Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr6
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: 44797108
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 921406 characters in sequence are not A, C, G, or T
File 129 of 144
Found at i:40162993 original size:76 final size:76
Alignment explanation
Indices: 40162812--40163029 Score: 265
Period size: 76 Copynumber: 2.8 Consensus size: 76
40162802 AACTGTTATC
* * *
40162812 GGTGGATTTAGCACTTAGAAACCACCAGTGATTCGGGGAATCAGCACTTAGCAACCCCCTTTTTT
1 GGTGGAATAAGCACTTAGCAACCACCAGTGATTCGGGGAATCAGCACTTAGCAA-CCCC-----T
*
40162877 TTTACATTCAAGGATAT
60 TTCACATTCAAGGATAT
* * * * *
40162894 GGTGGAATCAGCACTTAACAACCATCAGTGATTCAGGGAATCAGCAGTTAGCAACCCCTTTCACA
1 GGTGGAATAAGCACTTAGCAACCACCAGTGATTCGGGGAATCAGCACTTAGCAACCCCTTTCACA
40162959 TTCAAGGATAT
66 TTCAAGGATAT
** * *
40162970 GGTGGAATAAGCACTTAGCAACCACCAAAGAGTCGGGGAATCAACACTTAGCAACCCCTT
1 GGTGGAATAAGCACTTAGCAACCACCAGTGATTCGGGGAATCAGCACTTAGCAACCCCTT
40163030 GGGGAATCAG
Statistics
Matches: 119, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
76 68 0.57
81 4 0.03
82 47 0.39
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (76 bp):
GGTGGAATAAGCACTTAGCAACCACCAGTGATTCGGGGAATCAGCACTTAGCAACCCCTTTCACA
TTCAAGGATAT
Found at i:40163033 original size:26 final size:26
Alignment explanation
Indices: 40163004--40163055 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
40162994 CCAAAGAGTC
40163004 GGGGAATCAACACTTAGCAACCCCTT
1 GGGGAATCAACACTTAGCAACCCCTT
*
40163030 GGGGAATCAGCACTTAGCAACCCCTT
1 GGGGAATCAACACTTAGCAACCCCTT
40163056 TTGTCACGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.31, G:0.21, T:0.19
Consensus pattern (26 bp):
GGGGAATCAACACTTAGCAACCCCTT
Found at i:40168304 original size:3 final size:3
Alignment explanation
Indices: 40168296--40168333 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
40168286 TCTTAATACT
40168296 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
40168334 TAATAATAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:40168485 original size:10 final size:11
Alignment explanation
Indices: 40168468--40168496 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
40168458 TAAAAAATAC
40168468 CTTCTTTTTCT
1 CTTCTTTTTCT
40168479 C-TCTTTTTCT
1 CTTCTTTTTCT
40168489 CTTCTTTT
1 CTTCTTTT
40168497 CCGCAGCACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (11 bp):
CTTCTTTTTCT
Found at i:40168625 original size:27 final size:27
Alignment explanation
Indices: 40168587--40168669 Score: 103
Period size: 27 Copynumber: 3.1 Consensus size: 27
40168577 GTAGTGCCGC
* * *
40168587 CACCAATGGTGCCACCAATGGCATTGG
1 CACCATTGGTGCCGCCAATGGCTTTGG
* *
40168614 CACCATTGGTGCCGCTAATGGTTTTGG
1 CACCATTGGTGCCGCCAATGGCTTTGG
* *
40168641 CACCTTTGGTGCTGCCAATGGCTTTGG
1 CACCATTGGTGCCGCCAATGGCTTTGG
40168668 CA
1 CA
40168670 TGACCAAGGT
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.18, C:0.27, G:0.28, T:0.28
Consensus pattern (27 bp):
CACCATTGGTGCCGCCAATGGCTTTGG
Found at i:40168785 original size:28 final size:28
Alignment explanation
Indices: 40168726--40168787 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
40168716 TTTTTGATAT
* *
40168726 ATTTTGATAAATAAAAAAATTTATATAT
1 ATTTTGATAAATAAAAAAAGTTATATAC
*
40168754 ATTTTGCTAAATAAAAAAAAGTTATA-AC
1 ATTTTGATAAAT-AAAAAAAGTTATATAC
40168782 ATTTTG
1 ATTTTG
40168788 GTTATTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 18 0.60
29 12 0.40
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.40
Consensus pattern (28 bp):
ATTTTGATAAATAAAAAAAGTTATATAC
Found at i:40171057 original size:18 final size:17
Alignment explanation
Indices: 40170999--40171057 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 17
40170989 CATCACCCTT
40170999 TTTTATATTAAAATATTA
1 TTTT-TATTAAAATATTA
* **
40171017 TTATTTTTTAATTTATTGA
1 TT-TTTATTAAAATATT-A
*
40171036 TTTTCATTAAAATATTA
1 TTTTTATTAAAATATTA
40171053 TTTTT
1 TTTTT
40171058 TATAGTTGGC
Statistics
Matches: 31, Mismatches: 8, Indels: 5
0.70 0.18 0.11
Matches are distributed among these distances:
17 5 0.16
18 21 0.68
19 5 0.16
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (17 bp):
TTTTTATTAAAATATTA
Found at i:40174006 original size:25 final size:25
Alignment explanation
Indices: 40173941--40174010 Score: 86
Period size: 26 Copynumber: 2.7 Consensus size: 25
40173931 GAGTATCCCA
*
40173941 TCCTGTTATATGGCTCTTCGTGAGCT
1 TCCTATTA-ATGGCTCTTCGTGAGCT
* * *
40173967 TCTCGATTAAAGGCTCTTTGTGAGCT
1 TC-CTATTAATGGCTCTTCGTGAGCT
40173993 TCCTATTAATGGCTCTTC
1 TCCTATTAATGGCTCTTC
40174011 AGAGCTACTC
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
25 13 0.36
26 19 0.53
27 4 0.11
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.41
Consensus pattern (25 bp):
TCCTATTAATGGCTCTTCGTGAGCT
Found at i:40174175 original size:25 final size:25
Alignment explanation
Indices: 40174038--40174179 Score: 89
Period size: 25 Copynumber: 5.8 Consensus size: 25
40174028 CTTGCTTGAA
40174038 CTTCCCGATATATGGCT-ATCCA-GAG
1 CTTCCCGATATATGGCTCA--CATGAG
* *
40174063 CTTCCCG-T-TAGTGGTTCATATGAG
1 CTTCCCGATATA-TGGCTCACATGAG
* **
40174087 CTTCCTGAT-TATGGCTCTTATGAG
1 CTTCCCGATATATGGCTCACATGAG
* * * ** *
40174111 CTTCCCGTTACATAGCTCGGATAAG
1 CTTCCCGATATATGGCTCACATGAG
*
40174136 CTTCCC-ATTACATGGCTCACATGAG
1 CTTCCCGA-TATATGGCTCACATGAG
*
40174161 CTTCCCGCTATATGGCTCA
1 CTTCCCGATATATGGCTCA
40174180 AGAGAAGGCT
Statistics
Matches: 91, Mismatches: 19, Indels: 14
0.73 0.15 0.11
Matches are distributed among these distances:
23 3 0.03
24 32 0.35
25 56 0.62
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.32
Consensus pattern (25 bp):
CTTCCCGATATATGGCTCACATGAG
Found at i:40177122 original size:249 final size:248
Alignment explanation
Indices: 40176676--40177174 Score: 926
Period size: 249 Copynumber: 2.0 Consensus size: 248
40176666 AAAATTTATA
40176676 TGTTGAATCACTAAATTTGTGGTTAAAGTTTCAAACCCTCTAGGCCAGTATGTGATGGTAGACAA
1 TGTTGAATCACTAAATTTGTGGTTAAAGTTTCAAACCCTCTAGGCCAGTATGTGATGGTAGACAA
*
40176741 AATTTGTAAAAATTGTCCGTTAATGGTATGGGGTTATTATTTCTCGGGTGATTCGATGTTGTTGC
66 AATTTGTAAAAATTGTCCGTTAATGGTACGGGGTTATTATTTCTCGGGTGATTCGATGTTGTTGC
40176806 CATTTGATGAATTTGATGTAATATTGGGTATAGACTGGCTAACTCAGCATGATGCAGTGGTAAAT
131 CATTTGATGAATTTGATGTAATATTGGGTATAGACTGGCTAACTCAGCATGATGCAGTGGTAAAT
40176871 TGTAAACAAAAGTATATTGTGTTAAAATGTCAGAATGGTGAGTTACTCCATAT
196 TGTAAACAAAAGTATATTGTGTTAAAATGTCAGAATGGTGAGTTACTCCATAT
*
40176924 TGTTGAATCCACTAAATTTGTGGTTAAAGTTTCAAACCCTCTGGGCCAGTATGTGATGGTAGACA
1 TGTTGAAT-CACTAAATTTGTGGTTAAAGTTTCAAACCCTCTAGGCCAGTATGTGATGGTAGACA
* * * *
40176989 AAATTTGTAAAAATTGTCTGTTAATGGTACGGGGTTATTGTTTCTCGGTTGATTTGATGTTGTTG
65 AAATTTGTAAAAATTGTCCGTTAATGGTACGGGGTTATTATTTCTCGGGTGATTCGATGTTGTTG
*
40177054 CCATTTGATGAATTTGATGTAATATTGGGTATAGACTGGCTAACTCAGCATGATGTAGTGGTAAA
130 CCATTTGATGAATTTGATGTAATATTGGGTATAGACTGGCTAACTCAGCATGATGCAGTGGTAAA
40177119 TTGTAAACAAAAGTATATTGTGTTAAAATGTCAGAATGGTGAGTTACTCCATAT
195 TTGTAAACAAAAGTATATTGTGTTAAAATGTCAGAATGGTGAGTTACTCCATAT
40177173 TG
1 TG
40177175 AATCTGATGA
Statistics
Matches: 243, Mismatches: 7, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
248 8 0.03
249 235 0.97
ACGTcount: A:0.29, C:0.11, G:0.23, T:0.36
Consensus pattern (248 bp):
TGTTGAATCACTAAATTTGTGGTTAAAGTTTCAAACCCTCTAGGCCAGTATGTGATGGTAGACAA
AATTTGTAAAAATTGTCCGTTAATGGTACGGGGTTATTATTTCTCGGGTGATTCGATGTTGTTGC
CATTTGATGAATTTGATGTAATATTGGGTATAGACTGGCTAACTCAGCATGATGCAGTGGTAAAT
TGTAAACAAAAGTATATTGTGTTAAAATGTCAGAATGGTGAGTTACTCCATAT
Found at i:40180404 original size:17 final size:17
Alignment explanation
Indices: 40180373--40180406 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
40180363 TGAGTTCTAG
**
40180373 TAGCTATAGGTATCAAA
1 TAGCTATAGAAATCAAA
40180390 TAGCTATAGAAATCAAA
1 TAGCTATAGAAATCAAA
40180407 ATTAGAGGTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.12, G:0.15, T:0.26
Consensus pattern (17 bp):
TAGCTATAGAAATCAAA
Found at i:40181584 original size:26 final size:25
Alignment explanation
Indices: 40181555--40181604 Score: 82
Period size: 26 Copynumber: 2.0 Consensus size: 25
40181545 CCCGTTATAT
40181555 GGCTCTTCGTGAGCTTCCTGATTAAA
1 GGCTCTTCGTGAGCTTCCTG-TTAAA
*
40181581 GGCTCTTTGTGAGCTTCCTGTTAA
1 GGCTCTTCGTGAGCTTCCTGTTAA
40181605 TGGTTCTCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (25 bp):
GGCTCTTCGTGAGCTTCCTGTTAAA
Found at i:40184889 original size:171 final size:171
Alignment explanation
Indices: 40184604--40184926 Score: 522
Period size: 171 Copynumber: 1.9 Consensus size: 171
40184594 TTCTAGGAGA
* *
40184604 CCTATTGAATGTTAATTCAACTAAGCTATCTTGGTGTGAAGAAATTTCACTTAAAGAAGTGTTTC
1 CCTATTGAATATTAATTCAACTAAGCTAACTTGGTGTGAAGAAATTTCACTTAAAGAAGTGTTTC
*
40184669 TAATTGGGGTTAGTGCAACAGGGTCTAAGCACCTTCTAGTTTTCATTTGGTAAGGAGATTGATTT
66 TAATTGGGGTTAGTGCAACAGGGTCTAAGCACATTCTAGTTTTCATTTGGTAAGGAGATTGATTT
** *
40184734 CATGTTGTTGTATTGTTCTTGGGATGTCATGTTTTGGGTGG
131 CATGTCATTGTATTGCTCTTGGGATGTCATGTTTTGGGTGG
* *
40184775 CCTATTGAATATTAATTCAATTAAGCTAACTTGGTGTGGAGAAATTTCACTTAAAGAAGTGTTTC
1 CCTATTGAATATTAATTCAACTAAGCTAACTTGGTGTGAAGAAATTTCACTTAAAGAAGTGTTTC
* * * *
40184840 TAATTGGGG-TAGTGTAACATGGTCTATATCACATTCTAGTTTTCATTTGGTAGGGAGATTGATT
66 TAATTGGGGTTAGTGCAACAGGGTCTA-AGCACATTCTAGTTTTCATTTGGTAAGGAGATTGATT
40184904 TCATGTCATTGTATTGCTCTTGG
130 TCATGTCATTGTATTGCTCTTGG
40184927 AATTATGGTA
Statistics
Matches: 139, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
170 15 0.11
171 124 0.89
ACGTcount: A:0.25, C:0.12, G:0.23, T:0.40
Consensus pattern (171 bp):
CCTATTGAATATTAATTCAACTAAGCTAACTTGGTGTGAAGAAATTTCACTTAAAGAAGTGTTTC
TAATTGGGGTTAGTGCAACAGGGTCTAAGCACATTCTAGTTTTCATTTGGTAAGGAGATTGATTT
CATGTCATTGTATTGCTCTTGGGATGTCATGTTTTGGGTGG
Found at i:40186513 original size:23 final size:23
Alignment explanation
Indices: 40186468--40186515 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
40186458 AAAGTTGAAA
* *
40186468 TTTTATAATTTTTATTTTTATTT
1 TTTTACAATTTTTATTTTAATTT
40186491 TTTTACAATTTTT-TTTATAATTT
1 TTTTACAATTTTTATTT-TAATTT
40186514 TT
1 TT
40186516 AGTAAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 3 0.14
23 19 0.86
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (23 bp):
TTTTACAATTTTTATTTTAATTT
Found at i:40187129 original size:17 final size:19
Alignment explanation
Indices: 40187107--40187143 Score: 53
Period size: 16 Copynumber: 2.1 Consensus size: 19
40187097 ATAAAGGGTA
40187107 TTTTTTT-C-AATTTA-AT
1 TTTTTTTCCAAATTTATAT
40187123 TTTTTTTCCAAATTTATAT
1 TTTTTTTCCAAATTTATAT
40187142 TT
1 TT
40187144 ATTTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.39
17 1 0.06
18 6 0.33
19 4 0.22
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTTTTTCCAAATTTATAT
Found at i:40187413 original size:20 final size:18
Alignment explanation
Indices: 40187368--40187417 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
40187358 TAAATTTATG
*
40187368 ATAATTTTATAAATAAATA
1 ATAATTTTA-AATTAAATA
40187387 A-AATTTTAAATTAACATCA
1 ATAATTTTAAATTAA-AT-A
40187406 ATAATTTTAAAT
1 ATAATTTTAAAT
40187418 GCATCTATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 5 0.19
18 9 0.33
19 3 0.11
20 10 0.37
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (18 bp):
ATAATTTTAAATTAAATA
Found at i:40190507 original size:20 final size:20
Alignment explanation
Indices: 40190482--40190531 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
40190472 TGGCTTAAAA
40190482 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
40190502 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
40190519 GTGGTAGTGGATT
1 TTGGTAGTGGATT
40190532 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:40195146 original size:20 final size:20
Alignment explanation
Indices: 40195121--40195170 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
40195111 TGGCTTAAAA
40195121 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
40195141 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
40195158 GTGGTAGTGGATT
1 TTGGTAGTGGATT
40195171 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:40195739 original size:3 final size:3
Alignment explanation
Indices: 40195731--40195763 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
40195721 ATATATATAT
40195731 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
40195764 TGAAATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:40200304 original size:18 final size:19
Alignment explanation
Indices: 40200274--40200325 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
40200264 AATTCAACAT
*
40200274 TTCAAAATAATTT-TTAAAA
1 TTCAAAAT-ATTTATAAAAA
40200293 TTCAAAATATTTATAAAAA
1 TTCAAAATATTTATAAAAA
40200312 TTCAAAA-ATTTATA
1 TTCAAAATATTTATA
40200326 TTTTTTAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
18 11 0.35
19 20 0.65
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (19 bp):
TTCAAAATATTTATAAAAA
Found at i:40200351 original size:25 final size:27
Alignment explanation
Indices: 40200302--40200351 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
40200292 ATTCAAAATA
* *
40200302 TTTATAAAAATTCAAAAATTTATATTT
1 TTTAAAAAAATTCAAAAATTAATATTT
40200329 TTTAAAAAAATT-AAAAA-TAATAT
1 TTTAAAAAAATTCAAAAATTAATAT
40200352 ACAAAGAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 5 0.24
26 5 0.24
27 11 0.52
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (27 bp):
TTTAAAAAAATTCAAAAATTAATATTT
Found at i:40207283 original size:20 final size:20
Alignment explanation
Indices: 40207258--40207296 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
40207248 ACATATCAAA
40207258 ATTTTTAAAAATTTACTAAT
1 ATTTTTAAAAATTTACTAAT
*
40207278 ATTTTTAAAGATTTACTAA
1 ATTTTTAAAAATTTACTAA
40207297 AGTTATACCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.49
Consensus pattern (20 bp):
ATTTTTAAAAATTTACTAAT
Found at i:40207473 original size:21 final size:20
Alignment explanation
Indices: 40207436--40207495 Score: 66
Period size: 21 Copynumber: 3.0 Consensus size: 20
40207426 TGGTTAACTT
*
40207436 TTAGAAATATTGTTAAATCC
1 TTAGAAATATTGATAAATCC
* * * *
40207456 TTCATAAATTTTGGTAAAGCC
1 TT-AGAAATATTGATAAATCC
40207477 TTAGAAATATTGATAAATC
1 TTAGAAATATTGATAAATC
40207496 TTTTACAAGT
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
20 15 0.48
21 16 0.52
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (20 bp):
TTAGAAATATTGATAAATCC
Found at i:40221710 original size:78 final size:78
Alignment explanation
Indices: 40221580--40221738 Score: 223
Period size: 78 Copynumber: 2.0 Consensus size: 78
40221570 CTGTTCGCAC
* * *
40221580 TTTTTTCGTCATCGTCAATCCAAGATTGTTGCTCTACTGACCATCAATCTTGCGAGAGCATAATA
1 TTTTTTCGTCACCATCAATCCAAGATTGCTGCTCTACTGACCATCAATCTTGCG-GAGCATAATA
40221645 ACGTAATCTTAGGA
65 ACGTAATCTTAGGA
* * * *
40221659 TTTTTT-GTCACCATCAATTCAAGATTGCTGCTTTGA-TGACCATCATTCTTGCGGGGCATAATA
1 TTTTTTCGTCACCATCAATCCAAGATTGCTGCTCT-ACTGACCATCAATCTTGCGGAGCATAATA
40221722 ACGTAATCTTAGGA
65 ACGTAATCTTAGGA
40221736 TTT
1 TTT
40221739 GAAATATTCA
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
77 26 0.36
78 39 0.54
79 7 0.10
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.36
Consensus pattern (78 bp):
TTTTTTCGTCACCATCAATCCAAGATTGCTGCTCTACTGACCATCAATCTTGCGGAGCATAATAA
CGTAATCTTAGGA
Found at i:40227091 original size:45 final size:45
Alignment explanation
Indices: 40227005--40227128 Score: 153
Period size: 45 Copynumber: 2.8 Consensus size: 45
40226995 GTATGAATCC
* *
40227005 GCTATGATCATGAAG-TTCTTTTATGAATCCGCATGAATGAATTT
1 GCTATGATCATGAAGTTTCTTCTATGAATTCGCATGAATGAATTT
* * **
40227049 GCTATGATCATAAAGTTTCTTCTATGAATTCGTATGTTTGAATTT
1 GCTATGATCATGAAGTTTCTTCTATGAATTCGCATGAATGAATTT
* *
40227094 GCT-TTATCCATGAAGTTTCTTCTATGAATTTGCAT
1 GCTATGAT-CATGAAGTTTCTTCTATGAATTCGCAT
40227129 AGATGAGTCT
Statistics
Matches: 68, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
44 17 0.25
45 51 0.75
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.44
Consensus pattern (45 bp):
GCTATGATCATGAAGTTTCTTCTATGAATTCGCATGAATGAATTT
Found at i:40229636 original size:63 final size:61
Alignment explanation
Indices: 40229522--40229685 Score: 168
Period size: 63 Copynumber: 2.6 Consensus size: 61
40229512 CACCACATGA
* ** * * *
40229522 CCGTGTGCCAGGCTGTGTAACTCACTATTTGTGAATTACTGTCACATGGGCCAGGGGCACGAG
1 CCGTGTGCCAGGC-GTGTAACTCACTGTTTGTGAATTAAGGTCACACGGGCCAAGGACACG-G
* *
40229585 -CGTGTGTCCAGGTCGTGTAACTCACTGTTTGTGAATTAAGGTTACACGGGCCAAGGACATGG
1 CCGTGTG-CCAGG-CGTGTAACTCACTGTTTGTGAATTAAGGTCACACGGGCCAAGGACACGG
* * *
40229647 CCGTGTGACTAGGCCGTGTAACTCACTGTGTATGAATTA
1 CCGTGTG-CCAGG-CGTGTAACTCACTGTTTGTGAATTA
40229686 GTATCACATG
Statistics
Matches: 85, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
62 7 0.08
63 77 0.91
64 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.27
Consensus pattern (61 bp):
CCGTGTGCCAGGCGTGTAACTCACTGTTTGTGAATTAAGGTCACACGGGCCAAGGACACGG
Found at i:40231479 original size:45 final size:45
Alignment explanation
Indices: 40231407--40231523 Score: 198
Period size: 45 Copynumber: 2.6 Consensus size: 45
40231397 TTGATAAACA
* *
40231407 AATAAGATCATAGTTGAAAGACACTATGGCACTATATCAGAAATG
1 AATAAGACCATAGTTGAAAGACACTATGGCACTATACCAGAAATG
*
40231452 AATACGACCATAGTTGAAAGACACTATGGCACTATACCAGAAATG
1 AATAAGACCATAGTTGAAAGACACTATGGCACTATACCAGAAATG
*
40231497 AATAAGACCATGGTTGAAAGACACTAT
1 AATAAGACCATAGTTGAAAGACACTAT
40231524 AGCATTGTGT
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 67 1.00
ACGTcount: A:0.44, C:0.16, G:0.18, T:0.22
Consensus pattern (45 bp):
AATAAGACCATAGTTGAAAGACACTATGGCACTATACCAGAAATG
Found at i:40231641 original size:13 final size:13
Alignment explanation
Indices: 40231623--40231694 Score: 83
Period size: 13 Copynumber: 5.5 Consensus size: 13
40231613 TAAATGTGTA
40231623 ATATGAAATGGTT
1 ATATGAAATGGTT
*
40231636 ATATGAGATGGTT
1 ATATGAAATGGTT
40231649 AT-TCGAAATGGTT
1 ATAT-GAAATGGTT
* **
40231662 ATATAAAATGAAT
1 ATATGAAATGGTT
*
40231675 ATATGAAATGATT
1 ATATGAAATGGTT
40231688 ATATGAA
1 ATATGAA
40231695 TCAGTTATAT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
12 1 0.02
13 48 0.96
14 1 0.02
ACGTcount: A:0.43, C:0.01, G:0.19, T:0.36
Consensus pattern (13 bp):
ATATGAAATGGTT
Found at i:40231671 original size:39 final size:40
Alignment explanation
Indices: 40231614--40231689 Score: 91
Period size: 39 Copynumber: 1.9 Consensus size: 40
40231604 ATTAAATGAT
* ** * *
40231614 AAATGTGTAATATGAAATGGTTATATGAGATGGTTATTCG
1 AAATGTGTAATATAAAATGAATATATGAAATGATTATTCG
*
40231654 AAATG-GTTATATAAAATGAATATATGAAATGATTAT
1 AAATGTGTAATATAAAATGAATATATGAAATGATTAT
40231690 ATGAATCAGT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
39 25 0.83
40 5 0.17
ACGTcount: A:0.42, C:0.01, G:0.20, T:0.37
Consensus pattern (40 bp):
AAATGTGTAATATAAAATGAATATATGAAATGATTATTCG
Found at i:40231703 original size:26 final size:26
Alignment explanation
Indices: 40231623--40231745 Score: 74
Period size: 26 Copynumber: 4.7 Consensus size: 26
40231613 TAAATGTGTA
* *
40231623 ATATGAAATGGTTATATGAGAT-GGTT
1 ATATGAAATGATTATATGA-ATCAGTT
* * * *
40231649 AT-TCGAAATGGTTATATAAAATGA-AT
1 ATAT-GAAATGATTATAT-GAATCAGTT
40231675 ATATGAAATGATTATATGAATCAGTT
1 ATATGAAATGATTATATGAATCAGTT
* * *
40231701 ATATGGAAATAATTATATAAAGC-GCTT
1 ATAT-GAAATGATTATATGAATCAG-TT
* *
40231728 ATAAGAAATGTTTATATG
1 ATATGAAATGATTATATG
40231746 GATAGATATG
Statistics
Matches: 76, Mismatches: 14, Indels: 14
0.73 0.13 0.13
Matches are distributed among these distances:
25 5 0.07
26 49 0.64
27 22 0.29
ACGTcount: A:0.42, C:0.03, G:0.18, T:0.37
Consensus pattern (26 bp):
ATATGAAATGATTATATGAATCAGTT
Found at i:40231729 original size:27 final size:26
Alignment explanation
Indices: 40231674--40231736 Score: 65
Period size: 27 Copynumber: 2.4 Consensus size: 26
40231664 ATAAAATGAA
* * *
40231674 TATATGAAATGATTATATGAATCAGT
1 TATATGAAATAATTATATAAAGCAGT
40231700 TATATGGAAATAATTATATAAAGC-GCT
1 TATAT-GAAATAATTATATAAAGCAG-T
*
40231727 TATAAGAAAT
1 TATATGAAAT
40231737 GTTTATATGG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
26 11 0.35
27 20 0.65
ACGTcount: A:0.46, C:0.05, G:0.14, T:0.35
Consensus pattern (26 bp):
TATATGAAATAATTATATAAAGCAGT
Found at i:40235773 original size:15 final size:15
Alignment explanation
Indices: 40235753--40235788 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
40235743 TAAGGAAGGG
*
40235753 AATGATCTTGGTCTC
1 AATGATCATGGTCTC
40235768 AATGATCATGGTCTC
1 AATGATCATGGTCTC
40235783 AATGAT
1 AATGAT
40235789 GATTCAATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (15 bp):
AATGATCATGGTCTC
Found at i:40239852 original size:27 final size:27
Alignment explanation
Indices: 40239815--40239866 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
40239805 ATCGTCATCT
40239815 TTTTCACGTTCTTGCCAAAAAACTATC
1 TTTTCACGTTCTTGCCAAAAAACTATC
*
40239842 TTTTCATGTTCTTGCCAAAAAACTA
1 TTTTCACGTTCTTGCCAAAAAACTA
40239867 AGGCATTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (27 bp):
TTTTCACGTTCTTGCCAAAAAACTATC
Found at i:40240807 original size:40 final size:40
Alignment explanation
Indices: 40240763--40240889 Score: 146
Period size: 40 Copynumber: 3.2 Consensus size: 40
40240753 TGTTATACTC
* * *
40240763 TCTGTCTGGCGTGTTTCGGGTGTATTAGTTATTATGAGCT
1 TCTGTCTGGCGTGTTTCGGGTGGATTAGCTCTTATGAGCT
* **
40240803 TCTGTCTGGCGTGTATCGATTGGATTAGCTCTTATGAGCT
1 TCTGTCTGGCGTGTTTCGGGTGGATTAGCTCTTATGAGCT
* ** * *
40240843 TTTGTCTGGTATATTTCGGGTGGATTAGCTCTTACGAGCT
1 TCTGTCTGGCGTGTTTCGGGTGGATTAGCTCTTATGAGCT
*
40240883 CCTGTCT
1 TCTGTCT
40240890 AGTGTGTTCG
Statistics
Matches: 71, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 71 1.00
ACGTcount: A:0.13, C:0.17, G:0.28, T:0.43
Consensus pattern (40 bp):
TCTGTCTGGCGTGTTTCGGGTGGATTAGCTCTTATGAGCT
Found at i:40253428 original size:9 final size:8
Alignment explanation
Indices: 40253391--40253424 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
40253381 TAAAATATAT
40253391 ATTTTTATA
1 ATTTTTA-A
*
40253400 CTTTTTAA
1 ATTTTTAA
40253408 ATTTTTAA
1 ATTTTTAA
40253416 ATTTTTAA
1 ATTTTTAA
40253424 A
1 A
40253425 ATTTCAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 17 0.74
9 6 0.26
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (8 bp):
ATTTTTAA
Found at i:40255132 original size:13 final size:13
Alignment explanation
Indices: 40255114--40255140 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
40255104 TTAGTGTTAG
40255114 AGACTTTAGTTTT
1 AGACTTTAGTTTT
40255127 AGACTTTAGTTTT
1 AGACTTTAGTTTT
40255140 A
1 A
40255141 TTAGGTTGAT
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:0.26, C:0.07, G:0.15, T:0.52
Consensus pattern (13 bp):
AGACTTTAGTTTT
Found at i:40255767 original size:11 final size:11
Alignment explanation
Indices: 40255739--40255777 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
40255729 AATAACAAAA
*
40255739 AAAATAATAGC
1 AAAATAATAGT
*
40255750 AATATAATAGT
1 AAAATAATAGT
*
40255761 GAAATAATAGT
1 AAAATAATAGT
40255772 AAAATA
1 AAAATA
40255778 GTGACAAAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.62, C:0.03, G:0.10, T:0.26
Consensus pattern (11 bp):
AAAATAATAGT
Found at i:40261710 original size:153 final size:150
Alignment explanation
Indices: 40261391--40261740 Score: 373
Period size: 153 Copynumber: 2.3 Consensus size: 150
40261381 ACTATTATCA
* * **
40261391 TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAATTTTTACGGTTCACGTAAT
1 TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAATTTATACAATTCACGTAAT
* * * * * *
40261456 AGCCTTCACATAGTACTATACACGTGATCAAGTTTTACGATTCACGTAGTAGCCTTCACATAGTA
66 AGCCTTCACACAGTACTACACACGTGACCAAGTTCTACGATACACATAGTAGCCTTCACATAGTA
* *
40261521 CTACATATGTGACTAAAGCTT
131 CTACACATGTGACCAAA-CTT
* * * *
40261542 TTCGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTAT-CAATTCACGTA
1 TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCA--ATTTATACAATTCACGTA
* * * * * *
40261606 GTAGTCTTCACACAGTACTACACACGTGACCAAAGCTTCT-CGGTACATATTGTAGCCTTCACTT
64 ATAGCCTTCACACAGTACTACACACGTGACC-AAG-TTCTACGATACACATAGTAGCCTTCACAT
* *
40261670 AGTACTATACATGTGACCATTA-TT
127 AGTACTACACATGTGACCA-AACTT
* * *
40261694 TATCGATTCACGTAGTAGCCTTCAGACAGTACTACACACGTGACCAA
1 T-TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAA
40261741 CACTTTCACT
Statistics
Matches: 162, Mismatches: 31, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
151 41 0.25
152 38 0.23
153 79 0.49
154 4 0.02
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (150 bp):
TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAATTTATACAATTCACGTAAT
AGCCTTCACACAGTACTACACACGTGACCAAGTTCTACGATACACATAGTAGCCTTCACATAGTA
CTACACATGTGACCAAACTT
Found at i:40261738 original size:51 final size:51
Alignment explanation
Indices: 40261392--40261739 Score: 305
Period size: 51 Copynumber: 6.9 Consensus size: 51
40261382 CTATTATCAT
* *
40261392 TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAATT-TTTA
1 TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGA-CCATTATTTA
* * * * *
40261443 -CGGTTCACGTAATAGCCTTCACATAGTACTATACACGTGATCAAGT-TTTA
1 TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGA-CCATTATTTA
* * * *
40261493 -CGATTCACGTAGTAGCCTTCACATAGTACTACATATGTGACTA-AAGCTTT-
1 TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCATTA--TTTA
* * * * * *
40261543 TCGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTA
1 TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCATTATTTA
* * * * * *
40261594 TCAATTCACGTAGTAGTCTTCACACAGTACTACACACGTGACCA-AAGCTTC
1 TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCATTA-TTTA
* * ** * * * *
40261645 TCGGTACATATTGTAGCCTTCACTTAGTACTATACATGTGACCATTATTTA
1 TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCATTATTTA
* *
40261696 TCGATTCACGTAGTAGCCTTCAGACAGTACTACACACGTGACCA
1 TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCA
40261740 ACACTTTCAC
Statistics
Matches: 235, Mismatches: 54, Indels: 16
0.77 0.18 0.05
Matches are distributed among these distances:
49 2 0.01
50 84 0.36
51 147 0.63
52 2 0.01
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (51 bp):
TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCATTATTTA
Found at i:40261738 original size:102 final size:102
Alignment explanation
Indices: 40261392--40261740 Score: 445
Period size: 102 Copynumber: 3.4 Consensus size: 102
40261382 CTATTATCAT
* * * * * * *
40261392 TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AA-TTTTTACGGTTCACGTAA
1 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTT-CGGTACACATAG
* * * *
40261455 TAGCCTTCACATAGTACTATACACGTGATCAAGT-TTTA
65 TAGCCTTCACTTAGTACTATACATGTGA-CCATTATTTA
* * * *
40261493 -CGATTCACGTAGTAGCCTTCACATAGTACTACATATGTGACTAAAGCTTTTCGGTACACATAGT
1 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGGTACACATAGT
* *
40261557 AGCCTTCACTTAGTACTACACATGTGACCATCATTTA
66 AGCCTTCACTTAGTACTATACATGTGACCATTATTTA
* * * * *
40261594 TCAATTCACGTAGTAGTCTTCACACAGTACTACACACGTGACCAAAGCTTCTCGGTACATATTGT
1 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGGTACACATAGT
40261659 AGCCTTCACTTAGTACTATACATGTGACCATTATTTA
66 AGCCTTCACTTAGTACTATACATGTGACCATTATTTA
*
40261696 TCGATTCACGTAGTAGCCTTCAGACAGTACTACACACGTGACCAA
1 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAA
40261741 CACTTTCACT
Statistics
Matches: 215, Mismatches: 29, Indels: 7
0.86 0.12 0.03
Matches are distributed among these distances:
100 39 0.18
101 40 0.19
102 136 0.63
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (102 bp):
TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGGTACACATAGT
AGCCTTCACTTAGTACTATACATGTGACCATTATTTA
Found at i:40264404 original size:47 final size:48
Alignment explanation
Indices: 40264301--40264409 Score: 121
Period size: 47 Copynumber: 2.3 Consensus size: 48
40264291 TCTAACTACC
* * * *
40264301 GTCTTACATGTAATCACATATCACATACCGATGCCATAGCCCAGCTATA
1 GTCTTACACGGAATCACATAT-ACATAACGATGCCATAGCCCAGATATA
* * ** *
40264350 GTTTTACACGGAATCACATAT-CATAATGATGCCATATTCCAGATATG
1 GTCTTACACGGAATCACATATACATAACGATGCCATAGCCCAGATATA
40264397 GTCTTACACGGAA
1 GTCTTACACGGAA
40264410 ATTTCATAAT
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
47 32 0.64
49 18 0.36
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (48 bp):
GTCTTACACGGAATCACATATACATAACGATGCCATAGCCCAGATATA
Found at i:40266346 original size:51 final size:50
Alignment explanation
Indices: 40266278--40266633 Score: 307
Period size: 51 Copynumber: 7.0 Consensus size: 50
40266268 CTATTATCAT
* *
40266278 TCGATACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTA
1 TCGATACACATACTAGCCTTCACACAGTACTACACACGTGACCAAA-CTTA
* * * * ** * * *
40266329 TCGCTACATATTCTAGCCTCCACTTAGTACTACACATGTGACCATTATTTA
1 TCGATACACATACTAGCCTTCACACAGTACTACACACGTGACCA-AACTTA
* * *
40266380 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTA
1 TCGATACACATACTAGCCTTCACACAGTACTACACACGTGACCAAA-CTTA
* * * * ** * * *
40266431 TCGCTACATATTCTAGCCTCCACTTAGTACTACACATGTGACCATTATTTA
1 TCGATACACATACTAGCCTTCACACAGTACTACACACGTGACCA-AACTTA
* * *
40266482 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTA
1 TCGATACACATACTAGCCTTCACACAGTACTACACACGTGACCAAA-CTTA
* * * * ** * * *
40266533 TCGCTACATATTCTAGCCTCCACTTAGTACTACACATGTGACCATTATTTA
1 TCGATACACATACTAGCCTTCACACAGTACTACACACGTGACCA-AACTTA
* * *
40266584 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAACACTT
1 TCGATACACATACTAGCCTTCACACAGTACTACACACGTGACCAA-ACTT
40266634 TTACTTTCAT
Statistics
Matches: 228, Mismatches: 71, Indels: 12
0.73 0.23 0.04
Matches are distributed among these distances:
50 2 0.01
51 223 0.98
52 3 0.01
ACGTcount: A:0.30, C:0.29, G:0.13, T:0.28
Consensus pattern (50 bp):
TCGATACACATACTAGCCTTCACACAGTACTACACACGTGACCAAACTTA
Found at i:40266645 original size:102 final size:102
Alignment explanation
Indices: 40266278--40266628 Score: 693
Period size: 102 Copynumber: 3.4 Consensus size: 102
40266268 CTATTATCAT
*
40266278 TCGATACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTATCGCTACATATTCT
1 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTATCGCTACATATTCT
40266343 AGCCTCCACTTAGTACTACACATGTGACCATTATTTA
66 AGCCTCCACTTAGTACTACACATGTGACCATTATTTA
40266380 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTATCGCTACATATTCT
1 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTATCGCTACATATTCT
40266445 AGCCTCCACTTAGTACTACACATGTGACCATTATTTA
66 AGCCTCCACTTAGTACTACACATGTGACCATTATTTA
40266482 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTATCGCTACATATTCT
1 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTATCGCTACATATTCT
40266547 AGCCTCCACTTAGTACTACACATGTGACCATTATTTA
66 AGCCTCCACTTAGTACTACACATGTGACCATTATTTA
40266584 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAA
1 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAA
40266629 CACTTTTACT
Statistics
Matches: 248, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
102 248 1.00
ACGTcount: A:0.30, C:0.29, G:0.13, T:0.28
Consensus pattern (102 bp):
TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTATCGCTACATATTCT
AGCCTCCACTTAGTACTACACATGTGACCATTATTTA
Found at i:40267866 original size:23 final size:23
Alignment explanation
Indices: 40267834--40267881 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
40267824 CGTGGTAAAG
* *
40267834 GTGCTTCTACTTCGACCACTGCT
1 GTGCTACTACTTCGACCACTACT
*
40267857 GTGCTACTACTTCGATCACTACT
1 GTGCTACTACTTCGACCACTACT
40267880 GT
1 GT
40267882 TGTTGTATCC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.17, C:0.31, G:0.17, T:0.35
Consensus pattern (23 bp):
GTGCTACTACTTCGACCACTACT
Found at i:40268170 original size:28 final size:31
Alignment explanation
Indices: 40268123--40268180 Score: 77
Period size: 28 Copynumber: 2.0 Consensus size: 31
40268113 AAAATTCAAA
*
40268123 TTATTTTCACTATTTTAAATA-T-AAAATAT
1 TTATTTTCACTATTTAAAATAGTGAAAATAT
*
40268152 TTATTTTTA-TATTTAAAATAGTGAAAATA
1 TTATTTTCACTATTTAAAATAGTGAAAATA
40268181 ATTTGAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 10 0.40
29 9 0.36
30 6 0.24
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.50
Consensus pattern (31 bp):
TTATTTTCACTATTTAAAATAGTGAAAATAT
Found at i:40269309 original size:23 final size:24
Alignment explanation
Indices: 40269278--40269323 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
40269268 TGTCATAATT
40269278 TTTTATATAAGTA-TATTATAACAC
1 TTTTATATAA-TATTATTATAACAC
*
40269302 TTTT-TATAATATTTTTATAACA
1 TTTTATATAATATTATTATAACA
40269324 AACAAATTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 2 0.10
23 14 0.70
24 4 0.20
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (24 bp):
TTTTATATAATATTATTATAACAC
Found at i:40269782 original size:11 final size:11
Alignment explanation
Indices: 40269766--40269799 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
40269756 TTAATGCATT
*
40269766 CAACTCCCGCC
1 CAACTCCCACC
40269777 CAACTCCCACC
1 CAACTCCCACC
40269788 CAACTCCCACC
1 CAACTCCCACC
40269799 C
1 C
40269800 TACATATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.24, C:0.65, G:0.03, T:0.09
Consensus pattern (11 bp):
CAACTCCCACC
Found at i:40273333 original size:29 final size:26
Alignment explanation
Indices: 40273287--40273343 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 26
40273277 TCATATTTTG
*
40273287 AAAATCTTTTTTTTTATTTAAAATAAA
1 AAAATCTTTTTATTTATTTAAAA-AAA
*
40273314 AAAATACTTTTTAATTTATTTTAAAAAA
1 AAAAT-CTTTTT-ATTTATTTAAAAAAA
40273342 AA
1 AA
40273344 TTTATGTACT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 5 0.19
28 11 0.42
29 10 0.38
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (26 bp):
AAAATCTTTTTATTTATTTAAAAAAA
Found at i:40273859 original size:24 final size:23
Alignment explanation
Indices: 40273818--40273864 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
40273808 TTTTGTTTTC
*
40273818 ATTTAAAAAAATATTTTTCTAAT
1 ATTTAAAAAAATAATTTTCTAAT
* *
40273841 ATTTAAAAATTATAATTTTTTAAT
1 ATTTAAAAA-AATAATTTTCTAAT
40273865 TATAACCTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
ATTTAAAAAAATAATTTTCTAAT
Found at i:40274903 original size:29 final size:30
Alignment explanation
Indices: 40274867--40274934 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
40274857 TTATAGAGGT
* * *
40274867 TAGATCAAATTAGTCTCTATATTA-TTAAA
1 TAGATCAAATTAATCCCTATACTATTTAAA
40274896 TAGATCAAATTAATCCCTATACTATTTAAA
1 TAGATCAAATTAATCCCTATACTATTTAAA
*
40274926 -AAATCAAAT
1 TAGATCAAAT
40274935 AAGCCTAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 29 0.85
30 5 0.15
ACGTcount: A:0.46, C:0.13, G:0.04, T:0.37
Consensus pattern (30 bp):
TAGATCAAATTAATCCCTATACTATTTAAA
Found at i:40276204 original size:44 final size:44
Alignment explanation
Indices: 40276119--40276206 Score: 140
Period size: 44 Copynumber: 2.0 Consensus size: 44
40276109 AACCCAATGG
**
40276119 GACAAAACCTCGATTAAGGAAAAAAGAGTACAACGGGTATTTAC
1 GACAAAACCTCGATTAAGGAAAAAAGAGTACAACGCATATTTAC
* *
40276163 GACAAAACCTCGATTAAGGGAAAAAGAGTACAGCGCATATTTAC
1 GACAAAACCTCGATTAAGGAAAAAAGAGTACAACGCATATTTAC
40276207 TCCCTCTCAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.44, C:0.17, G:0.20, T:0.18
Consensus pattern (44 bp):
GACAAAACCTCGATTAAGGAAAAAAGAGTACAACGCATATTTAC
Found at i:40281609 original size:25 final size:25
Alignment explanation
Indices: 40281557--40281605 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
40281547 TTTTTGTATT
* * *
40281557 TTTAATTTTTTATAAAATAATATCA
1 TTTAATTTATTAAAAAATAATATAA
40281582 TTTAATTTATTAAAAAAT-ATATAA
1 TTTAATTTATTAAAAAATAATATAA
40281606 ATTTTGCACC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (25 bp):
TTTAATTTATTAAAAAATAATATAA
Found at i:40283893 original size:37 final size:37
Alignment explanation
Indices: 40283850--40283921 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
40283840 AGAGTTGCGA
40283850 TCTTAAATCAGCTAACTCAAATAAACTTAGGTTGCAG
1 TCTTAAATCAGCTAACTCAAATAAACTTAGGTTGCAG
* *
40283887 TCTTAAATCAGCTAACTTAATTAAACTTAGGTTGC
1 TCTTAAATCAGCTAACTCAAATAAACTTAGGTTGC
40283922 GATTGTTGCG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.33
Consensus pattern (37 bp):
TCTTAAATCAGCTAACTCAAATAAACTTAGGTTGCAG
Found at i:40286914 original size:18 final size:21
Alignment explanation
Indices: 40286830--40286944 Score: 78
Period size: 22 Copynumber: 5.4 Consensus size: 21
40286820 ATGTATGTAC
*
40286830 ATATAAATAT-ATATATATACTT
1 ATATAAATATAATAAATATA--T
* * *
40286852 ATAAAAATTTAGA-AAATATGT
1 ATATAAATATA-ATAAATATAT
* *
40286873 ATATAGATATGAATATATGTATAT
1 ATATAAATAT-AATA-A-ATATAT
40286897 ATATAAAT-T-ATAAA-ATAT
1 ATATAAATATAATAAATATAT
40286915 ATATAAATATCAATAAATATAT
1 ATATAAATAT-AATAAATATAT
40286937 ATATAAAT
1 ATATAAAT
40286945 CAAAGATATG
Statistics
Matches: 72, Mismatches: 11, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
18 12 0.17
19 1 0.01
20 1 0.01
21 17 0.24
22 22 0.31
23 7 0.10
24 12 0.17
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (21 bp):
ATATAAATATAATAAATATAT
Found at i:40286946 original size:20 final size:20
Alignment explanation
Indices: 40286892--40286947 Score: 71
Period size: 18 Copynumber: 2.8 Consensus size: 20
40286882 TGAATATATG
*
40286892 TATATATATAAAT-TATAAA
1 TATATATATAAATCAATAAA
40286911 -ATATATATAAATATCAATAAA
1 TATATATAT-AA-ATCAATAAA
40286932 TATATATATAAATCAA
1 TATATATATAAATCAA
40286948 AGATATGTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
18 8 0.25
19 2 0.06
20 7 0.22
21 7 0.22
22 8 0.25
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.38
Consensus pattern (20 bp):
TATATATATAAATCAATAAA
Found at i:40287078 original size:3 final size:3
Alignment explanation
Indices: 40287065--40287095 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
40287055 GCGTATATAT
40287065 ATA AGTA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA
40287096 TAAGGCAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:40287159 original size:3 final size:3
Alignment explanation
Indices: 40287145--40287179 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
40287135 ATGGAAATAT
*
40287145 AAC AAT AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
40287180 TAATATATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.69, C:0.29, G:0.00, T:0.03
Consensus pattern (3 bp):
AAC
Found at i:40289054 original size:44 final size:44
Alignment explanation
Indices: 40288959--40289072 Score: 120
Period size: 44 Copynumber: 2.6 Consensus size: 44
40288949 GACTCATATC
* * *
40288959 TTCAACTTGCCCCATTGCAACTTCAGGGGGATAAGACTTGTAAT
1 TTCAACCTGCCCCACTGCAACTTCAGGGGGACAAGACTTGTAAT
* * * * ** *
40289003 TTTAACCTGCCCCGCTGCAATTTCAGGGGGGCAAGGTTTGTTAT
1 TTCAACCTGCCCCACTGCAACTTCAGGGGGACAAGACTTGTAAT
* *
40289047 TTCAACCTGCTCTACTGCAACTTCAG
1 TTCAACCTGCCCCACTGCAACTTCAG
40289073 AGAGATAAGA
Statistics
Matches: 55, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
44 55 1.00
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.31
Consensus pattern (44 bp):
TTCAACCTGCCCCACTGCAACTTCAGGGGGACAAGACTTGTAAT
Found at i:40289922 original size:44 final size:44
Alignment explanation
Indices: 40289872--40290031 Score: 155
Period size: 44 Copynumber: 3.6 Consensus size: 44
40289862 AGTGGCTTAA
* *
40289872 ATCTGCTTCCTACTA-T-CTCAAGAAGATAAGATTTGCCATCTTCG
1 ATCTGC-TCC-ACTACTGCTCAAGAAGATAAGATCTACCATCTTCG
* * *
40289916 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTCG
1 ATCTGCTCCACTACTGCTCAAGAAGATAAGATCTACCATCTTCG
* * * * *
40289960 ATCTACTCCACTACTGCTTAGGGAGATAAGATCTACCATCTTCA
1 ATCTGCTCCACTACTGCTCAAGAAGATAAGATCTACCATCTTCG
* * *
40290004 ACCTACTCCACTGCTGCTC-AGAGAGATA
1 ATCTGCTCCACTACTGCTCAAGA-AGATA
40290032 GGACTGGTGG
Statistics
Matches: 101, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
42 4 0.04
43 5 0.05
44 92 0.91
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.29
Consensus pattern (44 bp):
ATCTGCTCCACTACTGCTCAAGAAGATAAGATCTACCATCTTCG
Found at i:40290032 original size:175 final size:175
Alignment explanation
Indices: 40289822--40290146 Score: 533
Period size: 175 Copynumber: 1.9 Consensus size: 175
40289812 AAGATCTGTA
* * * *
40289822 ATCTTTAACCTACTCCACTGCTGCTTAGGGAGATAGGATTAGTGGCTTAAATCTGCTTCCTACTA
1 ATCTTCAACCTACTCCACTGCTGCTCAGAGAGATAGGACTAGTGGCTTAAATCTGCTTCCTACTA
40289887 TCTCAAGAAGATAAGATTTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTAC
66 TCTCAAGAAGATAAGATTTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTAC
*
40289952 CATCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTACC
131 AATCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTACC
*
40289997 ATCTTCAACCTACTCCACTGCTGCTCAGAGAGATAGGACTGGTGGCTTAAATCTGCTTCCTACTA
1 ATCTTCAACCTACTCCACTGCTGCTCAGAGAGATAGGACTAGTGGCTTAAATCTGCTTCCTACTA
** * * *
40290062 TCTCGGGAAGATAAGATTTGCCGTCTTCGGTCTGCTCCACTATTGCTTAGGGAGATAAGATCTAC
66 TCTCAAGAAGATAAGATTTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTAC
* *
40290127 AATCTTTGATGTACTCCACT
131 AATCTTCGATCTACTCCACT
40290147 GCCGGTACAG
Statistics
Matches: 137, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
175 137 1.00
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.31
Consensus pattern (175 bp):
ATCTTCAACCTACTCCACTGCTGCTCAGAGAGATAGGACTAGTGGCTTAAATCTGCTTCCTACTA
TCTCAAGAAGATAAGATTTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTAC
AATCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTACC
Found at i:40290118 original size:44 final size:44
Alignment explanation
Indices: 40289895--40290124 Score: 207
Period size: 44 Copynumber: 5.2 Consensus size: 44
40289885 TATCTCAAGA
*
40289895 AGATAAGATTTGCCATCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATCTGCCATCTTCGATCTGCTCCACTACTGCTTAGGG
* *
40289939 AGATAAGATCTACCATCTTCGATCTACTCCACTACTGCTTAGGG
1 AGATAAGATCTGCCATCTTCGATCTGCTCCACTACTGCTTAGGG
* * * * * * *
40289983 AGATAAGATCTACCATCTTCAACCTACTCCACTGCTGCTCAGAG
1 AGATAAGATCTGCCATCTTCGATCTGCTCCACTACTGCTTAGGG
* **** ** *
40290027 AGATAGGA-CTGGTGGCTTAAATCTGCTTCCTACTA-T-C-TCGGG
1 AGATAAGATCTGCCATCTTCGATCTGC-TCC-ACTACTGCTTAGGG
* * * *
40290069 AAGATAAGATTTGCCGTCTTCGGTCTGCTCCACTATTGCTTAGGG
1 -AGATAAGATCTGCCATCTTCGATCTGCTCCACTACTGCTTAGGG
40290114 AGATAAGATCT
1 AGATAAGATCT
40290125 ACAATCTTTG
Statistics
Matches: 148, Mismatches: 31, Indels: 14
0.77 0.16 0.07
Matches are distributed among these distances:
42 6 0.04
43 22 0.15
44 113 0.76
45 7 0.05
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (44 bp):
AGATAAGATCTGCCATCTTCGATCTGCTCCACTACTGCTTAGGG
Found at i:40290302 original size:89 final size:89
Alignment explanation
Indices: 40290146--40290453 Score: 386
Period size: 89 Copynumber: 3.5 Consensus size: 89
40290136 TGTACTCCAC
* * ** *
40290146 TGCCGGTACAGGAAGACAAGATCTATTGCTTCTAGTCTACTCTACTGCAAACTC-AGGAAGGTCA
1 TGCCAGTACAGGAAGACAAGATCTATTGCTTCTAGTCTGCTCCGCTACAAACTCAAGGAA-GTCA
40290210 GGCTTGTGTCTTCGATCTGCTTCAT
65 GGCTTGTGTCTTCGATCTGCTTCAT
* * ** * *
40290235 TACCGGTACAGGAAGACAAGATCTGCTGCTTTTAGTCTGCTCCGTTACAAACTCAAGGAAG-CAA
1 TGCCAGTACAGGAAGACAAGATCTATTGCTTCTAGTCTGCTCCGCTACAAACTCAAGGAAGTC-A
* * *
40290299 GGCTAGTGTTTTTGATCTGCTTCAT
65 GGCTTGTGTCTTCGATCTGCTTCAT
* * * * *
40290324 TGCCAGTACAAGAAGACAAGATCTATTGTTTTTAGTCTGCTCCGCTACAAACTCAGGGAGGTCAG
1 TGCCAGTACAGGAAGACAAGATCTATTGCTTCTAGTCTGCTCCGCTACAAACTCAAGGAAGTCAG
*
40290389 GCTTGTGTCTTCGATCTGCTTCAC
66 GCTTGTGTCTTCGATCTGCTTCAT
* *
40290413 TGCCAGTACAGGAAGACAAAATCTGTTGCTTCTAGTCTGCT
1 TGCCAGTACAGGAAGACAAGATCTATTGCTTCTAGTCTGCT
40290454 TCTCTGTAAT
Statistics
Matches: 186, Mismatches: 30, Indels: 6
0.84 0.14 0.03
Matches are distributed among these distances:
88 1 0.01
89 179 0.96
90 6 0.03
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (89 bp):
TGCCAGTACAGGAAGACAAGATCTATTGCTTCTAGTCTGCTCCGCTACAAACTCAAGGAAGTCAG
GCTTGTGTCTTCGATCTGCTTCAT
Found at i:40293512 original size:12 final size:12
Alignment explanation
Indices: 40293481--40293514 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
40293471 CTTTTCTAGT
40293481 TGTTCTTGCATC
1 TGTTCTTGCATC
**
40293493 TGAGCTTGCATC
1 TGTTCTTGCATC
40293505 TGTTCTTGCA
1 TGTTCTTGCA
40293515 ATTTCTCTAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.44
Consensus pattern (12 bp):
TGTTCTTGCATC
Found at i:40296201 original size:35 final size:35
Alignment explanation
Indices: 40296155--40296223 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
40296145 GAAATGATCA
* *
40296155 AAAATTATGAAAGTA-AAAAAGATATATATATGTAT
1 AAAATTATGAAAATATAAAAA-ACATATATATGTAT
*
40296190 AAAATTATGAAAATATAAAAAACATATGTATGTA
1 AAAATTATGAAAATATAAAAAACATATATATGTA
40296224 CACATATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
35 25 0.83
36 5 0.17
ACGTcount: A:0.58, C:0.01, G:0.10, T:0.30
Consensus pattern (35 bp):
AAAATTATGAAAATATAAAAAACATATATATGTAT
Found at i:40296379 original size:20 final size:20
Alignment explanation
Indices: 40296324--40296380 Score: 64
Period size: 18 Copynumber: 2.9 Consensus size: 20
40296314 ATGAATATAT
*
40296324 GTATATATATAAAT-TATAA
1 GTATATATATAAATCAATAA
*
40296343 -AATATATATAAATATCAATAA
1 GTATATATAT-AA-ATCAATAA
40296364 GTATATATATAAATCAA
1 GTATATATATAAATCAA
40296381 AGATATGTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
18 8 0.26
19 2 0.06
20 7 0.23
21 6 0.19
22 8 0.26
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.37
Consensus pattern (20 bp):
GTATATATATAAATCAATAA
Found at i:40296516 original size:3 final size:3
Alignment explanation
Indices: 40296498--40296573 Score: 134
Period size: 3 Copynumber: 25.0 Consensus size: 3
40296488 ATGCATATAT
*
40296498 ATA AGTA ATT ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
40296544 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
40296574 TAAGACTAGT
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
3 67 0.96
4 3 0.04
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:40299615 original size:41 final size:41
Alignment explanation
Indices: 40299558--40299681 Score: 212
Period size: 41 Copynumber: 3.0 Consensus size: 41
40299548 TTTAACATAT
* *
40299558 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
*
40299599 TCACCGGCACGTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
*
40299640 TCACCCGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
40299681 T
1 T
40299682 AACTGGGTTG
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 78 1.00
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.28
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
Found at i:40305215 original size:41 final size:40
Alignment explanation
Indices: 40305158--40305343 Score: 284
Period size: 41 Copynumber: 4.5 Consensus size: 40
40305148 TTTAACATAT
* * *
40305158 TCACCAGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGG-TTATAACCTGGTTCAGA
40305199 TCACCGGCA-TGTAGCCTGCTAGGTTCATAACCTGGTTCAGA
1 TCACCGGCACT-TAGCCTGCTAGGTT-ATAACCTGGTTCAGA
*
40305240 TCACCGGCACTTAGCCTGCTAGGTTTGTAACCTGGTTCAGA
1 TCACCGGCACTTAGCCTGCTAGG-TTATAACCTGGTTCAGA
40305281 TCACCGGCACTTAGCCTGCTAGGTTCATAACCTGGTTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTT-ATAACCTGGTTCAGA
40305322 TCACCGGCACTTAGCCTGCTAG
1 TCACCGGCACTTAGCCTGCTAG
40305344 ACTTAAAGTC
Statistics
Matches: 135, Mismatches: 5, Indels: 10
0.90 0.03 0.07
Matches are distributed among these distances:
40 5 0.04
41 127 0.94
42 3 0.02
ACGTcount: A:0.22, C:0.29, G:0.23, T:0.27
Consensus pattern (40 bp):
TCACCGGCACTTAGCCTGCTAGGTTATAACCTGGTTCAGA
Found at i:40306697 original size:23 final size:23
Alignment explanation
Indices: 40306670--40306715 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 23
40306660 TAATTTGTTA
40306670 TATTAA-ACATATATTAACCTTAT
1 TATTAATAC-TATATTAACCTTAT
40306693 TATTAATGTACTATATTAACCTT
1 TATTAA--TACTATATTAACCTT
40306716 TACATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 6 0.30
25 12 0.60
26 2 0.10
ACGTcount: A:0.39, C:0.13, G:0.02, T:0.46
Consensus pattern (23 bp):
TATTAATACTATATTAACCTTAT
Found at i:40312582 original size:50 final size:50
Alignment explanation
Indices: 40311877--40312684 Score: 365
Period size: 50 Copynumber: 16.2 Consensus size: 50
40311867 AAAATGAGGT
* * * ** ** * *
40311877 AGCAAGATTCGCCATTGTGGCTTTAATCTGTTCCACTGCACCGCCTAGGG-
1 AGCAAGATTCGCTATTGTAGCTTTAATCTTTTTAACTGCAATGTC-GGGGA
* * * * *
40311927 AGTAAGATTTGCTGTTGAAGCTTTAATCTTTTTAACTGCAATGTCGGAGA
1 AGCAAGATTCGCTATTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGA
* * * * ** ** * **
40311977 AGCATGATTCGCTGTTGTGGCTTTAATCTATTCCACTGCACCGCCTAGGA
1 AGCAAGATTCGCTATTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGA
* * ** *
40312027 GGCAAGATTTGCTGCTGTAGCTTTAATCTTTTTAACCGCAATGTCGGGGA
1 AGCAAGATTCGCTATTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGA
* * * * ** ** * *
40312077 TGCAAGATTCACTGA-TGTGGCTTTAATCTGTTCCACTGCACCGCCAGGGA
1 AGCAAGATTCGCT-ATTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGA
** * * *
40312127 AATAAGATTCACTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGAGGA
1 AGCAAGATTCGCTATTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGA
* * * ** ** * * *
40312177 AGCAAGATTCACCGA-TGTGGCTTTAATCTGCTCCACTAC-ATCGCCTGGGA
1 AGCAAGATTC-GCTATTGTAGCTTTAATCTTTTTAACTGCAAT-GTCGGGGA
** *
40312227 AATAAGATTCGCTATTGTAGCTTTAATCTTTTTAACTGCAATGTTGGGGA
1 AGCAAGATTCGCTATTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGA
* * ** ** ** **
40312277 AGTAAGATTC-ATCGCTGTAGCTTTAATCTGCTGCACTGC-ATCACCTGGGG-
1 AGCAAGATTCGCT-ATTGTAGCTTTAATCTTTTTAACTGCAAT-GTC-GGGGA
* * * *
40312327 AGTAAGATTTGTTGTTGTAGC-TTAATCTTTTTAACTGCAATGTCGGGGA
1 AGCAAGATTCGCTATTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGA
* ** ** *
40312376 AGCAAGATTCACTGCTGTAGCTTTAATC-TGCTACACTGC-ATCGCCTGGGG-
1 AGCAAGATTCGCTATTGTAGCTTTAATCTTTTTA-ACTGCAAT-GTC-GGGGA
* * **
40312426 AGTAAGATTTGCCGTTGTAGC-TTAATCTTTTTAACTGCAATGTCGGGGA
1 AGCAAGATTCGCTATTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGA
* * * ** ** ** *
40312475 AGCAAGATTCACCGA-TGT-GACTTTAATCTCTTCCACTGCACCG-CTAAGTA
1 AGCAAGATTC-GCTATTGTAG-CTTTAATCTTTTTAACTGCAATGTC-GGGGA
**
40312525 AATAAGATTCGCTATTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGA
1 AGCAAGATTCGCTATTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGA
* * * ** ** ** ** *
40312575 AGCAAGATTCACCGA-TGT-GACCTTAATCCCTTCCACTGCACCG-CTAAGTA
1 AGCAAGATTC-GCTATTGTAG-CTTTAATCTTTTTAACTGCAATGTC-GGGGA
** *
40312625 AATAAGATTCGCTATTGTAGCTTTAATCTTTTTAACTGCAATGTTGGGGA
1 AGCAAGATTCGCTATTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGA
40312675 AGCAAGATTC
1 AGCAAGATTC
40312685 ACCGATGTGG
Statistics
Matches: 538, Mismatches: 187, Indels: 66
0.68 0.24 0.08
Matches are distributed among these distances:
48 9 0.02
49 76 0.14
50 436 0.81
51 17 0.03
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (50 bp):
AGCAAGATTCGCTATTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGA
Found at i:40312731 original size:100 final size:100
Alignment explanation
Indices: 40311877--40312733 Score: 1037
Period size: 100 Copynumber: 8.6 Consensus size: 100
40311867 AAAATGAGGT
* * *
40311877 AGCAAGATTCGCC-ATTGTGGCTTTAATCTGTTCCACTGCACCGCCTAGGG-AGTAAGATTTGCT
1 AGCAAGATTCACCGA-TGTGGCTTTAATCTGCTCCACTGCACCGCCT-GGGAAGTAAGATTCGCT
* *
40311940 GTTGAAGCTTTAATCTTTTTAACTGCAATGTCGGAGA
64 GTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGA
* * * * ** * * * * *
40311977 AGCATGATTCGCTGTTGTGGCTTTAATCTATTCCACTGCACCGCCTAGGAGGCAAGATTTGCTGC
1 AGCAAGATTCACCGATGTGGCTTTAATCTGCTCCACTGCACCGCCTGGGAAGTAAGATTCGCTGT
*
40312042 TGTAGCTTTAATCTTTTTAACCGCAATGTCGGGGA
66 TGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGA
* * * * * *
40312077 TGCAAGATTCACTGATGTGGCTTTAATCTGTTCCACTGCACCGCCAGGGAAATAAGATTCACTGT
1 AGCAAGATTCACCGATGTGGCTTTAATCTGCTCCACTGCACCGCCTGGGAAGTAAGATTCGCTGT
*
40312142 TGTAGCTTTAATCTTTTTAACTGCAATGTCGAGGA
66 TGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGA
* * * *
40312177 AGCAAGATTCACCGATGTGGCTTTAATCTGCTCCACTACATCGCCTGGGAAATAAGATTCGCTAT
1 AGCAAGATTCACCGATGTGGCTTTAATCTGCTCCACTGCACCGCCTGGGAAGTAAGATTCGCTGT
*
40312242 TGTAGCTTTAATCTTTTTAACTGCAATGTTGGGGA
66 TGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGA
* * * * * * * * * *
40312277 AGTAAGATTCATCGCTGTAGCTTTAATCTGCTGCACTGCATCACCTGGGGAGTAAGATTTGTTGT
1 AGCAAGATTCACCGATGTGGCTTTAATCTGCTCCACTGCACCGCCTGGGAAGTAAGATTCGCTGT
40312342 TGTAGC-TTAATCTTTTTAACTGCAATGTCGGGGA
66 TGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGA
* * * * * * * *
40312376 AGCAAGATTCACTGCTGTAGCTTTAATCTGCTACACTGCATCGCCTGGGGAGTAAGATTTGCCGT
1 AGCAAGATTCACCGATGTGGCTTTAATCTGCTCCACTGCACCGCCTGGGAAGTAAGATTCGCTGT
40312441 TGTAGC-TTAATCTTTTTAACTGCAATGTCGGGGA
66 TGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGA
* * * *
40312475 AGCAAGATTCACCGATGTGACTTTAATCT-CTTCCACTGCACCG-CTAAGTAAATAAGATTCGCT
1 AGCAAGATTCACCGATGTGGCTTTAATCTGC-TCCACTGCACCGCCT-GGGAAGTAAGATTCGCT
*
40312538 ATTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGA
64 GTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGA
* * * * * *
40312575 AGCAAGATTCACCGATGTGACCTTAATC-CCTTCCACTGCACCG-CTAAGTAAATAAGATTCGCT
1 AGCAAGATTCACCGATGTGGCTTTAATCTGC-TCCACTGCACCGCCT-GGGAAGTAAGATTCGCT
* *
40312638 ATTGTAGCTTTAATCTTTTTAACTGCAATGTTGGGGA
64 GTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGA
** *
40312675 AGCAAGATTCACCGATGTGGCTTTAATCTGCTCCACTGCATTGCTTGGGAAGTAAGATT
1 AGCAAGATTCACCGATGTGGCTTTAATCTGCTCCACTGCACCGCCTGGGAAGTAAGATT
40312734 TCTAGCTTCA
Statistics
Matches: 669, Mismatches: 80, Indels: 16
0.87 0.10 0.02
Matches are distributed among these distances:
98 3 0.00
99 174 0.26
100 490 0.73
101 2 0.00
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (100 bp):
AGCAAGATTCACCGATGTGGCTTTAATCTGCTCCACTGCACCGCCTGGGAAGTAAGATTCGCTGT
TGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGA
Found at i:40312972 original size:44 final size:44
Alignment explanation
Indices: 40312810--40313012 Score: 171
Period size: 44 Copynumber: 4.7 Consensus size: 44
40312800 TTCGGTCTAT
* * * * * *
40312810 TCCACTGTAATCTCAGGGAGATAAGA--CCT-GATACGATCTAC
1 TCCACTGTAATCTCAGAGAGATAAGATTTCTGGCTTCAATCTGC
* * *** * *
40312851 TCTACTGTAATTTCAGAGAGATAAGATCTT-TTATTTTAATCCGC
1 TCCACTGTAATCTCAGAGAGATAAGAT-TTCTGGCTTCAATCTGC
* * * * *
40312895 TCCACTATAATCTCAGGGAAATAGGATTACTGGCTTCAATCTGC
1 TCCACTGTAATCTCAGAGAGATAAGATTTCTGGCTTCAATCTGC
* *
40312939 GCCACTGTAATCTCAGAGAGATAAGATTTCTGGCTTCAATCTAC
1 TCCACTGTAATCTCAGAGAGATAAGATTTCTGGCTTCAATCTGC
* *
40312983 TCCACTGTAACCTCAGGGAGATAAGATTTC
1 TCCACTGTAATCTCAGAGAGATAAGATTTC
40313013 ACCATTTTCG
Statistics
Matches: 124, Mismatches: 33, Indels: 7
0.76 0.20 0.04
Matches are distributed among these distances:
41 23 0.19
43 2 0.02
44 99 0.80
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.31
Consensus pattern (44 bp):
TCCACTGTAATCTCAGAGAGATAAGATTTCTGGCTTCAATCTGC
Found at i:40313107 original size:234 final size:233
Alignment explanation
Indices: 40312727--40313405 Score: 1133
Period size: 234 Copynumber: 2.9 Consensus size: 233
40312717 GCTTGGGAAG
* * *
40312727 TAAGATTTCTAGCTTCAATCTGCTCCATTGTAACCTTAGGGAGATAAGATTCACCATTTTCGATT
1 TAAGATTTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATTCACCATTTTCGATT
* *
40312792 AGGAACTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATACGATCTACTCTACT
66 AGGAATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACT
* *
40312857 GTAATTTCAGAGAGATAAGATCTTTTATTTTAATCCGCTCCACTATAATCTCAGGGAAATAGGAT
131 GTAATTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAAATAGGAT
40312922 TACTGGCTTCAATCTGCGCCACTGTAATCTCAGAGAGA
196 TACTGGCTTCAATCTGCGCCACTGTAATCTCAGAGAGA
*
40312960 TAAGATTTCTGGCTTCAATCTACTCCACTGTAACCTCAGGGAGATAAGATTTCACCATTTTCGAT
1 TAAGATTTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGA-TTCACCATTTTCGAT
* *
40313025 TAGAAATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGAGCTGATGCGATCTACTCTAC
65 TAGGAATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTAC
* *
40313090 TGTAATTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCTACTGTAACCTCAGGGAAATAGGA
130 TGTAATTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAAATAGGA
* * * * *
40313155 TTACTAGCTTCGATCTGCTCCATTGTAATCTCAGGGAGA
195 TTACTGGCTTCAATCTGCGCCACTGTAATCTCAGAGAGA
*
40313194 TAAGATTTCTGACTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATTCACCATTTTCGATT
1 TAAGATTTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATTCACCATTTTCGATT
*
40313259 AGGAATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCAATCTACTCTACT
66 AGGAATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACT
* *
40313324 GTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCATGGAAATAGGAT
131 GTAATTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAAATAGGAT
** *
40313389 TTGTGGCTTAAATCTGC
196 TACTGGCTTCAATCTGC
40313406 TTCCTTACTC
Statistics
Matches: 414, Mismatches: 31, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
233 196 0.47
234 218 0.53
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.33
Consensus pattern (233 bp):
TAAGATTTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATTCACCATTTTCGATT
AGGAATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACT
GTAATTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAAATAGGAT
TACTGGCTTCAATCTGCGCCACTGTAATCTCAGAGAGA
Found at i:40313215 original size:44 final size:43
Alignment explanation
Indices: 40313044--40313244 Score: 167
Period size: 44 Copynumber: 4.7 Consensus size: 43
40313034 TTCGGTCTAT
* * * *
40313044 TCCACTGTAATCTCAGGGAGATAAGA--GCTGA-TGCGATCTAC
1 TCCACTGTAATCTCAGGGAGATAAGATTTCT-ACTTCAATCTGC
* * * * * *
40313085 TCTACTGTAATTTCAGAGAGATAAGATCCTT-TATTTTAATCCGC
1 TCCACTGTAATCTCAGGGAGATAAGAT--TTCTACTTCAATCTGC
* * * * * *
40313129 TCTACTGTAACCTCAGGGAAATAGGATTACTAGCTTCGATCTGC
1 TCCACTGTAATCTCAGGGAGATAAGATTTCTA-CTTCAATCTGC
*
40313173 TCCATTGTAATCTCAGGGAGATAAGATTTCTGACTTCAATCTGC
1 TCCACTGTAATCTCAGGGAGATAAGATTTCT-ACTTCAATCTGC
*
40313217 TCCACTGTAACCTCAGGGAGATAAGATT
1 TCCACTGTAATCTCAGGGAGATAAGATT
40313245 CACCATTTTC
Statistics
Matches: 124, Mismatches: 28, Indels: 13
0.75 0.17 0.08
Matches are distributed among these distances:
41 23 0.19
42 1 0.01
43 3 0.02
44 96 0.77
45 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (43 bp):
TCCACTGTAATCTCAGGGAGATAAGATTTCTACTTCAATCTGC
Found at i:40314489 original size:21 final size:21
Alignment explanation
Indices: 40314464--40314505 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
40314454 TAGCCTCTCC
40314464 ATTTTCACTTTTTCAT-TTTTT
1 ATTTTCA-TTTTTCATCTTTTT
40314485 ATTTTCATTTTTCATCTTTTT
1 ATTTTCATTTTTCATCTTTTT
40314506 TTTACTCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (21 bp):
ATTTTCATTTTTCATCTTTTT
Found at i:40322082 original size:34 final size:34
Alignment explanation
Indices: 40321985--40322070 Score: 127
Period size: 34 Copynumber: 2.5 Consensus size: 34
40321975 TAAAAGTTAT
* *
40321985 ATGATTTACGTGGTTTATAAGTTACATGAAATAC
1 ATGATTTACATGGTTTATAAGTTACATGAAATAA
* *
40322019 ATGAATTACATGGTTTATAAGCTACATGAAATAA
1 ATGATTTACATGGTTTATAAGTTACATGAAATAA
*
40322053 ATGATTTACATGGATTAT
1 ATGATTTACATGGTTTAT
40322071 TTGTTATATG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.37
Consensus pattern (34 bp):
ATGATTTACATGGTTTATAAGTTACATGAAATAA
Found at i:40326463 original size:63 final size:58
Alignment explanation
Indices: 40326386--40326505 Score: 165
Period size: 57 Copynumber: 2.1 Consensus size: 58
40326376 CATGTCCTTT
* * *
40326386 TCATTT-TTCATTTTCATTTT-AGTTTTGGAGAAAACCATATTCATTTCCAAATGATT-
1 TCATTTCTCCATTTTCATTTTCA-TGTTGGAGAAAACCATAATCATTTCCAAATGATTC
* *
40326442 TCATTTCTCCATTTTCATTTTCATGTTGGAGAAGACCATAATCATTTCCAAATGTTTC
1 TCATTTCTCCATTTTCATTTTCATGTTGGAGAAAACCATAATCATTTCCAAATGATTC
40326500 TCATTT
1 TCATTT
40326506 ATCTGTTTTC
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
56 6 0.11
57 43 0.77
58 7 0.12
ACGTcount: A:0.27, C:0.17, G:0.09, T:0.47
Consensus pattern (58 bp):
TCATTTCTCCATTTTCATTTTCATGTTGGAGAAAACCATAATCATTTCCAAATGATTC
Found at i:40340208 original size:22 final size:23
Alignment explanation
Indices: 40340180--40340223 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
40340170 TCATTTTCAT
40340180 TTTTTTAAAA-TTTTAAAAAATA
1 TTTTTTAAAATTTTTAAAAAATA
40340202 TTTTTTAAAATTTTTAAAAAAT
1 TTTTTTAAAATTTTTAAAAAAT
40340224 TATAATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTTTTAAAATTTTTAAAAAATA
Found at i:40340215 original size:39 final size:40
Alignment explanation
Indices: 40340132--40340215 Score: 91
Period size: 39 Copynumber: 2.1 Consensus size: 40
40340122 TTGTAAAATC
* * * ***
40340132 ATTTTCTTATTTTTTAAAATTTTAAAGACTTTTTATTTTC
1 ATTTTCATATTTTTTAAAATTTTAAAAAATTTTTATTAAA
40340172 ATTTTCAT-TTTTTTAAAATTTTAAAAAATATTTT-TTAAA
1 ATTTTCATATTTTTTAAAATTTTAAAAAAT-TTTTATTAAA
40340211 ATTTT
1 ATTTT
40340216 TAAAAAATTA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
39 26 0.70
40 11 0.30
ACGTcount: A:0.33, C:0.05, G:0.01, T:0.61
Consensus pattern (40 bp):
ATTTTCATATTTTTTAAAATTTTAAAAAATTTTTATTAAA
Found at i:40345606 original size:21 final size:20
Alignment explanation
Indices: 40345566--40345608 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
40345556 ACAAGTATTT
*
40345566 TTTTCAATTTCAACATAATA
1 TTTTCAATCTCAACATAATA
40345586 TTTTCAAGTCTCATACA-AATA
1 TTTTCAA-TCTCA-ACATAATA
40345607 TT
1 TT
40345609 CAAAAATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 7 0.35
21 10 0.50
22 3 0.15
ACGTcount: A:0.37, C:0.16, G:0.02, T:0.44
Consensus pattern (20 bp):
TTTTCAATCTCAACATAATA
Found at i:40347739 original size:38 final size:38
Alignment explanation
Indices: 40347639--40347766 Score: 141
Period size: 38 Copynumber: 3.3 Consensus size: 38
40347629 CCTAAACTAG
* * *
40347639 GACATATTTAAAACAT-ATATTTAAGATGTCTTAAATTAT
1 GACATAATTAAAAC-TCATATTAAAGATGT-TCAAATTAT
* * *
40347678 GACATAATTAAAAACCCTTATTAAAGATGTTCAGATTAT
1 GACATAATT-AAAACTCATATTAAAGATGTTCAAATTAT
** *
40347717 GACATAATTAAAACTCATATTAATTATGTTCAAATTAA
1 GACATAATTAAAACTCATATTAAAGATGTTCAAATTAT
40347755 GACATAATTAAA
1 GACATAATTAAA
40347767 GACTTAAACT
Statistics
Matches: 75, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
38 35 0.47
39 24 0.32
40 16 0.21
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.36
Consensus pattern (38 bp):
GACATAATTAAAACTCATATTAAAGATGTTCAAATTAT
Found at i:40353115 original size:22 final size:21
Alignment explanation
Indices: 40353066--40353108 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
40353056 AACAAATACC
*
40353066 TTCATTGCAAAGGGTAGGAAT
1 TTCATTGCAAAAGGTAGGAAT
40353087 TTCATTGCAAAAGGTAGGAAT
1 TTCATTGCAAAAGGTAGGAAT
40353108 T
1 T
40353109 GATATTGGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.35, C:0.09, G:0.26, T:0.30
Consensus pattern (21 bp):
TTCATTGCAAAAGGTAGGAAT
Found at i:40354445 original size:39 final size:38
Alignment explanation
Indices: 40354364--40354446 Score: 103
Period size: 39 Copynumber: 2.1 Consensus size: 38
40354354 TAGTATGAAC
* *
40354364 TAAAGACATGTATTAAAGACGTCTAAACTAGGACATATT
1 TAAA-ACATATATTAAAGACGTCTAAACTAGGACATAAT
* * *
40354403 TAAAACATATATTTAAGATGTCCTAAACTATGACATAAT
1 TAAAACATATATTAAAGACGT-CTAAACTAGGACATAAT
40354442 TAAAA
1 TAAAA
40354447 ACCCTTATTA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
38 14 0.37
39 24 0.63
ACGTcount: A:0.47, C:0.12, G:0.11, T:0.30
Consensus pattern (38 bp):
TAAAACATATATTAAAGACGTCTAAACTAGGACATAAT
Found at i:40354461 original size:40 final size:38
Alignment explanation
Indices: 40354364--40354463 Score: 103
Period size: 40 Copynumber: 2.6 Consensus size: 38
40354354 TAGTATGAAC
* * *
40354364 TAAAGACATGTATTAAAGACGTCTAAACTAGGACATAT
1 TAAAAACATATATTAAAGATGTCTAAACTAGGACATAT
* * *
40354402 TTAAAACATATATTTAAGATGTCCTAAACTATGACATAAT
1 TAAAAACATATATTAAAGATGT-CTAAACTAGGACAT-AT
*
40354442 TAAAAACCCT-TATTAAAGATGT
1 TAAAAA-CATATATTAAAGATGT
40354464 TCAGGTTATG
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
38 17 0.34
39 13 0.26
40 18 0.36
41 2 0.04
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.31
Consensus pattern (38 bp):
TAAAAACATATATTAAAGATGTCTAAACTAGGACATAT
Found at i:40359470 original size:39 final size:39
Alignment explanation
Indices: 40359426--40359505 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
40359416 ATATAAAATA
40359426 CAAATTAATTAAATATTAAATACAAAACAGAATTTGGTT
1 CAAATTAATTAAATATTAAATACAAAACAGAATTTGGTT
40359465 CAAATTAATTAAATATTAAATACAAAACAGAATTTGGTT
1 CAAATTAATTAAATATTAAATACAAAACAGAATTTGGTT
40359504 CA
1 CA
40359506 GTTTCGTGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.51, C:0.09, G:0.07, T:0.33
Consensus pattern (39 bp):
CAAATTAATTAAATATTAAATACAAAACAGAATTTGGTT
Found at i:40359923 original size:21 final size:21
Alignment explanation
Indices: 40359899--40359941 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
40359889 ATGTATTTTG
40359899 GAATTAAAAAATATATTAAAT
1 GAATTAAAAAATATATTAAAT
40359920 GAATTAAAAAATATATTAAAT
1 GAATTAAAAAATATATTAAAT
40359941 G
1 G
40359942 TAAAAATATG
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:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (21 bp):
GAATTAAAAAATATATTAAAT
Found at i:40360389 original size:30 final size:30
Alignment explanation
Indices: 40360328--40360389 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
40360318 GGAGGGGAGG
* * **
40360328 GGAGTAAAAGTTTTGGGGGGAAAGTGGAAA
1 GGAGTAAAAGTTTTGAGGGAAAAGTAAAAA
40360358 GGAGTAAAAGTTTTGAGGGAAAAGTAAAAA
1 GGAGTAAAAGTTTTGAGGGAAAAGTAAAAA
40360388 GG
1 GG
40360390 TTTAGGAGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.42, C:0.00, G:0.39, T:0.19
Consensus pattern (30 bp):
GGAGTAAAAGTTTTGAGGGAAAAGTAAAAA
Found at i:40360529 original size:9 final size:9
Alignment explanation
Indices: 40360512--40360542 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
40360502 TCGAGTTGAT
40360512 TCGAATAAC
1 TCGAATAAC
*
40360521 TCGATTAAC
1 TCGAATAAC
40360530 TCGAATAAC
1 TCGAATAAC
40360539 TCGA
1 TCGA
40360543 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:40360880 original size:24 final size:25
Alignment explanation
Indices: 40360853--40360900 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
40360843 TAAAAAAAAT
40360853 TATAACATTTTTTA-AATAAATAAG
1 TATAACATTTTTTATAATAAATAAG
** *
40360877 TATATTATTTTTTATAATATATAA
1 TATAACATTTTTTATAATAAATAA
40360901 CATGGATATG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (25 bp):
TATAACATTTTTTATAATAAATAAG
Found at i:40360965 original size:23 final size:23
Alignment explanation
Indices: 40360939--40360990 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
40360929 ATTTTTTGTC
40360939 ATAACA-TTTTATATAAGTA-TATT
1 ATAACACTTTT-TATAA-TATTATT
* *
40360962 ATAATACTTTTTATAATATTTTT
1 ATAACACTTTTTATAATATTATT
40360985 ATAACA
1 ATAACA
40360991 AGCAAATTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
22 2 0.08
23 18 0.75
24 4 0.17
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.50
Consensus pattern (23 bp):
ATAACACTTTTTATAATATTATT
Found at i:40360983 original size:11 final size:12
Alignment explanation
Indices: 40360960--40360988 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
40360950 TATAAGTATA
40360960 TTATAATACTTT
1 TTATAATACTTT
40360972 TTATAATA-TTT
1 TTATAATACTTT
40360983 TTATAA
1 TTATAA
40360989 CAAGCAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 9 0.53
12 8 0.47
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (12 bp):
TTATAATACTTT
Found at i:40369571 original size:20 final size:20
Alignment explanation
Indices: 40369543--40369581 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
40369533 GCTACTCATA
40369543 TTTTCAAAA-ACTTATCAGAG
1 TTTTCAAAACACTTA-CAGAG
*
40369563 TTTTTAAAACACTTACAGA
1 TTTTCAAAACACTTACAGA
40369582 ATCGATGCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.41, C:0.15, G:0.08, T:0.36
Consensus pattern (20 bp):
TTTTCAAAACACTTACAGAG
Found at i:40372738 original size:21 final size:22
Alignment explanation
Indices: 40372713--40372753 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
40372703 CGATTCAAAG
*
40372713 AAAATAAA-TTATTAAAAATTA
1 AAAATAAAGATATTAAAAATTA
40372734 AAAATAAAGATATTAAAAAT
1 AAAATAAAGATATTAAAAAT
40372754 ATATAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.29
Consensus pattern (22 bp):
AAAATAAAGATATTAAAAATTA
Found at i:40379134 original size:17 final size:19
Alignment explanation
Indices: 40379105--40379153 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
40379095 TATTTACTTT
40379105 CCCTCAAAC-TTTTA-TT-C
1 CCCT-AAACTTTTTATTTCC
40379122 CCCTAAACTTTTTATTTTCC
1 CCCTAAACTTTTTA-TTTCC
40379142 CCCTAAACTTTT
1 CCCTAAACTTTT
40379154 ACTTCTCACC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
16 4 0.14
17 9 0.32
19 2 0.07
20 13 0.46
ACGTcount: A:0.22, C:0.33, G:0.00, T:0.45
Consensus pattern (19 bp):
CCCTAAACTTTTTATTTCC
Found at i:40379165 original size:20 final size:20
Alignment explanation
Indices: 40379122--40379165 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
40379112 ACTTTTATTC
* *
40379122 CCCTAAACTTTTTATTTTCC
1 CCCTAAACTTTTTATTCTCA
40379142 CCCTAAAC-TTTTACTTCTCA
1 CCCTAAACTTTTTA-TTCTCA
40379162 CCCT
1 CCCT
40379166 TTACTCACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.20, C:0.36, G:0.00, T:0.43
Consensus pattern (20 bp):
CCCTAAACTTTTTATTCTCA
Found at i:40380553 original size:11 final size:12
Alignment explanation
Indices: 40380530--40380558 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
40380520 TATAAATATA
40380530 TTATAATACTTT
1 TTATAATACTTT
40380542 TTATAATA-TTT
1 TTATAATACTTT
40380553 TTATAA
1 TTATAA
40380559 CACACATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 9 0.53
12 8 0.47
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (12 bp):
TTATAATACTTT
Found at i:40389242 original size:5 final size:6
Alignment explanation
Indices: 40389225--40389250 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
40389215 ATTTTTTAAA
40389225 TATTTT TATTTT TATTTT TATTTT TA
1 TATTTT TATTTT TATTTT TATTTT TA
40389251 ATAAATTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TATTTT
Found at i:40389521 original size:21 final size:21
Alignment explanation
Indices: 40389480--40389580 Score: 62
Period size: 21 Copynumber: 4.6 Consensus size: 21
40389470 GAATTTTGAA
40389480 ATTTTTGTTTATATTTGTAAAATC
1 ATTTTT-TTTA-ATTT-TAAAATC
40389504 ATTTTTTTTAATTTTAAAGA-C
1 ATTTTTTTTAATTTTAAA-ATC
* * ***
40389525 TTTTTATTTTTATTTTTATTTTC
1 -ATTT-TTTTTAATTTTAAAATC
*
40389548 A-TTTTTTTAATTTTAAAATT
1 ATTTTTTTTAATTTTAAAATC
**
40389568 ATAATTTTTAATT
1 ATTTTTTTTAATT
40389581 ATAACCTTTT
Statistics
Matches: 59, Mismatches: 13, Indels: 13
0.69 0.15 0.15
Matches are distributed among these distances:
20 13 0.22
21 16 0.27
22 8 0.14
23 16 0.27
24 6 0.10
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (21 bp):
ATTTTTTTTAATTTTAAAATC
Found at i:40389539 original size:44 final size:43
Alignment explanation
Indices: 40389481--40389564 Score: 105
Period size: 44 Copynumber: 1.9 Consensus size: 43
40389471 AATTTTGAAA
*
40389481 TTTTTGTTTATATTTGTAAAATCATTTTTTTTAATTTTAAAGAC
1 TTTTTATTTATATTTGTAAAATCA-TTTTTTTAATTTTAAAGAC
* * ***
40389525 TTTTTATTTTTATTTTTATTTTCATTTTTTTAATTTTAAA
1 TTTTTATTTATATTTGTAAAATCATTTTTTTAATTTTAAA
40389565 ATTATAATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
43 16 0.47
44 18 0.53
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.67
Consensus pattern (43 bp):
TTTTTATTTATATTTGTAAAATCATTTTTTTAATTTTAAAGAC
Found at i:40389565 original size:64 final size:57
Alignment explanation
Indices: 40389482--40389618 Score: 130
Period size: 64 Copynumber: 2.2 Consensus size: 57
40389472 ATTTTGAAAT
** * *
40389482 TTTTGTTTATATTTGTAAAATCATTTTTTTTAATTTTAAAGACTTTTTATTTTTATTTTTATTTT
1 TTTT-TTTA-ATTT-TAAAATCATAATTTTTAA--TTAAA-ACCTTTTA--TTTAATTTT-TTTT
40389547 C
57 C
* *
40389548 ATTTTTTTAATTTTAAAATTATAATTTTTAATTATAACCTTTTATTTAATTTTTTTTC
1 -TTTTTTTAATTTTAAAATCATAATTTTTAATTAAAACCTTTTATTTAATTTTTTTTC
40389606 TTTTTTTAATTTT
1 TTTTTTTAATTTT
40389619 TATATAGTTT
Statistics
Matches: 64, Mismatches: 6, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
57 13 0.20
58 5 0.08
59 8 0.12
61 7 0.11
62 4 0.06
64 15 0.23
65 4 0.06
66 4 0.06
67 4 0.06
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.67
Consensus pattern (57 bp):
TTTTTTTAATTTTAAAATCATAATTTTTAATTAAAACCTTTTATTTAATTTTTTTTC
Found at i:40393554 original size:28 final size:28
Alignment explanation
Indices: 40393512--40393578 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
40393502 CCCTCCATTC
*
40393512 TTCCTTTCTCCTTTACTCAAAAACTTTGA
1 TTCCTTGC-CCTTTACTCAAAAACTTTGA
*
40393541 TTCCTTGCCCTTTACTCAAAGACTTTGA
1 TTCCTTGCCCTTTACTCAAAAACTTTGA
40393569 TTCCTTGCCC
1 TTCCTTGCCC
40393579 ACGCCTGACG
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
28 29 0.81
29 7 0.19
ACGTcount: A:0.19, C:0.31, G:0.07, T:0.42
Consensus pattern (28 bp):
TTCCTTGCCCTTTACTCAAAAACTTTGA
Found at i:40398567 original size:31 final size:33
Alignment explanation
Indices: 40398491--40398565 Score: 95
Period size: 30 Copynumber: 2.4 Consensus size: 33
40398481 TTTTAAGTTA
*
40398491 AAAATATTAAAAATAATATTTTTTATACTTTTT
1 AAAATTTTAAAAATAATATTTTTTATACTTTTT
* *
40398524 -AATTTTTAAAAAT-AT-TTTTTTTTA-TTTTT
1 AAAATTTTAAAAATAATATTTTTTATACTTTTT
40398553 AAAATTTTAAAAA
1 AAAATTTTAAAAA
40398566 ATTAATTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
29 5 0.14
30 19 0.51
31 2 0.05
32 11 0.30
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (33 bp):
AAAATTTTAAAAATAATATTTTTTATACTTTTT
Found at i:40403136 original size:25 final size:24
Alignment explanation
Indices: 40403099--40403150 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
40403089 TTGAATATTA
* *
40403099 TTTAATACTTTTTCATTTATGTAAT
1 TTTAATACATTTTCATTT-TATAAT
* *
40403124 TTTAATTCATTTTTATTTTATAAT
1 TTTAATACATTTTCATTTTATAAT
40403148 TTT
1 TTT
40403151 TTATAACAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 8 0.35
25 15 0.65
ACGTcount: A:0.27, C:0.06, G:0.02, T:0.65
Consensus pattern (24 bp):
TTTAATACATTTTCATTTTATAAT
Found at i:40405008 original size:21 final size:21
Alignment explanation
Indices: 40404969--40405008 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
40404959 AAACCAAAAC
*
40404969 AACCACACCCTCCGTCGGAGT
1 AACCACACCCTCCGACGGAGT
40404990 AACCACAACCCT-CGACGGA
1 AACCAC-ACCCTCCGACGGA
40405009 AGCTGAACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.30, C:0.42, G:0.17, T:0.10
Consensus pattern (21 bp):
AACCACACCCTCCGACGGAGT
Found at i:40408447 original size:126 final size:125
Alignment explanation
Indices: 40408005--40408527 Score: 724
Period size: 125 Copynumber: 4.2 Consensus size: 125
40407995 TAAGGTCAAA
* *
40408005 CAGGAACTACTGTAGTAAACAAGCGTCCACGTGGAAGCTTTTTTCAATAATTTTGCTGACAGTGC
1 CAGGAACTACTGTAG-AAAAAAGCGTCCACGTGGGAGCTTTTTTCAATAATTTTGCTGACAGTGC
* * * * * *
40408070 ATCTTGTTTGAAGCGTATTTGACACTATTATTTTAGAACAGTCTTCCCAAAATTATTTTTT
65 ATCCTGCTTGAAGCGTTTTTGACACTATTTTTTTAGAACCGTCTTCTCAAAATTATTTTTT
* * * * *
40408131 CAGAAACTACTGTAGAAAAAAGTGTCCACGTGGGAGCCTTTTTCAATAATTTTACTGACAGTGAA
1 CAGGAACTACTGTAGAAAAAAGCGTCCACGTGGGAGCTTTTTTCAATAATTTTGCTGACAGTGCA
* * *
40408196 TCTTGTTTGAAGCGTTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTT
66 TCCTGCTTGAAGCGTTTTTGACACTATTTTTTTAGAACCGTCTTCTCAAAATTATTTTTT
* *
40408256 -AGAAACTACTGTAGAAAAATAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGC
1 CAGGAACTACTGTAGAAAAA-AGCGTCCACGTGGGAGCTTTTTTCAATAATTTTGCTGACAGTGC
* *
40408320 ATCCTGCTTGAAGCGTTTTTGACATTATTTTTTTAAAACCGTCTTCTCAAAATTATTTTTT
65 ATCCTGCTTGAAGCGTTTTTGACACTATTTTTTTAGAACCGTCTTCTCAAAATTATTTTTT
* * * * *
40408381 CAGGAACTGCTGTAGAAAAAGAGCATCCACGTGGGATCTTTTTTCAGTAATTTTGCTGACAATGC
1 CAGGAACTACTGTAGAAAAA-AGCGTCCACGTGGGAGCTTTTTTCAATAATTTTGCTGACAGTGC
* * * *
40408446 ATCCTGCTTGAAGCGTTTTTGAAACTATTTTTTTAGAACCATCATCTTAAAATTATTTTTT
65 ATCCTGCTTGAAGCGTTTTTGACACTATTTTTTTAGAACCGTCTTCTCAAAATTATTTTTT
* * *
40408507 TAGGAACTACTGGAAAAAAAA
1 CAGGAACTACTGTAGAAAAAA
40408528 TAAAATCCTT
Statistics
Matches: 357, Mismatches: 38, Indels: 5
0.89 0.09 0.01
Matches are distributed among these distances:
124 19 0.05
125 195 0.55
126 143 0.40
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (125 bp):
CAGGAACTACTGTAGAAAAAAGCGTCCACGTGGGAGCTTTTTTCAATAATTTTGCTGACAGTGCA
TCCTGCTTGAAGCGTTTTTGACACTATTTTTTTAGAACCGTCTTCTCAAAATTATTTTTT
Found at i:40408623 original size:34 final size:33
Alignment explanation
Indices: 40408581--40408683 Score: 118
Period size: 34 Copynumber: 3.1 Consensus size: 33
40408571 AAACACAAAA
40408581 TTATTTAAAAAACTAAACCCTAATTTAATTAATT
1 TTATTTAAAAAACTAAACCCTAATTTAATTAA-T
* * * *
40408615 TTTTTTAAAAATCTAAACCCTAATTTTATTTAT
1 TTATTTAAAAAACTAAACCCTAATTTAATTAAT
** *
40408648 TTATTTAAAACCCCTAAAACCTAATTTAATT-AT
1 TTATTTAAAA-AACTAAACCCTAATTTAATTAAT
40408681 TTA
1 TTA
40408684 AAAAAACTCT
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
33 15 0.25
34 44 0.75
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.45
Consensus pattern (33 bp):
TTATTTAAAAAACTAAACCCTAATTTAATTAAT
Found at i:40409972 original size:17 final size:17
Alignment explanation
Indices: 40409950--40409999 Score: 91
Period size: 17 Copynumber: 2.9 Consensus size: 17
40409940 ATAGAAAGTC
40409950 AAAGATATGGGTATCAG
1 AAAGATATGGGTATCAG
*
40409967 AAAGATATAGGTATCAG
1 AAAGATATGGGTATCAG
40409984 AAAGATATGGGTATCA
1 AAAGATATGGGTATCA
40410000 AAACCTGAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.44, C:0.06, G:0.26, T:0.24
Consensus pattern (17 bp):
AAAGATATGGGTATCAG
Found at i:40413556 original size:17 final size:17
Alignment explanation
Indices: 40413534--40413592 Score: 95
Period size: 17 Copynumber: 3.6 Consensus size: 17
40413524 TATAGAAAGT
40413534 GAAAGATATGGGTATCA
1 GAAAGATATGGGTATCA
*
40413551 GAAAGATATAGGTATCA
1 GAAAGATATGGGTATCA
40413568 GAAAGATATGGGTATCA
1 GAAAGATATGGGTATCA
40413585 -AAA-ATATG
1 GAAAGATATG
40413593 AGATTTAAGG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
15 5 0.12
16 3 0.08
17 32 0.80
ACGTcount: A:0.46, C:0.05, G:0.25, T:0.24
Consensus pattern (17 bp):
GAAAGATATGGGTATCA
Found at i:40418802 original size:21 final size:21
Alignment explanation
Indices: 40418752--40418796 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
40418742 ATTGTTCAAC
**
40418752 TAAAAAAATTTTATCTATAAA
1 TAAAAAAAAGTTATCTATAAA
*
40418773 TAAAAAAAAGTTATTTATAAA
1 TAAAAAAAAGTTATCTATAAA
40418794 TAA
1 TAA
40418797 GGAAAAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (21 bp):
TAAAAAAAAGTTATCTATAAA
Found at i:40419247 original size:18 final size:17
Alignment explanation
Indices: 40419224--40419285 Score: 63
Period size: 18 Copynumber: 3.6 Consensus size: 17
40419214 AGGGAAAAGC
40419224 AAAAGAAAATGAAAAGAA
1 AAAAGAAAAT-AAAAGAA
* *
40419242 AAAAGAAAAAAAAAGTTA
1 AAAAGAAAATAAAAG-AA
* *
40419260 AAAAGCACATAAAAGAA
1 AAAAGAAAATAAAAGAA
40419277 AAAA-AAAAT
1 AAAAGAAAAT
40419286 TAAATTGCTC
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
16 3 0.09
17 10 0.29
18 22 0.63
ACGTcount: A:0.77, C:0.03, G:0.11, T:0.08
Consensus pattern (17 bp):
AAAAGAAAATAAAAGAA
Found at i:40419299 original size:26 final size:27
Alignment explanation
Indices: 40419241--40419308 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 27
40419231 AATGAAAAGA
*
40419241 AAAAAGAAAAAAAAAGTTAAAAAGCAC
1 AAAAAGAAAAAAAAAATTAAAAAGCAC
** *
40419268 ATAAAAGAAAAAAAAAATTAAATTGCTC
1 A-AAAAGAAAAAAAAAATTAAAAAGCAC
40419296 -AAAAGAAAAAAAA
1 AAAAAGAAAAAAAA
40419309 TATGGAGATC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 13 0.36
27 1 0.03
28 22 0.61
ACGTcount: A:0.74, C:0.06, G:0.09, T:0.12
Consensus pattern (27 bp):
AAAAAGAAAAAAAAAATTAAAAAGCAC
Found at i:40422035 original size:19 final size:17
Alignment explanation
Indices: 40422013--40422061 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
40422003 TTTCGCCTTT
40422013 TCTTTCTCTTTTTTTATC
1 TCTTTCTCTTTTTTT-TC
40422031 GTCTTTC-C-TTTTTTTC
1 -TCTTTCTCTTTTTTTTC
*
40422047 TCTTCCTCTTTTTTT
1 TCTTTCTCTTTTTTT
40422062 CTTTTGTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 5 0.19
16 3 0.11
17 12 0.44
18 1 0.04
19 6 0.22
ACGTcount: A:0.02, C:0.24, G:0.02, T:0.71
Consensus pattern (17 bp):
TCTTTCTCTTTTTTTTC
Found at i:40426485 original size:20 final size:20
Alignment explanation
Indices: 40426424--40426487 Score: 83
Period size: 20 Copynumber: 3.2 Consensus size: 20
40426414 CCAAGTCAAG
*
40426424 GTATCGATACTTTGCACAAA
1 GTATCTATACTTTGCACAAA
* *
40426444 ATATCTATACTTTGCACCAA
1 GTATCTATACTTTGCACAAA
**
40426464 GTATCTATACTTTTTACAAA
1 GTATCTATACTTTGCACAAA
40426484 GTAT
1 GTAT
40426488 ACTTTCACAA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.34, C:0.19, G:0.09, T:0.38
Consensus pattern (20 bp):
GTATCTATACTTTGCACAAA
Found at i:40426499 original size:15 final size:16
Alignment explanation
Indices: 40426469--40426502 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
40426459 ACCAAGTATC
*
40426469 TATACTTTTTACAAAG
1 TATACTTTTCACAAAG
40426485 TATAC-TTTCACAAAG
1 TATACTTTTCACAAAG
40426500 TAT
1 TAT
40426503 CGATACCTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.41
Consensus pattern (16 bp):
TATACTTTTCACAAAG
Found at i:40435265 original size:30 final size:30
Alignment explanation
Indices: 40435229--40435296 Score: 127
Period size: 30 Copynumber: 2.3 Consensus size: 30
40435219 CATTTAGAGA
40435229 GAGGATTGGGAGCTTCTTGGTGTAAGATCG
1 GAGGATTGGGAGCTTCTTGGTGTAAGATCG
40435259 GAGGATTGGGAGCTTCTTGGTGTAAGATCG
1 GAGGATTGGGAGCTTCTTGGTGTAAGATCG
*
40435289 GAGAATTG
1 GAGGATTG
40435297 AGTTGTCAGG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.22, C:0.09, G:0.40, T:0.29
Consensus pattern (30 bp):
GAGGATTGGGAGCTTCTTGGTGTAAGATCG
Found at i:40453515 original size:135 final size:135
Alignment explanation
Indices: 40453271--40453540 Score: 504
Period size: 135 Copynumber: 2.0 Consensus size: 135
40453261 CAGAAGGAAA
40453271 TACATCTTCAAAATCCTACAAAAGATCAACAAAACAACTAGGCAAATGTGTATTAGGGTTAGTCA
1 TACATCTTCAAAATCCTACAAAAGATCAACAAAACAACTAGGCAAATGTGTATTAGGGTTAGTCA
* *
40453336 AAACAAAGTTTTCCCTAAACCTAATAATTACAAATGTTTGTTTTGTACAAAGAGCAAATTTGATA
66 AAACAAAGTTTTCCATAAACCTAATAATTACAAATGTTTATTTTGTACAAAGAGCAAATTTGATA
40453401 TCTCG
131 TCTCG
40453406 TACATCTTCAAAATCCTACAAAAGATCAACAAAACAACTAGGCAAATGTGTATTAGGGTTAGTCA
1 TACATCTTCAAAATCCTACAAAAGATCAACAAAACAACTAGGCAAATGTGTATTAGGGTTAGTCA
* *
40453471 AGACAAAGTTTTCCATAAACCTAATAATTAGAAATGTTTATTTTGTACAAAGAGCAAATTTGATA
66 AAACAAAGTTTTCCATAAACCTAATAATTACAAATGTTTATTTTGTACAAAGAGCAAATTTGATA
40453536 TCTCG
131 TCTCG
40453541 AAACCTAGCG
Statistics
Matches: 131, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
135 131 1.00
ACGTcount: A:0.41, C:0.16, G:0.13, T:0.30
Consensus pattern (135 bp):
TACATCTTCAAAATCCTACAAAAGATCAACAAAACAACTAGGCAAATGTGTATTAGGGTTAGTCA
AAACAAAGTTTTCCATAAACCTAATAATTACAAATGTTTATTTTGTACAAAGAGCAAATTTGATA
TCTCG
Found at i:40457149 original size:67 final size:67
Alignment explanation
Indices: 40457041--40457168 Score: 229
Period size: 67 Copynumber: 1.9 Consensus size: 67
40457031 CAATTCAGAA
*
40457041 AGCACACTCCCGCAAACCTCATTTCTTACAGTGGGATTACTAGTCCAGGCTAAATCCCCTGCAAC
1 AGCACACTCCCGCAAACCTCATTTCTTACAGCGGGATTACTAGTCCAGGCTAAATCCCCTGCAAC
40457106 AG
66 AG
* *
40457108 AGCACACTCCCGCGAACCTCATTTCTTACAGCGGGATTACTAGTTCAGGCTAAATCCCCTG
1 AGCACACTCCCGCAAACCTCATTTCTTACAGCGGGATTACTAGTCCAGGCTAAATCCCCTG
40457169 TAATATAAAC
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 58 1.00
ACGTcount: A:0.27, C:0.33, G:0.17, T:0.23
Consensus pattern (67 bp):
AGCACACTCCCGCAAACCTCATTTCTTACAGCGGGATTACTAGTCCAGGCTAAATCCCCTGCAAC
AG
Found at i:40457364 original size:57 final size:60
Alignment explanation
Indices: 40457290--40457437 Score: 203
Period size: 57 Copynumber: 2.5 Consensus size: 60
40457280 ACCCTAATTT
* * * *
40457290 GGATTACCCGTCCGGGCTAGATCTTTTTCATACATATTCTTTGGGAGGGCTATATC-A-A
1 GGATCACCCGTCCGGGCTAGATCTTTTTCACACATATTCTTCGAGAGGGCTATATCGATA
*
40457348 -GATCACCCGTCCGGGCTAGATCTTTTTCACACTTATTCTTCGAGAGGGCTATATCAGGATA
1 GGATCACCCGTCCGGGCTAGATCTTTTTCACACATATTCTTCGAGAGGGCTATATC--GATA
40457409 GGATCACCCGTCCGGGCTAGATCCTTTTT
1 GGATCACCCGTCCGGGCTAGAT-CTTTTT
40457438 ACCGTCAATT
Statistics
Matches: 79, Mismatches: 5, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
57 50 0.63
60 1 0.01
61 1 0.01
62 21 0.27
63 6 0.08
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.32
Consensus pattern (60 bp):
GGATCACCCGTCCGGGCTAGATCTTTTTCACACATATTCTTCGAGAGGGCTATATCGATA
Found at i:40458149 original size:9 final size:9
Alignment explanation
Indices: 40458132--40458168 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
40458122 TGAGTTTTCG
40458132 AATTCGAAT
1 AATTCGAAT
*
40458141 AACTCGAAT
1 AATTCGAAT
40458150 AATTCGAAT
1 AATTCGAAT
40458159 AATTCGAAT
1 AATTCGAAT
40458168 A
1 A
40458169 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:40464303 original size:20 final size:18
Alignment explanation
Indices: 40464269--40464310 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 18
40464259 AAACATTATA
*
40464269 AATTAATTTTAATTAATT
1 AATTAATTTTAATTAAAT
40464287 AATTAACTTTCTAATTAAAT
1 AATTAA-TTT-TAATTAAAT
40464307 AATT
1 AATT
40464311 TTCTCAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.29
19 3 0.14
20 12 0.57
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (18 bp):
AATTAATTTTAATTAAAT
Done.