Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012103.1 Kokia drynarioides strain JFW-HI SEQ_127102, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 87334
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:491 original size:26 final size:26
Alignment explanation
Indices: 441--491 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
431 AAAAATCAAA
*
441 ATAGTTTTAAAAAAAATGAGAAAAGG
1 ATAGTTTTAAAAAAAATGAAAAAAGG
*
467 ATAGTTTTTAAAAAAAT-AAATAAAG
1 ATAGTTTTAAAAAAAATGAAA-AAAG
492 ATTTCGTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 2 0.09
26 20 0.91
ACGTcount: A:0.59, C:0.00, G:0.14, T:0.27
Consensus pattern (26 bp):
ATAGTTTTAAAAAAAATGAAAAAAGG
Found at i:541 original size:21 final size:21
Alignment explanation
Indices: 504--546 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
494 TTCGTTTTTT
*
504 TTTAAAGATCGAGGCTCGATC
1 TTTAAAGATCGAGGCTCAATC
*
525 TTTAAAGATTTGA-GCTCAATC
1 TTTAAAGA-TCGAGGCTCAATC
546 T
1 T
547 ATCCTTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (21 bp):
TTTAAAGATCGAGGCTCAATC
Found at i:1090 original size:30 final size:29
Alignment explanation
Indices: 1055--1588 Score: 194
Period size: 30 Copynumber: 18.2 Consensus size: 29
1045 GTTTTATTTC
*
1055 AAAATTATATTTTAACCCTCAAATTTCACA
1 AAAATTACATTTTAACCCTCAAATTTC-CA
* *
1085 AAAATTACATTTTGAA-CTTCAAACTTCTCA
1 AAAATTACATTTT-AACCCTCAAATTTC-CA
* *
1115 AAAATAACATTTTAACCCCTAAAATTTCCA
1 AAAATTACATTTTAA-CCCTCAAATTTCCA
* * * *
1145 AAAATTACATTTTGACCC-CTGAACTTCGTA
1 AAAATTACATTTTAACCCTC-AAATTTC-CA
* * * *
1175 AAAATTACATTTTGACCCTCGAACTTCTTA
1 AAAATTACATTTTAACCCTCAAATTTC-CA
* * * * *
1205 AAAATCACATTTTAACACAT-GAACTTCTCT
1 AAAATTACATTTTAAC-CCTCAAATTTC-CA
1235 AAAATTACATTTTAACCCTCAAACTTTTCC-
1 AAAATTACATTTTAACCCTCAAA--TTTCCA
* * * *
1265 AAAGTCACATTTTCACCCTAAACATTTCC-
1 AAAATTACATTTTAACCCTCAA-ATTTCCA
* * * * ** *
1294 AAAATTGCATTTTTAGCC-AAAACAT-AA
1 AAAATTACATTTTAACCCTCAAATTTCCA
* *
1321 AAAATTACCATTTTGACCC-CGAACTTTTCC-
1 AAAATTA-CATTTTAACCCTC-AA-ATTTCCA
* **
1351 AAAATTACATTTTTA-CCTCTAAACATCCA
1 AAAATTACATTTTAACCCTC-AAATTTCCA
*
1380 AAAATTACCATTTT-GCCCTCGAACA-TT-CA
1 AAAATTA-CATTTTAACCCTC-AA-ATTTCCA
* * **
1409 AAAATTATCATTTT-GCCCTTAAACATCC-
1 AAAATTA-CATTTTAACCCTCAAATTTCCA
*
1437 AAAATTACCATTTT-ACCCCCGAACATTT--A
1 AAAATTA-CATTTTAACCCTC-AA-ATTTCCA
* * **
1466 AAAATTATCATTTT-GCCCCCAAACATCCA
1 AAAATTA-CATTTTAACCCTCAAATTTCCA
**
1495 AAAATTACCATTTT-ACCCTCAAATTTTTA
1 AAAATTA-CATTTTAACCCTCAAATTTCCA
* *
1524 AAAATCACATTTTCGA-CCTCAAATTTTCCA
1 AAAATTACATTTT-AACCCTCAAA-TTTCCA
* ** *
1554 AAAGTTTGATTTTAATCC-CAAATTTTCCA
1 AAAATTACATTTTAACCCTCAAA-TTTCCA
1583 AAAATT
1 AAAATT
1589 TCGATCCCCG
Statistics
Matches: 391, Mismatches: 81, Indels: 65
0.73 0.15 0.12
Matches are distributed among these distances:
27 11 0.03
28 44 0.11
29 143 0.37
30 174 0.45
31 16 0.04
32 3 0.01
ACGTcount: A:0.38, C:0.24, G:0.04, T:0.34
Consensus pattern (29 bp):
AAAATTACATTTTAACCCTCAAATTTCCA
Found at i:1170 original size:60 final size:60
Alignment explanation
Indices: 1055--1257 Score: 223
Period size: 60 Copynumber: 3.4 Consensus size: 60
1045 GTTTTATTTC
* * *
1055 AAAATTATATTTTAACCCTCAAATTTCACAAAAATTACATTTTGA-ACTTCAAACTTCTCA
1 AAAATTACATTTTAACCCTCAAATTTCACAAAAATTACATTTTGACACAT-GAACTTCTCA
* * * *
1115 AAAATAACATTTTAACCCCTAAAATTTC-CAAAAATTACATTTTGACCCCTGAACTTCGT-A
1 AAAATTACATTTTAA-CCCTCAAATTTCACAAAAATTACATTTTGACACATGAACTTC-TCA
* * * ** * * *
1175 AAAATTACATTTTGACCCTCGAACTTCTTAAAAATCACATTTTAACACATGAACTTCTCT
1 AAAATTACATTTTAACCCTCAAATTTCACAAAAATTACATTTTGACACATGAACTTCTCA
1235 AAAATTACATTTTAACCCTCAAA
1 AAAATTACATTTTAACCCTCAAA
1258 CTTTTCCAAA
Statistics
Matches: 119, Mismatches: 19, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
59 10 0.08
60 95 0.80
61 14 0.12
ACGTcount: A:0.40, C:0.22, G:0.03, T:0.34
Consensus pattern (60 bp):
AAAATTACATTTTAACCCTCAAATTTCACAAAAATTACATTTTGACACATGAACTTCTCA
Found at i:1260 original size:90 final size:90
Alignment explanation
Indices: 1055--1260 Score: 236
Period size: 90 Copynumber: 2.3 Consensus size: 90
1045 GTTTTATTTC
* * *
1055 AAAATTATATTTTAACCCTCAAATTTCACAAAAATTACATTTTGAACTTCAAACTTCTCAAAAAT
1 AAAATTACATTTTAACCCTCAAACTTCACAAAAATTACATTTTGAACCTCAAACTTCTCAAAAAT
* *
1120 AACATTTTAACCCCTAAAATTTCCA
66 AACATTTTAACACATAAAATTTCCA
* * ** * * *
1145 AAAATTACATTTTGACCC-CTGAACTTCGTAAAAATTACATTTTGACCCTCGAACTTCTTAAAAA
1 AAAATTACATTTTAACCCTC-AAACTTCACAAAAATTACATTTTGAACCTCAAACTTCTCAAAAA
* * * *
1209 TCACATTTTAACACAT-GAACTTCTCT
65 TAACATTTTAACACATAAAATTTC-CA
1235 AAAATTACATTTTAACCCTCAAACTT
1 AAAATTACATTTTAACCCTCAAACTT
1261 TTCCAAAGTC
Statistics
Matches: 95, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
89 6 0.06
90 88 0.93
91 1 0.01
ACGTcount: A:0.40, C:0.22, G:0.03, T:0.34
Consensus pattern (90 bp):
AAAATTACATTTTAACCCTCAAACTTCACAAAAATTACATTTTGAACCTCAAACTTCTCAAAAAT
AACATTTTAACACATAAAATTTCCA
Found at i:1275 original size:90 final size:90
Alignment explanation
Indices: 1055--1393 Score: 222
Period size: 90 Copynumber: 3.8 Consensus size: 90
1045 GTTTTATTTC
* * *
1055 AAAATTATATTTTAACCCTCAAA--TTTCACAAAAATTACATTTTGAACTTCAAACTTCTCAAAA
1 AAAATTACATTTTAACCCTCAAACTTTTC-C-AAAATTACATTTTGACCCTCAAACTTCTCAAAA
* *
1118 ATAACATTTTAACCCCTAAAATTTCCA
64 ATAACATTTTAACACATAAAATTTCCA
* * * * * *
1145 AAAATTACATTTTGACCC-CTGAACTTCGT-AAAAATTACATTTTGACCCTCGAACTTCTTAAAA
1 AAAATTACATTTTAACCCTC-AAACTT-TTCCAAAATTACATTTTGACCCTCAAACTTCTCAAAA
* * * *
1208 ATCACATTTTAACACAT-GAACTTCTCT
64 ATAACATTTTAACACATAAAATTTC-CA
* * * *
1235 AAAATTACATTTTAACCCTCAAACTTTTCCAAAGTCACATTTTCACCCT-AAACATT-TCCAAAA
1 AAAATTACATTTTAACCCTCAAACTTTTCCAAAATTACATTTTGACCCTCAAAC-TTCTCAAAAA
** * *
1298 TTGCATTTTTAGC-CA-AAACA--T-AA
65 TAACA-TTTTAACACATAAA-ATTTCCA
* * * *
1321 AAAATTACCATTTTGACCC-CGAACTTTTCCAAAATTACATTTTTA-CCTCTAAACATC-CAAAA
1 AAAATTA-CATTTTAACCCTCAAACTTTTCCAAAATTACATTTTGACCCTC-AAACTTCTCAAAA
*
1383 ATTACCATTTT
64 A-TAACATTTT
1394 GCCCTCGAAC
Statistics
Matches: 193, Mismatches: 40, Indels: 36
0.72 0.15 0.13
Matches are distributed among these distances:
85 3 0.02
86 39 0.20
87 17 0.09
88 1 0.01
89 21 0.11
90 109 0.56
91 1 0.01
92 1 0.01
93 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.04, T:0.34
Consensus pattern (90 bp):
AAAATTACATTTTAACCCTCAAACTTTTCCAAAATTACATTTTGACCCTCAAACTTCTCAAAAAT
AACATTTTAACACATAAAATTTCCA
Found at i:1528 original size:29 final size:29
Alignment explanation
Indices: 1320--1517 Score: 186
Period size: 29 Copynumber: 6.8 Consensus size: 29
1310 CCAAAACATA
* *
1320 AAAAATTACCATTTTGACCC-CGAACTTTTC
1 AAAAATTACCATTTTG-CCCTCAAAC-ATTC
* ** *
1350 CAAAATTA-CATTTTTACCTCTAAACATCC
1 AAAAATTACCATTTTGCCCTC-AAACATTC
*
1379 AAAAATTACCATTTTGCCCTCGAACATTC
1 AAAAATTACCATTTTGCCCTCAAACATTC
* *
1408 AAAAATTATCATTTTGCCCTTAAACA-TC
1 AAAAATTACCATTTTGCCCTCAAACATTC
* * * * *
1436 CAAAATTACCATTTTACCCCCGAACATTT
1 AAAAATTACCATTTTGCCCTCAAACATTC
* * *
1465 AAAAATTATCATTTTGCCCCCAAACATCC
1 AAAAATTACCATTTTGCCCTCAAACATTC
*
1494 AAAAATTACCATTTTACCCTCAAA
1 AAAAATTACCATTTTGCCCTCAAA
1518 TTTTTAAAAA
Statistics
Matches: 134, Mismatches: 30, Indels: 9
0.77 0.17 0.05
Matches are distributed among these distances:
28 24 0.18
29 90 0.67
30 20 0.15
ACGTcount: A:0.37, C:0.27, G:0.04, T:0.32
Consensus pattern (29 bp):
AAAAATTACCATTTTGCCCTCAAACATTC
Found at i:1535 original size:28 final size:29
Alignment explanation
Indices: 1494--1550 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
1484 CCAAACATCC
*
1494 AAAAATTACCATTTT-ACCCTCAAATTTTT
1 AAAAATCACCATTTTCA-CCTCAAATTTTT
1523 AAAAATCA-CATTTTCGACCTCAAATTTT
1 AAAAATCACCATTTTC-ACCTCAAATTTT
1551 CCAAAAGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 6 0.24
29 18 0.72
30 1 0.04
ACGTcount: A:0.39, C:0.21, G:0.02, T:0.39
Consensus pattern (29 bp):
AAAAATCACCATTTTCACCTCAAATTTTT
Found at i:1535 original size:86 final size:86
Alignment explanation
Indices: 1235--1536 Score: 231
Period size: 86 Copynumber: 3.5 Consensus size: 86
1225 GAACTTCTCT
* * *
1235 AAAATTA-CATTTTAACCCTCAAACTTTTCCAAAGTCACATTTT-CACCCTAAACATTTCC-AAA
1 AAAATTACCATTTT-ACCCTCAAA-TTTTCCAAAATTACATTTTAC-CCCCAAACA--TCCAAAA
* *** * *
1297 ATT-GCATTTTTAGCCAAAACAT-AA
61 ATTACCATTTTGCCCCCAAACATCCA
* * *
1321 AAAATTACCATTTTGACCC-CGAACTTTTCCAAAATTACATTTTTACCTCTAAACATCCAAAAAT
1 AAAATTACCATTTT-ACCCTC-AAATTTTCCAAAATTACA-TTTTACCCCCAAACATCCAAAAAT
* * *
1385 TACCATTTTGCCCTCGAACATTCA
63 TACCATTTTGCCCCCAAACATCCA
* * * ** * **
1409 AAAATTATCATTTTGCCCTTAAA-CATCCAAAATTACCATTTTACCCCCGAACATTTAAAAATTA
1 AAAATTACCATTTTACCCTCAAATTTTCCAAAATTA-CATTTTACCCCCAAACATCCAAAAATTA
*
1473 TCATTTTGCCCCCAAACATCCA
65 CCATTTTGCCCCCAAACATCCA
** *
1495 AAAATTACCATTTTACCCTCAAATTTTTAAAAATCACATTTT
1 AAAATTACCATTTTACCCTCAAATTTTCCAAAATTACATTTT
1537 CGACCTCAAA
Statistics
Matches: 170, Mismatches: 36, Indels: 20
0.75 0.16 0.09
Matches are distributed among these distances:
85 3 0.02
86 102 0.60
87 50 0.29
88 15 0.09
ACGTcount: A:0.38, C:0.25, G:0.03, T:0.33
Consensus pattern (86 bp):
AAAATTACCATTTTACCCTCAAATTTTCCAAAATTACATTTTACCCCCAAACATCCAAAAATTAC
CATTTTGCCCCCAAACATCCA
Found at i:1536 original size:57 final size:58
Alignment explanation
Indices: 1320--1517 Score: 240
Period size: 57 Copynumber: 3.4 Consensus size: 58
1310 CCAAAACATA
* * * * *
1320 AAAAATTACCATTTTGACCC-CGAACTTTTCCAAAATTA-CATTTTTACCTCTAAACATCC
1 AAAAATTACCATTTT-ACCCTCAAAC-ATTCAAAAATTATCA-TTTTGCCCCTAAACATCC
* * *
1379 AAAAATTACCATTTTGCCCTCGAACATTCAAAAATTATCATTTTGCCCTTAAACATCC
1 AAAAATTACCATTTTACCCTCAAACATTCAAAAATTATCATTTTGCCCCTAAACATCC
* * * *
1437 -AAAATTACCATTTTACCCCCGAACATTTAAAAATTATCATTTTGCCCCCAAACATCC
1 AAAAATTACCATTTTACCCTCAAACATTCAAAAATTATCATTTTGCCCCTAAACATCC
1494 AAAAATTACCATTTTACCCTCAAA
1 AAAAATTACCATTTTACCCTCAAA
1518 TTTTTAAAAA
Statistics
Matches: 123, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
57 52 0.42
58 49 0.40
59 22 0.18
ACGTcount: A:0.37, C:0.27, G:0.04, T:0.32
Consensus pattern (58 bp):
AAAAATTACCATTTTACCCTCAAACATTCAAAAATTATCATTTTGCCCCTAAACATCC
Found at i:5796 original size:55 final size:55
Alignment explanation
Indices: 5734--5855 Score: 201
Period size: 55 Copynumber: 2.2 Consensus size: 55
5724 ACCATTCGTA
*
5734 CATATCCAATAAACTAAATTGATCATTCTTTAATACATACAAACATACCCATAAT
1 CATATCCAATAAACTAAATTGATCATTCTTTAATACATACAAACATACCAATAAT
* *
5789 CATATCCAATAAACTAAATTGATCATTCTTTAATATATACAAGCATACCAATAAT
1 CATATCCAATAAACTAAATTGATCATTCTTTAATACATACAAACATACCAATAAT
5844 CATA-CCATATAA
1 CATATCCA-ATAA
5856 TCATTCTTTC
Statistics
Matches: 63, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
54 3 0.05
55 60 0.95
ACGTcount: A:0.46, C:0.20, G:0.02, T:0.31
Consensus pattern (55 bp):
CATATCCAATAAACTAAATTGATCATTCTTTAATACATACAAACATACCAATAAT
Found at i:10256 original size:50 final size:50
Alignment explanation
Indices: 10139--10799 Score: 408
Period size: 50 Copynumber: 13.4 Consensus size: 50
10129 GGAAGGATTA
* * *
10139 AGGCCGCAACGGCAAATCCGGTACCTTAA-AAGATGTGAAGGGAAAGGTTA
1 AGGCCGCAACGGCGAACCCGGTACC-TAAGAAGATGTGAAGGGAAAGGTTG
* * ** ** *
10189 AGGCCGTAATGATGAACCCAATACCTAAGAAGATGTGATGGGAAAGGTTG
1 AGGCCGCAACGGCGAACCCGGTACCTAAGAAGATGTGAAGGGAAAGGTTG
* * * * * *
10239 AGGTCGCAACGACGAACCCAGCACC-ATGAAGA-GATGAAGGG-AAGAATTG
1 AGGCCGCAACGGCGAACCCGGTACCTAAGAAGATG-TGAAGGGAAAG-GTTG
** * * * *
10288 AGGCTACAACGGCAAAACCGGTACCTTAGAAGATGTGATGGGAAAGGTTG
1 AGGCCGCAACGGCGAACCCGGTACCTAAGAAGATGTGAAGGGAAAGGTTG
* * * ** * **
10338 AGCCCGCGATGGCGAACTGGGTACC-ATGAAGATACGAAGGGAAA-GTTG
1 AGGCCGCAACGGCGAACCCGGTACCTAAGAAGATGTGAAGGGAAAGGTTG
* * * *
10386 AGGCCGTAACGACGAACCTGGTACCTAAGAAGATGTGATGGGAAAGGTTG
1 AGGCCGCAACGGCGAACCCGGTACCTAAGAAGATGTGAAGGGAAAGGTTG
* * * * * *
10436 AGGCCGCAACGACGAACCCAGTA-CTATGAAGATTTGAAGGGAATGATTG
1 AGGCCGCAACGGCGAACCCGGTACCTAAGAAGATGTGAAGGGAAAGGTTG
* * * * * * *
10485 AGGTCACGATGGCGAATCCGGTACCTAAAAAGATGTGAGGGGAAAGGTTG
1 AGGCCGCAACGGCGAACCCGGTACCTAAGAAGATGTGAAGGGAAAGGTTG
* * * * ** *
10535 AGGCTGCAACGGCAAACCCGATACC-ATGAAGATACGAAGGGAAAGGTTC
1 AGGCCGCAACGGCGAACCCGGTACCTAAGAAGATGTGAAGGGAAAGGTTG
* ** * * *
10584 AGACCATAACGACGAACCCGGTACCTAAGAAGATGCGATGGGAAAGGTTG
1 AGGCCGCAACGGCGAACCCGGTACCTAAGAAGATGTGAAGGGAAAGGTTG
* * * * ** * * * * *
10634 AGCCCGCAATGACAAACTAGATACC-ACGGAGATATAAAGGGAAAGGTTG
1 AGGCCGCAACGGCGAACCCGGTACCTAAGAAGATGTGAAGGGAAAGGTTG
* * * * ** * * *
10683 AGGGCACAACGGCGAACTCGATACCTTGGAAGATGTGATGGGAATGATTG
1 AGGCCGCAACGGCGAACCCGGTACCTAAGAAGATGTGAAGGGAAAGGTTG
* ** * * * * *
10733 AGGTCATATCGGCGAATCCGATACC-ATGAAGATAT-AGAGGGAAAGGTTG
1 AGGCCGCAACGGCGAACCCGGTACCTAAGAAGATGTGA-AGGGAAAGGTTG
*
10782 AGGCAGCAACGGCGAACC
1 AGGCCGCAACGGCGAACC
10800 TAGCACCTTA
Statistics
Matches: 451, Mismatches: 148, Indels: 25
0.72 0.24 0.04
Matches are distributed among these distances:
48 27 0.06
49 201 0.45
50 219 0.49
51 4 0.01
ACGTcount: A:0.35, C:0.18, G:0.31, T:0.16
Consensus pattern (50 bp):
AGGCCGCAACGGCGAACCCGGTACCTAAGAAGATGTGAAGGGAAAGGTTG
Found at i:10321 original size:99 final size:98
Alignment explanation
Indices: 10210--10735 Score: 466
Period size: 99 Copynumber: 5.3 Consensus size: 98
10200 ATGAACCCAA
* * * *
10210 TACCTAAGAAGATGTGATGGGAAAGGTTGAGGTCGCAACGACGAACCCAGCACCATGAAGAGATG
1 TACCTAAGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGACGAACCCAGTACCATGAAGATACG
* * *
10275 AAGGGAAGAATTGAGGCTACAACGGCAAAACCGG
66 AAGGGAA-AATTGAGGCCACAACGACGAAACCGG
* * * * * ***
10309 TACCTTAGAAGATGTGATGGGAAAGGTTGAGCCCGCGATGGCGAACTGGGTACCATGAAGATACG
1 TACCTAAGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGACGAACCCAGTACCATGAAGATACG
* **
10374 AAGGGAAAGTTGAGGCCGTAACGACG-AACCTGG
66 AAGGGAAAATTGAGGCCACAACGACGAAACC-GG
* **
10407 TACCTAAGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGACGAACCCAGTACTATGAAGATTTG
1 TACCTAAGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGACGAACCCAGTACCATGAAGATACG
* * * * * *
10472 AAGGGAATGATTGAGGTCACGATGGCGAATCCGG
66 AAGGGAA-AATTGAGGCCACAACGACGAAACCGG
* * * * *
10506 TACCTAAAAAGATGTGAGGGGAAAGGTTGAGGCTGCAACGGCAAACCC-GATACCATGAAGATAC
1 TACCTAAGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGACGAACCCAG-TACCATGAAGATAC
* * * * *
10570 GAAGGGAAAGGTTCAGACCATAACGACGAACCCGG
65 GAAGGGAAA-ATTGAGGCCACAACGACGAAACCGG
* * * * * * * *
10605 TACCTAAGAAGATGCGATGGGAAAGGTTGAGCCCGCAATGAC-AAACTAGATACCACGGAGATAT
1 TACCTAAGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGACGAACCCAG-TACCATGAAGATAC
* * * * *
10669 AAAGGGAAAGGTTGAGGGCACAACGGCG-AACTCGA
65 GAAGGGAAA-ATTGAGGCCACAACGACGAAAC-CGG
** * *
10704 TACCTTGGAAGATGTGATGGGAATGATTGAGG
1 TACCTAAGAAGATGTGATGGGAAAGGTTGAGG
10736 TCATATCGGC
Statistics
Matches: 338, Mismatches: 82, Indels: 14
0.78 0.19 0.03
Matches are distributed among these distances:
97 4 0.01
98 82 0.24
99 249 0.74
100 3 0.01
ACGTcount: A:0.35, C:0.17, G:0.32, T:0.16
Consensus pattern (98 bp):
TACCTAAGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGACGAACCCAGTACCATGAAGATACG
AAGGGAAAATTGAGGCCACAACGACGAAACCGG
Found at i:10530 original size:197 final size:198
Alignment explanation
Indices: 10142--10642 Score: 621
Period size: 197 Copynumber: 2.5 Consensus size: 198
10132 AGGATTAAGG
* * * * ** * *
10142 CCGCAACGGCAAATCCGGTACCTTAAAAGATGTGAAGGGAAAGGTTAAGGCCGTAATGATGAACC
1 CCGCAACGGCAAACCCGATACCAT-GAAGATACGAAGGGAAAGGTTAAGGCCGTAACGACGAACC
** *
10207 CAATACCTAAGAAGATGTGATGGGAAAGGTTGAGGTCGCAACGACGAACCCAGCACCATGAAGAG
65 CGGTACCTAAGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGACGAACCCAGCACCATGAAGAG
* * *
10272 ATGAAGGGAAGAATTGAGGCTACAACGGCAAAACCGGTACCTTAGAAGATGTGATGGGAAAGGTT
130 ATGAAGGGAAGAATTGAGGCTACAACGGCAAAACCGGTACCTAAAAAGATGTGAGGGGAAAGGTT
10337 GAGC
195 GAGC
* * * ** * * *
10341 CCGCGATGGCGAACTGGGTACCATGAAGATACGAAGGGAAA-GTTGAGGCCGTAACGACGAACCT
1 CCGCAACGGCAAACCCGATACCATGAAGATACGAAGGGAAAGGTTAAGGCCGTAACGACGAACCC
* * **
10405 GGTACCTAAGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGACGAACCCAGTACTATGAAGATT
66 GGTACCTAAGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGACGAACCCAGCACCATGAAGAGA
* * * *
10470 TGAAGGGAATG-ATTGAGG-TCACGATGGCGAATCCGGTACCTAAAAAGATGTGAGGGGAAAGGT
131 TGAAGGGAA-GAATTGAGGCT-ACAACGGCAAAACCGGTACCTAAAAAGATGTGAGGGGAAAGGT
*
10533 TGAGG
194 TGAGC
* * * *
10538 CTGCAACGGCAAACCCGATACCATGAAGATACGAAGGGAAAGGTTCAGACCATAACGACGAACCC
1 CCGCAACGGCAAACCCGATACCATGAAGATACGAAGGGAAAGGTTAAGGCCGTAACGACGAACCC
* *
10603 GGTACCTAAGAAGATGCGATGGGAAAGGTTGAGCCCGCAA
66 GGTACCTAAGAAGATGTGATGGGAAAGGTTGAGGCCGCAA
10643 TGACAAACTA
Statistics
Matches: 257, Mismatches: 42, Indels: 7
0.84 0.14 0.02
Matches are distributed among these distances:
196 1 0.00
197 167 0.65
198 72 0.28
199 17 0.07
ACGTcount: A:0.35, C:0.18, G:0.31, T:0.16
Consensus pattern (198 bp):
CCGCAACGGCAAACCCGATACCATGAAGATACGAAGGGAAAGGTTAAGGCCGTAACGACGAACCC
GGTACCTAAGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGACGAACCCAGCACCATGAAGAGA
TGAAGGGAAGAATTGAGGCTACAACGGCAAAACCGGTACCTAAAAAGATGTGAGGGGAAAGGTTG
AGC
Found at i:12337 original size:21 final size:21
Alignment explanation
Indices: 12297--12337 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
12287 ATTTCGTATT
*
12297 TTTAAAGATCGAGGCTCGATC
1 TTTAAAGATCGAGGCCCGATC
12318 TTTAAAGATTCGA-GCCCGAT
1 TTTAAAGA-TCGAGGCCCGAT
12338 TTATGCTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (21 bp):
TTTAAAGATCGAGGCCCGATC
Found at i:12907 original size:30 final size:30
Alignment explanation
Indices: 12873--13282 Score: 254
Period size: 30 Copynumber: 13.8 Consensus size: 30
12863 TATTTTATTT
* *
12873 AAAAATTTCATTTTAACCCCTAAACTTTGC
1 AAAAATTACATTTTAACCCCTAAACTTTTC
* *
12903 AAAAATTACATTTTGA-CCCTCAAACTTATC
1 AAAAATTACATTTTAACCCCT-AAACTTTTC
* * * * *
12933 AAAAATCATATTTTGACCCTTGAA-TTTTC
1 AAAAATTACATTTTAACCCCTAAACTTTTC
** * * *
12962 TAAAAATTACATTTTAACCATTGAACTTCTA
1 -AAAAATTACATTTTAACCCCTAAACTTTTC
*
12993 AAAAATTACATTTTAACCCTTAAACTTCTT-
1 AAAAATTACATTTTAACCCCTAAACTT-TTC
* *
13023 AAAAATCACATTTTAACCTCTAAA-TTTTC
1 AAAAATTACATTTTAACCCCTAAACTTTTC
* * * *
13052 CAAAATTACATTTTAA-GCCTCGAACTTCTC
1 AAAAATTACATTTTAACCCCT-AAACTTTTC
* *
13082 TAAAATTACATTTTGA-CCCTCAAACTTTTC
1 AAAAATTACATTTTAACCCCT-AAACTTTTC
* *
13112 CAAAATCACATTTTAA-CCCTAAACTTTTC
1 AAAAATTACATTTTAACCCCTAAACTTTTC
* ** * * * *
13141 CAAAATTGA-ATTTTTGCCCCCAGAC-ATCC
1 AAAAATT-ACATTTTAACCCCTAAACTTTTC
* *
13170 AAAAATTTCCATTTTGACCCC-AAACTTTTC
1 AAAAA-TTACATTTTAACCCCTAAACTTTTC
* * * * * *
13200 CAAAATCACATTTTTACCCTTAAAC-ATCC
1 AAAAATTACATTTTAACCCCTAAACTTTTC
* * *
13229 AAAAAATACCATTTT-ACCCCTAAAC-ATCC
1 AAAAATTA-CATTTTAACCCCTAAACTTTTC
13258 AAAAATTACCATTTT-ACCCCTAAAC
1 AAAAATTA-CATTTTAACCCCTAAAC
13283 ATCCAAAATT
Statistics
Matches: 304, Mismatches: 61, Indels: 31
0.77 0.15 0.08
Matches are distributed among these distances:
28 4 0.01
29 110 0.36
30 183 0.60
31 7 0.02
ACGTcount: A:0.38, C:0.25, G:0.03, T:0.35
Consensus pattern (30 bp):
AAAAATTACATTTTAACCCCTAAACTTTTC
Found at i:13101 original size:89 final size:87
Alignment explanation
Indices: 12903--13219 Score: 318
Period size: 89 Copynumber: 3.6 Consensus size: 87
12893 TAAACTTTGC
* * * * *
12903 AAAAATTACATTTTGACCCTCAAACTTATCAAAAATCATATTTTGACCCTTGAATTTTCTAAAAA
1 AAAAATTACATTTTGACCCTCAAACTT-TTAAAAATCACATTTTAACCC-TAAATTTTC-CAAAA
*
12968 TTACATTTTAACCATTGAACTTCTA
63 TTACATTTTAACCATCGAACTTCTA
* *
12993 AAAAATTACATTTTAACCCTTAAACTTCTTAAAAATCACATTTTAACCTCTAAATTTTCCAAAAT
1 AAAAATTACATTTTGACCCTCAAACTT-TTAAAAATCACATTTTAACC-CTAAATTTTCCAAAAT
*
13058 TACATTTTAAGCC-TCGAACTTCTC
64 TACATTTTAA-CCATCGAACTTCTA
* *
13082 TAAAATTACATTTTGACCCTCAAACTTTTCCAAAATCACATTTTAACCCTAAACTTTTCCAAAAT
1 AAAAATTACATTTTGACCCTCAAACTTTT-AAAAATCACATTTTAACCCTAAA-TTTTCCAAAAT
** * * * *
13147 TGA-ATTTTTGCC-CCCAGACATCCA
64 T-ACATTTTAACCATCGA-ACTTCTA
* * * *
13171 AAAATTTCCATTTTGACCC-CAAACTTTTCCAAAATCACATTTTTACCCT
1 AAAAATTACATTTTGACCCTCAAACTTTT-AAAAATCACATTTTAACCCT
13220 TAAACATCCA
Statistics
Matches: 196, Mismatches: 25, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
88 40 0.20
89 102 0.52
90 53 0.27
91 1 0.01
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.36
Consensus pattern (87 bp):
AAAAATTACATTTTGACCCTCAAACTTTTAAAAATCACATTTTAACCCTAAATTTTCCAAAATTA
CATTTTAACCATCGAACTTCTA
Found at i:13156 original size:60 final size:59
Alignment explanation
Indices: 12881--13276 Score: 249
Period size: 59 Copynumber: 6.7 Consensus size: 59
12871 TTAAAAATTT
* *
12881 CATTTTAACCCCTAAACTTTGCAAAAATTACATTTTGACCCTCAAACTTATCAAAAATCA
1 CATTTTAA-CCCTAAACTTTTCAAAAATTACATTTTGACCCTCAAACTTTTCAAAAATCA
* * * * * ** * * *
12941 TATTTTGACCCTTGAA-TTTTCTAAAAATTACATTTTAACCATTGAACTTCTAAAAAATTA
1 CATTTTAACCC-TAAACTTTTC-AAAAATTACATTTTGACCCTCAAACTTTTCAAAAATCA
* * * *
13001 CATTTTAACCCTTAAACTTCTT-AAAAATCACATTTT-AACCTCTAAA-TTTTCCAAAATTA
1 CATTTTAACCC-TAAACTT-TTCAAAAATTACATTTTGACCCTC-AAACTTTTCAAAAATCA
* * * * *
13060 CATTTTAAGCCTCGAACTTCTCTAAAATTACATTTTGACCCTCAAACTTTTCCAAAATCA
1 CATTTTAACCCT-AAACTTTTCAAAAATTACATTTTGACCCTCAAACTTTTCAAAAATCA
* * * * *
13120 CATTTTAACCCTAAACTTTTCCAAAATTGA-ATTTTTG-CCCCCAGAC-ATCCAAAAATTTC-
1 CATTTTAACCCTAAACTTTTCAAAAATT-ACA-TTTTGACCCTCAAACTTTTCAAAAA--TCA
* * * * * * * *
13179 CATTTTGACCCCAAACTTTTCCAAAATCACATTTTTACCCTTAAAC-ATCCAAAAAAT-A
1 CATTTTAACCCTAAACTTTTCAAAAATTACATTTTGACCCTCAAACTTTTC-AAAAATCA
* * *
13237 CCATTTTACCCCTAAAC-ATCCAAAAATTACCATTTT-ACCC
1 -CATTTTAACCCTAAACTTTTCAAAAATTA-CATTTTGACCC
13277 CTAAACATCC
Statistics
Matches: 265, Mismatches: 52, Indels: 40
0.74 0.15 0.11
Matches are distributed among these distances:
58 26 0.10
59 126 0.48
60 109 0.41
61 2 0.01
62 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (59 bp):
CATTTTAACCCTAAACTTTTCAAAAATTACATTTTGACCCTCAAACTTTTCAAAAATCA
Found at i:13318 original size:27 final size:28
Alignment explanation
Indices: 13164--13345 Score: 181
Period size: 29 Copynumber: 6.4 Consensus size: 28
13154 TTGCCCCCAG
*
13164 ACATCCAAAAATTTCCATTTTGACCCC-AA
1 ACATCC-AAAATTACCATTTT-ACCCCTAA
* * *
13193 ACTTTTCCAAAATCA-CATTTTTACCCTTAA
1 AC--ATCCAAAATTACCA-TTTTACCCCTAA
*
13223 ACATCCAAAAAATACCATTTTACCCCTAA
1 ACATCC-AAAATTACCATTTTACCCCTAA
13252 ACATCCAAAAATTACCATTTTACCCCTAA
1 ACATCC-AAAATTACCATTTTACCCCTAA
* *
13281 ACATCCAAAATTACCATTTTA-CCTTGA
1 ACATCCAAAATTACCATTTTACCCCTAA
* *
13308 ACATCCAAAATTACCATTTTGCCCTTAA
1 ACATCCAAAATTACCATTTTACCCCTAA
**
13336 ATTTCCAAAA
1 ACATCCAAAA
13346 ATCACATTTT
Statistics
Matches: 131, Mismatches: 15, Indels: 15
0.81 0.09 0.09
Matches are distributed among these distances:
27 24 0.18
28 31 0.24
29 58 0.44
30 15 0.11
31 3 0.02
ACGTcount: A:0.39, C:0.29, G:0.02, T:0.31
Consensus pattern (28 bp):
ACATCCAAAATTACCATTTTACCCCTAA
Found at i:24343 original size:8 final size:8
Alignment explanation
Indices: 24330--24368 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
24320 TTAAATTACT
24330 TTTTATAA
1 TTTTATAA
24338 TTTTATAA
1 TTTTATAA
*
24346 TTCTAT-A
1 TTTTATAA
*
24353 TTTTAGAA
1 TTTTATAA
24361 TTTTATAA
1 TTTTATAA
24369 AAAATATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
7 5 0.19
8 21 0.81
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (8 bp):
TTTTATAA
Found at i:24514 original size:21 final size:20
Alignment explanation
Indices: 24480--24518 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
24470 ATTTTTATAA
24480 TTTTTTTATAATTTATATGT
1 TTTTTTTATAATTTATATGT
*
24500 TTTTTTTCTAGATTTATAT
1 TTTTTTTATA-ATTTATAT
24519 ATATTCTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.69
Consensus pattern (20 bp):
TTTTTTTATAATTTATATGT
Found at i:31582 original size:2 final size:2
Alignment explanation
Indices: 31575--31609 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
31565 CGAACATGAT
*
31575 TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
31610 GAAAAAAGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:31820 original size:22 final size:22
Alignment explanation
Indices: 31773--31822 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
31763 TTAATTAACC
*
31773 TTAATTAATCATAATTAATTCT
1 TTAATTAATCATAATTAATTCA
**
31795 TTAATTAAATCATTTTTAATT-A
1 TTAATT-AATCATAATTAATTCA
31817 TTAATT
1 TTAATT
31823 TAAGTTTAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 12 0.50
23 12 0.50
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (22 bp):
TTAATTAATCATAATTAATTCA
Found at i:32747 original size:25 final size:25
Alignment explanation
Indices: 32713--32762 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
32703 ATATATTGTT
*
32713 AAATTAATTTATTTTAATATTAAAA
1 AAATCAATTTATTTTAATATTAAAA
*
32738 AAATCAATTTATTTTAATGTTAAAA
1 AAATCAATTTATTTTAATATTAAAA
32763 TTATTAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (25 bp):
AAATCAATTTATTTTAATATTAAAA
Found at i:33017 original size:5 final size:5
Alignment explanation
Indices: 33007--33035 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
32997 ATTTATTATG
33007 TTAAA TTAAA -TAAA TTAAA TTAAA TTAAA
1 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA
33036 AATCATTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
TTAAA
Found at i:33022 original size:9 final size:10
Alignment explanation
Indices: 33007--33035 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
32997 ATTTATTATG
33007 TTAAATTAAA
1 TTAAATTAAA
33017 -TAAATTAAA
1 TTAAATTAAA
33026 TTAAATTAAA
1 TTAAATTAAA
33036 AATCATTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
TTAAATTAAA
Found at i:34229 original size:254 final size:254
Alignment explanation
Indices: 33780--34288 Score: 1000
Period size: 254 Copynumber: 2.0 Consensus size: 254
33770 TAGCTACTCA
*
33780 TCCGTTGAATCACTAATGGAGCACTGACATGGCCATTTTCATTGGCATAATAATAAATTTAGCCA
1 TCCGTTGAATCACTAACGGAGCACTGACATGGCCATTTTCATTGGCATAATAATAAATTTAGCCA
33845 TCTAATATTTATATATTTTATCAATTTGGTCTTAATTCTAAAAAATCAACAAGTTTAACCCTCAA
66 TCTAATATTTATATATTTTATCAATTTGGTCTTAATTCTAAAAAATCAACAAGTTTAACCCTCAA
33910 CTTTACATATTATGTCAATTTAGTATTGATTCTTAAATTTTCAATATTAAAAAAATAAAGAATTA
131 CTTTACATATTATGTCAATTTAGTATTGATTCTTAAATTTTCAATATTAAAAAAATAAAGAATTA
33975 TTTAAAAGTTCATCTTTATAAAAAATACATACAAAATTATAAATAAGTTATGTTAGGAG
196 TTTAAAAGTTCATCTTTATAAAAAATACATACAAAATTATAAATAAGTTATGTTAGGAG
34034 TCCGTTGAATCACTAACGGAGCACTGACATGGCCATTTTCATTGGCATAATAATAAATTTAGCCA
1 TCCGTTGAATCACTAACGGAGCACTGACATGGCCATTTTCATTGGCATAATAATAAATTTAGCCA
34099 TCTAATATTTATATATTTTATCAATTTGGTCTTAATTCTAAAAAATCAACAAGTTTAACCCTCAA
66 TCTAATATTTATATATTTTATCAATTTGGTCTTAATTCTAAAAAATCAACAAGTTTAACCCTCAA
*
34164 CTTTACATATTATGTCAATTTAGTATTGATTCTTAAATTTTCAATATTTAAAAAATAAAGAATTA
131 CTTTACATATTATGTCAATTTAGTATTGATTCTTAAATTTTCAATATTAAAAAAATAAAGAATTA
34229 TTTAAAAGTTCATCTTTATAAAAAATACATACAAAATTATAAATAAGTTATGTTAGGAG
196 TTTAAAAGTTCATCTTTATAAAAAATACATACAAAATTATAAATAAGTTATGTTAGGAG
34288 T
1 T
34289 AATTTATGGG
Statistics
Matches: 253, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
254 253 1.00
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (254 bp):
TCCGTTGAATCACTAACGGAGCACTGACATGGCCATTTTCATTGGCATAATAATAAATTTAGCCA
TCTAATATTTATATATTTTATCAATTTGGTCTTAATTCTAAAAAATCAACAAGTTTAACCCTCAA
CTTTACATATTATGTCAATTTAGTATTGATTCTTAAATTTTCAATATTAAAAAAATAAAGAATTA
TTTAAAAGTTCATCTTTATAAAAAATACATACAAAATTATAAATAAGTTATGTTAGGAG
Found at i:34324 original size:34 final size:34
Alignment explanation
Indices: 34281--34350 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
34271 ATAAGTTATG
*
34281 TTAGGAGTAATTTATGGGATTTGTATATATTGTT
1 TTAGGAGTAATTTATGAGATTTGTATATATTGTT
34315 TTAGGAGTAATTTATGAGATTTGTATATATTGTT
1 TTAGGAGTAATTTATGAGATTTGTATATATTGTT
34349 TT
1 TT
34351 CTTATTGCAG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.27, C:0.00, G:0.21, T:0.51
Consensus pattern (34 bp):
TTAGGAGTAATTTATGAGATTTGTATATATTGTT
Found at i:38834 original size:34 final size:34
Alignment explanation
Indices: 38791--38855 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
38781 GAGGAAGGTG
* * *
38791 TTAGGAGTAATTTATGTGATTTGTATATATTGTT
1 TTAGGAGTAATTTATGGGATCTATATATATTGTT
38825 TTAGGAGTAATTTATGGGATCTATATATATT
1 TTAGGAGTAATTTATGGGATCTATATATATT
38856 ATTTCCTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.29, C:0.02, G:0.20, T:0.49
Consensus pattern (34 bp):
TTAGGAGTAATTTATGGGATCTATATATATTGTT
Found at i:39358 original size:2 final size:2
Alignment explanation
Indices: 39351--39375 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39341 TATCCTCACC
39351 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
39376 CCCCAATCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:41449 original size:22 final size:22
Alignment explanation
Indices: 41424--41474 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
41414 TATGCTCTAT
*
41424 TATGATAAGATATGTTTTGATA
1 TATGATAAGATATGTTATGATA
* * *
41446 TATGTTAAGTTTTGTTATGATA
1 TATGATAAGATATGTTATGATA
41468 TATGATA
1 TATGATA
41475 TACTTCGATA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.49
Consensus pattern (22 bp):
TATGATAAGATATGTTATGATA
Found at i:43862 original size:13 final size:12
Alignment explanation
Indices: 43837--43866 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
43827 TCATTTTTTT
43837 AAAAATTTAAAA
1 AAAAATTTAAAA
*
43849 AAAAATTTAGAA
1 AAAAATTTAAAA
43861 AAAAAT
1 AAAAAT
43867 AAAAGCATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (12 bp):
AAAAATTTAAAA
Found at i:44165 original size:3 final size:3
Alignment explanation
Indices: 44159--44184 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
44149 ATAATAATAA
44159 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
44185 ATCGAATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:47170 original size:21 final size:21
Alignment explanation
Indices: 47146--47199 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 21
47136 ATAGCACTTC
47146 TTATAAATAAAAAA-TATTTTT
1 TTATAAATAAAAAATTA-TTTT
* *
47167 TTATAACTTTAAAAAGTTATTTT
1 TTATAA--ATAAAAAATTATTTT
47190 TTATAAATAA
1 TTATAAATAA
47200 GTTATAATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
21 9 0.33
23 16 0.59
24 2 0.07
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (21 bp):
TTATAAATAAAAAATTATTTT
Found at i:47444 original size:24 final size:24
Alignment explanation
Indices: 47417--47463 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
47407 AAATACAAAT
47417 GATTT-TTATAATAAAATTTTTTAG
1 GATTTATTAT-ATAAAATTTTTTAG
*
47441 GATTTATTATATAAGATTTTTTA
1 GATTTATTATATAAAATTTTTTA
47464 TCATAACCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (24 bp):
GATTTATTATATAAAATTTTTTAG
Found at i:48170 original size:12 final size:11
Alignment explanation
Indices: 48129--48164 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
48119 TTTAATTATT
48129 TTTTAAAA-TA
1 TTTTAAAATTA
48139 TTTTAAAATTA
1 TTTTAAAATTA
*
48150 ATTTAAAATTA
1 TTTTAAAATTA
48161 TTTT
1 TTTT
48165 TTAAATATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TTTTAAAATTA
Found at i:49185 original size:29 final size:29
Alignment explanation
Indices: 49151--49214 Score: 128
Period size: 29 Copynumber: 2.2 Consensus size: 29
49141 CATATGTATA
49151 TTTTAACATATAGGAATTAATTTATTTAT
1 TTTTAACATATAGGAATTAATTTATTTAT
49180 TTTTAACATATAGGAATTAATTTATTTAT
1 TTTTAACATATAGGAATTAATTTATTTAT
49209 TTTTAA
1 TTTTAA
49215 GTGAAAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (29 bp):
TTTTAACATATAGGAATTAATTTATTTAT
Found at i:49202 original size:25 final size:27
Alignment explanation
Indices: 49142--49214 Score: 92
Period size: 29 Copynumber: 2.5 Consensus size: 27
49132 TTATATTAAC
*
49142 ATATGTATATTTTAACATATAGGAATTA
1 ATATTTAT-TTTTAACATATAGGAATTA
49170 ATTTATTTATTTTTAACATATAGGAATTA
1 A--TATTTATTTTTAACATATAGGAATTA
49199 ATTTATTTATTTTTAA
1 A--TATTTATTTTTAA
49215 GTGAAAAAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
28 1 0.02
29 35 0.83
30 6 0.14
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.52
Consensus pattern (27 bp):
ATATTTATTTTTAACATATAGGAATTA
Found at i:54026 original size:48 final size:48
Alignment explanation
Indices: 53953--54069 Score: 135
Period size: 48 Copynumber: 2.4 Consensus size: 48
53943 AACATGCGAT
* * * * *
53953 AGCATTATCCAACTCCAACATACCTCCATTAAACTCGGTCTCCTTAGC
1 AGCAGTATCCAACTCCAACACACCTCCATCAAAATCGGTCACCTTAGC
* * *
54001 AGCAGTATCCAACTCTAATACACCTCCATCAAAATCGGTCACCTTAGT
1 AGCAGTATCCAACTCCAACACACCTCCATCAAAATCGGTCACCTTAGC
* * *
54049 AACAATATCCAAATCCAACAC
1 AGCAGTATCCAACTCCAACAC
54070 TTCTCCTTTT
Statistics
Matches: 56, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
48 56 1.00
ACGTcount: A:0.35, C:0.33, G:0.08, T:0.24
Consensus pattern (48 bp):
AGCAGTATCCAACTCCAACACACCTCCATCAAAATCGGTCACCTTAGC
Found at i:60265 original size:18 final size:17
Alignment explanation
Indices: 60230--60278 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
60220 AATTTTCAAT
*
60230 TTTCAATTC-ATATCAC
1 TTTCAATTCAATTTCAC
60246 TTTCAATTCCAATTTCAC
1 TTTCAATT-CAATTTCAC
*
60264 TTTCACTTTCAATTT
1 TTTCA-ATTCAATTT
60279 TGATCACAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 8 0.29
17 1 0.04
18 17 0.61
19 2 0.07
ACGTcount: A:0.27, C:0.24, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTCAATTCAATTTCAC
Found at i:63459 original size:30 final size:31
Alignment explanation
Indices: 63364--63478 Score: 102
Period size: 31 Copynumber: 3.9 Consensus size: 31
63354 TTAATATAAC
* * * *
63364 ATTTGGTACTTGAACTTAACACTTTTTCCTA
1 ATTTGGTACCTAAACTTGACAATTTTTCCTA
63395 ATTTGGTACCTAAACATT-----TTTTGT-CTA
1 ATTTGGTACCTAAAC-TTGACAATTTT-TCCTA
63422 ATTTGGTA-CTCAAACTTGACAATTTTTCCTA
1 ATTTGGTACCT-AAACTTGACAATTTTTCCTA
*
63453 A-TTGGTACCTAAACTTGACACTTTTT
1 ATTTGGTACCTAAACTTGACAATTTTT
63479 TTGAAGTTAG
Statistics
Matches: 71, Mismatches: 3, Indels: 21
0.75 0.03 0.22
Matches are distributed among these distances:
26 4 0.06
27 19 0.27
28 1 0.01
30 22 0.31
31 23 0.32
32 2 0.03
ACGTcount: A:0.27, C:0.18, G:0.10, T:0.44
Consensus pattern (31 bp):
ATTTGGTACCTAAACTTGACAATTTTTCCTA
Found at i:63497 original size:31 final size:30
Alignment explanation
Indices: 63427--63499 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 30
63417 GTCTAATTTG
* *
63427 GTACTCAAACTTGACAATTTTTCCTAATTG
1 GTACTTAAACTTGACAATTTTTCCTAATTA
* * *
63457 GTACCTAAACTTGACACTTTTT-TTGAAGTTA
1 GTACTTAAACTTGACAATTTTTCCT-AA-TTA
63488 GTACTTAAACTT
1 GTACTTAAACTT
63500 TTTGGAATCC
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
29 1 0.03
30 21 0.60
31 13 0.37
ACGTcount: A:0.30, C:0.18, G:0.11, T:0.41
Consensus pattern (30 bp):
GTACTTAAACTTGACAATTTTTCCTAATTA
Found at i:63872 original size:24 final size:25
Alignment explanation
Indices: 63826--63881 Score: 78
Period size: 24 Copynumber: 2.2 Consensus size: 25
63816 AACCAATTTA
63826 AAAAGTAAAGAAACTAAAACCAAAT
1 AAAAGTAAAGAAACTAAAACCAAAT
* *
63851 AAAAGTATAG-AATTAAAACCAAAT
1 AAAAGTAAAGAAACTAAAACCAAAT
63875 AACAAGT
1 AA-AAGT
63882 GGCTGTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 15 0.54
25 13 0.46
ACGTcount: A:0.64, C:0.11, G:0.09, T:0.16
Consensus pattern (25 bp):
AAAAGTAAAGAAACTAAAACCAAAT
Found at i:69114 original size:2 final size:2
Alignment explanation
Indices: 69107--69153 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
69097 CAAGTGTGAG
69107 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
69149 AT AT A
1 AT AT A
69154 CACACATTAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:71003 original size:4 final size:4
Alignment explanation
Indices: 70996--71042 Score: 94
Period size: 4 Copynumber: 11.8 Consensus size: 4
70986 TCAAAATGTA
70996 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TAT
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TAT
71043 ATATATAAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.26, C:0.23, G:0.00, T:0.51
Consensus pattern (4 bp):
TATC
Found at i:71363 original size:20 final size:19
Alignment explanation
Indices: 71312--71364 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
71302 TGGTGCAAAA
* *
71312 AGCAGATGAGAGGTCTCGG
1 AGCAGAAGAGGGGTCTCGG
*
71331 -GCAGAAGAAGGGTCTCGGG
1 AGCAGAAGAGGGGTCTC-GG
*
71350 AGCAGACGAGGGGTC
1 AGCAGAAGAGGGGTC
71365 ACATGGTTGA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
18 13 0.48
19 2 0.07
20 12 0.44
ACGTcount: A:0.26, C:0.17, G:0.45, T:0.11
Consensus pattern (19 bp):
AGCAGAAGAGGGGTCTCGG
Found at i:71905 original size:38 final size:38
Alignment explanation
Indices: 71863--72041 Score: 142
Period size: 38 Copynumber: 4.7 Consensus size: 38
71853 TATGTTTGCG
*
71863 ATCTGCCTCATGATTGAGGAAAGAGATTG-GTGTCTTCA
1 ATCTGCCTCATGATTGAGGTAAGAGATTGAGT-TCTTCA
*
71901 ATCTGCCTTC-TGATTAAGGT-A-A-ATTG-GATTCTTCA
1 ATCTGCC-TCATGATTGAGGTAAGAGATTGAG-TTCTTCA
* *
71936 ATCTGCCCCATGATTG-GGTAAGAGATTGGTGTGTCTTCA
1 ATCTGCCTCATGATTGAGGTAAGAGATT-GAGT-TCTTCA
* *
71975 CTTCTGTCCTC-TGATT-AGGGTAAGAGATTGAATTCTTCA
1 -ATCTG-CCTCATGATTGA-GGTAAGAGATTGAGTTCTTCA
* * *
72014 ATCAGCCTCATGATCGGGGTAAGAGATT
1 ATCTGCCTCATGATTGAGGTAAGAGATT
72042 AGATGGTGAC
Statistics
Matches: 114, Mismatches: 12, Indels: 30
0.73 0.08 0.19
Matches are distributed among these distances:
34 4 0.04
35 24 0.21
36 3 0.03
37 8 0.07
38 35 0.31
39 15 0.13
40 11 0.10
41 14 0.12
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (38 bp):
ATCTGCCTCATGATTGAGGTAAGAGATTGAGTTCTTCA
Found at i:72026 original size:78 final size:72
Alignment explanation
Indices: 71867--72041 Score: 199
Period size: 78 Copynumber: 2.3 Consensus size: 72
71857 TTTGCGATCT
* *
71867 GCCTCATGATTGAGGAAAGAGATTGGTGTCTTCAATCTGCCTTCTGATTAAGGTAAATTGGATTC
1 GCCTCATGATTG-GGTAAGAGATTGGTGTCTTCAATCTGCCTTCTGATTAAGGTAAATTGAATTC
*
71932 TTCAATCT
65 TTCAATCA
* * *
71940 GCCCCATGATTGGGTAAGAGATTGGTGTGTCTTCACTTCTGTCC-TCTGATTAGGGTAAGAGATT
1 GCCTCATGATTGGGTAAGAGATT-G-GTGTCTTCA-ATCTG-CCTTCTGATTAAGGT-A-A-ATT
72004 GAATTCTTCAATCA
59 GAATTCTTCAATCA
*
72018 GCCTCATGATCGGGGTAAGAGATT
1 GCCTCATGAT-TGGGTAAGAGATT
72042 AGATGGTGAC
Statistics
Matches: 86, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
72 10 0.12
73 12 0.14
74 9 0.10
75 15 0.17
76 3 0.03
77 1 0.01
78 24 0.28
79 12 0.14
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.34
Consensus pattern (72 bp):
GCCTCATGATTGGGTAAGAGATTGGTGTCTTCAATCTGCCTTCTGATTAAGGTAAATTGAATTCT
TCAATCA
Found at i:72514 original size:49 final size:49
Alignment explanation
Indices: 72441--74179 Score: 748
Period size: 49 Copynumber: 35.6 Consensus size: 49
72431 TGATACCAGA
*
72441 TTCGCCGTTACGACTTCAATCTTTCCCAGCATGTTTCTGAGGTACAAGG
1 TTCGCCGTTGCGACTTCAATCTTTCCCAGCATGTTTCTGAGGTACAAGG
* * * ** * * * * *
72490 TTCGTCGTTGCGACTTAAACCTTTCCCCCCATATCTTC-GTGCTACCAGA
1 TTCGCCGTTGCGACTTCAATCTTTCCCAGCATGT-TTCTGAGGTACAAGG
* * * * * *
72539 TTCGTCGTTGCGGCTTTAAT-TTTACCCAACATGTTTTTGAGGTACAATG
1 TTCGCCGTTGCGACTTCAATCTTT-CCCAGCATGTTTCTGAGGTACAAGG
** * * * * * * * *
72588 TTCGTTGTTACGACTTAAACCTTTCCC-CCATATCTTC-GTGGTACCAGA
1 TTCGCCGTTGCGACTTCAATCTTTCCCAGCATGT-TTCTGAGGTACAAGG
***
72636 TTCGTTATTGC-AGCTTCAATCTTTCCCAGCATGTTTCTGAGGTACAAGG
1 TTCGCCGTTGCGA-CTTCAATCTTTCCCAGCATGTTTCTGAGGTACAAGG
** * * * ** * * * * *
72685 TTTTCCGTTACGACTTAAACCTTTCCCTCCGTATCTTC-GTGGTACCAGA
1 TTCGCCGTTGCGACTTCAATCTTTCCCAGCATGT-TTCTGAGGTACAAGG
** *
72734 TTCATCGTTGCGGCTTCAATCTTTCCCAGCATGTTTCTGAGGTACAAGG
1 TTCGCCGTTGCGACTTCAATCTTTCCCAGCATGTTTCTGAGGTACAAGG
* * * * * * * * *
72783 TTAGCCGTTACGACTTAAATCTTTTCCTCCGTAT-CTTC-GTGGTACCAGA
1 TTCGCCGTTGCGACTTCAATC-TTTCC-CAGCATGTTTCTGAGGTACAAGG
* * * * *
72832 TTCACTGTTGCGGCTTCAATCTATCCCAACATGTTTCTGAGGTACAAGG
1 TTCGCCGTTGCGACTTCAATCTTTCCCAGCATGTTTCTGAGGTACAAGG
* * ** * * * * *
72881 TTC-CCGTTGCGACTTAAACCTTTCCCTCCGTATCTTC-GTGGTACTAGA
1 TTCGCCGTTGCGACTTCAATCTTTCCCAGCATGT-TTCTGAGGTACAAGG
* * * *
72929 TTCACCATTGCGGCTTCAATCTTTCCCAGCATGTTTCTGAGGTACAATG
1 TTCGCCGTTGCGACTTCAATCTTTCCCAGCATGTTTCTGAGGTACAAGG
* * * * * * *
72978 TTCGCCGTTGCGACTTAAACCCTTCCC-GTCATATCTT-TGTGGTACCAGA
1 TTCGCCGTTGCGACTTCAATCTTTCCCAG-CATGT-TTCTGAGGTACAAGG
* * *
73027 TTCGTCGTTGTGGCTTCAATCTTTCCCAGCATGTTTCTGAGGTACAAGG
1 TTCGCCGTTGCGACTTCAATCTTTCCCAGCATGTTTCTGAGGTACAAGG
** ** * * * * *
73076 TTTACCGTTGCGACTTCAATCTTTCCCTCCGTATCTTC-GTGGTACCAGA
1 TTCGCCGTTGCGACTTCAATCTTTCCCAGCATGT-TTCTGAGGTACAAGG
* * * *
73125 TTCACCGTTACGGCTTCAATCTTTCCCAGCATGTCTT-TGAGGTATAAGG
1 TTCGCCGTTGCGACTTCAATCTTTCCCAGCATGT-TTCTGAGGTACAAGG
* ** * * ** * * * *
73174 TTCACCGTCACGACTTAAACCTTTCCCTTC--GTATCTTCATGGTACCAGA
1 TTCGCCGTTGCGACTTCAATCTTTCCCAGCATGTTTC-TGA-GGTACAAGG
* * *
73223 TTCGCCATTGC-AGCTTCAATTTTTCCCAGCATGTTTTTGAGGTACAAGG
1 TTCGCCGTTGCGA-CTTCAATCTTTCCCAGCATGTTTCTGAGGTACAAGG
* * * * * * *
73272 TTCGCCGTTGCGATTTAAACCTTTCCCTCCGTAT-TTTC-GTGGTACCAA-A
1 TTCGCCGTTGCGACTTCAATCTTT-CC-CAGCATGTTTCTGAGGTA-CAAGG
* * * *
73321 TTCACCATTGC-AGCATCAATCTTTCCCAACATGTTTCTGAGGTACAAGG
1 TTCGCCGTTGCGA-CTTCAATCTTTCCCAGCATGTTTCTGAGGTACAAGG
* * * ** * *
73370 TTCGCCGTTGCGACTTAAACCCTTCCCCCCATATCTTC--ATGGTACCA-G
1 TTCGCCGTTGCGACTTCAATCTTTCCCAGCATGT-TTCTGA-GGTACAAGG
* ** * * *
73418 ATCTGTTGTTGCGGCTTCAATCTTTCCTAACATGTTTCTGAGGTACAAGG
1 TTC-GCCGTTGCGACTTCAATCTTTCCCAGCATGTTTCTGAGGTACAAGG
* * * * * * *
73468 TTCGCCGTTGCGACTTAAACCTTTCCTC-CCATATCTTC-GTGGTACCAGA
1 TTCGCCGTTGCGACTTCAATCTTTCC-CAGCATGT-TTCTGAGGTACAAGG
**** * * *
73517 TTTTTTGTTGCGCCTTCAATCTTTCCCAACATGTTTTTGAGGTACAAGG
1 TTCGCCGTTGCGACTTCAATCTTTCCCAGCATGTTTCTGAGGTACAAGG
** * * * * * * * *
73566 TTCATCGTTGCAACTTAAATCTTTCCC-TC-CGTATCTTCATGGTACCAGA
1 TTCGCCGTTGCGACTTCAATCTTTCCCAGCATGTTTC-TGA-GGTACAAGG
* * * * *
73615 TTCACTGTTGCGGCTTCAATCTTTCCCAACATGTTTATGAGGTACAAGG
1 TTCGCCGTTGCGACTTCAATCTTTCCCAGCATGTTTCTGAGGTACAAGG
* * * * * *** * * * * *
73664 TTCACTGTTACGACTTAAACCTTTCCTTTCTTATCTTC-GTGGTACCAGA
1 TTCGCCGTTGCGACTTCAATCTTTCCCAGCATGT-TTCTGAGGTACAAGG
*
73713 TTCACCGTTGC-AGCTTCAATCTTTCCCAGCATGTTTCTGAGGTACAAGG
1 TTCGCCGTTGCGA-CTTCAATCTTTCCCAGCATGTTTCTGAGGTACAAGG
* * * * * * * * * *
73762 TTCGCTGTTGCGACTTAAACCCTTCCC-CCATATCTTC-GTGGTGCCAGA
1 TTCGCCGTTGCGACTTCAATCTTTCCCAGCATGT-TTCTGAGGTACAAGG
** *
73810 TTCATCGTTGC-AGCTTCAATCTTTCCCAGCATGTTTTTGAGGTACAAGG
1 TTCGCCGTTGCGA-CTTCAATCTTTCCCAGCATGTTTCTGAGGTACAAGG
*** * * * * * * *
73859 TTCGCCGTTATTACTTAAATCTTTCCCTACGTAT-CTTC-GTGGTTCCAGA
1 TTCGCCGTTGCGACTTCAATCTTTCCC-A-GCATGTTTCTGAGGTACAAGG
* ** * * *
73908 TTTGTTGTTGTGGCTTCAATCTTTCCCAGCATGTTTCTAAGGTACAAGG
1 TTCGCCGTTGCGACTTCAATCTTTCCCAGCATGTTTCTGAGGTACAAGG
* * ** * * * * * *
73957 TTCGCCATTGCGACTTAAATCTTTCCCTTCGTATCTTC-GTGGTGCCAGA
1 TTCGCCGTTGCGACTTCAATCTTTCCCAGCATGT-TTCTGAGGTACAAGG
* ** * * * *
74006 TTCACTATTGCGGCTTCAATATTTCCTAGTATGTTTCTGAGGTACAAGG
1 TTCGCCGTTGCGACTTCAATCTTTCCCAGCATGTTTCTGAGGTACAAGG
* * * * * * *
74055 TTTGCCGTTGCGACTT-ACACCTTTCCC-TCTATATCTT-TGCGGTACCAGA
1 TTCGCCGTTGCGACTTCA-ATCTTTCCCAGC-ATGT-TTCTGAGGTACAAGG
* * * *
74104 TTTGCCGTTACGGCTTCAATCTTTCCCAACATGTTTCTGAGGTACAAGG
1 TTCGCCGTTGCGACTTCAATCTTTCCCAGCATGTTTCTGAGGTACAAGG
* * * *
74153 TTCGCCATTACGACTTTAACCTTTCCC
1 TTCGCCGTTGCGACTTCAATCTTTCCC
74180 TCTAAACTTG
Statistics
Matches: 1198, Mismatches: 418, Indels: 148
0.68 0.24 0.08
Matches are distributed among these distances:
46 1 0.00
47 16 0.01
48 160 0.13
49 941 0.79
50 63 0.05
51 17 0.01
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.36
Consensus pattern (49 bp):
TTCGCCGTTGCGACTTCAATCTTTCCCAGCATGTTTCTGAGGTACAAGG
Found at i:74183 original size:98 final size:98
Alignment explanation
Indices: 72385--74181 Score: 2217
Period size: 98 Copynumber: 18.4 Consensus size: 98
72375 TGTCTTTGAC
* * * *
72385 GTACAAAGTTCACCGTTGCGACTTAAACCTTTCCCTCCGTAT-TTCGTGATACCAGATTCGCCGT
1 GTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCGTATCTTCGTGGTACCAGATTCACCGT
* *
72449 TACGACTTCAATCTTTCCCAGCATGTTTCTGAG
66 TGCGGCTTCAATCTTTCCCAGCATGTTTCTGAG
* * * * **
72482 GTACAAGGTTCGTCGTTGCGACTTAAACCTTTCCCCCCATATCTTCGTGCTACCAGATTCGTCGT
1 GTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCGTATCTTCGTGGTACCAGATTCACCGT
* * *
72547 TGCGGCTTTAAT-TTTACCCAACATGTTTTTGAG
66 TGCGGCTTCAATCTTT-CCCAGCATGTTTCTGAG
* ** * * ****
72580 GTACAATGTTCGTTGTTACGACTTAAACCTTTCCC-CCATATCTTCGTGGTACCAGATTCGTTAT
1 GTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCGTATCTTCGTGGTACCAGATTCACCGT
*
72644 TGCAGCTTCAATCTTTCCCAGCATGTTTCTGAG
66 TGCGGCTTCAATCTTTCCCAGCATGTTTCTGAG
** * *
72677 GTACAAGGTTTTCCGTTACGACTTAAACCTTTCCCTCCGTATCTTCGTGGTACCAGATTCATCGT
1 GTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCGTATCTTCGTGGTACCAGATTCACCGT
72742 TGCGGCTTCAATCTTTCCCAGCATGTTTCTGAG
66 TGCGGCTTCAATCTTTCCCAGCATGTTTCTGAG
* * * * *
72775 GTACAAGGTTAGCCGTTACGACTTAAATCTTTTCCTCCGTATCTTCGTGGTACCAGATTCACTGT
1 GTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCGTATCTTCGTGGTACCAGATTCACCGT
* *
72840 TGCGGCTTCAATCTATCCCAACATGTTTCTGAG
66 TGCGGCTTCAATCTTTCCCAGCATGTTTCTGAG
* *
72873 GTACAAGGTTC-CCGTTGCGACTTAAACCTTTCCCTCCGTATCTTCGTGGTACTAGATTCACCAT
1 GTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCGTATCTTCGTGGTACCAGATTCACCGT
72937 TGCGGCTTCAATCTTTCCCAGCATGTTTCTGAG
66 TGCGGCTTCAATCTTTCCCAGCATGTTTCTGAG
* * * * **
72970 GTACAATGTTCGCCGTTGCGACTTAAACCCTTCCCGT-CATATCTTTGTGGTACCAGATTCGTCG
1 GTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCC-TCCGTATCTTCGTGGTACCAGATTCACCG
*
73034 TTGTGGCTTCAATCTTTCCCAGCATGTTTCTGAG
65 TTGCGGCTTCAATCTTTCCCAGCATGTTTCTGAG
** * *
73068 GTACAAGGTTTACCGTTGCGACTTCAATCTTTCCCTCCGTATCTTCGTGGTACCAGATTCACCGT
1 GTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCGTATCTTCGTGGTACCAGATTCACCGT
*
73133 TACGGCTTCAATCTTTCCCAGCATGTCTT-TGAG
66 TGCGGCTTCAATCTTTCCCAGCATGT-TTCTGAG
* * ** * * * *
73166 GTATAAGGTTCACCGTCACGACTTAAACCTTTCCCTTCGTATCTTCATGGTACCAGATTCGCCAT
1 GTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCGTATCTTCGTGGTACCAGATTCACCGT
* * *
73231 TGCAGCTTCAATTTTTCCCAGCATGTTTTTGAG
66 TGCGGCTTCAATCTTTCCCAGCATGTTTCTGAG
* * * *
73264 GTACAAGGTTCGCCGTTGCGATTTAAACCTTTCCCTCCGTATTTTCGTGGTACCAAATTCACCAT
1 GTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCGTATCTTCGTGGTACCAGATTCACCGT
* * *
73329 TGCAGCATCAATCTTTCCCAACATGTTTCTGAG
66 TGCGGCTTCAATCTTTCCCAGCATGTTTCTGAG
* * * * ***
73362 GTACAAGGTTCGCCGTTGCGACTTAAACCCTTCCCCCCATATCTTCATGGTACCAGA-TCTGTTG
1 GTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCGTATCTTCGTGGTACCAGATTC-ACCG
* *
73426 TTGCGGCTTCAATCTTTCCTAACATGTTTCTGAG
65 TTGCGGCTTCAATCTTTCCCAGCATGTTTCTGAG
* ****
73460 GTACAAGGTTCGCCGTTGCGACTTAAACCTTT-CCTCCCATATCTTCGTGGTACCAGATTTTTTG
1 GTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCT-CCGTATCTTCGTGGTACCAGATTCACCG
* * *
73524 TTGCGCCTTCAATCTTTCCCAACATGTTTTTGAG
65 TTGCGGCTTCAATCTTTCCCAGCATGTTTCTGAG
** * * * *
73558 GTACAAGGTTCATCGTTGCAACTTAAATCTTTCCCTCCGTATCTTCATGGTACCAGATTCACTGT
1 GTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCGTATCTTCGTGGTACCAGATTCACCGT
* *
73623 TGCGGCTTCAATCTTTCCCAACATGTTTATGAG
66 TGCGGCTTCAATCTTTCCCAGCATGTTTCTGAG
* * * * * *
73656 GTACAAGGTTCACTGTTACGACTTAAACCTTTCCTTTCTTATCTTCGTGGTACCAGATTCACCGT
1 GTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCGTATCTTCGTGGTACCAGATTCACCGT
*
73721 TGCAGCTTCAATCTTTCCCAGCATGTTTCTGAG
66 TGCGGCTTCAATCTTTCCCAGCATGTTTCTGAG
* * * * *
73754 GTACAAGGTTCGCTGTTGCGACTTAAACCCTTCCC-CCATATCTTCGTGGTGCCAGATTCATCGT
1 GTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCGTATCTTCGTGGTACCAGATTCACCGT
* *
73818 TGCAGCTTCAATCTTTCCCAGCATGTTTTTGAG
66 TGCGGCTTCAATCTTTCCCAGCATGTTTCTGAG
*** * * * ****
73851 GTACAAGGTTCGCCGTTATTACTTAAATCTTTCCCTACGTATCTTCGTGGTTCCAGATTTGTTGT
1 GTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCGTATCTTCGTGGTACCAGATTCACCGT
* *
73916 TGTGGCTTCAATCTTTCCCAGCATGTTTCTAAG
66 TGCGGCTTCAATCTTTCCCAGCATGTTTCTGAG
* * * * **
73949 GTACAAGGTTCGCCATTGCGACTTAAATCTTTCCCTTCGTATCTTCGTGGTGCCAGATTCACTAT
1 GTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCGTATCTTCGTGGTACCAGATTCACCGT
* * *
74014 TGCGGCTTCAATATTTCCTAGTATGTTTCTGAG
66 TGCGGCTTCAATCTTTCCCAGCATGTTTCTGAG
* * ** * * **
74047 GTACAAGGTTTGCCGTTGCGACTTACACCTTTCCCTCTATATCTTTGCGGTACCAGATTTGCCGT
1 GTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCGTATCTTCGTGGTACCAGATTCACCGT
* *
74112 TACGGCTTCAATCTTTCCCAACATGTTTCTGAG
66 TGCGGCTTCAATCTTTCCCAGCATGTTTCTGAG
* * *
74145 GTACAAGGTTCGCCATTACGACTTTAACCTTTCCCTC
1 GTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTC
74182 TAAACTTGTA
Statistics
Matches: 1479, Mismatches: 207, Indels: 27
0.86 0.12 0.02
Matches are distributed among these distances:
97 302 0.20
98 1170 0.79
99 7 0.00
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.36
Consensus pattern (98 bp):
GTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCGTATCTTCGTGGTACCAGATTCACCGT
TGCGGCTTCAATCTTTCCCAGCATGTTTCTGAG
Found at i:80875 original size:42 final size:42
Alignment explanation
Indices: 80820--81008 Score: 191
Period size: 42 Copynumber: 4.5 Consensus size: 42
80810 TATACTCTAT
* * *
80820 CGAGTCATAAGTCTTCCTTTAATCATATTCTCATTCTCATCC
1 CGAGACATGAGTCTTCCTTTAATCATATTCTCATGCTCATCC
* * **
80862 CGAGACATGAGTCTTCCTTTAATCATAATCTCATTCTCATAT
1 CGAGACATGAGTCTTCCTTTAATCATATTCTCATGCTCATCC
* * * **
80904 CGAGACATGAGTATTCCTTTAATAATATTTTCATGCTCATTT
1 CGAGACATGAGTCTTCCTTTAATCATATTCTCATGCTCATCC
* * * * *
80946 CGAGTCACGTGTCTTCCATTT-ATACAAATTCTCATGCTCAACC
1 CGAGACATGAGTCTTCC-TTTAAT-CATATTCTCATGCTCATCC
*
80989 CGAAACATGAGTCTTCCTTT
1 CGAGACATGAGTCTTCCTTT
81009 TTATACATCA
Statistics
Matches: 120, Mismatches: 25, Indels: 4
0.81 0.17 0.03
Matches are distributed among these distances:
42 91 0.76
43 29 0.24
ACGTcount: A:0.26, C:0.25, G:0.11, T:0.38
Consensus pattern (42 bp):
CGAGACATGAGTCTTCCTTTAATCATATTCTCATGCTCATCC
Found at i:84361 original size:7 final size:7
Alignment explanation
Indices: 84349--84426 Score: 147
Period size: 7 Copynumber: 11.1 Consensus size: 7
84339 TATATTGAAG
84349 GGGAGTT
1 GGGAGTT
84356 GGGAGTT
1 GGGAGTT
84363 GGGAGTT
1 GGGAGTT
84370 GGGAGTT
1 GGGAGTT
84377 GGGAGTT
1 GGGAGTT
84384 GGGAGTT
1 GGGAGTT
84391 GGGAGTT
1 GGGAGTT
*
84398 GGCAGTT
1 GGGAGTT
84405 GGGAGTT
1 GGGAGTT
84412 GGGAGTT
1 GGGAGTT
84419 GGGAGTT
1 GGGAGTT
84426 G
1 G
84427 TACTCATCAA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 69 1.00
ACGTcount: A:0.14, C:0.01, G:0.56, T:0.28
Consensus pattern (7 bp):
GGGAGTT
Found at i:84903 original size:58 final size:58
Alignment explanation
Indices: 84812--84926 Score: 185
Period size: 58 Copynumber: 2.0 Consensus size: 58
84802 GAAGCTAAGA
* * *
84812 GGCTGGCAGGGGTCATGATCCCCTTAAAGTGAAAAACTTTCTATTTAGGCCCTTAAAG
1 GGCTGGCAGGGGTCATGACCCCCTTAAAATGAAAAACTTTCTATTTAGACCCTTAAAG
* *
84870 GGCTGGCAGGGGTCATGGCCCCCTTAAAATGAAAAACTTTCTATTTTGACCCTTAAA
1 GGCTGGCAGGGGTCATGACCCCCTTAAAATGAAAAACTTTCTATTTAGACCCTTAAA
84927 ATTTTTTAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.28
Consensus pattern (58 bp):
GGCTGGCAGGGGTCATGACCCCCTTAAAATGAAAAACTTTCTATTTAGACCCTTAAAG
Found at i:86097 original size:21 final size:21
Alignment explanation
Indices: 86062--86102 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
86052 TTTTCAACAA
86062 AATTTCAATGTTTATATTTTTT
1 AATTTCAATGTTTAT-TTTTTT
*
86084 AATTT-AATTTTTATTTTTT
1 AATTTCAATGTTTATTTTTT
86103 GGTAAAGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 8 0.44
22 5 0.28
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.68
Consensus pattern (21 bp):
AATTTCAATGTTTATTTTTTT
Done.