatches: 19, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
68 82 1.00
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (68 bp):
AAACATGACATCATATTGTGTAAGACCATAGTTGAGCTACAGCAAAATATAAAGTCAGCCAAGAT
AGG
Found at i:561040 original size:68 final size:67
Alignment explanation
Indices: 560849--561040 Score: 177
Period size: 68 Copynumber: 2.8 Consensus size: 67
560839 GTCTATGGGA
* * * * * * *
560849 AAACATGGCATCATATTGTGTAAGACCATAGCTGGGCTACAGTAACATATAAAGTCTGCCAGGAT
1 AAACATGACAACATATAGTGTAAGACCATAG-TTGGCTACGGTAACATATAAAGTCAGCCAAGAT
*
560914 AGT
65 AGG
* * ** * * * * *
560917 AAACATGACATCATATTGTGTATTACCATAGTTGAGCTATGGCAAAATATGAAGTCAGTCAAGAT
1 AAACATGACAACATATAGTGTAAGACCATAGTTG-GCTACGGTAACATATAAAGTCAGCCAAGAT
560982 AGG
65 AGG
* * *
560985 AAACATGACAACTTATAGTGTAAGACCATAGTTAGGTTACGGTAGCATATAAAGTC
1 AAACATGACAACATATAGTGTAAGACCATAGTT-GGCTACGGTAACATATAAAGTC
561041 CACTAGGACA
Statistics
Matches: 98, Mismatches: 24, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
67 2 0.02
68 95 0.97
69 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.27
Consensus pattern (67 bp):
AAACATGACAACATATAGTGTAAGACCATAGTTGGCTACGGTAACATATAAAGTCAGCCAAGATA
GG
Found at i:563677 original size:14 final size:14
Alignment explanation
Indices: 563647--563680 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
563637 ATAGTTATGC
563647 TTTAATGTTCTATA
1 TTTAATGTTCTATA
563661 TTTATATGTTCTA-A
1 TTTA-ATGTTCTATA
563675 TTTAAT
1 TTTAAT
563681 TTATGATAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 2 0.11
14 9 0.47
15 8 0.42
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.59
Consensus pattern (14 bp):
TTTAATGTTCTATA
Found at i:566633 original size:13 final size:13
Alignment explanation
Indices: 566617--566641 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
566607 TGCCGTGGAA
566617 AAGTGCTTTTGAG
1 AAGTGCTTTTGAG
566630 AAGTGCTTTTGA
1 AAGTGCTTTTGA
566642 AAATTTGGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.28, T:0.40
Consensus pattern (13 bp):
AAGTGCTTTTGAG
Found at i:572017 original size:37 final size:37
Alignment explanation
Indices: 571975--572047 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
571965 AGTAAAGAAT
* *
571975 GTGTATCAATTATTTTTTTACATGTGTAGTCTAAAAG
1 GTGTATCAATTATTTTCTTACATGTGTAGCCTAAAAG
572012 GTGTATCAATTATTTTCTTACATGTGTAGCCTAAAA
1 GTGTATCAATTATTTTCTTACATGTGTAGCCTAAAA
572048 AGTTAAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.44
Consensus pattern (37 bp):
GTGTATCAATTATTTTCTTACATGTGTAGCCTAAAAG
Found at i:577224 original size:39 final size:39
Alignment explanation
Indices: 577181--577259 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
577171 CCTCTGTATG
577181 ACATTCGGTCGAGATACAATTTCTATTCTAAGCTCCATT
1 ACATTCGGTCGAGATACAATTTCTATTCTAAGCTCCATT
577220 ACATTCGGTCGAGATACAATTTCTATTCTAAGCTCCATT
1 ACATTCGGTCGAGATACAATTTCTATTCTAAGCTCCATT
577259 A
1 A
577260 AACAATTAAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35
Consensus pattern (39 bp):
ACATTCGGTCGAGATACAATTTCTATTCTAAGCTCCATT
Found at i:580459 original size:12 final size:12
Alignment explanation
Indices: 580442--580467 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
580432 TAGGGAAAAG
580442 ATAAATACAATT
1 ATAAATACAATT
580454 ATAAATACAATT
1 ATAAATACAATT
580466 AT
1 AT
580468 TAGTTAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.35
Consensus pattern (12 bp):
ATAAATACAATT
Done.