Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold153
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: 3137677
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 499 characters in sequence are not A, C, G, or T
File 9 of 24
Found at i:1216168 original size:15 final size:14
Alignment explanation
Indices: 1216148--1216177 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
1216138 TTATTTTTTA
1216148 AAAAAAATTATAATT
1 AAAAAAATTA-AATT
1216163 AAAAAAATTAAATT
1 AAAAAAATTAAATT
1216177 A
1 A
1216178 TATTTATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AAAAAAATTAAATT
Found at i:1216400 original size:30 final size:30
Alignment explanation
Indices: 1216357--1216421 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
1216347 ATTTTTAACT
*
1216357 TTTACCTTCTACTCAAATAAGTATTTAATC
1 TTTAACTTCTACTCAAATAAGTATTTAATC
* * *
1216387 TTTAACTTGTACTCAAATAAGTTTTTAATT
1 TTTAACTTCTACTCAAATAAGTATTTAATC
1216417 TTTAA
1 TTTAA
1216422 TTTATATTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.34, C:0.14, G:0.05, T:0.48
Consensus pattern (30 bp):
TTTAACTTCTACTCAAATAAGTATTTAATC
Found at i:1216435 original size:30 final size:30
Alignment explanation
Indices: 1216357--1216436 Score: 88
Period size: 30 Copynumber: 2.7 Consensus size: 30
1216347 ATTTTTAACT
* *
1216357 TTTACCTTCTACTCAAATAAGTATTTAATC
1 TTTAACTTATACTCAAATAAGTATTTAATC
* * *
1216387 TTTAACTTGTACTCAAATAAGTTTTTAATT
1 TTTAACTTATACTCAAATAAGTATTTAATC
* * *
1216417 TTTAATTTATATTTAAATAA
1 TTTAACTTATACTCAAATAA
1216437 ACTTTTAACA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.36, C:0.11, G:0.04, T:0.49
Consensus pattern (30 bp):
TTTAACTTATACTCAAATAAGTATTTAATC
Found at i:1216856 original size:2 final size:2
Alignment explanation
Indices: 1216849--1216883 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
1216839 TATAACACGC
*
1216849 TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1216884 GTGGATGGCC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1219008 original size:32 final size:33
Alignment explanation
Indices: 1218972--1219038 Score: 84
Period size: 31 Copynumber: 2.1 Consensus size: 33
1218962 TTTAATTAAA
*
1218972 AATATTAATATAAAATAAT-TTATA-AAATTTTT
1 AATATT-ATATAAAATAATGATATATAAATTTTT
* *
1219004 AATATTATTTTAAATAATGATATATAAATTTTT
1 AATATTATATAAAATAATGATATATAAATTTTT
1219037 AA
1 AA
1219039 ATTGAGCCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
31 10 0.33
32 10 0.33
33 10 0.33
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (33 bp):
AATATTATATAAAATAATGATATATAAATTTTT
Found at i:1220410 original size:34 final size:34
Alignment explanation
Indices: 1220364--1220548 Score: 257
Period size: 34 Copynumber: 5.5 Consensus size: 34
1220354 GTAAAAACCA
*
1220364 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
1220398 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
1220432 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
1220466 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
1220500 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
1220533 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
1220549 TCTCCCACTT
Statistics
Matches: 135, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
33 18 0.13
34 113 0.84
35 4 0.03
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:1224641 original size:19 final size:19
Alignment explanation
Indices: 1224614--1224676 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
1224604 TCACGTGTAC
* *
1224614 AGTAACCGTATACTTGAAT
1 AGTACCCGTATACGTGAAT
1224633 AGTACCCGTATACGTGAAT
1 AGTACCCGTATACGTGAAT
**
1224652 AGTACCTATATACGTGAAT
1 AGTACCCGTATACGTGAAT
1224671 AGTACC
1 AGTACC
1224677 TCGACAACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (19 bp):
AGTACCCGTATACGTGAAT
Found at i:1225027 original size:34 final size:34
Alignment explanation
Indices: 1224981--1225163 Score: 253
Period size: 34 Copynumber: 5.4 Consensus size: 34
1224971 GTAAAAACCA
*
1224981 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
1225015 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
1225049 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
1225083 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
1225117 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
1225150 CCATTTAATCAACA
1 CCATTTAATCAACA
1225164 CCACCTAATT
Statistics
Matches: 133, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
33 16 0.12
34 113 0.85
35 4 0.03
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:1227769 original size:24 final size:25
Alignment explanation
Indices: 1227728--1227784 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
1227718 AAATTTTAAT
* * *
1227728 AATATTTATTATAGTTTTATAATTA
1 AATATTAAATATAATTTTATAATTA
*
1227753 AA-ATTAAATATAATTTTATTATTA
1 AATATTAAATATAATTTTATAATTA
1227777 AATATTAA
1 AATATTAA
1227785 TTTGAATTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 20 0.74
25 7 0.26
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (25 bp):
AATATTAAATATAATTTTATAATTA
Found at i:1228003 original size:6 final size:6
Alignment explanation
Indices: 1227990--1228119 Score: 136
Period size: 6 Copynumber: 21.7 Consensus size: 6
1227980 GTGGTATTGG
* * * **
1227990 ATATAT ACATAT ACATACT -TATAT ATATAT ATATAT ATAGAT ATATGC
1 ATATAT ATATAT ATATA-T ATATAT ATATAT ATATAT ATATAT ATATAT
*
1228038 ATATAT ATATAT ATATAT ATATAT ATATAT GTATAT ATATAT ATATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
* * * * * *
1228086 ATAGAT AGATAG ATAGAT AAATAT ATGTAT ATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATAT
1228120 GTTATTAAGG
Statistics
Matches: 100, Mismatches: 22, Indels: 4
0.79 0.17 0.03
Matches are distributed among these distances:
5 1 0.01
6 98 0.98
7 1 0.01
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.43
Consensus pattern (6 bp):
ATATAT
Found at i:1228016 original size:4 final size:4
Alignment explanation
Indices: 1227990--1228119 Score: 136
Period size: 4 Copynumber: 32.5 Consensus size: 4
1227980 GTGGTATTGG
* * * **
1227990 ATAT ATAC ATAT ACAT ACT-T ATAT ATAT ATAT ATAT ATAG ATAT ATGC
1 ATAT ATAT ATAT ATAT A-TAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
*
1228038 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATGT ATAT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * * * *
1228086 ATAG ATAG ATAG ATAG ATAA ATAT ATGT ATAT AT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT AT
1228120 GTTATTAAGG
Statistics
Matches: 107, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
3 1 0.01
4 106 0.99
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.43
Consensus pattern (4 bp):
ATAT
Found at i:1229255 original size:20 final size:22
Alignment explanation
Indices: 1229208--1229256 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
1229198 TTACAAAATT
* *
1229208 TAATTTAATCTAATTAAAATTA
1 TAATTTAATCTAATAAAAATAA
*
1229230 TTATTTAA-C-AATAAAAATAA
1 TAATTTAATCTAATAAAAATAA
1229250 TAATTTA
1 TAATTTA
1229257 TTTAAATTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 15 0.65
21 1 0.04
22 7 0.30
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (22 bp):
TAATTTAATCTAATAAAAATAA
Found at i:1229845 original size:37 final size:38
Alignment explanation
Indices: 1229738--1229874 Score: 177
Period size: 38 Copynumber: 3.6 Consensus size: 38
1229728 TGGTTAATGG
* * *
1229738 TTAGAGAATTCAATTTGAAATTGACTAACGGTTGACAA
1 TTAGAGAATTCAATTTGGAATTGGCTAACGGCTGACAA
* * * **
1229776 TTAGAAAATTCAATTTGGAATTGGTTAGCGGCTGACGG
1 TTAGAGAATTCAATTTGGAATTGGCTAACGGCTGACAA
*
1229814 TTAGATAATTCAATTT-GAATTGGCTAACGGCTGACAA
1 TTAGAGAATTCAATTTGGAATTGGCTAACGGCTGACAA
*
1229851 CTAGAGAATTCAATTTGGAATTGG
1 TTAGAGAATTCAATTTGGAATTGG
1229875 ATAGTGGCTG
Statistics
Matches: 83, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
37 31 0.37
38 52 0.63
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (38 bp):
TTAGAGAATTCAATTTGGAATTGGCTAACGGCTGACAA
Found at i:1229861 original size:75 final size:76
Alignment explanation
Indices: 1229736--1229884 Score: 228
Period size: 75 Copynumber: 2.0 Consensus size: 76
1229726 ATTGGTTAAT
* * *
1229736 GGTTAGAGAATTCAATTTGAAATTGACTAACGGTTGACAATTAGAAAATTCAATTTGGAATTGGT
1 GGTTAGAGAATTCAATTTGAAATTGACTAACGGCTGACAACTAGAAAATTCAATTTGGAATTGGA
1229801 TAGCGGCTGAC
66 TAGCGGCTGAC
* * *
1229812 GGTTAGATAATTCAATTTG-AATTGGCTAACGGCTGACAACTAGAGAATTCAATTTGGAATTGGA
1 GGTTAGAGAATTCAATTTGAAATTGACTAACGGCTGACAACTAGAAAATTCAATTTGGAATTGGA
*
1229876 TAGTGGCTG
66 TAGCGGCTG
1229885 GAGGCTAGAA
Statistics
Matches: 66, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
75 48 0.73
76 18 0.27
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.32
Consensus pattern (76 bp):
GGTTAGAGAATTCAATTTGAAATTGACTAACGGCTGACAACTAGAAAATTCAATTTGGAATTGGA
TAGCGGCTGAC
Found at i:1229893 original size:38 final size:38
Alignment explanation
Indices: 1229777--1229898 Score: 140
Period size: 38 Copynumber: 3.2 Consensus size: 38
1229767 GGTTGACAAT
* *
1229777 TAGAAAATTCAATTTGGAATTGGTTAGCGGCTGACGGT
1 TAGAAAATTCAATTTGGAATTGGATAGCGGCTGACGGC
* * * **
1229815 TAGATAATTCAATTT-GAATTGGCTAACGGCTGACAAC
1 TAGAAAATTCAATTTGGAATTGGATAGCGGCTGACGGC
* *
1229852 TAGAGAATTCAATTTGGAATTGGATAGTGGCTGGA-GGC
1 TAGAAAATTCAATTTGGAATTGGATAGCGGCT-GACGGC
1229890 TAGAAAATT
1 TAGAAAATT
1229899 TAATAGAATT
Statistics
Matches: 69, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
37 31 0.45
38 36 0.52
39 2 0.03
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (38 bp):
TAGAAAATTCAATTTGGAATTGGATAGCGGCTGACGGC
Found at i:1238633 original size:20 final size:20
Alignment explanation
Indices: 1238608--1238646 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1238598 CTACTACCAG
1238608 TTTCATGTATCAATACAATT
1 TTTCATGTATCAATACAATT
*
1238628 TTTCATGTATCGATACAAT
1 TTTCATGTATCAATACAAT
1238647 GTATCGATAC
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:0.33, C:0.15, G:0.08, T:0.44
Consensus pattern (20 bp):
TTTCATGTATCAATACAATT
Found at i:1238650 original size:13 final size:13
Alignment explanation
Indices: 1238632--1238658 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1238622 ACAATTTTTC
1238632 ATGTATCGATACA
1 ATGTATCGATACA
1238645 ATGTATCGATACA
1 ATGTATCGATACA
1238658 A
1 A
1238659 AGCATAATGT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1239292 original size:22 final size:23
Alignment explanation
Indices: 1239251--1239293 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1239241 AGATAAACAT
*
1239251 ATTTCTCCCCCCTTTTTCAAAGC
1 ATTTCTCCCCCCTTTGTCAAAGC
*
1239274 ATTTCT-CCCTCTTTGTCAAA
1 ATTTCTCCCCCCTTTGTCAAA
1239294 TCTTAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.19, C:0.35, G:0.05, T:0.42
Consensus pattern (23 bp):
ATTTCTCCCCCCTTTGTCAAAGC
Found at i:1241310 original size:20 final size:20
Alignment explanation
Indices: 1241261--1241310 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
1241251 TTTTCACAAT
* *
1241261 TTGTATCGAGACATTGTTCA
1 TTGTATCGATACATTATTCA
1241281 TTGTATCGATACATTATTCA
1 TTGTATCGATACATTATTCA
1241301 TTGTATCGAT
1 TTGTATCGAT
1241311 CTATTGTATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.26, C:0.14, G:0.16, T:0.44
Consensus pattern (20 bp):
TTGTATCGATACATTATTCA
Found at i:1243735 original size:51 final size:52
Alignment explanation
Indices: 1243675--1243792 Score: 186
Period size: 51 Copynumber: 2.3 Consensus size: 52
1243665 TTATTTTTGA
*
1243675 GGGGATACTCCAACCCT-GATTTTATTTCTAAAATACCAATTTTCCACAATT
1 GGGGATACTCCAACCCTCGATTTTATTTCCAAAATACCAATTTTCCACAATT
* *
1243726 GGGGATACTCCAA-CTTCGATTTTATTTCCAAAATACCAATTTTTCACAATT
1 GGGGATACTCCAACCCTCGATTTTATTTCCAAAATACCAATTTTCCACAATT
*
1243777 AGGGATACTCCAACCC
1 GGGGATACTCCAACCC
1243793 CGTTATTTCA
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
50 2 0.03
51 57 0.95
52 1 0.02
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.33
Consensus pattern (52 bp):
GGGGATACTCCAACCCTCGATTTTATTTCCAAAATACCAATTTTCCACAATT
Found at i:1243810 original size:28 final size:28
Alignment explanation
Indices: 1243778--1243847 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
1243768 TTCACAATTA
* *
1243778 GGGATACTCCAACCCCGTTATTTC-ATTG
1 GGGATACTCCAACCCCATTATTTCTA-AG
1243806 GGGATACTCCAACCCCATTATTTCTAAG
1 GGGATACTCCAACCCCATTATTTCTAAG
*
1243834 GGGATACTTCAACC
1 GGGATACTCCAACC
1243848 TCGGCCTTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
28 37 0.97
29 1 0.03
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.29
Consensus pattern (28 bp):
GGGATACTCCAACCCCATTATTTCTAAG
Found at i:1243888 original size:79 final size:78
Alignment explanation
Indices: 1243805--1244059 Score: 268
Period size: 79 Copynumber: 3.3 Consensus size: 78
1243795 TTATTTCATT
* * **
1243805 GGGGATACTCCAACCCCATTA-TTTCTAAGGGGATACTTCAACCTCGGCCTTATTTCTAAATCAT
1 GGGGATACTCCAACCCCATTATTTTC-GAGGGGATACTCCAACC-CGGATTTATTTCTAAATCAT
*
1243869 CGATTTTTCATAATC
64 CAATTTTTCATAATC
* * *
1243884 GGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTCATTTTCAAAAT-AT
1 GGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCGGATTT-A-TTTCTAAATCAT
*
1243948 CTATTTTT-ATAATC
64 CAATTTTTCATAATC
* * ** * * *
1243962 AGAGATACTCCAACCCTGTTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCTGGAA-CAC
1 GGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAA-CCCGGATTTATTTCT-AAATCAT
*
1244026 CAATTTTCCATAATC
64 CAATTTTTCATAATC
1244041 GGGGATACTCC-ACCCCATT
1 GGGGATACTCCAACCCCATT
1244060 GTTATCTCCA
Statistics
Matches: 147, Mismatches: 22, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
77 4 0.03
78 64 0.44
79 67 0.46
80 12 0.08
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (78 bp):
GGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCGGATTTATTTCTAAATCATCA
ATTTTTCATAATC
Found at i:1244032 original size:78 final size:77
Alignment explanation
Indices: 1243805--1244056 Score: 274
Period size: 78 Copynumber: 3.2 Consensus size: 77
1243795 TTATTTCATT
* * * * **
1243805 GGGGATACTCCAACCCCATTA-TTTCTAAGGGGATACTTCAACCTCGGCCTTATTTCTAAATCAT
1 GGGGATACTCCAACCCCGTTATTTTC-GAGGGGATACTCCAACCCCGGTTTTATTTCTAAA-CAT
*
1243869 CGATTTTTCATAATC
64 CAATTTTT-ATAATC
* * * *
1243884 GGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTCATTTTCAAAATATC
1 GGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTTTTA-TTTCTAAACATC
*
1243949 TATTTTTATAATC
65 AATTTTTATAATC
* * * * *
1243962 AGAGATACTCCAACCCTGTTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCTGGAACACC
1 GGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCT-AAACATC
*
1244027 AATTTTCCATAATC
65 AATTTT-TATAATC
1244041 GGGGATACTCC-ACCCC
1 GGGGATACTCCAACCCC
1244057 ATTGTTATCT
Statistics
Matches: 144, Mismatches: 25, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
77 4 0.03
78 66 0.46
79 63 0.44
80 11 0.08
ACGTcount: A:0.26, C:0.27, G:0.15, T:0.32
Consensus pattern (77 bp):
GGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAACATCA
ATTTTTATAATC
Found at i:1245214 original size:13 final size:13
Alignment explanation
Indices: 1245196--1245222 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1245186 ATAGTAACCC
1245196 ATGTATCGATACA
1 ATGTATCGATACA
1245209 ATGTATCGATACA
1 ATGTATCGATACA
1245222 A
1 A
1245223 GGAATGTTGT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1251392 original size:33 final size:33
Alignment explanation
Indices: 1251355--1251423 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
1251345 CTGTTACAAG
1251355 CAATGTAACGATACAAT-TCATCATGTATCGATA
1 CAATGTAACGATACAATGTCAT-ATGTATCGATA
* *
1251388 CAATGTATCGATACAATGTCCTATGTATCGATA
1 CAATGTAACGATACAATGTCATATGTATCGATA
1251421 CAA
1 CAA
1251424 ACAGTGGTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 30 0.91
34 3 0.09
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (33 bp):
CAATGTAACGATACAATGTCATATGTATCGATA
Found at i:1251395 original size:13 final size:13
Alignment explanation
Indices: 1251377--1251406 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1251367 ACAATTCATC
1251377 ATGTATCGATACA
1 ATGTATCGATACA
1251390 ATGTATCGATACA
1 ATGTATCGATACA
1251403 ATGT
1 ATGT
1251407 CCTATGTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1251496 original size:19 final size:20
Alignment explanation
Indices: 1251452--1251506 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
1251442 CTTCAAGTTT
* **
1251452 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATAGAA
1251472 CATGTATCGATACAA-AGAA
1 CATGTATCGATACAATAGAA
1251491 CATGTATCGATACAAT
1 CATGTATCGATACAAT
1251507 GTATCGAGAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (20 bp):
CATGTATCGATACAATAGAA
Found at i:1251519 original size:32 final size:33
Alignment explanation
Indices: 1251473--1251537 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
1251463 ACAATTGTCC
*
1251473 ATGTATCGATACAAAG-A-ACATGTATCGATACA
1 ATGTATCGAGACAAAGCATA-ATGTATCGATACA
1251505 ATGTATCGAGACAAAGCATAATGTATCGATACA
1 ATGTATCGAGACAAAGCATAATGTATCGATACA
1251538 TTCAAGGGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 15 0.50
33 14 0.47
34 1 0.03
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.25
Consensus pattern (33 bp):
ATGTATCGAGACAAAGCATAATGTATCGATACA
Found at i:1254823 original size:20 final size:20
Alignment explanation
Indices: 1254779--1254852 Score: 76
Period size: 21 Copynumber: 3.6 Consensus size: 20
1254769 TTCTATAATT
* * *
1254779 TGTATTGATACAGATAGTGAA
1 TGTATCGATACATA-AGTAAA
1254800 TGTATCGATACATAAGTAAA
1 TGTATCGATACATAAGTAAA
**
1254820 TGTATCGATACATATCTAAAA
1 TGTATCGATACATAAGT-AAA
*
1254841 TATATCGATACA
1 TGTATCGATACA
1254853 GGACCATGTC
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
20 20 0.43
21 26 0.57
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (20 bp):
TGTATCGATACATAAGTAAA
Found at i:1257402 original size:13 final size:13
Alignment explanation
Indices: 1257384--1257409 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1257374 TACAGCAAGT
1257384 ATGTATCGATACA
1 ATGTATCGATACA
1257397 ATGTATCGATACA
1 ATGTATCGATACA
1257410 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1259134 original size:21 final size:21
Alignment explanation
Indices: 1259101--1259145 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1259091 TTGCAAGTTG
*
1259101 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1259123 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
1259143 AAA
1 AAA
1259146 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1260969 original size:15 final size:15
Alignment explanation
Indices: 1260949--1260979 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1260939 TAAAAATGTC
*
1260949 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1260964 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1260979 C
1 C
1260980 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1263054 original size:13 final size:13
Alignment explanation
Indices: 1263036--1263074 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1263026 ACATTTTTCT
1263036 TTGTATCGATACA
1 TTGTATCGATACA
1263049 TTGTATCGATACA
1 TTGTATCGATACA
*
1263062 CTGTATCGATACA
1 TTGTATCGATACA
1263075 GGAGGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1263238 original size:20 final size:19
Alignment explanation
Indices: 1263197--1263239 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
1263187 ATCTTTTACA
1263197 AAATACTTGTTTTTCACTTC
1 AAATACTTGTTTTTCAC-TC
1263217 AAATCACTTCGTTTTTCA-TC
1 AAAT-ACTT-GTTTTTCACTC
1263237 AAA
1 AAA
1263240 ACCAGCATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.30, C:0.21, G:0.05, T:0.44
Consensus pattern (19 bp):
AAATACTTGTTTTTCACTC
Found at i:1264884 original size:18 final size:18
Alignment explanation
Indices: 1264863--1264900 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1264853 ATAAATTTTG
1264863 ATATGTGTGAATTACTTT
1 ATATGTGTGAATTACTTT
1264881 ATATGTGTGAATTACTTT
1 ATATGTGTGAATTACTTT
1264899 AT
1 AT
1264901 TAAGGGGGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.05, G:0.16, T:0.50
Consensus pattern (18 bp):
ATATGTGTGAATTACTTT
Found at i:1265606 original size:13 final size:13
Alignment explanation
Indices: 1265588--1265613 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1265578 TACAGCAAGT
1265588 ATGTATCGATACA
1 ATGTATCGATACA
1265601 ATGTATCGATACA
1 ATGTATCGATACA
1265614 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1266982 original size:81 final size:80
Alignment explanation
Indices: 1266692--1266972 Score: 334
Period size: 81 Copynumber: 3.5 Consensus size: 80
1266682 TCACCATCTG
*
1266692 GGATACTCTAACCTCACCATTTCCAAGAGGATACTCTAACCCCATTTTTACTCCTAAAAATATC-
1 GGATACTCTAACCCCACCATTTCCAAGAGGATACTCTAA-CCCATTTTTACTCCTAAAAATATCA
*
1266756 AAATTTCCCATCTTCGA
65 AAATTT-TCATCTTCGA
* * *
1266773 GGATACT-TCAACCCCATCATTTTCAAG-GGCATACTCTAACCCATTTTTACTCCTAAAAATATT
1 GGATACTCT-AACCCCACCATTTCCAAGAGG-ATACTCTAACCCATTTTTACTCCTAAAAATATC
* *
1266836 AAATTTTTCATTTTCGA
64 AAAATTTTCATCTTCGA
* ** ** * * *
1266853 GGATATTCTAACCCTGCCATTTCTGAGGGGATACTCTAGCCTCATTTTTACTTCTAAAAATATCA
1 GGATACTCTAACCCCACCATTTCCAAGAGGATACTCTAACC-CATTTTTACTCCTAAAAATATCA
1266918 AAATTTTCATCTTCGA
65 AAATTTTCATCTTCGA
* * *
1266934 GGATACTCTAACCCCACTATCTCCAAGAAGATACTCTAA
1 GGATACTCTAACCCCACCATTTCCAAGAGGATACTCTAA
1266973 TACCTTTTTT
Statistics
Matches: 165, Mismatches: 29, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
80 62 0.38
81 103 0.62
ACGTcount: A:0.31, C:0.26, G:0.09, T:0.33
Consensus pattern (80 bp):
GGATACTCTAACCCCACCATTTCCAAGAGGATACTCTAACCCATTTTTACTCCTAAAAATATCAA
AATTTTCATCTTCGA
Found at i:1271475 original size:54 final size:53
Alignment explanation
Indices: 1271329--1271501 Score: 197
Period size: 53 Copynumber: 3.2 Consensus size: 53
1271319 TCACAAACAT
* *
1271329 ACTATCACAAATTTTTGTCCCATTTAAATTTTATTACTATTCTATTACAAATA
1 ACTATCACAAATTTTTGTCCCATTTAAATTTTGTCACTATTCTATTACAAATA
* * * * *
1271382 ATTGTCATAAATTTTTGCCCCATTTAAATTTTGTCACTATTCTGTTACAAATA
1 ACTATCACAAATTTTTGTCCCATTTAAATTTTGTCACTATTCTATTACAAATA
* * * *
1271435 ACTATCACAAATTTTTTATCTCATTTAAATTTCGTCACTATT-TAATTATAAA-A
1 ACTATCACAAA-TTTTTGTCCCATTTAAATTTTGTCACTATTCT-ATTACAAATA
*
1271488 TTCTATCACAAATT
1 -ACTATCACAAATT
1271502 GAAATTGCAT
Statistics
Matches: 100, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
53 58 0.58
54 42 0.42
ACGTcount: A:0.35, C:0.17, G:0.03, T:0.45
Consensus pattern (53 bp):
ACTATCACAAATTTTTGTCCCATTTAAATTTTGTCACTATTCTATTACAAATA
Found at i:1271745 original size:20 final size:20
Alignment explanation
Indices: 1271682--1271746 Score: 87
Period size: 20 Copynumber: 3.2 Consensus size: 20
1271672 TGTCATTAAA
*
1271682 TCCGTCACAACTTGTGACAT
1 TCCGTCACAACTTGTGACAG
* *
1271702 TCCATCAGAACTTGTGA-AG
1 TCCGTCACAACTTGTGACAG
1271721 TTCCGTCACAACTTGTGACAG
1 -TCCGTCACAACTTGTGACAG
1271742 TCCGT
1 TCCGT
1271747 TATAATTTCC
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
19 1 0.03
20 35 0.92
21 2 0.05
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.29
Consensus pattern (20 bp):
TCCGTCACAACTTGTGACAG
Found at i:1274389 original size:18 final size:18
Alignment explanation
Indices: 1274346--1274393 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
1274336 CAAATAAATG
* *
1274346 ATCATCATTTTCATCATC
1 ATCATCATCTTCATAATC
1274364 ATCATCATCTTCATAATC
1 ATCATCATCTTCATAATC
1274382 AT-ATTCATCTTC
1 ATCA-TCATCTTC
1274394 TTCATCACCC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 1 0.04
18 26 0.96
ACGTcount: A:0.29, C:0.27, G:0.00, T:0.44
Consensus pattern (18 bp):
ATCATCATCTTCATAATC
Found at i:1276575 original size:207 final size:207
Alignment explanation
Indices: 1276214--1276627 Score: 738
Period size: 207 Copynumber: 2.0 Consensus size: 207
1276204 CCATCCTAGC
*
1276214 CTTCATATTATCTTTGGATTTACCTTTAATATCCATTAGCGTGTTAAATATGTTCTCAAACACAT
1 CTTCATATTATCTTTGGATTTACCTTTAATATCCATTACCGTGTTAAATATGTTCTCAAACACAT
*
1276279 TTTGCTCAATATGCGTAAAATCCAAATTGTGACGAATCATGTTTGAGTGCCAATAAGGTAACTCC
66 TTTGCTCAATATGCGTAAAATCAAAATTGTGACGAATCATGTTTGAGTGCCAATAAGGTAACTCC
* *
1276344 TAAAAGATACTTTTCTTTACCCAATTATGTGTTTCTCCAAAGCCATATATTTTCTCCTTCTCATG
131 CAAAAGATACTTTTCTTCACCCAATTATGTGTTTCTCCAAAGCCATATATTTTCTCCTTCTCATG
1276409 TAATTTATCAAA
196 TAATTTATCAAA
*
1276421 CTTCATATTATCTTTGGATTTACCTTTAATATCCATTACCGTGTTAAATATGTTCTCAAGCACAT
1 CTTCATATTATCTTTGGATTTACCTTTAATATCCATTACCGTGTTAAATATGTTCTCAAACACAT
* * *
1276486 TTTGCTCAATATGCGTAACATCAAAATTGTGATGAGTCATGTTTGAGTGCCAATAAGGTAACTCC
66 TTTGCTCAATATGCGTAAAATCAAAATTGTGACGAATCATGTTTGAGTGCCAATAAGGTAACTCC
* *
1276551 CAAAAGATATTTTTCTTCACCCAATTATGTGTTTCTCCAAAGCCATCTATTTTCTCCTTCTCATG
131 CAAAAGATACTTTTCTTCACCCAATTATGTGTTTCTCCAAAGCCATATATTTTCTCCTTCTCATG
1276616 TAATTTATCAAA
196 TAATTTATCAAA
1276628 GATCACATTA
Statistics
Matches: 197, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
207 197 1.00
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (207 bp):
CTTCATATTATCTTTGGATTTACCTTTAATATCCATTACCGTGTTAAATATGTTCTCAAACACAT
TTTGCTCAATATGCGTAAAATCAAAATTGTGACGAATCATGTTTGAGTGCCAATAAGGTAACTCC
CAAAAGATACTTTTCTTCACCCAATTATGTGTTTCTCCAAAGCCATATATTTTCTCCTTCTCATG
TAATTTATCAAA
Found at i:1280491 original size:12 final size:12
Alignment explanation
Indices: 1280473--1280529 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 12
1280463 ATTTAAATTT
1280473 TATTATAAATAA
1 TATTATAAATAA
*
1280485 TAATATAAA-AA
1 TATTATAAATAA
* * *
1280496 TATTTTTAATAT
1 TATTATAAATAA
*
1280508 TATTTTAAATAA
1 TATTATAAATAA
*
1280520 TAGTATAAAT
1 TATTATAAAT
1280530 TTTCGAGTTA
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
11 8 0.23
12 27 0.77
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (12 bp):
TATTATAAATAA
Found at i:1281349 original size:36 final size:37
Alignment explanation
Indices: 1281279--1281350 Score: 87
Period size: 36 Copynumber: 2.0 Consensus size: 37
1281269 TTGGAATGGT
* *
1281279 TTTTCATTATTTTTTTTTTTGTTGCTATTTTAAACAG
1 TTTTCATTATTTTTTTTTTTATTACTATTTTAAACAG
1281316 TTTT-ATT-TTTTATTTTTTTATTAC-ATTTATAAACA
1 TTTTCATTATTTT-TTTTTTTATTACTATTT-TAAACA
1281351 AAAACTACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
35 8 0.26
36 19 0.61
37 4 0.13
ACGTcount: A:0.24, C:0.07, G:0.04, T:0.65
Consensus pattern (37 bp):
TTTTCATTATTTTTTTTTTTATTACTATTTTAAACAG
Found at i:1283190 original size:22 final size:23
Alignment explanation
Indices: 1283162--1283206 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
1283152 TTGCTCTCAA
*
1283162 TTTTTTAAAATCTT-TCTTTATT
1 TTTTTTAAAATCTTATATTTATT
*
1283184 TTTTTTAATATCTTATATTTATT
1 TTTTTTAAAATCTTATATTTATT
1283207 ACTAATATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (23 bp):
TTTTTTAAAATCTTATATTTATT
Found at i:1283487 original size:27 final size:25
Alignment explanation
Indices: 1283457--1283534 Score: 79
Period size: 24 Copynumber: 3.1 Consensus size: 25
1283447 CAAGTTTGGA
*
1283457 TTAATATTTAAATTATAATAAATATTT
1 TTAAAATTT-AATTATAA-AAATATTT
*
1283484 TTAAAATTTAATTATAAAAATATAT
1 TTAAAATTTAATTATAAAAATATTT
* *
1283509 AT-AAATATTAA-TATAAAATTATTT
1 TTAAAAT-TTAATTATAAAAATATTT
1283533 TT
1 TT
1283535 TATATTTTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
24 16 0.36
25 12 0.27
26 8 0.18
27 8 0.18
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
TTAAAATTTAATTATAAAAATATTT
Found at i:1287262 original size:18 final size:18
Alignment explanation
Indices: 1287236--1287330 Score: 87
Period size: 18 Copynumber: 5.6 Consensus size: 18
1287226 TAATTCATGT
1287236 ATTTATATTATATTAATA
1 ATTTATATTATATTAATA
*
1287254 ATTTTTATTATATT-ATA
1 ATTTATATTATATTAATA
1287271 A-TTATATT-T-TTAAAATA
1 ATTTATATTATATT--AATA
* *
1287288 TTTTATATT-TA-TAAAA
1 ATTTATATTATATTAATA
*
1287304 ATTT-TAATATATTAATA
1 ATTTATATTATATTAATA
1287321 ATTTATATTA
1 ATTTATATTA
1287331 AAAAAATTTT
Statistics
Matches: 61, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
14 2 0.03
15 4 0.07
16 14 0.23
17 15 0.25
18 26 0.43
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTATATTATATTAATA
Found at i:1287264 original size:23 final size:22
Alignment explanation
Indices: 1287238--1287282 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
1287228 ATTCATGTAT
1287238 TTATATTAT-ATTAATAATTTTTA
1 TTATATTATAATT-AT-ATTTTTA
1287261 TTATATTATAATTATATTTTTA
1 TTATATTATAATTATATTTTTA
1287283 AAATATTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 7 0.33
23 11 0.52
24 3 0.14
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TTATATTATAATTATATTTTTA
Found at i:1287339 original size:32 final size:33
Alignment explanation
Indices: 1287284--1287347 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1287274 ATATTTTTAA
* * *
1287284 AATATTTTATATTTATAAAAATTTTAATATATT
1 AATAATTTATATTTAAAAAAATTTTAAAATATT
1287317 AATAATTTATA-TTAAAAAAATTTTAAAATAT
1 AATAATTTATATTTAAAAAAATTTTAAAATAT
1287348 ATAAATATCA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 18 0.64
33 10 0.36
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (33 bp):
AATAATTTATATTTAAAAAAATTTTAAAATATT
Found at i:1287361 original size:32 final size:32
Alignment explanation
Indices: 1287300--1287362 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
1287290 TTATATTTAT
* *
1287300 AAAAATTTTAATATATTAATAATTTATATTAA
1 AAAAATTTTAATATATAAATAATTCATATTAA
1287332 AAAAATTTTAAAATATATAAAT-A-TCATATTA
1 AAAAATTTT--AATATATAAATAATTCATATTA
1287363 TATTATATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 16 0.59
33 1 0.04
34 10 0.37
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (32 bp):
AAAAATTTTAATATATAAATAATTCATATTAA
Found at i:1287365 original size:5 final size:5
Alignment explanation
Indices: 1287352--1287411 Score: 63
Period size: 5 Copynumber: 12.2 Consensus size: 5
1287342 AAATATATAA
* *
1287352 ATATC ATATT ATATT ATATT ATATTT TTATT ATA-T ATATT ATATT -TA-T
1 ATATT ATATT ATATT ATATT ATA-TT ATATT ATATT ATATT ATATT ATATT
1287400 ATAATT ATATT A
1 AT-ATT ATATT A
1287412 AAATATCTGG
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
3 1 0.02
4 7 0.15
5 32 0.68
6 7 0.15
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (5 bp):
ATATT
Found at i:1287365 original size:50 final size:50
Alignment explanation
Indices: 1287259--1287375 Score: 116
Period size: 49 Copynumber: 2.4 Consensus size: 50
1287249 TAATAATTTT
* * * * * **
1287259 TATTATATT-ATAATTATATTTTTAAAATATTTTATATTTATAAAAATTT
1 TATTATATTAATAATTATATATTAAAAAAATTTTAAATATATAAAAATCA
* *
1287308 TAATATATTAATAATT-TATATTAAAAAAATTTTAAAATATATAAATATCA
1 TATTATATTAATAATTATATATTAAAAAAATTTT-AAATATATAAAAATCA
1287358 TATTATATT-AT-ATTATAT
1 TATTATATTAATAATTATAT
1287376 TTTTATTATA
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
48 3 0.05
49 27 0.49
50 25 0.45
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (50 bp):
TATTATATTAATAATTATATATTAAAAAAATTTTAAATATATAAAAATCA
Found at i:1287407 original size:26 final size:26
Alignment explanation
Indices: 1287345--1287407 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
1287335 AATTTTAAAA
*
1287345 TATATAAATATCATATTATATTATAT
1 TATATAATTATCATATTATATTATAT
** *
1287371 TATATTTTTATTATA-TATATTATATT
1 TATATAATTATCATATTATATTATA-T
1287397 TATATAATTAT
1 TATATAATTAT
1287408 ATTAAAATAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
25 9 0.30
26 21 0.70
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (26 bp):
TATATAATTATCATATTATATTATAT
Found at i:1287702 original size:19 final size:19
Alignment explanation
Indices: 1287678--1287714 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1287668 TTGATTAAAA
*
1287678 ATAATTATAATATTATATT
1 ATAATTATAATAATATATT
*
1287697 ATAATTATTATAATATAT
1 ATAATTATAATAATATAT
1287715 AATGCATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATAATTATAATAATATATT
Found at i:1288244 original size:27 final size:27
Alignment explanation
Indices: 1288206--1288260 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
1288196 CATTTCAGCC
1288206 AGATTAAGAAATGAATATTAGATATTA
1 AGATTAAGAAATGAATATTAGATATTA
1288233 AGATTAAGAAATGAATATTAGATATTA
1 AGATTAAGAAATGAATATTAGATATTA
1288260 A
1 A
1288261 TATATGTCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.15, T:0.33
Consensus pattern (27 bp):
AGATTAAGAAATGAATATTAGATATTA
Found at i:1291253 original size:20 final size:20
Alignment explanation
Indices: 1291216--1291256 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1291206 GATTTAGTAA
*
1291216 TTTATGTATCTGTATTATAT
1 TTTATGTATCTATATTATAT
* *
1291236 TTTATGTATTTATTTTATAT
1 TTTATGTATCTATATTATAT
1291256 T
1 T
1291257 ATAATCGTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.66
Consensus pattern (20 bp):
TTTATGTATCTATATTATAT
Found at i:1291705 original size:14 final size:14
Alignment explanation
Indices: 1291688--1291741 Score: 54
Period size: 15 Copynumber: 3.7 Consensus size: 14
1291678 AGTAATGGAA
**
1291688 ATATTTTAGGTTTT
1 ATATTTTAAATTTT
1291702 ATATTATTAAATTTT
1 ATATT-TTAAATTTT
* *
1291717 GTATTTTAATTTTT
1 ATATTTTAAATTTT
1291731 ATACTTTTAAA
1 ATA-TTTTAAA
1291742 ATTGTAACAA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
14 15 0.47
15 17 0.53
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61
Consensus pattern (14 bp):
ATATTTTAAATTTT
Found at i:1292375 original size:41 final size:42
Alignment explanation
Indices: 1292318--1292488 Score: 267
Period size: 41 Copynumber: 4.1 Consensus size: 42
1292308 CATCTACATC
* *
1292318 TTTTTTTT-CCAACATATTATATTTAATAGTTGAAATTTTAA
1 TTTTTTTTCCCAACATATTATATTTAGTACTTGAAATTTTAA
1292359 TTTTTTTT-CCAACATATTATATTTAGTACTTGAAATTTT-A
1 TTTTTTTTCCCAACATATTATATTTAGTACTTGAAATTTTAA
* * *
1292399 TTTTTTTTCCCAACATATTATATTTAGCACTTAAAATTTTGA
1 TTTTTTTTCCCAACATATTATATTTAGTACTTGAAATTTTAA
*
1292441 TTTTTTTTCCCAACATATTATATTTAGTATTTGAAATTTTAA
1 TTTTTTTTCCCAACATATTATATTTAGTACTTGAAATTTTAA
1292483 TTTTTT
1 TTTTTT
1292489 AATATTTAAA
Statistics
Matches: 120, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
40 9 0.08
41 66 0.55
42 45 0.38
ACGTcount: A:0.30, C:0.10, G:0.05, T:0.55
Consensus pattern (42 bp):
TTTTTTTTCCCAACATATTATATTTAGTACTTGAAATTTTAA
Found at i:1292466 original size:83 final size:81
Alignment explanation
Indices: 1292318--1292488 Score: 261
Period size: 83 Copynumber: 2.1 Consensus size: 81
1292308 CATCTACATC
* * *
1292318 TTTTTTTTCCAACATATTATATTTAATAGTTGAAATTTTAATTTTTTTTCCAACATATTATATTT
1 TTTTTTTTCCAACATATTATATTTAACACTTAAAATTTTAATTTTTTTTCCAACATATTATATTT
1292383 AGTACTTGAAATTTTA
66 AGTACTTGAAATTTTA
* *
1292399 TTTTTTTTCCCAACATATTATATTTAGCACTTAAAATTTTGATTTTTTTTCCCAACATATTATAT
1 TTTTTTTT-CCAACATATTATATTTAACACTTAAAATTTTAATTTTTTTT-CCAACATATTATAT
*
1292464 TTAGTATTTGAAATTTTA
64 TTAGTACTTGAAATTTTA
*
1292482 ATTTTTT
1 TTTTTTT
1292489 AATATTTAAA
Statistics
Matches: 81, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
81 8 0.10
82 36 0.44
83 37 0.46
ACGTcount: A:0.30, C:0.10, G:0.05, T:0.55
Consensus pattern (81 bp):
TTTTTTTTCCAACATATTATATTTAACACTTAAAATTTTAATTTTTTTTCCAACATATTATATTT
AGTACTTGAAATTTTA
Found at i:1292865 original size:7 final size:7
Alignment explanation
Indices: 1292853--1292989 Score: 66
Period size: 7 Copynumber: 20.3 Consensus size: 7
1292843 TTGACGTAAT
1292853 ATATTTA
1 ATATTTA
1292860 ATATTTA
1 ATATTTA
1292867 ATA--T-
1 ATATTTA
1292871 ATGATTT-
1 AT-ATTTA
1292878 ATATTT-
1 ATATTTA
1292884 ATATTTA
1 ATATTTA
1292891 ATA--TA
1 ATATTTA
1292896 ATATATTAA
1 ATAT-TT-A
1292905 ATATTT-
1 ATATTTA
*
1292911 ATATATA
1 ATATTTA
1292918 ATATTT-
1 ATATTTA
1292924 ATATTTA
1 ATATTTA
*
1292931 AAATTATA
1 ATATT-TA
1292939 ATATAATTA
1 ATAT--TTA
1292948 ATAATTT-
1 AT-ATTTA
1292955 ATA-TT-
1 ATATTTA
1292960 ATATTT-
1 ATATTTA
* *
1292966 ATTTTTT
1 ATATTTA
1292973 ATATTTA
1 ATATTTA
*
1292980 TATAATTA
1 -ATATTTA
1292988 AT
1 AT
1292990 GTAAAAAATG
Statistics
Matches: 105, Mismatches: 8, Indels: 34
0.71 0.05 0.23
Matches are distributed among these distances:
4 2 0.02
5 12 0.11
6 29 0.28
7 34 0.32
8 16 0.15
9 9 0.09
10 3 0.03
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (7 bp):
ATATTTA
Found at i:1292890 original size:31 final size:29
Alignment explanation
Indices: 1292852--1292932 Score: 89
Period size: 27 Copynumber: 2.9 Consensus size: 29
1292842 ATTGACGTAA
**
1292852 TATATTTAATATTTAATATATGATTTATATT
1 TATATTTAATATTTAATATAT--TAAATATT
1292883 TATATTTAATA--TAATATATTAAATATT
1 TATATTTAATATTTAATATATTAAATATT
*
1292910 TATATATAATATTT-ATAT-TTAAA
1 TATATTTAATATTTAATATATTAAA
1292933 ATTATAATAT
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
27 21 0.47
28 4 0.09
29 9 0.20
31 11 0.24
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (29 bp):
TATATTTAATATTTAATATATTAAATATT
Found at i:1292895 original size:40 final size:39
Alignment explanation
Indices: 1292849--1292989 Score: 124
Period size: 42 Copynumber: 3.3 Consensus size: 39
1292839 ATAATTGACG
*
1292849 TAATATATTTAATATTTAATATATGATTTATATTTATATT
1 TAATATAATTAATATTTAATATAT-ATTTATATTTATATT
*
1292889 TAATATAATATATTAAATATTTATATATAATATTTATATTTAAAATT
1 T-A-AT-ATA-ATT-AATATTTA-ATAT-ATATTTATATTT-ATATT
*
1292936 ATAATATAATTAATAATTT-ATATTATATTTATTTTTTATATT
1 -TAATATAATTAAT-ATTTAATA-TATATTTA-TATTTATATT
1292978 T-ATATAATTAAT
1 TAATATAATTAAT
1292990 GTAAAAAATG
Statistics
Matches: 85, Mismatches: 4, Indels: 24
0.75 0.04 0.21
Matches are distributed among these distances:
40 12 0.14
41 2 0.02
42 16 0.19
43 11 0.13
44 9 0.11
45 11 0.13
46 16 0.19
47 7 0.08
48 1 0.01
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (39 bp):
TAATATAATTAATATTTAATATATATTTATATTTATATT
Found at i:1292913 original size:13 final size:13
Alignment explanation
Indices: 1292878--1292928 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
1292868 TATATGATTT
*
1292878 ATATTTATATTTA
1 ATATTTATATTAA
*
1292891 ATATAATATATTAA
1 ATAT-TTATATTAA
1292905 ATATTTATA-TATA
1 ATATTTATATTA-A
1292918 ATATTTATATT
1 ATATTTATATT
1292929 TAAAATTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
12 2 0.06
13 18 0.56
14 12 0.38
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
ATATTTATATTAA
Found at i:1292915 original size:29 final size:26
Alignment explanation
Indices: 1292852--1292989 Score: 70
Period size: 24 Copynumber: 5.7 Consensus size: 26
1292842 ATTGACGTAA
1292852 TATATTTA-ATATTTAATATATGATT
1 TATATTTATATATTTAATATATGATT
1292877 TATA-TT-TATATTTAATATA--A--
1 TATATTTATATATTTAATATATGATT
*
1292897 TATA-TTAAATATTTATATATAAT-ATT
1 TATATTTATATATTTA-ATAT-ATGATT
*
1292923 TATATTTA-AAATTATAATATA--ATT
1 TATATTTATATATT-TAATATATGATT
* * * **
1292947 AATAATT-TATA-TTATATTTATTTTT
1 TATATTTATATATTTA-ATATATGATT
*
1292972 TATATTTATATAATTAAT
1 TATATTTATATATTTAAT
1292990 GTAAAAAATG
Statistics
Matches: 89, Mismatches: 9, Indels: 29
0.70 0.07 0.23
Matches are distributed among these distances:
20 6 0.07
21 7 0.08
22 7 0.08
23 6 0.07
24 25 0.28
25 12 0.13
26 18 0.20
27 8 0.09
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (26 bp):
TATATTTATATATTTAATATATGATT
Found at i:1294720 original size:22 final size:22
Alignment explanation
Indices: 1294695--1294736 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1294685 AAATAGTAAT
1294695 TTATCAAAAAATAAATTATATC
1 TTATCAAAAAATAAATTATATC
* *
1294717 TTATTAAAAAGTAAATTATA
1 TTATCAAAAAATAAATTATA
1294737 ACATGAGCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (22 bp):
TTATCAAAAAATAAATTATATC
Found at i:1296730 original size:19 final size:20
Alignment explanation
Indices: 1296706--1296743 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1296696 TTAAAAATTA
*
1296706 ATTTT-ATATACAAATATAG
1 ATTTTAATAAACAAATATAG
1296725 ATTTTAATAAACAAATATA
1 ATTTTAATAAACAAATATA
1296744 TTAAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (20 bp):
ATTTTAATAAACAAATATAG
Found at i:1298749 original size:3 final size:3
Alignment explanation
Indices: 1298743--1298784 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
1298733 ATAATTCCTA
1298743 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1298785 TTCATCACCC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1299130 original size:7 final size:7
Alignment explanation
Indices: 1299120--1299148 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
1299110 AGGGTTGAGA
1299120 TTTTATT
1 TTTTATT
1299127 TTTTATT
1 TTTTATT
1299134 TTTTATT
1 TTTTATT
1299141 TTTTATT
1 TTTTATT
1299148 T
1 T
1299149 ATTTTCATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTATT
Found at i:1299669 original size:22 final size:22
Alignment explanation
Indices: 1299644--1299685 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1299634 TTTTAAAAAA
1299644 TATTTTTAT-ATTAATATTTATT
1 TATTTTTATAATTAA-ATTTATT
1299666 TATTTTTATAATTAAATTTA
1 TATTTTTATAATTAAATTTA
1299686 AATGAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TATTTTTATAATTAAATTTATT
Found at i:1300139 original size:16 final size:16
Alignment explanation
Indices: 1300115--1300160 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
1300105 TATAATTAAA
1300115 ATAAT-ATATTAAAAC
1 ATAATAATATTAAAAC
*
1300130 ATAATAATATTAACAC
1 ATAATAATATTAAAAC
1300146 ATACA-AATATTAAAA
1 ATA-ATAATATTAAAA
1300161 TAAAACAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 5 0.19
16 21 0.78
17 1 0.04
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (16 bp):
ATAATAATATTAAAAC
Found at i:1303063 original size:16 final size:15
Alignment explanation
Indices: 1303042--1303100 Score: 73
Period size: 16 Copynumber: 3.7 Consensus size: 15
1303032 AAGTGATCAT
1303042 AATTTAAAATAATATA
1 AATTTAAAATAAT-TA
*
1303058 AATTTAAAAATGATTCA
1 AATTT-AAAATAATT-A
1303075 AATTTAAAATAATTTA
1 AATTTAAAATAA-TTA
1303091 AATTTAAAAT
1 AATTTAAAAT
1303101 GACACCGATT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
16 23 0.61
17 15 0.39
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (15 bp):
AATTTAAAATAATTA
Found at i:1303162 original size:15 final size:16
Alignment explanation
Indices: 1303132--1303180 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
1303122 ATAATTTAAA
*
1303132 TTTAAATTAAGTAAAAT
1 TTTAATTTAA-TAAAAT
*
1303149 TTTATTTTAA-AAAAT
1 TTTAATTTAATAAAAT
*
1303164 ATTAATTTAATAAAAT
1 TTTAATTTAATAAAAT
1303180 T
1 T
1303181 GATAACTACA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
15 13 0.50
16 5 0.19
17 8 0.31
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (16 bp):
TTTAATTTAATAAAAT
Found at i:1304117 original size:16 final size:17
Alignment explanation
Indices: 1304086--1304119 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1304076 ATAATTTTTA
1304086 TATTTATTTTTAAATAT
1 TATTTATTTTTAAATAT
1304103 TATTTATTTTT-AATAT
1 TATTTATTTTTAAATAT
1304119 T
1 T
1304120 TCAATAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TATTTATTTTTAAATAT
Found at i:1308155 original size:22 final size:22
Alignment explanation
Indices: 1308101--1308155 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
1308091 ATTATTTATA
* *
1308101 TTTATCATTTTATTATTATCCT
1 TTTATTATTTTATTATTATCAT
* *
1308123 TTAATTTTTTTATTATTAT-AT
1 TTTATTATTTTATTATTATCAT
1308144 TATTATTATTTT
1 T-TTATTATTTT
1308156 TAATTTTGAT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 2 0.08
22 24 0.92
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTATTATTTTATTATTATCAT
Found at i:1309961 original size:118 final size:118
Alignment explanation
Indices: 1309753--1309991 Score: 478
Period size: 118 Copynumber: 2.0 Consensus size: 118
1309743 AGATTCCCTT
1309753 TTCTGCCAGAATATGGTGCCAGTAAAAGTCCAAATCTCTAAGCTATAAAGCACATAAAACAAAAA
1 TTCTGCCAGAATATGGTGCCAGTAAAAGTCCAAATCTCTAAGCTATAAAGCACATAAAACAAAAA
1309818 TCGAAAGATCATTATTGGTTAATTATATAAAACTTCTATCTAAATTTAAAGCA
66 TCGAAAGATCATTATTGGTTAATTATATAAAACTTCTATCTAAATTTAAAGCA
1309871 TTCTGCCAGAATATGGTGCCAGTAAAAGTCCAAATCTCTAAGCTATAAAGCACATAAAACAAAAA
1 TTCTGCCAGAATATGGTGCCAGTAAAAGTCCAAATCTCTAAGCTATAAAGCACATAAAACAAAAA
1309936 TCGAAAGATCATTATTGGTTAATTATATAAAACTTCTATCTAAATTTAAAGCA
66 TCGAAAGATCATTATTGGTTAATTATATAAAACTTCTATCTAAATTTAAAGCA
1309989 TTC
1 TTC
1309992 ATTAGTATAC
Statistics
Matches: 121, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
118 121 1.00
ACGTcount: A:0.43, C:0.16, G:0.12, T:0.29
Consensus pattern (118 bp):
TTCTGCCAGAATATGGTGCCAGTAAAAGTCCAAATCTCTAAGCTATAAAGCACATAAAACAAAAA
TCGAAAGATCATTATTGGTTAATTATATAAAACTTCTATCTAAATTTAAAGCA
Found at i:1310967 original size:20 final size:19
Alignment explanation
Indices: 1310942--1310999 Score: 80
Period size: 19 Copynumber: 3.0 Consensus size: 19
1310932 CTGCCAGTTT
1310942 CATGTATCGATACAATTGTA
1 CATGTATCGATAC-ATTGTA
* *
1310962 CATGTATCGATACAGTGAA
1 CATGTATCGATACATTGTA
*
1310981 CACGTATCGATACATTGTA
1 CATGTATCGATACATTGTA
1311000 TCGATACAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 20 0.61
20 13 0.39
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (19 bp):
CATGTATCGATACATTGTA
Found at i:1321810 original size:1 final size:1
Alignment explanation
Indices: 1321800--1321860 Score: 59
Period size: 1 Copynumber: 61.0 Consensus size: 1
1321790 TGGCAAAAGG
* * * ** * *
1321800 AAAAAGAAAAAAAAAACAAAACAAAAAAAAGGAAAAAGAAAAAAAAAACAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1321861 GTGAAGATTT
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.89, C:0.05, G:0.07, T:0.00
Consensus pattern (1 bp):
A
Found at i:1321813 original size:16 final size:16
Alignment explanation
Indices: 1321794--1321845 Score: 70
Period size: 16 Copynumber: 3.2 Consensus size: 16
1321784 GATGCATGGC
1321794 AAAAGGAAAAAGAAAA
1 AAAAGGAAAAAGAAAA
* *
1321810 AAAA-AACAAAACAAAA
1 AAAAGGA-AAAAGAAAA
1321826 AAAAGGAAAAAGAAAA
1 AAAAGGAAAAAGAAAA
1321842 AAAA
1 AAAA
1321846 AACAAAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
15 1 0.03
16 28 0.93
17 1 0.03
ACGTcount: A:0.85, C:0.04, G:0.12, T:0.00
Consensus pattern (16 bp):
AAAAGGAAAAAGAAAA
Found at i:1321830 original size:32 final size:31
Alignment explanation
Indices: 1321794--1321861 Score: 127
Period size: 32 Copynumber: 2.2 Consensus size: 31
1321784 GATGCATGGC
1321794 AAAAGGAAAAAGAAAAAAAAAACAAAACAAAA
1 AAAAGGAAAAAGAAAAAAAAAACAAAA-AAAA
1321826 AAAAGGAAAAAGAAAAAAAAAACAAAAAAAA
1 AAAAGGAAAAAGAAAAAAAAAACAAAAAAAA
1321857 AAAAG
1 AAAAG
1321862 TGAAGATTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 9 0.25
32 27 0.75
ACGTcount: A:0.85, C:0.04, G:0.10, T:0.00
Consensus pattern (31 bp):
AAAAGGAAAAAGAAAAAAAAAACAAAAAAAA
Found at i:1321847 original size:27 final size:25
Alignment explanation
Indices: 1321800--1321860 Score: 88
Period size: 27 Copynumber: 2.4 Consensus size: 25
1321790 TGGCAAAAGG
*
1321800 AAAAAGAAAAAAAAAACAAAACAAA
1 AAAAAGAAAAAAAAAAAAAAACAAA
1321825 AAAAAGGAAAAAGAAAAAAAAAACAAA
1 AAAAA-GAAAAA-AAAAAAAAAACAAA
1321852 AAAAA-AAAA
1 AAAAAGAAAA
1321861 GTGAAGATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
25 9 0.27
26 6 0.18
27 18 0.55
ACGTcount: A:0.89, C:0.05, G:0.07, T:0.00
Consensus pattern (25 bp):
AAAAAGAAAAAAAAAAAAAAACAAA
Found at i:1321852 original size:16 final size:16
Alignment explanation
Indices: 1321801--1321860 Score: 79
Period size: 16 Copynumber: 3.8 Consensus size: 16
1321791 GGCAAAAGGA
1321801 AAAAGAAAAAAAAAAC
1 AAAAGAAAAAAAAAAC
* *
1321817 AAAACAAAAAAAAGGA-
1 AAAAGAAAAAAAA-AAC
1321833 AAAAGAAAAAAAAAAC
1 AAAAGAAAAAAAAAAC
1321849 AAAA-AAAAAAAA
1 AAAAGAAAAAAAA
1321861 GTGAAGATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
15 9 0.24
16 28 0.74
17 1 0.03
ACGTcount: A:0.88, C:0.05, G:0.07, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAAAAAAAC
Found at i:1328167 original size:3 final size:3
Alignment explanation
Indices: 1328159--1328195 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
1328149 TCCGAGTCAC
* *
1328159 CAT CAT CAT CAT TAT CAT CAT CAT CAT CAT CTT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
1328196 GTCTTTGATG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.30, C:0.32, G:0.00, T:0.38
Consensus pattern (3 bp):
CAT
Found at i:1328993 original size:15 final size:16
Alignment explanation
Indices: 1328970--1329001 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1328960 CATTGTTGCG
1328970 TTTTCCATTCTTGAGC
1 TTTTCCATTCTTGAGC
1328986 TTTT-CATTCTTGAGC
1 TTTTCCATTCTTGAGC
1329001 T
1 T
1329002 GAAGAAGATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.12, C:0.22, G:0.12, T:0.53
Consensus pattern (16 bp):
TTTTCCATTCTTGAGC
Found at i:1330103 original size:22 final size:22
Alignment explanation
Indices: 1330054--1330103 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
1330044 GTATTTTTAC
*
1330054 TTAAAAACATTTGAATTAAGGT
1 TTAAAAACATTTGAATTAAGCT
* *
1330076 TCAAAAACATTTG-TTTATAGCT
1 TTAAAAACATTTGAATTA-AGCT
1330098 TTAAAA
1 TTAAAA
1330104 CTTTCATTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 3 0.13
22 20 0.87
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (22 bp):
TTAAAAACATTTGAATTAAGCT
Found at i:1331972 original size:22 final size:25
Alignment explanation
Indices: 1331946--1332000 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
1331936 GTTATTTTTG
1331946 AAGTTATT-AATAT-TATAT-TTAA
1 AAGTTATTAAATATATATATATTAA
*
1331968 AAGTTATTAAATTTATATATATTAA
1 AAGTTATTAAATATATATATATTAA
1331993 AAGTTATT
1 AAGTTATT
1332001 TAAAAAATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 8 0.28
23 4 0.14
24 5 0.17
25 12 0.41
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.49
Consensus pattern (25 bp):
AAGTTATTAAATATATATATATTAA
Found at i:1332059 original size:20 final size:21
Alignment explanation
Indices: 1331982--1332140 Score: 135
Period size: 21 Copynumber: 7.3 Consensus size: 21
1331972 TATTAAATTT
*
1331982 ATATATATTAAAAGTTATTTAAA
1 ATAT-TATTAAAA-TTATATAAA
* *
1332005 AAATTATTAAAATTATATCAA
1 ATATTATTAAAATTATATAAA
* *
1332026 ATATTAAATAAAATTATAT-TA
1 ATATT-ATTAAAATTATATAAA
*
1332047 CTATTATTAAAATTATATAAA
1 ATATTATTAAAATTATATAAA
*
1332068 ATATT-TTCAAATTATATTAAA
1 ATATTATTAAAATTATA-TAAA
*
1332089 TATTACTTATCAAAATTATATTAAA
1 -A-TA-TTATTAAAATTATA-TAAA
* *
1332114 A-ATTATCAAAATCATATAAA
1 ATATTATTAAAATTATATAAA
1332134 ATATTAT
1 ATATTAT
1332141 CGAATTTAAT
Statistics
Matches: 114, Mismatches: 14, Indels: 18
0.78 0.10 0.12
Matches are distributed among these distances:
20 27 0.24
21 43 0.38
22 22 0.19
23 5 0.04
24 3 0.03
25 14 0.12
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (21 bp):
ATATTATTAAAATTATATAAA
Found at i:1332107 original size:45 final size:47
Alignment explanation
Indices: 1332041--1332139 Score: 123
Period size: 46 Copynumber: 2.1 Consensus size: 47
1332031 AAATAAAATT
* * * *
1332041 ATATTACTATTATTAAAATTATA-TAAAATATTTTC-AAATTATATTAA
1 ATATTAC-ATTATCAAAATTATATTAAAA-ATTATCAAAATCATATAAA
1332088 ATATTAC-TTATCAAAATTATATTAAAAATTATCAAAATCATATAAA
1 ATATTACATTATCAAAATTATATTAAAAATTATCAAAATCATATAAA
1332134 ATATTA
1 ATATTA
1332140 TCGAATTTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
45 18 0.39
46 21 0.46
47 7 0.15
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (47 bp):
ATATTACATTATCAAAATTATATTAAAAATTATCAAAATCATATAAA
Found at i:1332141 original size:21 final size:22
Alignment explanation
Indices: 1331982--1332170 Score: 130
Period size: 21 Copynumber: 8.8 Consensus size: 22
1331972 TATTAAATTT
*
1331982 ATATATATTAAAAGTTAT-TTAAA
1 ATAT-TATCAAAA-TTATATTAAA
* * *
1332005 AAATTATTAAAATTATA-TCAA
1 ATATTATCAAAATTATATTAAA
1332026 ATATTAAAT-AAAATTATATT--A
1 ATATT--ATCAAAATTATATTAAA
* *
1332047 CTATTATTAAAATTATA-TAAA
1 ATATTATCAAAATTATATTAAA
*
1332068 ATATTTTC-AAATTATATTAAA
1 ATATTATCAAAATTATATTAAA
1332089 TATTACTTATCAAAATTATATTAAA
1 -A-TA-TTATCAAAATTATATTAAA
*
1332114 A-ATTATCAAAATCATA-TAAA
1 ATATTATCAAAATTATATTAAA
* * *
1332134 ATATTATCGAATTTA-ATCAAA
1 ATATTATCAAAATTATATTAAA
*
1332155 A-ATTATCAAATTTATA
1 ATATTATCAAAATTATA
1332171 CATCAAAATT
Statistics
Matches: 137, Mismatches: 14, Indels: 32
0.75 0.08 0.17
Matches are distributed among these distances:
19 3 0.02
20 35 0.26
21 54 0.39
22 19 0.14
23 8 0.06
24 5 0.04
25 13 0.09
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.41
Consensus pattern (22 bp):
ATATTATCAAAATTATATTAAA
Found at i:1332924 original size:17 final size:16
Alignment explanation
Indices: 1332898--1332933 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1332888 TCAATCGACA
1332898 AAAATAAAAAATAACTC
1 AAAAT-AAAAATAACTC
*
1332915 AAAATTAAAATAACTC
1 AAAATAAAAATAACTC
1332931 AAA
1 AAA
1332934 TCTAAATAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.69, C:0.11, G:0.00, T:0.19
Consensus pattern (16 bp):
AAAATAAAAATAACTC
Found at i:1332940 original size:15 final size:15
Alignment explanation
Indices: 1332905--1332950 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
1332895 ACAAAAATAA
1332905 AAAATAACTCAAAATT
1 AAAATAACTC-AAATT
1332921 AAAATAACTCAAATCT
1 AAAATAACTCAAAT-T
*
1332937 -AAATAACTTAAATT
1 AAAATAACTCAAATT
1332951 CGAAATTATC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 1 0.04
15 16 0.57
16 11 0.39
ACGTcount: A:0.59, C:0.13, G:0.00, T:0.28
Consensus pattern (15 bp):
AAAATAACTCAAATT
Found at i:1335489 original size:151 final size:151
Alignment explanation
Indices: 1335313--1335625 Score: 608
Period size: 151 Copynumber: 2.1 Consensus size: 151
1335303 AAGTGTTGGT
1335313 TGTCTGAATTTTTTTTTTTTTTTGGGCTAGAAAATCAAATTTAAGATACTTAAATTTAGAGTCTC
1 TGTCTGAA-TTTTTTTTTTTTTTGGGCTAGAAAATCAAATTTAAGATACTTAAATTTAGAGTCTC
1335378 TAGTCAGTCCTTTCAAGACTAAACAAAACCTTAAAAGTTACTTGGATTTTATGTTTAGTTCATGG
65 TAGTCAGTCCTTTCAAGACTAAACAAAACCTTAAAAGTTACTTGGATTTTATGTTTAGTTCATGG
1335443 CTAATTGGCTACATATTTGCCA
130 CTAATTGGCTACATATTTGCCA
1335465 TGTCTGAATTTTTTTTTTTTTTGGGCTAGAAAATCAAATTTAAGATACTTAAATTTAGAGTCTCT
1 TGTCTGAATTTTTTTTTTTTTTGGGCTAGAAAATCAAATTTAAGATACTTAAATTTAGAGTCTCT
1335530 AGTCAGTCCTTTCAAGACTAAACAAAACCTTAAAAGTTACTTGGATTTTATGTTTAGTTCATGGC
66 AGTCAGTCCTTTCAAGACTAAACAAAACCTTAAAAGTTACTTGGATTTTATGTTTAGTTCATGGC
1335595 TAATTGGCTACATATTTGCCA
131 TAATTGGCTACATATTTGCCA
*
1335616 TGTCTTAATT
1 TGTCTGAATT
1335626 ATGCATCTTC
Statistics
Matches: 160, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
151 152 0.95
152 8 0.05
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (151 bp):
TGTCTGAATTTTTTTTTTTTTTGGGCTAGAAAATCAAATTTAAGATACTTAAATTTAGAGTCTCT
AGTCAGTCCTTTCAAGACTAAACAAAACCTTAAAAGTTACTTGGATTTTATGTTTAGTTCATGGC
TAATTGGCTACATATTTGCCA
Found at i:1337897 original size:34 final size:34
Alignment explanation
Indices: 1337854--1337929 Score: 152
Period size: 34 Copynumber: 2.2 Consensus size: 34
1337844 ATCGTGTAAT
1337854 TGTAGTTTCTGTATACGTACAATGATTTTGATAA
1 TGTAGTTTCTGTATACGTACAATGATTTTGATAA
1337888 TGTAGTTTCTGTATACGTACAATGATTTTGATAA
1 TGTAGTTTCTGTATACGTACAATGATTTTGATAA
1337922 TGTAGTTT
1 TGTAGTTT
1337930 ATTTACGGTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.28, C:0.08, G:0.18, T:0.46
Consensus pattern (34 bp):
TGTAGTTTCTGTATACGTACAATGATTTTGATAA
Found at i:1338433 original size:25 final size:24
Alignment explanation
Indices: 1338387--1338463 Score: 88
Period size: 23 Copynumber: 3.2 Consensus size: 24
1338377 TTTTTTTGTG
1338387 TAAATTATATAA-AT-ATAAAATTT
1 TAAATTATA-AATATGATAAAATTT
1338410 TAAATTATTAAATATGATAAAATTT
1 TAAATTA-TAAATATGATAAAATTT
* *
1338435 TTAA-TATAAATATGATATATATTT
1 TAAATTATAAATATGATA-AAATTT
1338459 TAAAT
1 TAAAT
1338464 ATTTTCATAT
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
23 20 0.43
24 14 0.30
25 12 0.26
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (24 bp):
TAAATTATAAATATGATAAAATTT
Found at i:1338448 original size:23 final size:23
Alignment explanation
Indices: 1338401--1338465 Score: 85
Period size: 24 Copynumber: 2.7 Consensus size: 23
1338391 TTATATAAAT
1338401 ATAAAATTTTAAATTATTAAATATG
1 ATAAAATTTTAAA-TA-TAAATATG
*
1338426 ATAAAATTTTTAATATAAATATG
1 ATAAAATTTTAAATATAAATATG
*
1338449 ATATATATTTTAAATAT
1 ATA-AAATTTTAAATAT
1338466 TTTCATATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
23 11 0.31
24 13 0.36
25 12 0.33
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (23 bp):
ATAAAATTTTAAATATAAATATG
Found at i:1338925 original size:9 final size:9
Alignment explanation
Indices: 1338907--1338941 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
1338897 ATATAATATT
1338907 TTAAATAAAA
1 TTAAA-AAAA
1338917 TTAAAAAAA
1 TTAAAAAAA
1338926 TTAAAAAAA
1 TTAAAAAAA
*
1338935 TCAAAAA
1 TTAAAAA
1338942 TTAATTCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 19 0.79
10 5 0.21
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (9 bp):
TTAAAAAAA
Found at i:1339317 original size:19 final size:20
Alignment explanation
Indices: 1339280--1339317 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
1339270 AAAATTAGAT
**
1339280 ATAAATATTAAATTCAAAAA
1 ATAAATATTAAATAAAAAAA
1339300 ATAAAT-TTAAATAAAAAA
1 ATAAATATTAAATAAAAAA
1339318 TTTAGTCTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (20 bp):
ATAAATATTAAATAAAAAAA
Found at i:1339778 original size:2 final size:2
Alignment explanation
Indices: 1339766--1339801 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1339756 TTAATTTGCT
*
1339766 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1339802 CACACACACA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1340079 original size:3 final size:3
Alignment explanation
Indices: 1340073--1340115 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
1340063 CTTCTTCTTC
* *
1340073 TTA TTA TTA TTA TTA TCA TTA TTA TTA TTA TTA TCA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1340116 CATCTTTTCT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:1340742 original size:6 final size:6
Alignment explanation
Indices: 1340731--1340859 Score: 74
Period size: 6 Copynumber: 21.7 Consensus size: 6
1340721 CGTGATTTTG
* * *
1340731 TTATAT TTATAT ATTTTA- TTATA- TTATAA TTATAT TTA-AT TTTTATT
1 TTATAT TTATAT -TTATAT TTATAT TTATAT TTATAT TTATAT TTATA-T
* * * * *
1340778 TTATTT TTATAT ATTGATAAT TTATA- TTATA- TAAAAT TTAAAAT ATATAT
1 TTATAT TTATAT -TT-AT-AT TTATAT TTATAT TTATAT TT-ATAT TTATAT
*
1340828 TTATA- TTATAT TTTTAT TTAT-T TTATAT TTAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTAT
1340860 TATATTCATA
Statistics
Matches: 97, Mismatches: 15, Indels: 22
0.72 0.11 0.16
Matches are distributed among these distances:
5 31 0.32
6 43 0.44
7 17 0.18
8 4 0.04
9 2 0.02
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (6 bp):
TTATAT
Found at i:1340839 original size:11 final size:11
Alignment explanation
Indices: 1340731--1340870 Score: 60
Period size: 11 Copynumber: 12.5 Consensus size: 11
1340721 CGTGATTTTG
1340731 TTATATTTATA
1 TTATATTTATA
*
1340742 -TATTTTATTATA
1 TTA-TAT-TTATA
*
1340754 TTATAATTATA
1 TTATATTTATA
*
1340765 TT-TAATTTTTA
1 TTAT-ATTTATA
* *
1340776 TTTTATTTTTA
1 TTATATTTATA
*
1340787 -TATATTGATAA
1 TTATATTTAT-A
1340798 TT-TATATTATA
1 TTATAT-TTATA
* * *
1340809 TAAAATTTAAAA
1 TTATATTT-ATA
1340821 TATATATTTATA
1 T-TATATTTATA
*
1340833 TTATATTTTTA
1 TTATATTTATA
1340844 TT-TATTTTATA
1 TTATA-TTTATA
1340855 TT-TA-TTATA
1 TTATATTTATA
1340864 TTCATAT
1 TT-ATAT
1340871 AAGTTAAATT
Statistics
Matches: 97, Mismatches: 17, Indels: 29
0.68 0.12 0.20
Matches are distributed among these distances:
9 7 0.07
10 11 0.11
11 53 0.55
12 19 0.20
13 7 0.07
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (11 bp):
TTATATTTATA
Found at i:1340847 original size:17 final size:18
Alignment explanation
Indices: 1340825--1340862 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
1340815 TTAAAATATA
1340825 TATTTATATTATATTT-T
1 TATTTATATTATATTTAT
*
1340842 TATTTATTTTATATTTAT
1 TATTTATATTATATTTAT
1340860 TAT
1 TAT
1340863 ATTCATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TATTTATATTATATTTAT
Found at i:1340870 original size:6 final size:5
Alignment explanation
Indices: 1340731--1340870 Score: 54
Period size: 5 Copynumber: 29.2 Consensus size: 5
1340721 CGTGATTTTG
* *
1340731 TTATA TT-TA -TATA TTTTA TTATA TTATAA TTATA TT-TAA TT-T- TTATT
1 TTATA TTATA TTATA TTATA TTATA TTAT-A TTATA TTAT-A TTATA TTATA
* * * **
1340778 TTAT- TTTTA -TATA TTGATAA TTTATA TTATA TAAAA TT-TA AAATA
1 TTATA TTATA TTATA TT-AT-A -TTATA TTATA TTATA TTATA TTATA
*
1340823 -TATA TTTATA TTATA TT-T- TTAT- TTATT TTATA TT-TA TTATA TTCATA
1 TTATA -TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TT-ATA
1340870 T
1 T
1340871 AAGTTAAATT
Statistics
Matches: 105, Mismatches: 12, Indels: 35
0.69 0.08 0.23
Matches are distributed among these distances:
3 5 0.05
4 26 0.25
5 53 0.50
6 16 0.15
7 3 0.03
8 2 0.02
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:1341243 original size:21 final size:17
Alignment explanation
Indices: 1341202--1341236 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1341192 CAGTCACTTG
1341202 CTTTCTGATCTTCCTTC
1 CTTTCTGATCTTCCTTC
1341219 CTTTCTGATCTTCCTTC
1 CTTTCTGATCTTCCTTC
1341236 C
1 C
1341237 AACCTTTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.06, C:0.37, G:0.06, T:0.51
Consensus pattern (17 bp):
CTTTCTGATCTTCCTTC
Found at i:1350624 original size:55 final size:55
Alignment explanation
Indices: 1350531--1350643 Score: 163
Period size: 55 Copynumber: 2.1 Consensus size: 55
1350521 TTATATAAAA
* * * *
1350531 ACGTCACGTAAGATAATGAGTTCGATGTAGAATTATTATAGAATTAAGTGATTTT
1 ACGTCACGTAAGATAACGAGTTCAATATAGAATCATTATAGAATTAAGTGATTTT
* * *
1350586 ACGTCACGTAAGGTAACGAGTTTAATATGGAATCATTATAGAATTAAGTGATTTT
1 ACGTCACGTAAGATAACGAGTTCAATATAGAATCATTATAGAATTAAGTGATTTT
1350641 ACG
1 ACG
1350644 CGAAGAATGC
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.35
Consensus pattern (55 bp):
ACGTCACGTAAGATAACGAGTTCAATATAGAATCATTATAGAATTAAGTGATTTT
Found at i:1359270 original size:20 final size:20
Alignment explanation
Indices: 1359247--1359342 Score: 113
Period size: 20 Copynumber: 4.8 Consensus size: 20
1359237 AAAGTACCCA
1359247 AATGTATCGATACATTCTTC
1 AATGTATCGATACATTCTTC
* * *
1359267 AATGTATCGACACATGT-ATG
1 AATGTATCGATACAT-TCTTC
* *
1359287 AATGTATGGATATATTCTTC
1 AATGTATCGATACATTCTTC
*
1359307 AATGTATCGATATATTCTTC
1 AATGTATCGATACATTCTTC
*
1359327 AATGTATTGATACATT
1 AATGTATCGATACATT
1359343 ATGTGTTTTT
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
19 1 0.02
20 61 0.97
21 1 0.02
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.41
Consensus pattern (20 bp):
AATGTATCGATACATTCTTC
Found at i:1360279 original size:21 final size:22
Alignment explanation
Indices: 1360246--1360286 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1360236 AGCCTTTGAC
*
1360246 CATGCATTTTTTTATTATGTTT
1 CATGCATTTTTTTAATATGTTT
1360268 CATGCA-TTTTTTAATATGT
1 CATGCATTTTTTTAATATGT
1360287 CCAGTATCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.22, C:0.10, G:0.10, T:0.59
Consensus pattern (22 bp):
CATGCATTTTTTTAATATGTTT
Found at i:1370483 original size:43 final size:43
Alignment explanation
Indices: 1370422--1370511 Score: 162
Period size: 43 Copynumber: 2.1 Consensus size: 43
1370412 CCTTTTTCAT
*
1370422 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
*
1370465 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
1370508 CTTT
1 CTTT
1370512 TCCATCTTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:1370543 original size:52 final size:52
Alignment explanation
Indices: 1370465--1370564 Score: 155
Period size: 52 Copynumber: 1.9 Consensus size: 52
1370455 ACATTGGCAC
* *
1370465 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACACCTTTTCCAT
* * *
1370517 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCTTTT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACACCTTTT
1370565 TTCTCAGCTT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 43 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (52 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACACCTTTTCCAT
Found at i:1371464 original size:13 final size:13
Alignment explanation
Indices: 1371446--1371470 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1371436 CATAAAGTGT
1371446 TGTATCGATACAA
1 TGTATCGATACAA
1371459 TGTATCGATACA
1 TGTATCGATACA
1371471 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1371470 original size:33 final size:33
Alignment explanation
Indices: 1371426--1371492 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1371416 TTCAACGATT
1371426 TGTATCAATACATAAAGTGTTGTATCGATACAA
1 TGTATCAATACATAAAGTGTTGTATCGATACAA
* *** *
1371459 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCAATACATAAAGTGTTGTATCGATACAA
1371492 T
1 T
1371493 TTAAGCTACT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCAATACATAAAGTGTTGTATCGATACAA
Found at i:1371551 original size:13 final size:13
Alignment explanation
Indices: 1371533--1371557 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1371523 ATCACTTAAA
1371533 TGTATCGATACAT
1 TGTATCGATACAT
1371546 TGTATCGATACA
1 TGTATCGATACA
1371558 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1371610 original size:52 final size:51
Alignment explanation
Indices: 1371546--1371694 Score: 244
Period size: 52 Copynumber: 2.9 Consensus size: 51
1371536 ATCGATACAT
**
1371546 TGTATCGATACACTGATCTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACT-ATCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
*
1371598 TGTATCGATACACTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTAT-CAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1371650 TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACACTA-TCAATGTATCGATACATGCAGGCAAATTT
1371695 TCATATTTCG
Statistics
Matches: 91, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
51 2 0.02
52 88 0.97
53 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Consensus pattern (51 bp):
TGTATCGATACACTATCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:1377755 original size:6 final size:6
Alignment explanation
Indices: 1377739--1377786 Score: 62
Period size: 6 Copynumber: 8.0 Consensus size: 6
1377729 TCCTTTACAC
* *
1377739 CAAAAA AAAAAA C-AAAA CAAAAA CAAAACA AAAAAA CAAAAA CAAAAA
1 CAAAAA CAAAAA CAAAAA CAAAAA CAAAA-A CAAAAA CAAAAA CAAAAA
1377787 AAACCAAGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
5 5 0.14
6 26 0.72
7 5 0.14
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (6 bp):
CAAAAA
Found at i:1377774 original size:19 final size:18
Alignment explanation
Indices: 1377739--1377789 Score: 77
Period size: 19 Copynumber: 2.8 Consensus size: 18
1377729 TCCTTTACAC
*
1377739 CAAAAA-AAAAAACAAAA
1 CAAAAACAAAAAAAAAAA
1377756 CAAAAACAAAACAAAAAAA
1 CAAAAACAAAA-AAAAAAA
1377775 CAAAAACAAAAAAAA
1 CAAAAACAAAAAAAA
1377790 CCAAGAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
17 6 0.19
18 8 0.26
19 17 0.55
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (18 bp):
CAAAAACAAAAAAAAAAA
Found at i:1377776 original size:24 final size:25
Alignment explanation
Indices: 1377739--1377799 Score: 83
Period size: 25 Copynumber: 2.5 Consensus size: 25
1377729 TCCTTTACAC
1377739 CAAAA-AAAAAAAC-AAAACAAAAA
1 CAAAACAAAAAAACAAAAACAAAAA
1377762 CAAAACAAAAAAACAAAAACAAAAA
1 CAAAACAAAAAAACAAAAACAAAAA
*
1377787 -AAACCAAGAAAAA
1 CAAAACAA-AAAAA
1377800 ATAGCCAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
23 5 0.15
24 14 0.41
25 15 0.44
ACGTcount: A:0.84, C:0.15, G:0.02, T:0.00
Consensus pattern (25 bp):
CAAAACAAAAAAACAAAAACAAAAA
Found at i:1377798 original size:10 final size:9
Alignment explanation
Indices: 1377743--1377800 Score: 55
Period size: 10 Copynumber: 5.9 Consensus size: 9
1377733 TTACACCAAA
1377743 AAAAAAAAC
1 AAAAAAAAC
1377752 AAAACAAAAAC
1 -AAA-AAAAAC
1377763 AAAACAAAA-
1 AAAA-AAAAC
1377772 AAACAAAAAC
1 AAA-AAAAAC
1377782 AAAAAAAACC
1 AAAAAAAA-C
1377792 AAGAAAAAA
1 AA-AAAAAA
1377801 TAGCCAAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
9 13 0.31
10 17 0.40
11 12 0.29
ACGTcount: A:0.84, C:0.14, G:0.02, T:0.00
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:1379079 original size:28 final size:28
Alignment explanation
Indices: 1379030--1380087 Score: 1071
Period size: 28 Copynumber: 37.1 Consensus size: 28
1379020 CGTTCATCTC
* *
1379030 TTCAAAGCCCACAAGTCAATGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCTT
*
1379058 TTCAAGAGCCCACAAGTTA-TGGCACTCTT
1 TTCAA-AGCCCACAAGTCAGTGGCAC-CTT
* *
1379087 TTCAAAGCCCACAAATCAGTGGCACTTTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CTT
1379116 TTCAAAG-CCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CTT
* * *
1379144 TTC-AAGCCTACAAGACAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCTT
*
1379171 TTCAAAGCCCACAAGTCAATGGCATCC-T
1 TTCAAAGCCCACAAGTCAGTGGCA-CCTT
*
1379199 TTCAAAGCCCACAAATCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CTT
1379228 TTCAAAGCCCACAAGTCAGTGGCA-CTCT
1 TTCAAAGCCCACAAGTCAGTGGCACCT-T
* *
1379256 TTCAAAGCTCACAAGTCAATGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CTT
* *
1379285 TTCAAAACCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCTT
* *
1379313 TTCAAAGCCCATAAGTCAGTGGCACTTTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CTT
* *
1379342 TTCAAAGCCCATAAATCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CTT
* *
1379371 TTCAAAGCAC-CAAGTCAGTAGCACCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCTT
* * *
1379398 TTTAAAGCCCACAAATCAGTGGTACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CTT
1379427 TTCAAAGCCCACAAGTCAGTGGCACCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCTT
* *
1379455 TTCAAAGCCTACAAGTCAGTGACA-CTCT
1 TTCAAAGCCCACAAGTCAGTGGCACCT-T
*
1379483 TTCAAAGCCCACACGAGTC-GATGGTAACTCTT
1 TTCAAAGCCCACA--AGTCAG-TGG-CAC-CTT
* *
1379515 TTCAAAG-CCACAAATCAATGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CTT
* *
1379543 TTCAAAGCCCATAAGTCAGTGACATCC-T
1 TTCAAAGCCCACAAGTCAGTGGCA-CCTT
*
1379571 TTCAAAGCCCACAAATCAGTGGCACTCTTTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-C--TT
* *
1379602 TTCAAAGCCCACAAATCAATGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CTT
* * *
1379631 TTCAAAGTCCACATGAGTCGGTGGTAACTCTT
1 TTCAAAGCCCACA--AGTCAGTGG-CAC-CTT
* * *
1379663 TTCAAAGTCTACAAGTCAGTGGCATTCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-CCTT
*
1379692 TTCAAAG-AC-CAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CTT
* *
1379719 TTCAAAGCCCACAAGTCGGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCTT
1379747 TTCAAAGCCCACAAGTCAGTGGCATCC-T
1 TTCAAAGCCCACAAGTCAGTGGCA-CCTT
1379775 TTCAAAGCCCACAAGTCAGTGGC-CC-T
1 TTCAAAGCCCACAAGTCAGTGGCACCTT
1379801 TTCAAAGCCCATGCAAGTCAGTGGCACAC-T
1 TTCAAAGCCCA--CAAGTCAGTGGCAC-CTT
*
1379831 TTCAAAGCCCACAAATCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CTT
*
1379860 TTC-AAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCTT
*
1379887 TTCAAAGCCCACAAGTTAGTGGCATCC-T
1 TTCAAAGCCCACAAGTCAGTGGCA-CCTT
* *
1379915 TTCAAAGCCTACAAGTCAGTGACACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CTT
* * *
1379944 TT-AAA-CCCACGCAAGTCAATAGTACC-T
1 TTCAAAGCCCA--CAAGTCAGTGGCACCTT
* *
1379971 TTCAAAGCCCA-TAGTTAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CTT
* *
1379999 TTCAAAGCCCATAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCTT
* *
1380027 TTCAAAGCTCATAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CTT
*
1380056 TTCAAAGCCCACCCAAGTCAGTGGCAACTT
1 TTCAAAGCCCA--CAAGTCAGTGGCACCTT
1380086 TT
1 TT
1380088 TTCAAGCCCA
Statistics
Matches: 877, Mismatches: 98, Indels: 108
0.81 0.09 0.10
Matches are distributed among these distances:
26 22 0.03
27 61 0.07
28 427 0.49
29 253 0.29
30 35 0.04
31 51 0.06
32 26 0.03
33 2 0.00
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.25
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCACCTT
Found at i:1379163 original size:56 final size:58
Alignment explanation
Indices: 1379030--1380099 Score: 1198
Period size: 57 Copynumber: 18.7 Consensus size: 58
1379020 CGTTCATCTC
* * *
1379030 TTCAAAGCCCACAAGTCAATGGCAC-CCTTTCAAGAGCCCACAAGTTA-TGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAA-AGCCCACAAGTCAGTGGCACTCTT
* *
1379087 TTCAAAGCCCACAAATCAGTGGCACTTTTTTCAAAG-CCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTT
* * * * *
1379144 TTC-AAGCCTACAAGACAGTGGCAC-CCTTTCAAAGCCCACAAGTCAATGGCA-TCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTT
*
1379199 TTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTC-T
1 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTT
* * * *
1379256 TTCAAAGCTCACAAGTCAATGGCACTCTTTTCAAAACCCACAAGTCAGTGGCAC-CCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTT
* * * *
1379313 TTCAAAGCCCATAAGTCAGTGGCACTTTTTTCAAAGCCCATAAATCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTT
* * * * *
1379371 TTCAAAGCAC-CAAGTCAGTAGCAC-CTTTTTAAAGCCCACAAATCAGTGGTACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTT
* *
1379427 TTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCCTACAAGTCAGTGACACTC-T
1 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTT
* * *
1379483 TTCAAAGCCCACACGAGTC-GATGGTAACTCTTTTCAAAG-CCACAAATCAATGGCACTCTT
1 TTCAAAGCCCACA--AGTCAG-TGG-CACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTT
* * * *
1379543 TTCAAAGCCCATAAGTCAGTGACA-TCCTTTCAAAGCCCACAAATCAGTGGCACTCTTTT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTC--TT
* * * * *
1379602 TTCAAAGCCCACAAATCAATGGCACTCTTTTCAAAGTCCACATGAGTCGGTGGTAACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACA--AGTCAGTGG-CACTCTT
* * * *
1379663 TTCAAAGTCTACAAGTCAGTGGCATTCTTTTCAAAG-AC-CAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTT
* * *
1379719 TTCAAAGCCCACAAGTCGGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCA-TCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTT
*
1379775 TTCAAAGCCCACAAGTCAGTGGC-C-C-TTTCAAAGCCCATGCAAGTCAGTGGCACAC-T
1 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCA--CAAGTCAGTGGCACTCTT
* *
1379831 TTCAAAGCCCACAAATCAGTGGCACTCTTTTC-AAGCCCACAAGTCAGTGGCAC-CCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTT
* * * *
1379887 TTCAAAGCCCACAAGTTAGTGGCA-TCCTTTCAAAGCCTACAAGTCAGTGACACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTT
* * * * *
1379944 TT-AAA-CCCACGCAAGTCAATAGTAC-C-TTTCAAAGCCCA-TAGTTAGTGGCACTCTT
1 TTCAAAGCCCA--CAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTT
* * * *
1379999 TTCAAAGCCCATAAGTCAGTGGCAC-CCTTTCAAAGCTCATAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTT
*
1380056 TTCAAAGCCCACCCAAGTCAGTGGCAACTTTTTTC-AAGCCCACA
1 TTCAAAGCCCA--CAAGTCAGTGGC-ACTCTTTTCAAAGCCCACA
1380100 CAAGTTAGTG
Statistics
Matches: 862, Mismatches: 106, Indels: 87
0.82 0.10 0.08
Matches are distributed among these distances:
54 12 0.01
55 63 0.07
56 295 0.34
57 299 0.35
58 40 0.05
59 57 0.07
60 48 0.06
61 37 0.04
62 7 0.01
63 4 0.00
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.25
Consensus pattern (58 bp):
TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTT
Found at i:1380686 original size:20 final size:20
Alignment explanation
Indices: 1380661--1380738 Score: 104
Period size: 20 Copynumber: 3.9 Consensus size: 20
1380651 AAAGTACCCA
*
1380661 AATGTATCGATACATTCTTT
1 AATGTATCGATACATTCTTC
* *
1380681 AATGTATCGATACATGT-ATG
1 AATGTATCGATACAT-TCTTC
*
1380701 AATGTATCGATATATTCTTC
1 AATGTATCGATACATTCTTC
1380721 AATGTATCGATACATTCT
1 AATGTATCGATACATTCT
1380739 GTGTTTTTAC
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
19 1 0.02
20 48 0.96
21 1 0.02
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.41
Consensus pattern (20 bp):
AATGTATCGATACATTCTTC
Found at i:1384182 original size:35 final size:35
Alignment explanation
Indices: 1384143--1384215 Score: 110
Period size: 35 Copynumber: 2.1 Consensus size: 35
1384133 TATGTTATTA
*
1384143 TTTTTTTCTTCAATATCTATATTATATATAAAACC
1 TTTTTTTCTTCAATATCTATACTATATATAAAACC
* * *
1384178 TTTTTTTCTTTAATATTTATACTATATATAAAGCC
1 TTTTTTTCTTCAATATCTATACTATATATAAAACC
1384213 TTT
1 TTT
1384216 GGCTAAGTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.32, C:0.12, G:0.01, T:0.55
Consensus pattern (35 bp):
TTTTTTTCTTCAATATCTATACTATATATAAAACC
Found at i:1384782 original size:27 final size:27
Alignment explanation
Indices: 1384730--1384780 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
1384720 AATTAAAATC
*
1384730 AATTTAAATTTATAAAATTTTATTTAA
1 AATTTAAATTTATAAAATTATATTTAA
1384757 AATTT-AATTTATATAAATTA-ATTT
1 AATTTAAATTTATA-AAATTATATTT
1384781 TATCAACTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
AATTTAAATTTATAAAATTATATTTAA
Done.