Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A09
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: 77927517
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1491452 characters in sequence are not A, C, G, or T
File 180 of 250
Found at i:57044582 original size:47 final size:47
Alignment explanation
Indices: 57044447--57044653 Score: 175
Period size: 47 Copynumber: 4.3 Consensus size: 47
57044437 ATAGTAAAAT
** * *
57044447 TATGGTCTTGCACA-TAGTCACATATCACATACCGAGGCCATAGCCCAGC
1 TATGGTCTTATACAGTAG-CACATATCAC--ACCGATGCCATAGCCCAGA
* * * * * *
57044496 CATGGTCTTATAC-GGATCACATATCACACTGATGTCATATCCCAGA
1 TATGGTCTTATACAGTAGCACATATCACACCGATGCCATAGCCCAGA
* *
57044542 TATGGTCTTATACAGTAGCACATATCACACCGATGCCATATCCCGGA
1 TATGGTCTTATACAGTAGCACATATCACACCGATGCCATAGCCCAGA
* * * * *
57044589 TATGGTCTTATACGGAAGCACAAATCACATTTCTCCGAAGCCATAGCCCAGC
1 TATGGTCTTATACAGTAGCACATATCACA-----CCGATGCCATAGCCCAGA
57044641 TATGGTCTTATAC
1 TATGGTCTTATAC
57044654 GGAAATCACA
Statistics
Matches: 128, Mismatches: 23, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
46 26 0.20
47 54 0.42
48 10 0.08
49 11 0.09
52 27 0.21
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (47 bp):
TATGGTCTTATACAGTAGCACATATCACACCGATGCCATAGCCCAGA
Found at i:57047911 original size:18 final size:18
Alignment explanation
Indices: 57047870--57047904 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
57047860 GTACTAGGTA
*
57047870 GATAAAAATGAATACTAC
1 GATAAAAATGAATAATAC
57047888 GATAAAAA-GAATAATAC
1 GATAAAAATGAATAATAC
57047905 ATATAAAGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.60, C:0.09, G:0.11, T:0.20
Consensus pattern (18 bp):
GATAAAAATGAATAATAC
Found at i:57048224 original size:7 final size:7
Alignment explanation
Indices: 57048212--57048237 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
57048202 AAATAGTATT
57048212 TAATATA
1 TAATATA
57048219 TAATATA
1 TAATATA
57048226 TAATATA
1 TAATATA
57048233 TAATA
1 TAATA
57048238 ACAAGAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
TAATATA
Found at i:57048361 original size:19 final size:18
Alignment explanation
Indices: 57048321--57048359 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
57048311 TTTTAAAATG
*
57048321 AAATAATATATAATAGAT
1 AAATAATAAATAATAGAT
57048339 AAATAAATAAATAATA-AT
1 AAAT-AATAAATAATAGAT
57048357 AAA
1 AAA
57048360 ATGTGTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (18 bp):
AAATAATAAATAATAGAT
Found at i:57048519 original size:24 final size:24
Alignment explanation
Indices: 57048469--57048522 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
57048459 TATAATATTT
*
57048469 ATAAAAATAATAAGTGGTATAGAA
1 ATAAAAATAATAAATGGTATAGAA
* *
57048493 ATAAAACATAATAAATGTTATA-TA
1 ATAAAA-ATAATAAATGGTATAGAA
57048517 ATAAAA
1 ATAAAA
57048523 TATATAGGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.61, C:0.02, G:0.09, T:0.28
Consensus pattern (24 bp):
ATAAAAATAATAAATGGTATAGAA
Found at i:57048639 original size:47 final size:44
Alignment explanation
Indices: 57048588--57048688 Score: 102
Period size: 47 Copynumber: 2.2 Consensus size: 44
57048578 TAAAATAATG
*
57048588 TATAAATAATA-AT-AAATATATAATATATGTGAAAATATAACAATATA
1 TATAAATAATATATAAAATA-ATAAT-T-TGAGAAAA-ATAACAA-ATA
*
57048635 TATAAAAAATGATATAAAATAATAATTTGAGAAAAATAACAAATA
1 TATAAATAAT-ATATAAAATAATAATTTGAGAAAAATAACAAATA
57048680 -AT-AATAATA
1 TATAAATAATA
57048689 CACATAATAA
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
42 1 0.02
43 5 0.10
44 2 0.04
45 3 0.06
46 7 0.15
47 16 0.33
48 2 0.04
49 7 0.15
50 5 0.10
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (44 bp):
TATAAATAATATATAAAATAATAATTTGAGAAAAATAACAAATA
Found at i:57048801 original size:19 final size:22
Alignment explanation
Indices: 57048764--57048805 Score: 63
Period size: 19 Copynumber: 2.0 Consensus size: 22
57048754 AATAAAACAA
57048764 ATAATAAATATATATATATAGG
1 ATAATAAATATATATATATAGG
57048786 ATAATAAA-ATA-A-ATATAGG
1 ATAATAAATATATATATATAGG
57048805 A
1 A
57048806 CTGAATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 8 0.40
20 1 0.05
21 3 0.15
22 8 0.40
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.31
Consensus pattern (22 bp):
ATAATAAATATATATATATAGG
Found at i:57051714 original size:18 final size:20
Alignment explanation
Indices: 57051691--57051728 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
57051681 CTTCTTACAC
57051691 AAACT-CAAAT-ACACCATT
1 AAACTCCAAATGACACCATT
*
57051709 AAACTCCCAATGACACCATT
1 AAACTCCAAATGACACCATT
57051729 TTGTCAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 4 0.24
20 8 0.47
ACGTcount: A:0.45, C:0.32, G:0.03, T:0.21
Consensus pattern (20 bp):
AAACTCCAAATGACACCATT
Found at i:57053397 original size:22 final size:22
Alignment explanation
Indices: 57053370--57053413 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
57053360 TTAACCAAAT
*
57053370 AAATTGATAAATATAAAGATTA
1 AAATTGATAAATATAAAAATTA
57053392 AAATTGATAAATATAAAAATTA
1 AAATTGATAAATATAAAAATTA
57053414 TAAAAACTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (22 bp):
AAATTGATAAATATAAAAATTA
Found at i:57057692 original size:132 final size:130
Alignment explanation
Indices: 57057359--57057735 Score: 504
Period size: 131 Copynumber: 2.9 Consensus size: 130
57057349 TAAGAATTCT
* *
57057359 TTAAAACGAAGGTAATATTCGATATTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGC
1 TTAAAACGAAGGTAATATTCGATATTTGGCAATTCGCGGAATCGTGCCCTATCGTGCTGGGTTGC
* * *
57057424 AATTTCTCGTTTGCTCAAAGTAATCGAAGGTTCCTTTAGAATTTCACCCATGTCTTTAAAAAATC
66 AATTTCTCGTTTGTTCAAAATAATCGAAGGTTCCTTTAGAATTTCACTCATGTCTTTAAAAAAT-
57057489 C
130 C
* ** * * *
57057490 TTTAAACGAAGGCGATGTTCGATATTTGGCGATTCGCGGAATCGTGCCCTATCGTGCTGGGTTTC
1 TTAAAACGAAGGTAATATTCGATATTTGGCAATTCGCGGAATCGTGCCCTATCGTGCTGGGTTGC
* * *
57057555 AATTTCTCGATTGTTCAAAATAATCGAAGGTCCCTTTTGAATTTCACTCATGTCTTTAAAAAACT
66 AATTTCTCGTTTGTTCAAAATAATCGAAGGTTCCTTTAGAATTTCACTCATGTCTTTAAAAAA-T
57057620 C
130 C
* * * * *
57057621 TTCAAAACGAAGGTAATACTCGATGTTTGGCAATTCGGGGAATCGTGCCTTATCGTGCTAGGTTG
1 TT-AAAACGAAGGTAATATTCGATATTTGGCAATTCGCGGAATCGTGCCCTATCGTGCTGGGTTG
* ** *
57057686 CGATTTC-CTGTTTGTTCAAAATAATCGAATATTCCTTTGGAATTTCACTC
65 CAATTTCTC-GTTTGTTCAAAATAATCGAAGGTTCCTTTAGAATTTCACTC
57057736 GTGCTTCCTA
Statistics
Matches: 212, Mismatches: 31, Indels: 5
0.85 0.12 0.02
Matches are distributed among these distances:
131 118 0.56
132 94 0.44
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (130 bp):
TTAAAACGAAGGTAATATTCGATATTTGGCAATTCGCGGAATCGTGCCCTATCGTGCTGGGTTGC
AATTTCTCGTTTGTTCAAAATAATCGAAGGTTCCTTTAGAATTTCACTCATGTCTTTAAAAAATC
Found at i:57065293 original size:181 final size:176
Alignment explanation
Indices: 57064971--57065293 Score: 448
Period size: 176 Copynumber: 1.8 Consensus size: 176
57064961 AAAATGATTG
* * * * *
57064971 AACAACCTATGCATCACAAAGGCCCGGGCCTAGGAGAAGTGAAAACTCCAAAAGAATGAATAATA
1 AACAACCTATGCATCACAAAGACCAGGGCATAGGAGAAGTGAAAACTCCAAAAGAACGAAAAATA
**
57065036 ACAAATAACATTGCAGTTTAGACAACATAAGAAAGTTTGGAACAACCTCAGACATTTTCCATTTT
66 ACAAATAACATTGCAGTTTAGACAACATAAGAAAGCCTGGAACAACCTCAGACATTTTCCATTTT
*
57065101 AATCTTTTGACTCATCCTGAAGAGGTTCAGACAATGAGCAATGGCA
131 AATCATTTGACTCATCCTGAAGAGGTTCAGACAATGAGCAATGGCA
* * *
57065147 AACAACCTATGCCTCACAAAGACTAGGGCATAGGAGAAGTGAAAACTTCAAAAGAACGAAAAATA
1 AACAACCTATGCATCACAAAGACCAGGGCATAGGAGAAGTGAAAACTCCAAAAGAACGAAAAATA
* * * ** *
57065212 TTGCAAATGATATTGCAGTTGTTTAGACAACATAAGAAAGCCTGGAACAACCTCAGATGTTTTCT
66 --ACAAATAACATTGCA---GTTTAGACAACATAAGAAAGCCTGGAACAACCTCAGACATTTTCC
57065277 ATTTTAATCATTTGACT
126 ATTTTAATCATTTGACT
57065294 AACCTGCCAA
Statistics
Matches: 125, Mismatches: 17, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
176 57 0.46
178 12 0.10
181 56 0.45
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.24
Consensus pattern (176 bp):
AACAACCTATGCATCACAAAGACCAGGGCATAGGAGAAGTGAAAACTCCAAAAGAACGAAAAATA
ACAAATAACATTGCAGTTTAGACAACATAAGAAAGCCTGGAACAACCTCAGACATTTTCCATTTT
AATCATTTGACTCATCCTGAAGAGGTTCAGACAATGAGCAATGGCA
Found at i:57066268 original size:3 final size:3
Alignment explanation
Indices: 57066262--57066314 Score: 52
Period size: 3 Copynumber: 17.7 Consensus size: 3
57066252 TCCTCCTCCG
* * * * * *
57066262 CTT CTT CTT CTT CTT CTT CAT CAT CAT CTA CAT CTT CGT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
57066310 CTT CT
1 CTT CT
57066315 CTCTCGTCGT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.09, C:0.34, G:0.02, T:0.55
Consensus pattern (3 bp):
CTT
Found at i:57073390 original size:58 final size:58
Alignment explanation
Indices: 57073300--57073415 Score: 232
Period size: 58 Copynumber: 2.0 Consensus size: 58
57073290 GGTCCATCTA
57073300 AGACTAAGGATTACCTGTACAGATCAACAGAAAAAAAGGTGAGTTTTCGTAAACTTAG
1 AGACTAAGGATTACCTGTACAGATCAACAGAAAAAAAGGTGAGTTTTCGTAAACTTAG
57073358 AGACTAAGGATTACCTGTACAGATCAACAGAAAAAAAGGTGAGTTTTCGTAAACTTAG
1 AGACTAAGGATTACCTGTACAGATCAACAGAAAAAAAGGTGAGTTTTCGTAAACTTAG
57073416 TGTGTAATCC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.24
Consensus pattern (58 bp):
AGACTAAGGATTACCTGTACAGATCAACAGAAAAAAAGGTGAGTTTTCGTAAACTTAG
Found at i:57079507 original size:27 final size:27
Alignment explanation
Indices: 57079450--57079507 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
57079440 ACTATATTTT
* *
57079450 AAAAGTTAAAATGTTATAAAATTTTAC
1 AAAAGTTAAAATGATATAAAATTATAC
57079477 AAAAGTTAAAAATGAT-TAAAATATATA-
1 AAAAGTT-AAAATGATATAAAAT-TATAC
57079504 AAAA
1 AAAA
57079508 TTAGTTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 17 0.63
28 10 0.37
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.31
Consensus pattern (27 bp):
AAAAGTTAAAATGATATAAAATTATAC
Found at i:57081954 original size:46 final size:46
Alignment explanation
Indices: 57081904--57082079 Score: 209
Period size: 46 Copynumber: 3.8 Consensus size: 46
57081894 TGATTGAGCA
57081904 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
57081950 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
57081995 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
57082043 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
57082080 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 9, Indels: 20
0.79 0.06 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 5 0.05
46 61 0.55
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:57082060 original size:93 final size:93
Alignment explanation
Indices: 57081901--57082072 Score: 310
Period size: 93 Copynumber: 1.8 Consensus size: 93
57081891 GGATGATTGA
*
57081901 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
57081966 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
57081994 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCTGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC-GAACTCGTTGAG
57082058 TTGAGTCCGAGTTCG
65 TTGAGTCCGAGTTCG
57082073 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
92 2 0.03
93 74 0.97
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:57085963 original size:20 final size:20
Alignment explanation
Indices: 57085935--57085973 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
57085925 CATTAGAAAA
57085935 TAATAAAA-TAAATAAATAAT
1 TAATAAAATTAAA-AAATAAT
*
57085955 TAATGAAATTAAAAAATAA
1 TAATAAAATTAAAAAATAA
57085974 ATCTTAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (20 bp):
TAATAAAATTAAAAAATAAT
Found at i:57087666 original size:53 final size:51
Alignment explanation
Indices: 57087518--57087677 Score: 196
Period size: 52 Copynumber: 3.1 Consensus size: 51
57087508 TAACGGAAAA
* *
57087518 GATGTGATATGTGCTTCCGTATAAGACCATAGCTGGGTTATGGCATCGGTAC
1 GATGTGATATGTG-TTCCGTATAAGACCATAGCTGGGATATGGCATCGGTAT
* * *
57087570 AATGTGAT-TCGTGTTCCTGTATAAGACCATAGCTGGGCTATGGCATCGGTGT
1 GATGTGATAT-GTGTTCC-GTATAAGACCATAGCTGGGATATGGCATCGGTAT
* **
57087622 GATGTGATAATATGATTCCGTATAAGACCATATTTGGGATATGGCATCGGTAT
1 GATGTGAT-ATGTG-TTCCGTATAAGACCATAGCTGGGATATGGCATCGGTAT
57087675 GAT
1 GAT
57087678 ATGTGATCCG
Statistics
Matches: 93, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
51 5 0.05
52 48 0.52
53 35 0.38
54 5 0.05
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.33
Consensus pattern (51 bp):
GATGTGATATGTGTTCCGTATAAGACCATAGCTGGGATATGGCATCGGTAT
Found at i:57092857 original size:66 final size:66
Alignment explanation
Indices: 57092772--57092904 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
57092762 TAAAAATAAT
*
57092772 TATATAAAGAAATTCAATTTAAATTTTTTTATCCATATTTTAATTATCAAATTTTTATTTGGTTA
1 TATATAAAGAAATTCAATTTAAAGTTTTTTATCCATATTTTAATTATCAAATTTTTATTTGGTTA
57092837 A
66 A
* * *
57092838 TATATAAAGAAATTTAATTTAAAGTTTTTTATCCCTATTTTAATTATCGAATTTTTATTTGGTTA
1 TATATAAAGAAATTCAATTTAAAGTTTTTTATCCATATTTTAATTATCAAATTTTTATTTGGTTA
57092903 A
66 A
57092904 T
1 T
57092905 TTAGTCATTC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.52
Consensus pattern (66 bp):
TATATAAAGAAATTCAATTTAAAGTTTTTTATCCATATTTTAATTATCAAATTTTTATTTGGTTA
A
Found at i:57098604 original size:61 final size:60
Alignment explanation
Indices: 57098456--57098642 Score: 173
Period size: 61 Copynumber: 3.1 Consensus size: 60
57098446 TTAGCACTAG
* * ** *
57098456 AACTTGACAATTTTTCTCAATTTGGTACCTAAGTTTTTTTTTTGTCCAA-TT-CAACACATA
1 AACTTGACACTTTTTCTTAATTTGGTACCT-AGTTTTTTTTTTGTCCAATTTGGTAC-CCTA
* * * * * *
57098516 AGCTTGATACTTTTTCCCTAATCTGGTACTTGAGTTTTTTTTTTGTCTAATTTGGTACCCTA
1 AACTTGACACTTTTT-CTTAATTTGGTACCT-AGTTTTTTTTTTGTCCAATTTGGTACCCTA
* *** *
57098578 AACTTGACACTTTGTCTTAATTTGGTACCTAAACTTTTTTTTATCCAATTTGGTA-CCTA
1 AACTTGACACTTTTTCTTAATTTGGTACCTAGTTTTTTTTTTGTCCAATTTGGTACCCTA
57098637 AACTTG
1 AACTTG
57098643 TCAAATGTTA
Statistics
Matches: 101, Mismatches: 23, Indels: 7
0.77 0.18 0.05
Matches are distributed among these distances:
59 10 0.10
60 32 0.32
61 40 0.40
62 17 0.17
63 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.11, T:0.47
Consensus pattern (60 bp):
AACTTGACACTTTTTCTTAATTTGGTACCTAGTTTTTTTTTTGTCCAATTTGGTACCCTA
Found at i:57100972 original size:55 final size:55
Alignment explanation
Indices: 57100857--57100975 Score: 152
Period size: 55 Copynumber: 2.2 Consensus size: 55
57100847 CTTAAACTTT
* *
57100857 TAAGTCAGTATTGTCCACGGGTAGGCCACACGAGCATGTGCCATAGCTGTGTCTA
1 TAAGTCAGTATTGTCCACGGGTAGGCCACACGAGCATGTGCCATAGCCGTGCCTA
* * * *
57100912 TAAGTCAGTATTGTCCACGGGTAGGCTACACG-GACGTGTGTCATGGCCGTGCCCTA
1 TAAGTCAGTATTGTCCACGGGTAGGCCACACGAG-CATGTGCCATAGCCGTG-CCTA
57100968 -AAGTCAGT
1 TAAGTCAGT
57100976 GTTGCACACG
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
54 1 0.02
55 52 0.93
56 3 0.05
ACGTcount: A:0.23, C:0.24, G:0.29, T:0.25
Consensus pattern (55 bp):
TAAGTCAGTATTGTCCACGGGTAGGCCACACGAGCATGTGCCATAGCCGTGCCTA
Found at i:57101537 original size:25 final size:26
Alignment explanation
Indices: 57101509--57101560 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
57101499 GGTTCATTAT
*
57101509 ATTAAATTTAAAAAAATTGAA-ATAA
1 ATTAAATTGAAAAAAATTGAACATAA
**
57101534 ATTAAATTGAAAGTAATTGAACATAA
1 ATTAAATTGAAAAAAATTGAACATAA
57101560 A
1 A
57101561 AAAAATAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.31
Consensus pattern (26 bp):
ATTAAATTGAAAAAAATTGAACATAA
Found at i:57103089 original size:19 final size:19
Alignment explanation
Indices: 57103065--57103103 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
57103055 TTAACATTAC
57103065 TTTAATGTTTATATTAGAG
1 TTTAATGTTTATATTAGAG
57103084 TTTAATGTTTATATTAGAG
1 TTTAATGTTTATATTAGAG
57103103 T
1 T
57103104 AGTATTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (19 bp):
TTTAATGTTTATATTAGAG
Found at i:57109179 original size:20 final size:21
Alignment explanation
Indices: 57109145--57109198 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
57109135 TGATGATATT
*
57109145 TTATGATTA-TTTAATTAGATA
1 TTAT-ATTATTTTAATGAGATA
57109166 -TATATTATTTTAATGAGATA
1 TTATATTATTTTAATGAGATA
*
57109186 TTTTATTATTTTA
1 TTATATTATTTTA
57109199 TTATTATTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 4 0.14
20 14 0.48
21 11 0.38
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (21 bp):
TTATATTATTTTAATGAGATA
Found at i:57109202 original size:3 final size:3
Alignment explanation
Indices: 57109184--57109232 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
57109174 TTTAATGAGA
*
57109184 TAT T-T TAT TAT T-T TAT TAT TAT T-T CAT TAT TAT T-T TAT TAT TAAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT
57109229 TAT T
1 TAT T
57109233 TAGTATAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
2 7 0.18
3 29 0.74
4 3 0.08
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:57109204 original size:11 final size:11
Alignment explanation
Indices: 57109188--57109226 Score: 69
Period size: 11 Copynumber: 3.5 Consensus size: 11
57109178 ATGAGATATT
57109188 TTATTATTTTA
1 TTATTATTTTA
*
57109199 TTATTATTTCA
1 TTATTATTTTA
57109210 TTATTATTTTA
1 TTATTATTTTA
57109221 TTATTA
1 TTATTA
57109227 ATTATTTAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:57109212 original size:19 final size:19
Alignment explanation
Indices: 57109184--57109225 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
57109174 TTTAATGAGA
*
57109184 TATTTTATTATT-TTATTAT
1 TATTTCATTATTATT-TTAT
57109203 TATTTCATTATTATTTTAT
1 TATTTCATTATTATTTTAT
57109222 TATT
1 TATT
57109226 AATTATTTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (19 bp):
TATTTCATTATTATTTTAT
Found at i:57109656 original size:11 final size:11
Alignment explanation
Indices: 57109624--57109656 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
57109614 TTGATATGTT
57109624 AGTGAAGAGAA
1 AGTGAAGAGAA
57109635 AGT-AAGAGAA
1 AGTGAAGAGAA
*
57109645 AGTGATGAGAA
1 AGTGAAGAGAA
57109656 A
1 A
57109657 TGGTGTAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.55, C:0.00, G:0.33, T:0.12
Consensus pattern (11 bp):
AGTGAAGAGAA
Found at i:57111412 original size:23 final size:23
Alignment explanation
Indices: 57111378--57111490 Score: 104
Period size: 23 Copynumber: 4.8 Consensus size: 23
57111368 CCCGATATAT
57111378 GGCTCTTCGTGAGCTTCCCGATA
1 GGCTCTTCGTGAGCTTCCCGATA
*
57111401 GGCTCTTTGTGAGCTTCCCGATA
1 GGCTCTTCGTGAGCTTCCCGATA
* * * *
57111424 GTGCT-TGCTTGAACTTCCCTATATA
1 G-GCTCTTCGTGAGCTTCCC--GATA
* *
57111449 TGGCTATCCG-GAGCTTCCCGATA
1 -GGCTCTTCGTGAGCTTCCCGATA
*
57111472 GGCTCTTCATGAGCTTCCC
1 GGCTCTTCGTGAGCTTCCC
57111491 AATATGGTTC
Statistics
Matches: 71, Mismatches: 13, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
22 6 0.08
23 45 0.63
24 3 0.04
25 14 0.20
26 3 0.04
ACGTcount: A:0.15, C:0.29, G:0.23, T:0.33
Consensus pattern (23 bp):
GGCTCTTCGTGAGCTTCCCGATA
Found at i:57113839 original size:15 final size:15
Alignment explanation
Indices: 57113819--57113847 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
57113809 ATGATCAATG
57113819 AAAAGCTTGTTCACC
1 AAAAGCTTGTTCACC
57113834 AAAAGCTTGTTCAC
1 AAAAGCTTGTTCAC
57113848 TATATTCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (15 bp):
AAAAGCTTGTTCACC
Found at i:57122486 original size:10 final size:10
Alignment explanation
Indices: 57122471--57122526 Score: 53
Period size: 10 Copynumber: 5.7 Consensus size: 10
57122461 TTTGTTTTGG
57122471 TTTTTTACTT
1 TTTTTTACTT
*
57122481 TTTTTTTCTT
1 TTTTTTACTT
57122491 TCTTTTTA--T
1 T-TTTTTACTT
*
57122500 TTATTTACTT
1 TTTTTTACTT
**
57122510 TTTTTTAAGT
1 TTTTTTACTT
57122520 TTTTTTA
1 TTTTTTA
57122527 TTTGTCCTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
8 5 0.14
9 2 0.05
10 25 0.68
11 5 0.14
ACGTcount: A:0.12, C:0.07, G:0.02, T:0.79
Consensus pattern (10 bp):
TTTTTTACTT
Found at i:57122489 original size:28 final size:29
Alignment explanation
Indices: 57122458--57122515 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
57122448 TCCTGTCGAA
* *
57122458 TTCTTTGTTTTGGTTT-TTTACTTTTTTT
1 TTCTTTCTTTTGATTTATTTACTTTTTTT
*
57122486 TTCTTTCTTTTTATTTATTTACTTTTTTT
1 TTCTTTCTTTTGATTTATTTACTTTTTTT
57122515 T
1 T
57122516 AAGTTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 13 0.50
29 13 0.50
ACGTcount: A:0.07, C:0.09, G:0.05, T:0.79
Consensus pattern (29 bp):
TTCTTTCTTTTGATTTATTTACTTTTTTT
Found at i:57122495 original size:14 final size:15
Alignment explanation
Indices: 57122474--57122515 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
57122464 GTTTTGGTTT
*
57122474 TTTACTTTTTTTTTC
1 TTTACTTTTTTTTTA
*
57122489 TTT-CTTTTTATTTA
1 TTTACTTTTTTTTTA
57122503 TTTACTTTTTTTT
1 TTTACTTTTTTTT
57122516 AAGTTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTACTTTTTTTTTA
Found at i:57122525 original size:29 final size:28
Alignment explanation
Indices: 57122474--57122529 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
57122464 GTTTTGGTTT
*
57122474 TTTACTTTTTTTTTCTTTCTTTTTATTTA
1 TTTACTTTTTTTTAC-TTCTTTTTATTTA
*
57122503 TTTACTTTTTTTTAAGTT-TTTTTATTT
1 TTTACTTTTTTTT-ACTTCTTTTTATTT
57122530 GTCCTTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 9 0.38
29 15 0.62
ACGTcount: A:0.12, C:0.07, G:0.02, T:0.79
Consensus pattern (28 bp):
TTTACTTTTTTTTACTTCTTTTTATTTA
Found at i:57122573 original size:29 final size:27
Alignment explanation
Indices: 57122493--57122575 Score: 73
Period size: 29 Copynumber: 2.9 Consensus size: 27
57122483 TTTTTCTTTC
*
57122493 TTTTTATTTAT-TTACTTTT-TTTTAAGTT
1 TTTTTATTTGTCTTA-TTTTATTTT-A-TT
57122521 TTTTTATTTGTCCTTATTTTATTTTATT
1 TTTTTATTTGT-CTTATTTTATTTTATT
57122549 TTATTTATTTGT-TTATTATTGATTTTA
1 TT-TTTATTTGTCTTATT-TT-ATTTTA
57122576 AAAAACTTGA
Statistics
Matches: 48, Mismatches: 1, Indels: 11
0.80 0.02 0.18
Matches are distributed among these distances:
27 5 0.10
28 16 0.33
29 20 0.42
30 7 0.15
ACGTcount: A:0.18, C:0.04, G:0.05, T:0.73
Consensus pattern (27 bp):
TTTTTATTTGTCTTATTTTATTTTATT
Found at i:57122638 original size:20 final size:22
Alignment explanation
Indices: 57122603--57122646 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
57122593 ATTTGAAATG
57122603 TTTTATAATAT-TTTTTTAAAA
1 TTTTATAATATATTTTTTAAAA
57122624 TTTTA-AATATATTTTTTAAAA
1 TTTTATAATATATTTTTTAAAA
57122645 TT
1 TT
57122647 ATTTTTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TTTTATAATATATTTTTTAAAA
Found at i:57122651 original size:12 final size:13
Alignment explanation
Indices: 57122624--57122659 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
57122614 TTTTTTAAAA
57122624 TTTT-AAATATATT
1 TTTTAAAAT-TATT
57122637 TTTTAAAATTATT
1 TTTTAAAATTATT
57122650 TTTTAAAATT
1 TTTTAAAATT
57122660 TTAAATATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 18 0.82
14 4 0.18
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TTTTAAAATTATT
Found at i:57122661 original size:21 final size:19
Alignment explanation
Indices: 57122603--57122689 Score: 69
Period size: 21 Copynumber: 4.6 Consensus size: 19
57122593 ATTTGAAATG
57122603 TTTTATAATATTTTTTTAAAA
1 TTTTA-AATA-TTTTTTAAAA
57122624 TTTTAAATATATTTTTTAAAA
1 TTTT-AA-ATATTTTTTAAAA
57122645 ---T---TATTTTTTAAAA
1 TTTTAAATATTTTTTAAAA
57122658 TTTTAAATATTTTTTAATAA
1 TTTTAAATATTTTTTAA-AA
* *
57122678 TATAAAATATTT
1 TTTTAAATATTT
57122690 AAATATTTTA
Statistics
Matches: 55, Mismatches: 2, Indels: 19
0.72 0.03 0.25
Matches are distributed among these distances:
13 12 0.22
16 1 0.02
18 1 0.02
19 10 0.18
20 12 0.22
21 15 0.27
22 4 0.07
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTTAAATATTTTTTAAAA
Found at i:57122685 original size:20 final size:19
Alignment explanation
Indices: 57122640--57122689 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
57122630 ATATATTTTT
*
57122640 TAAAATTATTTTTTAAAATT
1 TAAAA-TATTTTTTAAAATA
*
57122660 TTAAATATTTTTTAATAATA
1 TAAAATATTTTTTAA-AATA
57122680 TAAAATATTT
1 TAAAATATTT
57122690 AAATATTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TAAAATATTTTTTAAAATA
Found at i:57122758 original size:70 final size:70
Alignment explanation
Indices: 57122680--57122880 Score: 224
Period size: 70 Copynumber: 2.9 Consensus size: 70
57122670 TTTAATAATA
*
57122680 TAAAATATTTAAATATTTTAAAGATATGACCTTTCAAATTTATTATTAGTTTTATAATATTTTAA
1 TAAAATATTTAAAT-TTTTAAAGATATGACCTTTCAAATTTATTATTTGTTTTATAATATTTTAA
57122745 -AT-TT
65 TATGTT
* *
57122749 TAAATATATTTAATTTGTTTTAAA-ATAT----TTTTAATATTT-TTAATTTGTTTTATAATATT
1 TAAA-ATATTTAA-AT-TTTTAAAGATATGACCTTTCAA-ATTTATT-ATTTGTTTTATAATA-T
*
57122808 TTTAATTTGTT
60 TTTAATATGTT
57122819 TAAAATATATT--ATTTTTAAAGATATGACCTTTCAAATTTATTATTTGTTTTATAATATTTTA
1 TAAAATAT-TTAAATTTTTAAAGATATGACCTTTCAAATTTATTATTTGTTTTATAATATTTTA
57122881 GATGTATATT
Statistics
Matches: 111, Mismatches: 7, Indels: 28
0.76 0.05 0.19
Matches are distributed among these distances:
66 14 0.13
67 23 0.21
68 6 0.05
69 14 0.13
70 39 0.35
71 15 0.14
ACGTcount: A:0.37, C:0.03, G:0.04, T:0.56
Consensus pattern (70 bp):
TAAAATATTTAAATTTTTAAAGATATGACCTTTCAAATTTATTATTTGTTTTATAATATTTTAAT
ATGTT
Found at i:57122764 original size:16 final size:17
Alignment explanation
Indices: 57122729--57122761 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
57122719 TTATTATTAG
57122729 TTTTATAATATTTTAAA
1 TTTTATAATATTTTAAA
57122746 TTTTA-AATATATTTAA
1 TTTTATAATAT-TTTAA
57122762 TTTGTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTTATAATATTTTAAA
Found at i:57122771 original size:20 final size:20
Alignment explanation
Indices: 57122746--57122829 Score: 62
Period size: 21 Copynumber: 4.7 Consensus size: 20
57122736 ATATTTTAAA
57122746 TTTTAAATATATTTAATTTG
1 TTTTAAATATATTTAATTTG
57122766 TTTT-AA-A-A--T-A-TT-
1 TTTTAAATATATTTAATTTG
*
57122778 -TTTA-ATATTTTTAATTTG
1 TTTTAAATATATTTAATTTG
*
57122796 TTTTATAATATTTTTAATTTG
1 TTTTA-AATATATTTAATTTG
*
57122817 TTTAAAATATATT
1 TTTTAAATATATT
57122830 ATTTTTAAAG
Statistics
Matches: 50, Mismatches: 3, Indels: 22
0.67 0.04 0.29
Matches are distributed among these distances:
11 4 0.08
12 1 0.02
13 2 0.04
14 1 0.02
15 2 0.04
16 1 0.02
17 3 0.06
18 1 0.02
19 6 0.12
20 11 0.22
21 18 0.36
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (20 bp):
TTTTAAATATATTTAATTTG
Found at i:57122774 original size:21 final size:20
Alignment explanation
Indices: 57122729--57122791 Score: 62
Period size: 21 Copynumber: 3.3 Consensus size: 20
57122719 TTATTATTAG
*
57122729 TTTTATAATAT-TTTAA-A-
1 TTTTAAAATATATTTAATAT
*
57122746 TTTT-AAATATATTTAATTT
1 TTTTAAAATATATTTAATAT
*
57122765 GTTTTAAAATATTTTTAATAT
1 -TTTTAAAATATATTTAATAT
57122786 TTTTAA
1 TTTTAA
57122792 TTTGTTTTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
16 5 0.14
17 9 0.24
20 10 0.27
21 13 0.35
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
TTTTAAAATATATTTAATAT
Found at i:57122806 original size:21 final size:20
Alignment explanation
Indices: 57122776--57122819 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 20
57122766 TTTTAAAATA
57122776 TTTTTAATATTTTTAATTTG
1 TTTTTAATATTTTTAATTTG
57122796 TTTTATAATATTTTTAATTTG
1 TTTT-TAATATTTTTAATTTG
57122817 TTT
1 TTT
57122820 AAAATATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (20 bp):
TTTTTAATATTTTTAATTTG
Found at i:57122821 original size:9 final size:9
Alignment explanation
Indices: 57122729--57122813 Score: 57
Period size: 9 Copynumber: 8.9 Consensus size: 9
57122719 TTATTATTAG
57122729 TTTTATAATA
1 TTTT-TAATA
57122739 -TTTTAA-A
1 TTTTTAATA
*
57122746 TTTTAAATA
1 TTTTTAATA
* *
57122755 TATTTAATT
1 TTTTTAATA
57122764 TGTTTTAAAATA
1 T-TTTT--AATA
57122776 TTTTTAATA
1 TTTTTAATA
*
57122785 TTTTTAATTTG
1 TTTTTAA--TA
57122796 TTTTATAATA
1 TTTT-TAATA
57122806 TTTTTAAT
1 TTTTTAAT
57122814 TTGTTTAAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 17
0.70 0.10 0.20
Matches are distributed among these distances:
7 1 0.02
8 8 0.14
9 26 0.44
10 8 0.14
11 9 0.15
12 7 0.12
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (9 bp):
TTTTTAATA
Found at i:57122821 original size:30 final size:30
Alignment explanation
Indices: 57122745--57122821 Score: 111
Period size: 30 Copynumber: 2.6 Consensus size: 30
57122735 AATATTTTAA
* *
57122745 ATTTTAAATATATTTAATTTGTTTTAAAAT
1 ATTTTTAATATTTTTAATTTGTTTTAAAAT
*
57122775 ATTTTTAATATTTTTAATTTGTTTTATAAT
1 ATTTTTAATATTTTTAATTTGTTTTAAAAT
57122805 ATTTTTAAT-TTGTTTAA
1 ATTTTTAATATT-TTTAA
57122822 AATATATTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
29 2 0.05
30 41 0.95
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (30 bp):
ATTTTTAATATTTTTAATTTGTTTTAAAAT
Found at i:57128798 original size:40 final size:40
Alignment explanation
Indices: 57128743--57128821 Score: 149
Period size: 40 Copynumber: 2.0 Consensus size: 40
57128733 TAGATGAAGT
*
57128743 GTGATCCATATTTGCTCCATAAGACATTTTAATATTTGCG
1 GTGATCCATATTTGCTCCAAAAGACATTTTAATATTTGCG
57128783 GTGATCCATATTTGCTCCAAAAGACATTTTAATATTTGC
1 GTGATCCATATTTGCTCCAAAAGACATTTTAATATTTGC
57128822 ATAATTTGAG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (40 bp):
GTGATCCATATTTGCTCCAAAAGACATTTTAATATTTGCG
Found at i:57129098 original size:20 final size:20
Alignment explanation
Indices: 57129073--57129110 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
57129063 TTTTTTAAAA
*
57129073 TTTTTAATTTAAATTTTTAC
1 TTTTTAATATAAATTTTTAC
*
57129093 TTTTTAATATATATTTTT
1 TTTTTAATATAAATTTTT
57129111 TAAATAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTTAATATAAATTTTTAC
Found at i:57129112 original size:14 final size:15
Alignment explanation
Indices: 57129093--57129133 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
57129083 AAATTTTTAC
*
57129093 TTTTT-AATATATAT
1 TTTTTAAATAAATAT
57129107 TTTTTAAATAAATAT
1 TTTTTAAATAAATAT
*
57129122 TTTTAAAATAAA
1 TTTTTAAATAAA
57129134 GTCATATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 5 0.21
15 19 0.79
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TTTTTAAATAAATAT
Found at i:57129133 original size:19 final size:19
Alignment explanation
Indices: 57129111--57129157 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
57129101 ATATATTTTT
57129111 TAAATAAATATTTTTAAAA
1 TAAATAAATATTTTTAAAA
* **
57129130 TAAAGT-CATATTTTTTTAA
1 TAAA-TAAATATTTTTAAAA
57129149 TAAATAAAT
1 TAAATAAAT
57129158 CCTTTTTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
18 1 0.05
19 20 0.91
20 1 0.05
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (19 bp):
TAAATAAATATTTTTAAAA
Found at i:57129436 original size:19 final size:19
Alignment explanation
Indices: 57129412--57129483 Score: 64
Period size: 19 Copynumber: 4.0 Consensus size: 19
57129402 GTTTTATATT
57129412 ATTAAAAAATATATTTAAA
1 ATTAAAAAATATATTTAAA
*
57129431 ATTAAAAAATAT-TTT--C
1 ATTAAAAAATATATTTAAA
*
57129447 A--AAAATATATATTTAAA
1 ATTAAAAAATATATTTAAA
**
57129464 ATTTTAAAATATATTATAAA
1 ATTAAAAAATATATT-TAAA
57129484 TCATTTCAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
14 8 0.20
15 3 0.07
16 1 0.02
17 1 0.02
18 3 0.07
19 21 0.51
20 4 0.10
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (19 bp):
ATTAAAAAATATATTTAAA
Found at i:57129462 original size:33 final size:32
Alignment explanation
Indices: 57129407--57129480 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 32
57129397 TAAATGTTTT
57129407 ATATTATTAAAAAATATATTTAAAATTAAAAA
1 ATATTATTAAAAAATATATTTAAAATTAAAAA
*
57129439 ATATT-TTCAAAAATATATATTTAAAATTTTAAAAT
1 ATATTATT-AAAAA-ATATATTTAAAA--TTAAAAA
57129474 ATATTAT
1 ATATTAT
57129481 AAATCATTTC
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
31 2 0.06
32 10 0.28
33 12 0.33
35 11 0.31
36 1 0.03
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (32 bp):
ATATTATTAAAAAATATATTTAAAATTAAAAA
Found at i:57129538 original size:4 final size:4
Alignment explanation
Indices: 57129522--57129614 Score: 91
Period size: 4 Copynumber: 22.2 Consensus size: 4
57129512 TAAAATCAAT
* * *
57129522 AATA AACA AATA AATAA AATA AATA AATA AAGA CAATA AAGA CAATA AA-A
1 AATA AATA AATA AAT-A AATA AATA AATA AATA -AATA AATA -AATA AATA
57129572 AACTTA AA-A AAGTA AATA AATA AATA AATA AATA AATA AATA A
1 AA--TA AATA AA-TA AATA AATA AATA AATA AATA AATA AATA A
57129615 GAAAGAAAAA
Statistics
Matches: 75, Mismatches: 6, Indels: 16
0.77 0.06 0.16
Matches are distributed among these distances:
3 6 0.08
4 53 0.71
5 13 0.17
6 3 0.04
ACGTcount: A:0.73, C:0.04, G:0.03, T:0.19
Consensus pattern (4 bp):
AATA
Found at i:57138366 original size:13 final size:13
Alignment explanation
Indices: 57138332--57138371 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
57138322 AAAAAATAAT
*
57138332 AAAAATTATAAAC
1 AAAAATTATAAAA
**
57138345 AAATTTTATAAAA
1 AAAAATTATAAAA
57138358 AAAAATTATAAAA
1 AAAAATTATAAAA
57138371 A
1 A
57138372 TTTTTAATTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAAATTATAAAA
Found at i:57143174 original size:25 final size:27
Alignment explanation
Indices: 57143137--57143189 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
57143127 TCAAACATGC
57143137 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
57143163 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
57143189 A
1 A
57143190 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:57144707 original size:26 final size:26
Alignment explanation
Indices: 57144671--57144754 Score: 159
Period size: 26 Copynumber: 3.2 Consensus size: 26
57144661 CATGAAATTC
57144671 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
57144697 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
*
57144723 TTATCATGGAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
57144749 TTATCA
1 TTATCA
57144755 ATTTGTATCA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 57 1.00
ACGTcount: A:0.37, C:0.26, G:0.05, T:0.32
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:57152206 original size:11 final size:11
Alignment explanation
Indices: 57152192--57152232 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
57152182 TTTTTTCTCT
57152192 CTATTTTGCTA
1 CTATTTTGCTA
*
57152203 CTATTTTACTA
1 CTATTTTGCTA
* *
57152214 TTATATTGCTA
1 CTATTTTGCTA
57152225 CTATTTTG
1 CTATTTTG
57152233 TTGTTATTGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.22, C:0.15, G:0.07, T:0.56
Consensus pattern (11 bp):
CTATTTTGCTA
Found at i:57152470 original size:12 final size:12
Alignment explanation
Indices: 57152455--57152488 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
57152445 ATATATTTTT
*
57152455 AAAATTATATAA
1 AAAATAATATAA
57152467 AAAATAATATAA
1 AAAATAATATAA
*
57152479 AAATTAATAT
1 AAAATAATAT
57152489 GGGCGAGCCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATAATATAA
Found at i:57153284 original size:18 final size:18
Alignment explanation
Indices: 57153261--57153295 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
57153251 TTTTTTTGAA
57153261 GAAGAAGATAGAGAAAAT
1 GAAGAAGATAGAGAAAAT
57153279 GAAGAAGATAGAGAAAA
1 GAAGAAGATAGAGAAAA
57153296 AGTTTGGGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.29, T:0.09
Consensus pattern (18 bp):
GAAGAAGATAGAGAAAAT
Found at i:57158464 original size:29 final size:29
Alignment explanation
Indices: 57158424--57158479 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
57158414 TTAAATTAAA
* *
57158424 TAATTTTAAAAGATATTTTATT-TAAATAT
1 TAATTGTAAAAG-TATATTATTATAAATAT
57158453 TAATTGTAAAAGTATATTATTATAAAT
1 TAATTGTAAAAGTATATTATTATAAAT
57158480 TGGATTGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 8 0.33
29 16 0.67
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.48
Consensus pattern (29 bp):
TAATTGTAAAAGTATATTATTATAAATAT
Found at i:57162883 original size:6 final size:6
Alignment explanation
Indices: 57162872--57162900 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
57162862 AACAAATATT
57162872 TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
57162901 GTATAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:57162907 original size:18 final size:18
Alignment explanation
Indices: 57162872--57162907 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
57162862 AACAAATATT
*
57162872 TTTAAATTTAAATTTAAA
1 TTTAAATTTAAATATAAA
*
57162890 TTTAAATTTAAGTATAAA
1 TTTAAATTTAAATATAAA
57162908 AATATATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
TTTAAATTTAAATATAAA
Found at i:57164588 original size:17 final size:17
Alignment explanation
Indices: 57164566--57164601 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
57164556 AGAAGAACCG
57164566 AGGAAAGAAGAAA-AGAA
1 AGGAAAG-AGAAAGAGAA
57164583 AGGAAAGAGAAAGAGAA
1 AGGAAAGAGAAAGAGAA
57164600 AG
1 AG
57164602 AGAGGGAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (17 bp):
AGGAAAGAGAAAGAGAA
Found at i:57164596 original size:6 final size:6
Alignment explanation
Indices: 57164568--57164604 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
57164558 AAGAACCGAG
57164568 GAAAGAA GAAA-A GAAAG- GAAAGA GAAAGA GAAAGA GA
1 GAAAG-A GAAAGA GAAAGA GAAAGA GAAAGA GAAAGA GA
57164605 GGGAAGAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
5 10 0.36
6 14 0.50
7 4 0.14
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (6 bp):
GAAAGA
Found at i:57165159 original size:12 final size:12
Alignment explanation
Indices: 57165142--57165168 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
57165132 ATGTTTTTTC
57165142 TATTATTATATA
1 TATTATTATATA
57165154 TATTATTATATA
1 TATTATTATATA
57165166 TAT
1 TAT
57165169 ACATTGTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TATTATTATATA
Found at i:57165417 original size:30 final size:30
Alignment explanation
Indices: 57165383--57165451 Score: 120
Period size: 30 Copynumber: 2.3 Consensus size: 30
57165373 TTAGCCTTTG
*
57165383 CCACCACCAACTCCACTAGCCACACTTGCT
1 CCACCACCAACTACACTAGCCACACTTGCT
*
57165413 CCACCACCTACTACACTAGCCACACTTGCT
1 CCACCACCAACTACACTAGCCACACTTGCT
57165443 CCACCACCA
1 CCACCACCA
57165452 CTTGTACCTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.28, C:0.51, G:0.06, T:0.16
Consensus pattern (30 bp):
CCACCACCAACTACACTAGCCACACTTGCT
Found at i:57166053 original size:25 final size:25
Alignment explanation
Indices: 57165995--57166059 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
57165985 ATTCTAAATT
*
57165995 CTATATTACGTATATATATATTATA
1 CTATATTATGTATATATATATTATA
* *
57166020 CTATTTTATGTATATATCT-TTAATA
1 CTATATTATGTATATATATATT-ATA
* *
57166045 TTATATTATTTATAT
1 CTATATTATGTATAT
57166060 TTTTTTTTCT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
24 2 0.06
25 31 0.94
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.55
Consensus pattern (25 bp):
CTATATTATGTATATATATATTATA
Found at i:57166132 original size:25 final size:24
Alignment explanation
Indices: 57166081--57166143 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 24
57166071 CATGTTATCT
*
57166081 TATGTATATATTTTAATTATATAATG
1 TATGTAT-T-TTTTAACTATATAATG
*
57166107 TATGTATTTTTTACACTATATTATG
1 TATGTATTTTTTA-ACTATATAATG
**
57166132 TACATATTTTTT
1 TATGTATTTTTT
57166144 TTATATCTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
24 5 0.16
25 20 0.62
26 7 0.22
ACGTcount: A:0.32, C:0.05, G:0.06, T:0.57
Consensus pattern (24 bp):
TATGTATTTTTTAACTATATAATG
Found at i:57166233 original size:25 final size:24
Alignment explanation
Indices: 57166205--57166260 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
57166195 GTTATATTTT
*
57166205 CACTATTTTAT-GTATATACTTCAAA
1 CACTATTATATAGTATAT--TTCAAA
*
57166230 CACTA-TATATAGTATATTTCTAA
1 CACTATTATATAGTATATTTCAAA
57166253 CACTATTA
1 CACTATTA
57166261 CTATTTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 10 0.37
24 6 0.22
25 11 0.41
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.43
Consensus pattern (24 bp):
CACTATTATATAGTATATTTCAAA
Found at i:57179187 original size:93 final size:93
Alignment explanation
Indices: 57179059--57179230 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
57179049 GCCCATAAGT
* * * *
57179059 GAACTCGGACTTAACTCAATGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
57179124 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
*
57179152 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
57179217 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
57179231 CAAATATCCT
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:57179226 original size:46 final size:46
Alignment explanation
Indices: 57179051--57179226 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
57179041 TGTAACCCGC
* * * *
57179051 CCATAAGTGAACTCGGACTTAACTCAATGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
57179097 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--T
* *** *
57179143 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
57179190 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
57179227 TGCCCAAATA
Statistics
Matches: 109, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
46 68 0.62
47 32 0.29
49 4 0.04
50 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:57179245 original size:46 final size:44
Alignment explanation
Indices: 57179102--57179245 Score: 116
Period size: 46 Copynumber: 3.1 Consensus size: 44
57179092 CGCATCCATA
* *
57179102 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCA---A-ATC-CT
* * *
57179151 --CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGC--ATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCCCAAATCC-T
57179194 AAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAATATCCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCC-AA-ATCCT
57179241 AGTGA
1 AGTGA
57179246 CATGTCACTT
Statistics
Matches: 77, Mismatches: 8, Indels: 23
0.71 0.07 0.21
Matches are distributed among these distances:
42 1 0.01
43 4 0.05
44 4 0.05
46 33 0.43
47 28 0.36
48 4 0.05
49 3 0.04
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.22
Consensus pattern (44 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAATCCT
Found at i:57181189 original size:14 final size:13
Alignment explanation
Indices: 57181167--57181210 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
57181157 TGCCGAGGTA
57181167 TTTTTAATTTCTG
1 TTTTTAATTTCTG
*
57181180 TTTTTCAATTTTTG
1 TTTTT-AATTTCTG
57181194 -TTTTAATTTCTG
1 TTTTTAATTTCTG
57181206 TTTTT
1 TTTTT
57181211 CAAAAATCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 7 0.26
13 13 0.48
14 7 0.26
ACGTcount: A:0.14, C:0.07, G:0.07, T:0.73
Consensus pattern (13 bp):
TTTTTAATTTCTG
Found at i:57181201 original size:12 final size:12
Alignment explanation
Indices: 57181168--57181209 Score: 57
Period size: 12 Copynumber: 3.3 Consensus size: 12
57181158 GCCGAGGTAT
57181168 TTTTAATTTCTG
1 TTTTAATTTCTG
*
57181180 TTTTTCAATTTTTG
1 -TTTT-AATTTCTG
57181194 TTTTAATTTCTG
1 TTTTAATTTCTG
57181206 TTTT
1 TTTT
57181210 TCAAAAATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 11 0.42
13 8 0.31
14 7 0.27
ACGTcount: A:0.14, C:0.07, G:0.07, T:0.71
Consensus pattern (12 bp):
TTTTAATTTCTG
Found at i:57181255 original size:99 final size:99
Alignment explanation
Indices: 57181095--57181461 Score: 431
Period size: 99 Copynumber: 3.8 Consensus size: 99
57181085 ATTTCCGTTT
* * * * *
57181095 TTTTAATTTATGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGCTGAGCCTCGGGGCATGC
1 TTTTAATTTATGCTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACACGC
* *
57181160 CGAGGTATTTTTAATTTCTGTTTTTCAATTTTTG
66 TGAGGTATTTTCAATTTCTGTTTTTCAATTTTTG
* * *
57181194 TTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAG-AGTTGAGTTGAGCCTCAGGGCACG
1 TTTTAATTTATGCTTTTCAAAAATCAACTCATATTGCGAGAAG-TGAGTTGAGCCTCAGGACACG
57181258 CTGAGGTATTTTCAATTTCTGTTTTTCAATTTTTG
65 CTGAGGTATTTTCAATTTCTGTTTTTCAATTTTTG
** * * * *
57181293 CCTTACAAATTCTGCTTTTC--AAATCAACTCATATTGCGAGAAGTGAGTTAAGCCTCAAGACAC
1 --TTTTAATTTATGCTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACAC
57181356 GCTGAGGTATTTTCAA-------TTTTC-A--TTT-
64 GCTGAGGTATTTTCAATTTCTGTTTTTCAATTTTTG
* *
57181381 TTTTAATTTATG-TTCTAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACACGC
1 TTTTAATTTATGCTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACACGC
*
57181445 TGAGGTAATTTCAATTT
66 TGAGGTATTTTCAATTT
57181462 TTGTCAAAAC
Statistics
Matches: 235, Mismatches: 24, Indels: 27
0.82 0.08 0.09
Matches are distributed among these distances:
85 3 0.01
86 8 0.03
87 56 0.24
89 3 0.01
91 1 0.00
92 5 0.02
98 1 0.00
99 142 0.60
100 2 0.01
101 14 0.06
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (99 bp):
TTTTAATTTATGCTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACACGC
TGAGGTATTTTCAATTTCTGTTTTTCAATTTTTG
Found at i:57181630 original size:71 final size:72
Alignment explanation
Indices: 57181398--57181950 Score: 601
Period size: 71 Copynumber: 7.6 Consensus size: 72
57181388 TTATGTTCTA
* * *
57181398 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAA--TT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTT
57181461 -TTTGTC
66 GTTTGTC
* *
57181467 AAAACT-AACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGAC-CGTTGAGGT-ATTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTT-
* *
57181529 AGTTTTTC
65 TGTTTGTC
* * *
57181537 AAAAAAATCAACTCATATTGCGATAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
1 --AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATT
57181602 TT-TTTGTC
64 TTGTTTGTC
*
57181610 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTT-
***
57181675 TGGTTTAAAAA
65 T-GTTT--GTC
* * *
57181686 AAAAATCAGCTCATATTGCGAGA-GTGAGGGGTTGAACCTCAAGACACGTTGAGGTATTTTCAAT
1 AAAAATCAACTCATATTGCGAGAGGTGA---GTTGAGCCTCAAGACACGTTGAGGTAATTTCAAT
57181750 TTTGTTT-TC
63 TTTGTTTGTC
* * * *
57181759 AAAAAATCAA-TCATATTGCGATAGGGTGAGGTTGAGCCTC--GAGATGCTGAGGTAATTTCAAT
1 -AAAAATCAACTCATATTGCGAGA-GGTGA-GTTGAGCCTCAAGACACGTTGAGGTAATTTCAAT
57181821 TTTGTTTGTC
63 TTTGTTTGTC
* * *
57181831 AAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGATATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTT-
57181896 TGTCTT-TC
65 TGT-TTGTC
* * *
57181904 AAAAAAAAATCAGCGCATATTGCGAGAGGTGAGTTGAACCTCAAGAC
1 ----AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGAC
57181951 GCTGAGGTGT
Statistics
Matches: 411, Mismatches: 43, Indels: 52
0.81 0.08 0.10
Matches are distributed among these distances:
66 7 0.02
67 8 0.02
68 34 0.08
69 5 0.01
70 15 0.04
71 99 0.24
72 38 0.09
73 65 0.16
74 21 0.05
75 18 0.04
76 26 0.06
77 40 0.10
78 35 0.09
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.31
Consensus pattern (72 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTT
GTTTGTC
Found at i:57181761 original size:149 final size:145
Alignment explanation
Indices: 57181397--57181972 Score: 622
Period size: 149 Copynumber: 4.0 Consensus size: 145
57181387 TTTATGTTCT
* *
57181397 AAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAA-TT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTT
* * * *
57181461 TTTGTC-AAAACT-AACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGAC-CGTTGAGGTA-TTT
66 TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTT
* * *
57181522 CAATTTCAGTTTTTCA
131 CAATTTCTG-GTTTAA
* *
57181538 AAAAAATCAACTCATATTGCGATAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTT
*
57181603 TTTTGTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTT
66 TTTT-TCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTT
57181667 TCAATTTCTGGTTTAAAA
130 TCAATTTCTGGTTT--AA
* * * *
57181685 AAAAAATCAGCTCATATTGCGAGA-GTGAGGGGTTGAACCTCAAGACACGTTGAGGTATTTTCAA
1 AAAAAATCAACTCATATTGCGAGAGGTGA---GTTGAGCCTCAAGACACGCTGAGGTAATTTCAA
* * *
57181749 TTTTGTTTTCAAAAAATCAA-TCATATTGCGATAGGGTGAGGTTGAGCCTC--GAGATGCTGAGG
63 TTTT-TTTTCAAAAAATCAACTCATATTGCGAGA-GGTGA-GTTGAGCCTCAAGACACGCTGAGG
* **
57181811 TAATTTCAATTT-T-GTTTGT
125 TATTTTCAATTTCTGGTTTAA
* * * * *
57181830 CAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGATATTTTCAATTT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTT
* * *
57181895 CTGTCTTTCAAAAAAAAATCAGCGCATATTGCGAGAGGTGAGTTGAACCTCAAG--ACGCTGAGG
66 -T-T-TTTC---AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGG
* *
57181958 TGTTTTCCATTTCTG
125 TATTTTCAATTTCTG
57181973 TTCTTCAATT
Statistics
Matches: 376, Mismatches: 34, Indels: 42
0.83 0.08 0.09
Matches are distributed among these distances:
141 60 0.16
142 5 0.01
143 41 0.11
144 38 0.10
145 38 0.10
146 19 0.05
147 53 0.14
148 16 0.04
149 79 0.21
150 17 0.05
151 10 0.03
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (145 bp):
AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTT
TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTT
CAATTTCTGGTTTAA
Found at i:57181860 original size:221 final size:217
Alignment explanation
Indices: 57181398--57181980 Score: 762
Period size: 221 Copynumber: 2.7 Consensus size: 217
57181388 TTATGTTCTA
* * * *
57181398 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTT-
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
* * * * * *
57181462 T-TGT---CAAAACT-AACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGAC-CGTTGAGGTA-T
66 TGTTTAAAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACACGTTGAGGTATT
*
57181520 TTCAATTTCAGTTTTTCAAAAAAATCAACTCATATTGCGATAGGTGAGTTGAGCCTCAGGACACG
131 TTCAATTTCTG-TTTTC-AAAAAATCAACTCATATTGCGATAGGTGAGTTGAGCCTCA-GACACG
57181585 CTGAGGTAATTTCAATTTTTTTGTC
193 CTGAGGTAATTTCAATTTTTTTGTC
57181610 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
57181675 TGGTTTAAAAAAAAAATCAGCTCATATTGCGAGA-GTGAGGGGTTGAACCTCAAGACACGTTGAG
66 T-GTTT-AAAAAAAAATCAGCTCATATTGCGAGAGGTGA---GTTGAACCTCAAGACACGTTGAG
57181739 GTATTTTCAATTT-TGTTTTCAAAAAATCAA-TCATATTGCGATAGGGTGAGGTTGAGCCTC-GA
126 GTATTTTCAATTTCTGTTTTCAAAAAATCAACTCATATTGCGATA-GGTGA-GTTGAGCCTCAGA
* *
57181801 GATGCTGAGGTAATTTCAATTTTGTTTGTC
189 CACGCTGAGGTAATTTCAATTTT-TTTGTC
* *
57181831 AAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGATATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
* *
57181896 TGTCTTTCAAAAAAAAATCAGCGCATATTGCGAGAGGTGAGTTGAACCTCAAG--ACGCTGAGGT
66 TG--TTT-AAAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACACGTTGAGGT
* *
57181959 GTTTTCCATTTCTGTTCTTCAA
128 ATTTTCAATTTCTGTT-TTCAA
57181981 TTTCTGTGTG
Statistics
Matches: 330, Mismatches: 20, Indels: 34
0.86 0.05 0.09
Matches are distributed among these distances:
212 60 0.18
213 1 0.00
215 2 0.01
218 18 0.05
219 13 0.04
220 69 0.21
221 85 0.26
222 58 0.18
223 15 0.05
224 9 0.03
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.32
Consensus pattern (217 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
TGTTTAAAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACACGTTGAGGTATT
TTCAATTTCTGTTTTCAAAAAATCAACTCATATTGCGATAGGTGAGTTGAGCCTCAGACACGCTG
AGGTAATTTCAATTTTTTTGTC
Found at i:57182088 original size:15 final size:14
Alignment explanation
Indices: 57182052--57182084 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
57182042 CGCTGAGGTA
57182052 TTTTCAAATTCTGT
1 TTTTCAAATTCTGT
*
57182066 TTTTCAAATTTTGT
1 TTTTCAAATTCTGT
57182080 TTTTC
1 TTTTC
57182085 CAAAAAATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.18, C:0.12, G:0.06, T:0.64
Consensus pattern (14 bp):
TTTTCAAATTCTGT
Found at i:57182184 original size:83 final size:82
Alignment explanation
Indices: 57181886--57182209 Score: 283
Period size: 83 Copynumber: 3.7 Consensus size: 82
57181876 GTTGAGATAT
* * * * * *
57181886 TTTCAATTTCTGTCTTTCAAAAAAAAATCAGCGCATATTGCGAGAGGTGAGTTGAACCTCAAGAC
1 TTTCAATTT-TGTTTTTC--AAAAAAATCAACTCATATTGCGAGAGGTGAGTTCAGCCTCAGGAC
* *
57181951 GCTGAGGTGTTTTCCATTTC
63 GCTGAGGTATTTTCAATTTC
* * *
57181971 TGTTCTTCAATTTCTGTGTGTTTCAAAAAAATCAGCCCATA-TGCGAGTGGTGAGTTGAGCATTG
1 ---T-TTCAATTT-TGT-T-TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTT---CA--G
* * *
57182035 ACTCA-CACGCTGAGGTATTTTCAAATTCTGTT
54 CCTCAGGACGCTGAGGTATTTTC-AA-T-T-TC
*
57182067 TTTCAAATTTTGTTTTTCCAAAAAATCAACTCATATTGCGAGAGGTGAGTTCAGCCTCAGGACGC
1 TTTC-AATTTTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTCAGCCTCAGGACGC
*
57182132 TGAGATATTTTCAATTTC
65 TGAGGTATTTTCAATTTC
* *
57182150 TTTCAATTTATGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
1 TTTCAATTT-TGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTCAGCCTCAG
57182210 ATCACACGCC
Statistics
Matches: 199, Mismatches: 21, Indels: 37
0.77 0.08 0.14
Matches are distributed among these distances:
82 5 0.03
83 52 0.26
84 1 0.01
85 1 0.01
86 7 0.04
87 15 0.08
88 17 0.09
89 28 0.14
90 18 0.09
91 20 0.10
92 21 0.11
93 11 0.06
94 1 0.01
95 1 0.01
96 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (82 bp):
TTTCAATTTTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTCAGCCTCAGGACGCT
GAGGTATTTTCAATTTC
Found at i:57182273 original size:174 final size:177
Alignment explanation
Indices: 57181885--57182298 Score: 443
Period size: 174 Copynumber: 2.3 Consensus size: 177
57181875 CGTTGAGATA
* * * *
57181885 TTTTC-AATTTCTGTCTTTCAAAAAAAAATCAGCGCATATTGCGAGAGGTGAGTTGAACCTCAAG
1 TTTTCAAATTT-TGTCTTTC--CAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG
* * * * * *
57181949 ACGCTGAGGTGTTTTCCATTTCTGTTCTTCAATTTCTGTGTGTTTCAAAAAAATCAGCCCATATG
63 ACGCTGAGATATTTTCAATTTC--TTCTTCAATTTATGTGTGTGTCAAAAAAATCAACCCATATG
* * * *
57182014 CGAGTGGTGAGTTGAGCATTGACTCACACGCTGAGGTATTTTCAAATTCTGT
126 CGAGAGGTGAGTTGAGCATAGACTCACACGCCGAGGGATTTTCAAATTCTGT
* * *
57182066 TTTTCAAATTTTGTTTTTCCAAAAAATCAACTCATATTGCGAGAGGTGAGTTCAGCCTCAGGACG
1 TTTTCAAATTTTGTCTTTCCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACG
*
57182131 CTGAGATATTTTCAATTTC-T-TTCAATTTATGT-T-TGTCAAAAAAATCAACTCATATTGCGAG
66 CTGAGATATTTTCAATTTCTTCTTCAATTTATGTGTGTGTCAAAAAAATCAACCCATA-TGCGAG
* *
57182192 AGGTGAGTTGAGCCTCAGA-TCACACGCCGAGGGATTTTCAATTGATT-TTT
130 AGGTGAGTTGAGCAT-AGACTCACACGCCGAGGGATTTTCAA---ATTCTGT
* * * *
57182242 TTTTC-AATTTATG-CTTTGC-AACAATCAACTCATATTACAAGAGGTGAGTTGAGCCTC
1 TTTTCAAATTT-TGTCTTTCCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
57182299 GGGTCACATA
Statistics
Matches: 200, Mismatches: 26, Indels: 21
0.81 0.11 0.09
Matches are distributed among these distances:
173 18 0.09
174 74 0.37
175 22 0.11
176 10 0.05
177 3 0.01
179 56 0.28
181 12 0.06
182 5 0.03
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (177 bp):
TTTTCAAATTTTGTCTTTCCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACG
CTGAGATATTTTCAATTTCTTCTTCAATTTATGTGTGTGTCAAAAAAATCAACCCATATGCGAGA
GGTGAGTTGAGCATAGACTCACACGCCGAGGGATTTTCAAATTCTGT
Found at i:57182289 original size:91 final size:92
Alignment explanation
Indices: 57182150--57182323 Score: 244
Period size: 91 Copynumber: 1.9 Consensus size: 92
57182140 TTTCAATTTC
* *
57182150 TTTCAATTTATGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCAC
1 TTTCAATTTATGTTTGTC-AAAAAATCAACTCATATTACAAGAGGTGAGTTGAGCCTCAGATCAC
*
57182215 ACGCCGAGGGATTTTCAATTGATTTTTT
65 ACACCGAGGGATTTTCAATTGATTTTTT
* * *
57182243 TTTCAATTTATGCTTTG-C-AACAATCAACTCATATTACAAGAGGTGAGTTGAGCCTCGGGTCAC
1 TTTCAATTTATG-TTTGTCAAAAAATCAACTCATATTACAAGAGGTGAGTTGAGCCTCAGATCAC
* *
57182306 ATACCGAGGTATTTTCAA
65 ACACCGAGGGATTTTCAA
57182324 AATCTGTTTT
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
91 55 0.76
93 13 0.18
94 4 0.06
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (92 bp):
TTTCAATTTATGTTTGTCAAAAAATCAACTCATATTACAAGAGGTGAGTTGAGCCTCAGATCACA
CACCGAGGGATTTTCAATTGATTTTTT
Found at i:57182410 original size:87 final size:90
Alignment explanation
Indices: 57181996--57182421 Score: 330
Period size: 87 Copynumber: 4.8 Consensus size: 90
57181986 GTGTGTTTCA
* * * * * *
57181996 AAAAAATCAGCCCATA-TGCGAGTGGTGAGTTGAGCATTGACTCACACGCTGAGGTATTTTCAAA
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACACGCTGAGGTATTTTCAAA
* *
57182060 TTCTGTTTTTCAAATTT-TG-TTTTT
66 ATCTGTTTTTC-AATTTATGCTTTGT
* *
57182084 CCAAAAAATCAACTCATATTGCGAGAGGTGAGTTCAGCCTCAGG-----ACGCTGAGATATTTTC
1 --AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGCTCACACGCTGAGGTATTTTC
*
57182144 --AAT-T-TCTTTCAATTTATG-TTTGT
63 AAAATCTGTTTTTCAATTTATGCTTTGT
* * * *
57182167 CAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCCGAGGGATTTTCA
1 --AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACACGCTGAGGTATTTTCA
* * *
57182232 ATTGATTTTTTTTTCAATTTATGCTTTG-
64 A--AATCTGTTTTTCAATTTATGCTTTGT
* * * * * ** *
57182260 CAACAATCAACTCATATTACAAGAGGTGAGTTGAGCCTCGGGTCACATACCGAGGTATTTTCAAA
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACACGCTGAGGTATTTTCAAA
*
57182325 ATCTGTTTTACAAATTT-TG-TTT-T
66 ATCTGTTTTTC-AATTTATGCTTTGT
* * * ** * *
57182348 -AAAAATCAACTCATATTGTGAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTCAAT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACACGCTGAGGTATTTTCAAA
*
57182412 TTCTGTTTTT
66 ATCTGTTTTT
57182422 AATGTCTAGT
Statistics
Matches: 273, Mismatches: 46, Indels: 37
0.77 0.13 0.10
Matches are distributed among these distances:
82 6 0.02
83 50 0.18
84 1 0.00
85 2 0.01
87 88 0.32
88 3 0.01
89 10 0.04
90 19 0.07
91 75 0.27
92 2 0.01
93 13 0.05
94 4 0.01
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (90 bp):
AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACACGCTGAGGTATTTTCAAA
ATCTGTTTTTCAATTTATGCTTTGT
Found at i:57182434 original size:87 final size:87
Alignment explanation
Indices: 57182173--57182454 Score: 199
Period size: 87 Copynumber: 3.2 Consensus size: 87
57182163 TTGTCAAAAA
* * * * ** ** *
57182173 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCCGAGGGATTTTCAATTGAT
1 AATCAACTCATATTGCAAGAAGTGAGTTGAGCCTCGGCTCACATACCGAGCTATTTTCAA--AAT
* * ** ** *
57182238 TTTTTTTTCAATTTATGCTTTGCAAC
64 CTGTTTTAAAATTTA-G-TTTTAAAG
* * * *
57182264 AATCAACTCATATTACAAGAGGTGAGTTGAGCCTCGGGTCACATACCGAGGTATTTTCAAAATCT
1 AATCAACTCATATTGCAAGAAGTGAGTTGAGCCTCGGCTCACATACCGAGCTATTTTCAAAATCT
*
57182329 GTTTTACAAATTTTGTTTTAAA-
66 GTTTTA-AAATTTAGTTTTAAAG
** * * * * **
57182351 AATCAACTCATATTGTGAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTCAATTTCT
1 AATCAACTCATATTGCAAGAAGTGAGTTGAGCCTCGGCTCACATACCGAGCTATTTTCAAAATCT
*
57182416 GTTTT-TAATGTCTAGTTTTAAAG
66 GTTTTAAAAT-T-TAGTTTTAAAG
* *
57182439 AGTCAATTCATATTGC
1 AATCAACTCATATTGC
57182455 GTGAAATGAG
Statistics
Matches: 155, Mismatches: 32, Indels: 11
0.78 0.16 0.06
Matches are distributed among these distances:
85 3 0.02
86 1 0.01
87 67 0.43
88 18 0.12
89 8 0.05
90 5 0.03
91 53 0.34
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.37
Consensus pattern (87 bp):
AATCAACTCATATTGCAAGAAGTGAGTTGAGCCTCGGCTCACATACCGAGCTATTTTCAAAATCT
GTTTTAAAATTTAGTTTTAAAG
Found at i:57182561 original size:21 final size:21
Alignment explanation
Indices: 57182535--57182574 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
57182525 TTTTATATCC
57182535 TTGAAGTTACAGTGAAGCTAA
1 TTGAAGTTACAGTGAAGCTAA
* *
57182556 TTGAAGTTGCAGTGGAGCT
1 TTGAAGTTACAGTGAAGCT
57182575 GATCGATGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.10, G:0.30, T:0.30
Consensus pattern (21 bp):
TTGAAGTTACAGTGAAGCTAA
Found at i:57194005 original size:71 final size:70
Alignment explanation
Indices: 57193906--57194081 Score: 212
Period size: 71 Copynumber: 2.5 Consensus size: 70
57193896 CTTTCCAAGG
** *
57193906 AAAATCAACTCATATTGCGAG-AGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTT
1 AAAATCAACTCATATTGCGAGAAG-TGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTTA
57193970 TGTTTTT
65 TG-TTTT
** * *
57193977 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTAT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTTAT
57194042 GTTTT
66 GTTTT
** * * *
57194047 -AAATTGACTCAGATTGCGAGAGGTGAGTTAAGCCT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT
57194082 TTTAATTTTT
Statistics
Matches: 92, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
69 30 0.33
70 4 0.04
71 56 0.61
72 2 0.02
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (70 bp):
AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTTAT
GTTTT
Found at i:57194237 original size:54 final size:54
Alignment explanation
Indices: 57194175--57194314 Score: 210
Period size: 54 Copynumber: 2.6 Consensus size: 54
57194165 TGTTTTAATT
*
57194175 TCAACTCATATTGCGAGAAGTGAGTTGAGCCTTTCAATTTATA-TTTTTCAAAAA
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTCAATTTATACTTTTTC-AAAA
* * * *
57194229 TCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTTTCAAAA
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTCAATTTATACTTTTTCAAAA
*
57194283 TCAGCTCATATTGCGAGAGGTGAGTTGAGCCT
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCT
57194315 CAGGTCACGC
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
54 71 0.92
55 6 0.08
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (54 bp):
TCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTCAATTTATACTTTTTCAAAA
Found at i:57194430 original size:88 final size:87
Alignment explanation
Indices: 57194273--57194489 Score: 323
Period size: 88 Copynumber: 2.5 Consensus size: 87
57194263 TAATTTCTAC
* *
57194273 TTTTTC-AAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCCGAGGTATTTTC
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCCGAGGTATTTTC
57194337 AATTTCTATTTT-CATTATT-ATG
66 AATTTCTATTTTCCA--ATTCATG
* * *
57194359 TTTTTGAAAGAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTT
1 TTTTTCAAA-AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCCGAGGTATTTT
*
57194424 CAATTTCTATTTTCCAATTCCTG
65 CAATTTCTATTTTCCAATTCATG
*
57194447 TTTTTCAAAAATCAACTCATGTTGCGAGAGGTGAGTTGAGCCT
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
57194490 TTCAATTTAT
Statistics
Matches: 119, Mismatches: 8, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
86 5 0.04
87 38 0.32
88 74 0.62
89 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.36
Consensus pattern (87 bp):
TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCCGAGGTATTTTC
AATTTCTATTTTCCAATTCATG
Found at i:57194592 original size:54 final size:54
Alignment explanation
Indices: 57194445--57194636 Score: 225
Period size: 56 Copynumber: 3.6 Consensus size: 54
57194435 TTCCAATTCC
*
57194445 TGTTTTTCAAAAATCAACTCATGTTGCGAGAGGTGAGTTGAGCCTTTCAATTTA
1 TGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTCAATTTA
* * *
57194499 TATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTT
1 TGTTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTCAATTTA
* * * *
57194555 TGTTTTTCAAAAAGCAACTCATATTGTGAGAGTTGAGTT-ATACCTTT---TTGT-
1 TGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGA-GCCTTTCAATT-TA
*
57194606 T-TTTTTCAAAAATCAATTCATATTGCGAGAG
1 TGTTTTTCAAAAATCAACTCATATTGCGAGAG
57194637 ACAAGTTGAA
Statistics
Matches: 122, Mismatches: 12, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
50 27 0.22
51 3 0.02
52 1 0.01
53 1 0.01
54 40 0.33
56 50 0.41
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (54 bp):
TGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTCAATTTA
Found at i:57194791 original size:44 final size:44
Alignment explanation
Indices: 57194680--57194774 Score: 190
Period size: 44 Copynumber: 2.2 Consensus size: 44
57194670 GAATAAAGAT
57194680 TGGAGCTAATTGAAGATGTCAGATTTTGTCTCCTGAAGTTACAG
1 TGGAGCTAATTGAAGATGTCAGATTTTGTCTCCTGAAGTTACAG
57194724 TGGAGCTAATTGAAGATGTCAGATTTTGTCTCCTGAAGTTACAG
1 TGGAGCTAATTGAAGATGTCAGATTTTGTCTCCTGAAGTTACAG
57194768 TGGAGCT
1 TGGAGCT
57194775 GATCGAGGAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 51 1.00
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.34
Consensus pattern (44 bp):
TGGAGCTAATTGAAGATGTCAGATTTTGTCTCCTGAAGTTACAG
Found at i:57196751 original size:18 final size:18
Alignment explanation
Indices: 57196717--57196751 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
57196707 GTTACGTACG
*
57196717 TATATATTATATGTATTT
1 TATATATTATATATATTT
*
57196735 TATATATTATGTATATT
1 TATATATTATATATATT
57196752 ATTTTTTTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (18 bp):
TATATATTATATATATTT
Found at i:57199432 original size:9 final size:9
Alignment explanation
Indices: 57199418--57199587 Score: 56
Period size: 9 Copynumber: 17.9 Consensus size: 9
57199408 TTTTTTCGAT
57199418 TAAAAAATA
1 TAAAAAATA
*
57199427 TAAAAATTA
1 TAAAAAATA
* *
57199436 GAAGAAATA
1 TAAAAAATA
*
57199445 AAAAAAATA
1 TAAAAAATA
* *
57199454 TTAAATATAA
1 TAAAAAAT-A
**
57199464 TATTAAATA
1 TAAAAAATA
*
57199473 TTAAAAATA
1 TAAAAAATA
57199482 TTAAAATTAATA
1 -TAAAA--AATA
**
57199494 T-AAACTTA
1 TAAAAAATA
* *
57199502 TTAAAATTA
1 TAAAAAATA
57199511 TAAAAAATATTA
1 T-AAAAA-A-TA
57199523 TATAAAAACTTA
1 TA-AAAAA--TA
* *
57199535 TAAATATTA
1 TAAAAAATA
57199544 TAAAAAATA
1 TAAAAAATA
*
57199553 -AAAAAATC
1 TAAAAAATA
*
57199561 TAATAAATTA
1 TAA-AAAATA
*
57199571 TAAAAAAAA
1 TAAAAAATA
*
57199580 TATAAAAT
1 TAAAAAAT
57199588 TAATAAAACT
Statistics
Matches: 116, Mismatches: 33, Indels: 24
0.67 0.19 0.14
Matches are distributed among these distances:
8 10 0.09
9 61 0.53
10 23 0.20
11 6 0.05
12 16 0.14
ACGTcount: A:0.66, C:0.02, G:0.01, T:0.31
Consensus pattern (9 bp):
TAAAAAATA
Found at i:57199471 original size:28 final size:28
Alignment explanation
Indices: 57199419--57199494 Score: 77
Period size: 28 Copynumber: 2.8 Consensus size: 28
57199409 TTTTTCGATT
* *
57199419 AAAAAATATAAAAATTAGA-A-GAAATAA
1 AAAAAATATTAAAATTA-ATATTAAATAA
*
57199446 AAAAAATATT-AAATATAATATTAAATAT
1 AAAAAATATTAAAAT-TAATATTAAATAA
*
57199474 TAAAAATATTAAAATTAATAT
1 AAAAAATATTAAAATTAATAT
57199495 AAACTTATTA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
26 5 0.12
27 12 0.29
28 20 0.49
29 4 0.10
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (28 bp):
AAAAAATATTAAAATTAATATTAAATAA
Found at i:57199516 original size:29 final size:29
Alignment explanation
Indices: 57199456--57199610 Score: 97
Period size: 28 Copynumber: 5.2 Consensus size: 29
57199446 AAAAAATATT
* * * *
57199456 AAATATAATATTAAA-TATTAAAAATATTA
1 AAAT-TAATATAAAATTAATAAAATTATAA
* *
57199485 AAATTAATATAAACTTATTAAAATTATAAA
1 AAATTAATATAAAATTAATAAAATTAT-AA
*
57199515 AAATATTATATAAAAACTT-ATAAATATTATAA
1 AAAT-TAATAT-AAAA-TTAATAAA-ATTATAA
*
57199547 AAAATAA-A-AAAATCTAAT-AAATTATAA
1 AAATTAATATAAAAT-TAATAAAATTATAA
* *
57199574 AAA-AAATATAAAATTAATAAAACTTATTTA
1 AAATTAATATAAAATTAATAAAA-TTA-TAA
57199604 AAATTAA
1 AAATTAA
57199611 AAAATGTGTT
Statistics
Matches: 100, Mismatches: 12, Indels: 26
0.72 0.09 0.19
Matches are distributed among these distances:
26 2 0.02
27 16 0.16
28 23 0.23
29 20 0.20
30 11 0.11
31 9 0.09
32 12 0.12
33 7 0.07
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (29 bp):
AAATTAATATAAAATTAATAAAATTATAA
Found at i:57199536 original size:10 final size:9
Alignment explanation
Indices: 57199474--57199615 Score: 56
Period size: 9 Copynumber: 14.8 Consensus size: 9
57199464 TATTAAATAT
57199474 TAAAAA-TA
1 TAAAAATTA
*
57199482 TTAAAATTAA
1 TAAAAATT-A
*
57199492 TATAAACTTA
1 TA-AAAATTA
*
57199502 TTAAAATTA
1 TAAAAATTA
57199511 TAAAAAATATTATA
1 T--AAAA-A-T-TA
57199525 TAAAAACTTA
1 TAAAAA-TTA
*
57199535 TAAATATTA
1 TAAAAATTA
*
57199544 TAAAAAATA
1 TAAAAATTA
*
57199553 AAAAAATCTA
1 TAAAAAT-TA
*
57199563 -ATAAATTA
1 TAAAAATTA
**
57199571 TAAAAAAAA
1 TAAAAATTA
57199580 TATAAAATTAA
1 TA-AAAATT-A
*
57199591 TAAAACTTA
1 TAAAAATTA
*
57199600 TTTAAAATTA
1 -TAAAAATTA
57199610 -AAAAAT
1 TAAAAAT
57199616 GTGTTAGAAT
Statistics
Matches: 99, Mismatches: 22, Indels: 26
0.67 0.15 0.18
Matches are distributed among these distances:
8 12 0.12
9 36 0.36
10 29 0.29
11 13 0.13
12 5 0.05
13 1 0.01
14 3 0.03
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (9 bp):
TAAAAATTA
Found at i:57199544 original size:33 final size:32
Alignment explanation
Indices: 57199487--57199552 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 32
57199477 AAATATTAAA
*
57199487 ATTAATATAAACTTATTAAAATTATAAAAAAT
1 ATTAATAAAAACTTATTAAAATTATAAAAAAT
57199519 ATTATATAAAAACTTA-TAAATATTATAAAAAAT
1 ATTA-ATAAAAACTTATTAAA-ATTATAAAAAAT
57199552 A
1 A
57199553 AAAAAATCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
32 8 0.26
33 23 0.74
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (32 bp):
ATTAATAAAAACTTATTAAAATTATAAAAAAT
Found at i:57199570 original size:27 final size:27
Alignment explanation
Indices: 57199490--57199594 Score: 81
Period size: 27 Copynumber: 3.6 Consensus size: 27
57199480 TATTAAAATT
* *
57199490 AATATAAACTTATTAAAATTATAAAAAA
1 AATATAAAATTAAT-AAATTATAAAAAA
57199518 TATTATATAAAAACTT-ATAAATATTATAAAAAA
1 -A--ATAT-AAAA-TTAAT-AA-ATTATAAAAAA
57199551 TAA-A-AAAATCTAATAAATTATAAAAAA
1 -AATATAAAAT-TAATAAATTATAAAAAA
57199578 AATATAAAATTAATAAA
1 AATATAAAATTAATAAA
57199595 ACTTATTTAA
Statistics
Matches: 65, Mismatches: 2, Indels: 20
0.75 0.02 0.23
Matches are distributed among these distances:
26 2 0.03
27 20 0.31
28 12 0.18
29 3 0.05
30 1 0.02
31 5 0.08
32 7 0.11
33 15 0.23
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (27 bp):
AATATAAAATTAATAAATTATAAAAAA
Found at i:57199643 original size:15 final size:15
Alignment explanation
Indices: 57199623--57199652 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
57199613 AATGTGTTAG
57199623 AATTCTTAAAAAATA
1 AATTCTTAAAAAATA
57199638 AATTCTTAAAAAATA
1 AATTCTTAAAAAATA
57199653 TTAAAGTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (15 bp):
AATTCTTAAAAAATA
Found at i:57200162 original size:21 final size:22
Alignment explanation
Indices: 57200133--57200187 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
57200123 TAATATGTTT
* *
57200133 TATGATTTTTTTAGAATTTTAA
1 TATGATTTTTATAAAATTTTAA
57200155 TATG-TTTTTATAAAATTTTAA
1 TATGATTTTTATAAAATTTTAA
57200176 -AT-ATTTTATATA
1 TATGATTTT-TATA
57200188 TGTTTTATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 6 0.21
21 19 0.66
22 4 0.14
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.58
Consensus pattern (22 bp):
TATGATTTTTATAAAATTTTAA
Found at i:57200173 original size:29 final size:30
Alignment explanation
Indices: 57200118--57200193 Score: 84
Period size: 29 Copynumber: 2.5 Consensus size: 30
57200108 AGTTTATATC
*** *
57200118 AATTTTAATATG-TTTTATGATTTTTTTAG
1 AATTTTAATATGTTTTTATGAAAATTTTAA
57200147 AATTTTAATATGTTTTTAT-AAAATTTTAA
1 AATTTTAATATGTTTTTATGAAAATTTTAA
57200176 ATATTTTATATATGTTTT
1 A-ATTTTA-ATATGTTTT
57200194 ATTAATTTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
29 19 0.47
30 12 0.30
31 9 0.22
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.61
Consensus pattern (30 bp):
AATTTTAATATGTTTTTATGAAAATTTTAA
Found at i:57205059 original size:28 final size:28
Alignment explanation
Indices: 57205023--57205077 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
57205013 AATTTAATGA
*
57205023 TATTCTTATT-TCATATTTTTATATTATT
1 TATTCTTATTATCAT-TTTTTAAATTATT
* *
57205051 TATTTTTATTATTATTTTTTAAATTAT
1 TATTCTTATTATCATTTTTTAAATTAT
57205078 GCGGTCATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 20 0.87
29 3 0.13
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (28 bp):
TATTCTTATTATCATTTTTTAAATTATT
Found at i:57205063 original size:16 final size:15
Alignment explanation
Indices: 57205036--57205067 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
57205026 TCTTATTTCA
57205036 TATTTTTATATTATT
1 TATTTTTATATTATT
57205051 TATTTTTATTATTATT
1 TATTTTTA-TATTATT
57205067 T
1 T
57205068 TTTAAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (15 bp):
TATTTTTATATTATT
Found at i:57207030 original size:11 final size:11
Alignment explanation
Indices: 57207006--57207048 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
57206996 TTCTAATATG
*
57207006 TATATATATTA
1 TATATATTTTA
*
57207017 TATGTATTTTA
1 TATATATTTTA
* *
57207028 TATATATTATG
1 TATATATTTTA
57207039 TATATATTTT
1 TATATATTTT
57207049 TAATGCCATT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (11 bp):
TATATATTTTA
Found at i:57207221 original size:12 final size:12
Alignment explanation
Indices: 57207174--57207226 Score: 63
Period size: 12 Copynumber: 4.2 Consensus size: 12
57207164 CCATGTTGTG
57207174 TATATATTATTAT
1 TATA-ATTATTAT
57207187 TACTAATTATTAT
1 TA-TAATTATTAT
*
57207200 TGCTAA-TATTAT
1 T-ATAATTATTAT
57207212 TATAATTATTAT
1 TATAATTATTAT
57207224 TAT
1 TAT
57207227 GTTAGTGTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
11 3 0.09
12 16 0.46
13 14 0.40
14 2 0.06
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.57
Consensus pattern (12 bp):
TATAATTATTAT
Found at i:57207333 original size:3 final size:3
Alignment explanation
Indices: 57207320--57207420 Score: 50
Period size: 3 Copynumber: 34.3 Consensus size: 3
57207310 TGTATTTTAA
* * * *
57207320 TAT TGT TAT TAT TA- TAT CAT TAT TAT TTT TTT TAT ATAT TAT TCA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT T-AT
* * * * *
57207365 TAC TAT CAT TAT TA- TAT TAT TAT CAC TAT TA- CATT TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT
*
57207408 TAG TAT TAT TAT T
1 TAT TAT TAT TAT T
57207421 GCTATCATTA
Statistics
Matches: 73, Mismatches: 17, Indels: 16
0.69 0.16 0.15
Matches are distributed among these distances:
2 8 0.11
3 60 0.82
4 5 0.07
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:57207380 original size:23 final size:26
Alignment explanation
Indices: 57207350--57207409 Score: 76
Period size: 23 Copynumber: 2.5 Consensus size: 26
57207340 TATTATTTTT
57207350 TTTA-TATATTATTCAT-ACTA-T-CA
1 TTTATTATATTATT-ATCACTATTACA
57207373 -TTATTATATTATTATCACTATTACA
1 TTTATTATATTATTATCACTATTACA
57207398 TTTATTATATTA
1 TTTATTATATTA
57207410 GTATTATTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
22 5 0.16
23 13 0.41
24 1 0.03
25 2 0.06
26 11 0.34
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (26 bp):
TTTATTATATTATTATCACTATTACA
Found at i:57207385 original size:26 final size:27
Alignment explanation
Indices: 57207351--57207414 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 27
57207341 ATTATTTTTT
57207351 TTATA-TATTATTCA-TACTATCA-TTA
1 TTATATTATTATTCACTACTA-CATTTA
*
57207376 TTATATTATTA-TCACTATTACATTTA
1 TTATATTATTATTCACTACTACATTTA
*
57207402 TTATATTAGTATT
1 TTATATTATTATT
57207415 ATTATTGCTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
25 10 0.30
26 22 0.67
27 1 0.03
ACGTcount: A:0.34, C:0.09, G:0.02, T:0.55
Consensus pattern (27 bp):
TTATATTATTATTCACTACTACATTTA
Found at i:57216199 original size:23 final size:23
Alignment explanation
Indices: 57216173--57216217 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
57216163 TGGGTATGTG
*
57216173 ATGACGTTATCTT-ATAAATATGC
1 ATGAAGTTATCTTGA-AAATATGC
*
57216196 ATGAATTTATCTTGAAAATATG
1 ATGAAGTTATCTTGAAAATATG
57216218 TTGAATTGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (23 bp):
ATGAAGTTATCTTGAAAATATGC
Found at i:57217820 original size:51 final size:49
Alignment explanation
Indices: 57217786--57217879 Score: 134
Period size: 49 Copynumber: 1.9 Consensus size: 49
57217776 GATCGAAGTT
* * *
57217786 ATCAGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACA
1 ATCAGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCAACA
* * *
57217835 ATCTGGTACACGTAGTAGCCTGCACTTAGAACTACACACGTGACC
1 ATCAGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACC
57217880 TTATAATAGC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 39 1.00
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21
Consensus pattern (49 bp):
ATCAGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCAACA
Found at i:57217878 original size:127 final size:127
Alignment explanation
Indices: 57217652--57217880 Score: 395
Period size: 127 Copynumber: 1.8 Consensus size: 127
57217642 CACTTGTAGC
* **
57217652 CGAAGCTATCTGGTACGCATAGTAGCCTGCACTGAGTACTACACATGCGACCAATTATCCGGTAC
1 CGAAGCTATCAGGTACGCATAGTAGCCTGCACTGAGTACTACACATGCGACCAACAATCCGGTAC
*
57217717 ACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACTACACACGTGAT
66 ACGTAGTAGCCTGCACTTAGAACTACACACGTGACCTAACCATCTGATACTACACACGTGAT
* * *
57217779 CGAAGTTATCAGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACAATCTGGTAC
1 CGAAGCTATCAGGTACGCATAGTAGCCTGCACTGAGTACTACACATGCGACCAACAATCCGGTAC
57217844 ACGTAGTAGCCTGCACTTAGAACTACACACGTGACCT
66 ACGTAGTAGCCTGCACTTAGAACTACACACGTGACCT
57217881 TATAATAGCT
Statistics
Matches: 95, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
127 95 1.00
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (127 bp):
CGAAGCTATCAGGTACGCATAGTAGCCTGCACTGAGTACTACACATGCGACCAACAATCCGGTAC
ACGTAGTAGCCTGCACTTAGAACTACACACGTGACCTAACCATCTGATACTACACACGTGAT
Found at i:57218560 original size:30 final size:30
Alignment explanation
Indices: 57218526--57218585 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
57218516 CTTTAATACG
57218526 AACTTTGGCAAAATTATCA-TTTTGCCCCTA
1 AACTTTGGCAAAATTA-CACTTTTGCCCCTA
* * *
57218556 AACTTTTGTATAATTACACTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTGCCCCTA
57218586 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 2 0.08
30 24 0.92
ACGTcount: A:0.28, C:0.23, G:0.08, T:0.40
Consensus pattern (30 bp):
AACTTTGGCAAAATTACACTTTTGCCCCTA
Found at i:57220934 original size:21 final size:21
Alignment explanation
Indices: 57220908--57220956 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
57220898 AATTTGACAC
57220908 AAATAAATAATG--AATATATTT
1 AAATAAA-AATGACAATAT-TTT
*
57220929 AAATAAAAATTACAATATTTT
1 AAATAAAAATGACAATATTTT
57220950 AAATAAA
1 AAATAAA
57220957 CTAACGGCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 3 0.12
21 17 0.68
22 5 0.20
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (21 bp):
AAATAAAAATGACAATATTTT
Found at i:57231499 original size:26 final size:26
Alignment explanation
Indices: 57231470--57231551 Score: 137
Period size: 26 Copynumber: 3.2 Consensus size: 26
57231460 TGGTACAAAT
*
57231470 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGATTAGGTAAATGTTCCA
*
57231496 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGATTAGGTAAATGTTCCA
*
57231522 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGATTAGGTAAATGTTCCA
57231548 TGAT
1 TGAT
57231552 GGGCATTTCT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 52 1.00
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.37
Consensus pattern (26 bp):
TGATAATGGATTAGGTAAATGTTCCA
Found at i:57238532 original size:26 final size:26
Alignment explanation
Indices: 57238503--57238610 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
57238493 TGGTACAAAT
57238503 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
57238529 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
57238555 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
57238581 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
57238607 TGAT
1 TGAT
57238611 GGGCATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:57246252 original size:15 final size:15
Alignment explanation
Indices: 57246232--57246264 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
57246222 TTTCTCCTCA
*
57246232 GCTGGCTTTTTCTCG
1 GCTGGCTTCTTCTCG
57246247 GCTGGCTTCTTCTCG
1 GCTGGCTTCTTCTCG
57246262 GCT
1 GCT
57246265 TTGGGTGCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.30, G:0.27, T:0.42
Consensus pattern (15 bp):
GCTGGCTTCTTCTCG
Found at i:57248499 original size:21 final size:22
Alignment explanation
Indices: 57248475--57248516 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
57248465 AAATTACGTT
*
57248475 AAAAGAAATGAAGAAG-AGAAA
1 AAAACAAATGAAGAAGCAGAAA
*
57248496 AAAACAAATGGAGAAGCAGAA
1 AAAACAAATGAAGAAGCAGAA
57248517 GACAGAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.67, C:0.05, G:0.24, T:0.05
Consensus pattern (22 bp):
AAAACAAATGAAGAAGCAGAAA
Found at i:57252532 original size:26 final size:26
Alignment explanation
Indices: 57252495--57252603 Score: 182
Period size: 26 Copynumber: 4.2 Consensus size: 26
57252485 ATGAAATGCC
* *
57252495 TATCATGAAACATTTACCTAAACCAT
1 TATCATGGAACATTTACCTAACCCAT
57252521 TATCATGGAACATTTACCTAACCCAT
1 TATCATGGAACATTTACCTAACCCAT
* *
57252547 TATCATGGAATATTTACCTAATCCAT
1 TATCATGGAACATTTACCTAACCCAT
57252573 TATCATGGAACATTTACCTAACCCAT
1 TATCATGGAACATTTACCTAACCCAT
57252599 TATCA
1 TATCA
57252604 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.33
Consensus pattern (26 bp):
TATCATGGAACATTTACCTAACCCAT
Found at i:57255584 original size:23 final size:22
Alignment explanation
Indices: 57255558--57255626 Score: 61
Period size: 23 Copynumber: 3.1 Consensus size: 22
57255548 TGTTCATATT
*
57255558 TTATTTTTAATCTTGTTTCTAAA
1 TTATTTTTAATCATG-TTCTAAA
* *
57255581 TTATTTGT-AT-ATGTTCATAAT
1 TTATTTTTAATCATGTTC-TAAA
*
57255602 TTATTTTTAATCCTGCTTCTAAA
1 TTATTTTTAATCATG-TTCTAAA
57255625 TT
1 TT
57255627 TATCTATTCA
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
20 3 0.08
21 12 0.33
22 4 0.11
23 14 0.39
24 3 0.08
ACGTcount: A:0.26, C:0.10, G:0.06, T:0.58
Consensus pattern (22 bp):
TTATTTTTAATCATGTTCTAAA
Found at i:57255648 original size:39 final size:39
Alignment explanation
Indices: 57255537--57255705 Score: 189
Period size: 39 Copynumber: 4.2 Consensus size: 39
57255527 AATTTCGAGC
*
57255537 CTAAATTT-TACTGTTCATATTTTATTTTTAATCTTGTTT
1 CTAAATTTAT-CTGTTCATATTTTATTTTTAATCCTGTTT
* * *
57255576 CTAAATTATTTGTATATGTTCATAATTTATTTTTAATCCTGCTT
1 CT-AA--A-TT-TATCTGTTCATATTTTATTTTTAATCCTGTTT
* *
57255620 CTAAATTTATCTATTCATATTTTATTTTTAATCCTATTT
1 CTAAATTTATCTGTTCATATTTTATTTTTAATCCTGTTT
*
57255659 CTAAATTTATCTGGTT-ATATTTTATTTTTAATCCTGGTT
1 CTAAATTTATCT-GTTCATATTTTATTTTTAATCCTGTTT
*
57255698 CAAAATTT
1 CTAAATTT
57255706 GTAATTTAAA
Statistics
Matches: 110, Mismatches: 13, Indels: 14
0.80 0.09 0.10
Matches are distributed among these distances:
39 69 0.63
40 6 0.05
41 1 0.01
42 1 0.01
43 4 0.04
44 28 0.25
45 1 0.01
ACGTcount: A:0.27, C:0.11, G:0.05, T:0.57
Consensus pattern (39 bp):
CTAAATTTATCTGTTCATATTTTATTTTTAATCCTGTTT
Found at i:57255705 original size:78 final size:79
Alignment explanation
Indices: 57255550--57255705 Score: 199
Period size: 83 Copynumber: 1.9 Consensus size: 79
57255540 AATTTTACTG
* * *
57255550 TTCATATTTTATTTTTAATCTTGTTTCTAAATTATTTGTATATGTTCATAATTTATTTTTAATCC
1 TTCATATTTTATTTTTAATCCTATTTCTAAATTATCTG----TGTTCATAATTTATTTTTAATCC
*
57255615 TGCTTCTAAATTTATCTA
62 TGCTTCAAAATTTATCTA
* *
57255633 TTCATATTTTATTTTTAATCCTATTTCTAAATTTATCTG-GTT-ATATTTTATTTTTAATCCTGG
1 TTCATATTTTATTTTTAATCCTATTTCTAAA-TTATCTGTGTTCATAATTTATTTTTAATCCTGC
57255696 TTCAAAATTT
65 TTCAAAATTT
57255706 GTAATTTAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
78 28 0.42
79 3 0.05
83 29 0.44
84 6 0.09
ACGTcount: A:0.26, C:0.11, G:0.05, T:0.58
Consensus pattern (79 bp):
TTCATATTTTATTTTTAATCCTATTTCTAAATTATCTGTGTTCATAATTTATTTTTAATCCTGCT
TCAAAATTTATCTA
Done.