Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010362.1 Kokia drynarioides strain JFW-HI SEQ_125233, 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: 86795
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Warning! 15 characters in sequence are not A, C, G, or T
Found at i:598 original size:29 final size:29
Alignment explanation
Indices: 559--904 Score: 376
Period size: 30 Copynumber: 11.8 Consensus size: 29
549 GAGGGTCCCT
**
559 AAACTATCCAAAAATTCCATTTTTACCCTT
1 AAACT-TCCAAAAATTCCATTTTTACCCCA
* * *
589 GAACTTCCAAAAA-TCCTATTTTTGACCTCG
1 AAACTTCCAAAAATTCC-ATTTTT-ACCCCA
*
619 AAACTTCCAAAAATTCCATTTTTACCCCT
1 AAACTTCCAAAAATTCCATTTTTACCCCA
648 AAACTTCCAAAAA-TCCTATTTTTAACCCCA
1 AAACTTCCAAAAATTCC-ATTTTT-ACCCCA
*
678 AAACTTCCAAAAATTCCATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCA
* * *
707 GAACTTCCAAAAATCCCATTTTAAACCCCA
1 AAACTTCCAAAAATTCCATTTT-TACCCCA
*
737 AAACTTCCAAAAATTCCA-TTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCA
* * *
765 AAACTTCTAAAAATCCCATTTTTAACCCAA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCA
* *
795 AAACTTCCAAAAAATCCATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCA
* * *
824 GAACTTCCAAAAATCCCATCTTTGACCCCA
1 AAACTTCCAAAAATTCCAT-TTTTACCCCA
* * * *
854 AAACTTTCAAAAATTCTATTTTTAGCCCT
1 AAACTTCCAAAAATTCCATTTTTACCCCA
*
883 GAACTTCC-AAAATTCCATTTTT
1 AAACTTCCAAAAATTCCATTTTT
905 GACACTGAAA
Statistics
Matches: 265, Mismatches: 41, Indels: 22
0.81 0.12 0.07
Matches are distributed among these distances:
28 40 0.15
29 102 0.38
30 117 0.44
31 6 0.02
ACGTcount: A:0.36, C:0.30, G:0.02, T:0.32
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCCA
Found at i:657 original size:59 final size:59
Alignment explanation
Indices: 559--907 Score: 477
Period size: 59 Copynumber: 5.9 Consensus size: 59
549 GAGGGTCCCT
* * * *
559 AAACTATCCAAAAATTCCATTTTTACCCTTGAACTTCCAAAAATCCTATTTTTGACCTCG
1 AAACT-TCCAAAAATTCCATTTTTACCCCTGAACTTCCAAAAATCCCATTTTTGACCCCA
* * *
619 AAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATCCTATTTTTAACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCCTGAACTTCCAAAAATCCCATTTTTGACCCCA
* **
678 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTAAACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCCTGAACTTCCAAAAATCCCATTTTTGACCCCA
** * * *
737 AAACTTCCAAAAATTCCA-TTTTACCCCCAAACTTCTAAAAATCCCATTTTTAACCCAA
1 AAACTTCCAAAAATTCCATTTTTACCCCTGAACTTCCAAAAATCCCATTTTTGACCCCA
* * *
795 AAACTTCCAAAAAATCCATTTTTACCCCCGAACTTCCAAAAATCCCATCTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCCTGAACTTCCAAAAATCCCATTTTTGACCCCA
* * * *
854 AAACTTTCAAAAATTCTATTTTTAGCCCTGAACTTCC-AAAATTCCATTTTTGAC
1 AAACTTCCAAAAATTCCATTTTTACCCCTGAACTTCCAAAAATCCCATTTTTGAC
908 ACTGAAACTT
Statistics
Matches: 262, Mismatches: 26, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
58 68 0.26
59 189 0.72
60 5 0.02
ACGTcount: A:0.36, C:0.30, G:0.03, T:0.31
Consensus pattern (59 bp):
AAACTTCCAAAAATTCCATTTTTACCCCTGAACTTCCAAAAATCCCATTTTTGACCCCA
Found at i:935 original size:117 final size:116
Alignment explanation
Indices: 559--1025 Score: 491
Period size: 117 Copynumber: 4.0 Consensus size: 116
549 GAGGGTCCCT
** * * *
559 AAACTATCCAAAAATTCCATTTTTACCCTTGAACTTCCAAAAATCCTATTTTTGACCTCGAAACT
1 AAACT-TCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCA-TTTTGACCCCAAAACT
* *
624 TCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATCCTATTTTTAACCCCA
64 TCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAATTCC-ATTTTTAACCCAA
*
678 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTAAACCCCAAAACTT
1 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTT-GACCCCAAAACTT
* * *
743 CCAAAAATTCCA-TTTTACCCCCAAACTTCTAAAAATCCCATTTTTAACCCAA
65 CCAAAAATTCCATTTTTACCCCTAAACTTC-CAAAATTCCATTTTTAACCCAA
*
795 AAACTTCCAAAAAATCCATTTTTACCCCCGAACTTCCAAAAATCCCATCTTTGACCCCAAAACTT
1 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCAT-TTTGACCCCAAAACTT
* * * * * * **
860 TCAAAAATTCTATTTTTAGCCCTGAACTTCCAAAATTCCATTTTTGACACTG
65 CCAAAAATTCCATTTTTACCCCTAAACTTCCAAAATTCCATTTTTAACCCAA
*** ** * *
912 AAACTTTTGAAAATTACCA-TTTTACCCCCG-GTTGTCCAAAAA-CTCCATTTTCGACCTCGAAA
1 AAACTTCCAAAAATT-CCATTTTTACCCCCGAACT-TCCAAAAATC-CCATTTT-GACCCCAAAA
**
974 C-TCTC-AAAATTACCA-TTTTACCCCTAAA-TGTTTAAAATTTCCATTTTTAACC
62 CTTC-CAAAAATT-CCATTTTTACCCCTAAACT-TCCAAAA-TTCCATTTTTAACC
1026 TCGAATTTAC
Statistics
Matches: 296, Mismatches: 40, Indels: 26
0.82 0.11 0.07
Matches are distributed among these distances:
115 1 0.00
116 28 0.09
117 175 0.59
118 87 0.29
119 5 0.02
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.32
Consensus pattern (116 bp):
AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTGACCCCAAAACTTC
CAAAAATTCCATTTTTACCCCTAAACTTCCAAAATTCCATTTTTAACCCAA
Found at i:962 original size:176 final size:175
Alignment explanation
Indices: 559--940 Score: 471
Period size: 176 Copynumber: 2.2 Consensus size: 175
549 GAGGGTCCCT
*** * *
559 AAACTATCCAAAAATTCCATTTTTACCCTTGAACTTCCAAAAATCCTATTTTTGACCTCGAAACT
1 AAACT-TCCAAAAATTCCA-TTTTACCCCCAAACTTCCAAAAATCC-ATTTTTAACCTCAAAACT
* * * *
624 TCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATCCTATTTTTAACCCCAAAACTTCCAAA
63 TCCAAAAAATCCATTTTTACCCCCAAACTTCCAAAAATCCCATCTTTAACCCCAAAACTTCCAAA
*
689 AATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTAAACCCCA
128 AATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTAAACACCA
*
737 AAACTTCCAAAAATTCCATTTTACCCCCAAACTTCTAAAAATCCCATTTTTAACC-CAAAAACTT
1 AAACTTCCAAAAATTCCATTTTACCCCCAAACTTCCAAAAAT-CCATTTTTAACCTC-AAAACTT
* * *
801 CCAAAAAATCCATTTTTACCCCCGAACTTCCAAAAATCCCATCTTTGACCCCAAAACTTTCAAAA
64 CCAAAAAATCCATTTTTACCCCCAAACTTCCAAAAATCCCATCTTTAACCCCAAAACTTCCAAAA
* * * * ** **
866 ATTCTATTTTTAGCCCTGAACTTCC-AAAATTCCATTTTTGACACTG
129 ATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTAAACACCA
***
912 AAACTTTTGAAAATTACCATTTTACCCCC
1 AAACTTCCAAAAATT-CCATTTTACCCCC
941 GGTTGTCCAA
Statistics
Matches: 176, Mismatches: 25, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
175 28 0.16
176 128 0.73
177 15 0.09
178 5 0.03
ACGTcount: A:0.36, C:0.30, G:0.03, T:0.31
Consensus pattern (175 bp):
AAACTTCCAAAAATTCCATTTTACCCCCAAACTTCCAAAAATCCATTTTTAACCTCAAAACTTCC
AAAAAATCCATTTTTACCCCCAAACTTCCAAAAATCCCATCTTTAACCCCAAAACTTCCAAAAAT
TCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTAAACACCA
Found at i:992 original size:176 final size:175
Alignment explanation
Indices: 559--997 Score: 469
Period size: 176 Copynumber: 2.5 Consensus size: 175
549 GAGGGTCCCT
***
559 AAACTATCCAAAAATTCCATTTTTACCCTTGAACTTCCAAAAATCCTATTTTTGACCTCGAAACT
1 AAACT-TCCAAAAATTCCA-TTTTACCCCCAAACTTCCAAAAATCC-ATTTTTGACCTCGAAACT
* * *
624 TCCAAAAATT-CCATTTTTACCCCTAAACTTCCAAAAATCCTATTTTTAACCCCAAAACTTCCAA
63 TCC-AAAATTACCATTTTTACCCCCAAACTTCCAAAAATCCCATCTTTAACCCCAAAACTTCCAA
*
688 AAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTAAACCCCA
127 AAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTAAACACCA
* * *
737 AAACTTCCAAAAATTCCATTTTACCCCCAAACTTCTAAAAATCCCATTTTTAACC-CAAAAACTT
1 AAACTTCCAAAAATTCCATTTTACCCCCAAACTTCCAAAAAT-CCATTTTTGACCTC-GAAACTT
* * * *
801 CCAAAA-AATCCATTTTTACCCCCGAACTTCCAAAAATCCCATCTTTGACCCCAAAACTTTCAAA
64 CCAAAATTA-CCATTTTTACCCCCAAACTTCCAAAAATCCCATCTTTAACCCCAAAACTTCCAAA
* * * * ** **
865 AATTCTATTTTTAGCCCTGAACTTCC-AAAATTCCATTTTTGACACTG
128 AATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTAAACACCA
*** *** *
912 AAACTTTTGAAAATTACCATTTTACCCCC-GGTTGTCCAAAAACTCCATTTTCGACCTCGAAAC-
1 AAACTTCCAAAAATT-CCATTTTACCCCCAAACT-TCCAAAAA-TCCATTTTTGACCTCGAAACT
975 TCTCAAAATTACCA-TTTTACCCC
63 TC-CAAAATTACCATTTTTACCCC
998 TAAATGTTTA
Statistics
Matches: 218, Mismatches: 33, Indels: 23
0.80 0.12 0.08
Matches are distributed among these distances:
175 44 0.20
176 151 0.69
177 18 0.08
178 5 0.02
ACGTcount: A:0.35, C:0.30, G:0.04, T:0.31
Consensus pattern (175 bp):
AAACTTCCAAAAATTCCATTTTACCCCCAAACTTCCAAAAATCCATTTTTGACCTCGAAACTTCC
AAAATTACCATTTTTACCCCCAAACTTCCAAAAATCCCATCTTTAACCCCAAAACTTCCAAAAAT
TCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTAAACACCA
Found at i:6283 original size:49 final size:47
Alignment explanation
Indices: 6202--6296 Score: 129
Period size: 49 Copynumber: 2.0 Consensus size: 47
6192 TATTACATAC
* *
6202 AACAAATTTAAAAAATATATAATATGTCAAATACACTTAAAAACATTAA
1 AACAAATTTAAAAAATAAATAATATGTAAAATACA-TTAAAAA-ATTAA
*
6251 AACAAATATTAAAAAATAAATAA-ATTTAAAATACATTAAAAAATTA
1 AACAAAT-TTAAAAAATAAATAATATGTAAAATACATTAAAAAATTA
6297 TCTTAAGATA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
47 4 0.10
48 7 0.17
49 17 0.40
50 14 0.33
ACGTcount: A:0.63, C:0.07, G:0.01, T:0.28
Consensus pattern (47 bp):
AACAAATTTAAAAAATAAATAATATGTAAAATACATTAAAAAATTAA
Found at i:6487 original size:20 final size:20
Alignment explanation
Indices: 6408--6487 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
6398 AAAACGCATA
* * *
6408 AAAAATAACATCCAAACAAC
1 AAAAATAACAACAAAACAGC
6428 AAAAATAACAACCAAAACAACAGC
1 AAAAATAACAA-C--AA-AACAGC
**
6452 AAAAATAACAGTAAAACAGC
1 AAAAATAACAACAAAACAGC
6472 AAAAATAACAACAAAA
1 AAAAATAACAACAAAA
6488 ATAGCAACAA
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
20 30 0.61
21 3 0.06
23 1 0.02
24 15 0.31
ACGTcount: A:0.69, C:0.20, G:0.04, T:0.07
Consensus pattern (20 bp):
AAAAATAACAACAAAACAGC
Found at i:6488 original size:56 final size:56
Alignment explanation
Indices: 6421--6566 Score: 167
Period size: 56 Copynumber: 2.6 Consensus size: 56
6411 AATAACATCC
*
6421 AAACAACAAAAATAACAACCAAAACAACAGCAAAAATAACA-GTAAAACAGCAA-AA
1 AAACAACAAAAATAACAACCAAAACAACAGCAAAAATAACACG-AAAACAACAATAA
* * * * *
6476 ATAACAACAAAAATAGCAACAAAAACAGCAGCAAAAATAACACGAAAATAACAATCA
1 A-AACAACAAAAATAACAACCAAAACAACAGCAAAAATAACACGAAAACAACAATAA
*
6533 AAACAATAAAAA-AACAACTC-AAA-AACAGCAAAAA
1 AAACAACAAAAATAACAAC-CAAAACAACAGCAAAAA
6567 AATCAACCAA
Statistics
Matches: 77, Mismatches: 10, Indels: 9
0.80 0.10 0.09
Matches are distributed among these distances:
54 10 0.13
55 9 0.12
56 55 0.71
57 3 0.04
ACGTcount: A:0.68, C:0.19, G:0.05, T:0.07
Consensus pattern (56 bp):
AAACAACAAAAATAACAACCAAAACAACAGCAAAAATAACACGAAAACAACAATAA
Found at i:6499 original size:11 final size:12
Alignment explanation
Indices: 6422--6535 Score: 85
Period size: 12 Copynumber: 9.8 Consensus size: 12
6412 ATAACATCCA
6422 AACAACAAAAAT
1 AACAACAAAAAT
* *
6434 AACAACCAAAAC
1 AACAACAAAAAT
*
6446 AACAGCAAAAAT
1 AACAACAAAAAT
**
6458 ---AACAGTAA-
1 AACAACAAAAAT
*
6466 AACAGCAAAAAT
1 AACAACAAAAAT
6478 AACAACAAAAAT
1 AACAACAAAAAT
* *
6490 AGCAACAAAAAC
1 AACAACAAAAAT
* *
6502 AGCAGCAAAAAT
1 AACAACAAAAAT
*
6514 AAC-ACGAAAAT
1 AACAACAAAAAT
6525 AACAATCAAAA
1 AACAA-CAAAA
6536 CAATAAAAAA
Statistics
Matches: 76, Mismatches: 20, Indels: 11
0.71 0.19 0.10
Matches are distributed among these distances:
9 5 0.07
11 14 0.18
12 53 0.70
13 4 0.05
ACGTcount: A:0.68, C:0.19, G:0.06, T:0.07
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:6499 original size:44 final size:44
Alignment explanation
Indices: 6408--6566 Score: 119
Period size: 44 Copynumber: 3.6 Consensus size: 44
6398 AAAACGCATA
* * *
6408 AAAAATAACATCCAAACAACAAAAATAACAACCAAAACAACAGC
1 AAAAATAACATCAAAACAACAAAAATAACAACAAAAACAACAAC
* * *
6452 AAAAATAACAGT-AAAACAGCAAAAATAACAACAAAAATAGCAAC
1 AAAAATAACA-TCAAAACAACAAAAATAACAACAAAAACAACAAC
* * * * *
6496 AAAAACAGCAGCAAAAATAACACGAAAATAACAATC-AAAACAATAA-
1 AAAAATAACATC-AAAACAACA--AAAATAACAA-CAAAAACAACAAC
* *
6542 AAAAACAAC-TCAAAAACAGCAAAAA
1 AAAAATAACATC-AAAACAACAAAAA
6567 AATCAACCAA
Statistics
Matches: 91, Mismatches: 18, Indels: 13
0.75 0.15 0.11
Matches are distributed among these distances:
43 4 0.04
44 44 0.48
45 17 0.19
46 8 0.09
47 17 0.19
48 1 0.01
ACGTcount: A:0.68, C:0.19, G:0.05, T:0.08
Consensus pattern (44 bp):
AAAAATAACATCAAAACAACAAAAATAACAACAAAAACAACAAC
Found at i:6557 original size:22 final size:22
Alignment explanation
Indices: 6421--6578 Score: 69
Period size: 21 Copynumber: 7.1 Consensus size: 22
6411 AATAACATCC
6421 AAACAACAAAAATAACAAC-C-A
1 AAACAACAAAAA-AACAACTCAA
* * ***
6442 AAACAACAGCAAAAATAACAGTA
1 AAACAACA-AAAAAACAACTCAA
*
6465 AAACAGCAAAAATAACAA--CAA
1 AAACAACAAAAA-AACAACTCAA
* * * *
6486 AAATAGCAACAAAAACAGCAGCAA
1 AAACAACAA-AAAAACAAC-TCAA
*
6510 AAATAACACGAAAATAACAA-TC-A
1 AAACAACA--AAAA-AACAACTCAA
*
6533 AAACAATAAAAAAACAACTCAA
1 AAACAACAAAAAAACAACTCAA
*
6555 AAACAGCAAAAAAATCAAC-CAA
1 AAACAACAAAAAAA-CAACTCAA
6577 AA
1 AA
6579 TAGTAAAAAA
Statistics
Matches: 106, Mismatches: 17, Indels: 27
0.71 0.11 0.18
Matches are distributed among these distances:
20 5 0.05
21 32 0.30
22 27 0.25
23 23 0.22
24 11 0.10
25 3 0.03
26 5 0.05
ACGTcount: A:0.68, C:0.20, G:0.05, T:0.07
Consensus pattern (22 bp):
AAACAACAAAAAAACAACTCAA
Found at i:6586 original size:21 final size:22
Alignment explanation
Indices: 6520--6589 Score: 67
Period size: 21 Copynumber: 3.3 Consensus size: 22
6510 AAATAACACG
* *
6520 AAAATAACAA-TC-AAAACAAT
1 AAAAAAACAACTCAAAAACAGT
*
6540 AAAAAAACAACTCAAAAACAGC
1 AAAAAAACAACTCAAAAACAGT
*
6562 AAAAAAATCAAC-C-AAAATAGT
1 AAAAAAA-CAACTCAAAAACAGT
6583 AAAAAAA
1 AAAAAAA
6590 GCACTAAAAC
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
20 9 0.21
21 15 0.36
22 14 0.33
23 4 0.10
ACGTcount: A:0.71, C:0.16, G:0.03, T:0.10
Consensus pattern (22 bp):
AAAAAAACAACTCAAAAACAGT
Found at i:16327 original size:21 final size:20
Alignment explanation
Indices: 16303--16350 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
16293 TTTTTTAATC
*
16303 ATTAAATATATTATTTTTATA
1 ATTAAATA-AGTATTTTTATA
*
16324 ATTAAA-AAGTATATTTATTA
1 ATTAAATAAGTATTTTTA-TA
16344 ATTAAAT
1 ATTAAAT
16351 TAAATTTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 8 0.35
20 9 0.39
21 6 0.26
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
ATTAAATAAGTATTTTTATA
Found at i:18040 original size:22 final size:22
Alignment explanation
Indices: 18008--18054 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
17998 AACATTCTGT
18008 TTTTCTCTGCATATTTGCACGC
1 TTTTCTCTGCATATTTGCACGC
*
18030 TTTTCTTTGCATATTTGCACGC
1 TTTTCTCTGCATATTTGCACGC
18052 TTT
1 TTT
18055 GGTCTTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.13, C:0.23, G:0.13, T:0.51
Consensus pattern (22 bp):
TTTTCTCTGCATATTTGCACGC
Found at i:24059 original size:63 final size:63
Alignment explanation
Indices: 23960--24084 Score: 241
Period size: 63 Copynumber: 2.0 Consensus size: 63
23950 GTATTAAAAT
23960 ATCCTTCTGTATACAGAGTAAGTGATATCACTATGAGAGTGTTTTTATCTTTTTATCTTTTAA
1 ATCCTTCTGTATACAGAGTAAGTGATATCACTATGAGAGTGTTTTTATCTTTTTATCTTTTAA
*
24023 ATCCTTCTGTATACAGAGTAAGTGATATCACTATGAGGGTGTTTTTATCTTTTTATCTTTTA
1 ATCCTTCTGTATACAGAGTAAGTGATATCACTATGAGAGTGTTTTTATCTTTTTATCTTTTA
24085 TTTATTTATC
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.46
Consensus pattern (63 bp):
ATCCTTCTGTATACAGAGTAAGTGATATCACTATGAGAGTGTTTTTATCTTTTTATCTTTTAA
Found at i:26506 original size:25 final size:24
Alignment explanation
Indices: 26478--26553 Score: 89
Period size: 24 Copynumber: 3.1 Consensus size: 24
26468 AGAAATAATC
*
26478 TTTCAGTTAAATTTTAATTTATTTG
1 TTTCAATTAAATTTT-ATTTATTTG
*
26503 TTTCAATTAAACTTTATTTATTTG
1 TTTCAATTAAATTTTATTTATTTG
* * * *
26527 TTTTAATTAAATTCTGTTTAGTTG
1 TTTCAATTAAATTTTATTTATTTG
26551 TTT
1 TTT
26554 GAGTCAAATT
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
24 31 0.70
25 13 0.30
ACGTcount: A:0.26, C:0.05, G:0.08, T:0.61
Consensus pattern (24 bp):
TTTCAATTAAATTTTATTTATTTG
Found at i:26717 original size:14 final size:14
Alignment explanation
Indices: 26698--26728 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
26688 TTTTGAAGAA
26698 TTTAGTGTTTACGT
1 TTTAGTGTTTACGT
*
26712 TTTAGTGTTTATGT
1 TTTAGTGTTTACGT
26726 TTT
1 TTT
26729 GAGGGTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.03, G:0.19, T:0.65
Consensus pattern (14 bp):
TTTAGTGTTTACGT
Found at i:30089 original size:214 final size:207
Alignment explanation
Indices: 29668--30099 Score: 677
Period size: 214 Copynumber: 2.1 Consensus size: 207
29658 AAATATGGAC
*
29668 ATGGAACTTCATAAATGCAGCATTTAGCTATATAAGTTCATATGCTTGGTCCCACTTAATTGGTT
1 ATGGAACCTCATAAATGCAGCATTTAGCTATATAAGTTCATATGCTTGGTCCCACTTAATTGGTT
*
29733 GACATTTGCATTACAAGATCTTATAGACAACCGAGCAATGTTGTTGTATTACCCACGGTTCCACT
66 GACATTTGCATTACAAGATCTTATAGACAACAGAGCAATGTTGTTGTATTACCCACGGTTCCACT
* * *
29798 TAATTTCAAATTTATTGCAATCCATTTTCTTCTCCGACATTTGTACTTTATTTAATGCAACCAAG
131 TAAATTCAAATTTATTGCAATCCATTTTCTTCTCCAACATTTGTACTTTATTAAATGCAACCAAG
29863 TGTTTAAGAGTA
196 TGTTTAAGAGTA
*
29875 ATGGAACCTCATTAATGCAGCATTTAGCTATATAAGTTCATATGCTTGGTCCCACTTAATTGGTT
1 ATGGAACCTCATAAATGCAGCATTTAGCTATATAAGTTCATATGCTTGGTCCCACTTAATTGGTT
** *
29940 GACATTTGCATTACGTGATCTTATAGACAACAGAGCAATGTTGTTTGTTGTTGTATTACCGACGG
66 GACATTTGCATTACAAGATCTTATAGACAACAGAGCAA-------TGTTGTTGTATTACCCACGG
**
30005 TTCCACTTAAATTCAAATTTATTGTGATCCATTTTCTTCTCCAATC-TTTGTACTTTATTAAATG
124 TTCCACTTAAATTCAAATTTATTGCAATCCATTTTCTTCTCCAA-CATTTGTACTTTATTAAATG
*
30069 CAACCAAGTGTTTTAGAGTA
188 CAACCAAGTGTTTAAGAGTA
30089 ATGGAACCTCA
1 ATGGAACCTCA
30100 ATCTGCAGCA
Statistics
Matches: 205, Mismatches: 12, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
207 98 0.48
214 106 0.52
215 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (207 bp):
ATGGAACCTCATAAATGCAGCATTTAGCTATATAAGTTCATATGCTTGGTCCCACTTAATTGGTT
GACATTTGCATTACAAGATCTTATAGACAACAGAGCAATGTTGTTGTATTACCCACGGTTCCACT
TAAATTCAAATTTATTGCAATCCATTTTCTTCTCCAACATTTGTACTTTATTAAATGCAACCAAG
TGTTTAAGAGTA
Found at i:37767 original size:13 final size:13
Alignment explanation
Indices: 37749--37774 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
37739 CATCGAAGAT
37749 GTAAATTGACTTC
1 GTAAATTGACTTC
37762 GTAAATTGACTTC
1 GTAAATTGACTTC
37775 CAAACGTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
GTAAATTGACTTC
Found at i:38669 original size:23 final size:24
Alignment explanation
Indices: 38638--38697 Score: 68
Period size: 28 Copynumber: 2.4 Consensus size: 24
38628 GCCTACACAC
*
38638 CAAGGATAT-TCGAATTGTTTCAG
1 CAAGAATATATCGAATTGTTTCAG
38661 CAAGAATATGAAACTCGAATTGTTTCAG
1 CAAGAATAT---A-TCGAATTGTTTCAG
38689 CAAGAATAT
1 CAAGAATAT
38698 GAAACATGTC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
23 8 0.26
28 23 0.74
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.30
Consensus pattern (24 bp):
CAAGAATATATCGAATTGTTTCAG
Found at i:38687 original size:28 final size:28
Alignment explanation
Indices: 38647--38702 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
38637 CCAAGGATAT
38647 TCGAATTGTTTCAGCAAGAATATGAAAC
1 TCGAATTGTTTCAGCAAGAATATGAAAC
38675 TCGAATTGTTTCAGCAAGAATATGAAAC
1 TCGAATTGTTTCAGCAAGAATATGAAAC
38703 ATGTCTGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (28 bp):
TCGAATTGTTTCAGCAAGAATATGAAAC
Found at i:46711 original size:39 final size:40
Alignment explanation
Indices: 46657--46736 Score: 144
Period size: 39 Copynumber: 2.0 Consensus size: 40
46647 TATGCACTCA
46657 ATGGACACCTTTTGAAGAGTCACAACCC-TTTCAAATTGG
1 ATGGACACCTTTTGAAGAGTCACAACCCTTTTCAAATTGG
*
46696 ATGGACACCTTTTGAAGAGTCACAACCCTTTTCATATTGG
1 ATGGACACCTTTTGAAGAGTCACAACCCTTTTCAAATTGG
46736 A
1 A
46737 CATACCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
39 28 0.72
40 11 0.28
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (40 bp):
ATGGACACCTTTTGAAGAGTCACAACCCTTTTCAAATTGG
Found at i:46752 original size:39 final size:38
Alignment explanation
Indices: 46661--46753 Score: 107
Period size: 39 Copynumber: 2.4 Consensus size: 38
46651 CACTCAATGG
* *
46661 ACACCTTTTGAAGAGTCACAACCCTTTCAAATTGGATGG
1 ACACCTTTGGAAGAGTCACAACCCTTTCAAATTGGA-GC
* *
46700 ACACCTTTTGAAGAGTCACAACCCTTTTCATATTGGA-C
1 ACACCTTTGGAAGAGTCACAACCC-TTTCAAATTGGAGC
*
46738 ATACCTCTTGGAAGAG
1 ACACCT-TTGGAAGAG
46754 ACTTGTCCCA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
38 5 0.10
39 32 0.67
40 11 0.23
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (38 bp):
ACACCTTTGGAAGAGTCACAACCCTTTCAAATTGGAGC
Found at i:51656 original size:39 final size:40
Alignment explanation
Indices: 51602--51677 Score: 136
Period size: 39 Copynumber: 1.9 Consensus size: 40
51592 CACTTAATGG
51602 ACACCTTTTGAAGAGTCACAACC-CTTTCAAATTGGATGA
1 ACACCTTTTGAAGAGTCACAACCTCTTTCAAATTGGATGA
*
51641 ACACCTTTTGAAGAGTCACAACCTCTTTCATATTGGA
1 ACACCTTTTGAAGAGTCACAACCTCTTTCAAATTGGA
51678 CATACCTCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 23 0.66
40 12 0.34
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (40 bp):
ACACCTTTTGAAGAGTCACAACCTCTTTCAAATTGGATGA
Found at i:51693 original size:39 final size:38
Alignment explanation
Indices: 51602--51694 Score: 107
Period size: 39 Copynumber: 2.4 Consensus size: 38
51592 CACTTAATGG
*
51602 ACACCTTTTGAAGAGTCACAACCCTTTCAAATTGGATGA
1 ACACCTTTGGAAGAGTCACAACCCTTTCAAATTGGA-GA
* * *
51641 ACACCTTTTGAAGAGTCACAACCTCTTTCATATTGGA-C
1 ACACCTTTGGAAGAGTCACAACC-CTTTCAAATTGGAGA
*
51679 ATACCTCTTGGAAGAG
1 ACACCT-TTGGAAGAG
51695 ACTTGTCCCA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
38 5 0.10
39 31 0.65
40 12 0.25
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (38 bp):
ACACCTTTGGAAGAGTCACAACCCTTTCAAATTGGAGA
Found at i:57309 original size:15 final size:15
Alignment explanation
Indices: 57291--57320 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
57281 AATGAAACTA
57291 GATGAATGGAAAAAG
1 GATGAATGGAAAAAG
*
57306 GATGAATGGTAAAAG
1 GATGAATGGAAAAAG
57321 TATTATAATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.33, T:0.17
Consensus pattern (15 bp):
GATGAATGGAAAAAG
Found at i:73697 original size:15 final size:14
Alignment explanation
Indices: 73672--73701 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
73662 ACTCAATCCG
73672 AAATCGAATCTGAA
1 AAATCGAATCTGAA
73686 AAATCTGAATCTGAA
1 AAATC-GAATCTGAA
73701 A
1 A
73702 TGATCAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.50, C:0.13, G:0.13, T:0.23
Consensus pattern (14 bp):
AAATCGAATCTGAA
Found at i:74430 original size:23 final size:25
Alignment explanation
Indices: 74390--74439 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
74380 TATATTAATG
74390 TTTTTTGCTGTTTCTGG-TG-TATT
1 TTTTTTGCTGTTTCTGGTTGATATT
74413 TTTTTGTGCTGTTT-TGGTTGATATT
1 TTTTT-TGCTGTTTCTGGTTGATATT
74438 TT
1 TT
74440 GGTGCTCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 8 0.33
24 10 0.42
25 6 0.25
ACGTcount: A:0.06, C:0.06, G:0.22, T:0.66
Consensus pattern (25 bp):
TTTTTTGCTGTTTCTGGTTGATATT
Found at i:74444 original size:23 final size:23
Alignment explanation
Indices: 74395--74450 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
74385 TAATGTTTTT
* *
74395 TGCTGTTTCTGGTGTATTTTTTTG
1 TGCTGTTT-TGGTGTATATTTTGG
74419 TGCTGTTTTGGT-TGATATTTTGG
1 TGCTGTTTTGGTGT-ATATTTTGG
*
74442 TGCTCTTTT
1 TGCTGTTTT
74451 TTACCGTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 1 0.04
23 19 0.68
24 8 0.29
ACGTcount: A:0.05, C:0.09, G:0.25, T:0.61
Consensus pattern (23 bp):
TGCTGTTTTGGTGTATATTTTGG
Found at i:74478 original size:12 final size:12
Alignment explanation
Indices: 74457--74500 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
74447 TTTTTTACCG
*
74457 TTTTGATGTTGT
1 TTTTGCTGTTGT
*
74469 TTTTGCTGTTAT
1 TTTTGCTGTTGT
*
74481 TTTTGTTGTTGT
1 TTTTGCTGTTGT
74493 TTTTGCTG
1 TTTTGCTG
74501 CTACTTTTGT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.05, C:0.05, G:0.23, T:0.68
Consensus pattern (12 bp):
TTTTGCTGTTGT
Found at i:74485 original size:24 final size:23
Alignment explanation
Indices: 74457--74529 Score: 80
Period size: 24 Copynumber: 3.2 Consensus size: 23
74447 TTTTTTACCG
74457 TTTTGATGTTGTTTTTGCTGTTAT
1 TTTTG-TGTTGTTTTTGCTGTTAT
*
74481 TTTTGTTGTTGTTTTTGCTGCTA-
1 TTTTG-TGTTGTTTTTGCTGTTAT
* *
74504 CTTT-TGTTGTTTTTGTTGTT-T
1 TTTTGTGTTGTTTTTGCTGTTAT
74525 TTTTG
1 TTTTG
74530 CTATTTTGGT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
21 17 0.41
23 3 0.07
24 21 0.51
ACGTcount: A:0.04, C:0.05, G:0.21, T:0.70
Consensus pattern (23 bp):
TTTTGTGTTGTTTTTGCTGTTAT
Found at i:74522 original size:12 final size:11
Alignment explanation
Indices: 74457--74529 Score: 51
Period size: 12 Copynumber: 6.5 Consensus size: 11
74447 TTTTTTACCG
*
74457 TTTTGATGTTGT
1 TTTTGTTGTT-T
*
74469 TTTTGCTGTTAT
1 TTTTGTTGTT-T
74481 TTTTGTTGTTGT
1 TTTTGTTGTT-T
* **
74493 TTTTGCTGCTAC
1 TTTTGTTG-TTT
74505 TTTTGTTG--T
1 TTTTGTTGTTT
74514 TTTTGTTGTTT
1 TTTTGTTGTTT
74525 TTTTG
1 TTTTG
74530 CTATTTTGGT
Statistics
Matches: 49, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
9 8 0.16
11 6 0.12
12 34 0.69
13 1 0.02
ACGTcount: A:0.04, C:0.05, G:0.21, T:0.70
Consensus pattern (11 bp):
TTTTGTTGTTT
Found at i:75088 original size:13 final size:13
Alignment explanation
Indices: 75070--75098 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
75060 GACACTCTTA
75070 AATTTTGCATTAT
1 AATTTTGCATTAT
75083 AATTTTGCATTAT
1 AATTTTGCATTAT
75096 AAT
1 AAT
75099 AAAATTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (13 bp):
AATTTTGCATTAT
Found at i:79386 original size:28 final size:28
Alignment explanation
Indices: 79355--79599 Score: 93
Period size: 28 Copynumber: 8.6 Consensus size: 28
79345 TACAAAGGCA
*
79355 GCCACAAAGGCATCCTTTTTAAAGATTT
1 GCCACAAAGGCATCCTTTATAAAGATTT
* * * *
79383 GCCACTAAGGCTTTCC-TTATAGAGGTTT
1 GCCACAAAGGC-ATCCTTTATAAAGATTT
** * *
79411 GCCACAAAGATTATCCTTTA-ACAGATATC
1 GCCACAAAG-GCATCCTTTATAAAGAT-TT
* * * * ** *
79440 ACCACAAAGGCTTTCCTGTCTAGTGTTTT
1 GCCACAAAGGC-ATCCTTTATAAAGATTT
* *
79469 GCCACAAAGGCATCCTTTAATAGAGATCT
1 GCCACAAAGGCATCCTTT-ATAAAGATTT
* * * *
79498 -CCACAAAGGCTTTCTTATCTAAAGTTTT
1 GCCACAAAGGCATCCTT-TATAAAGATTT
* * * *
79526 TCCACAAAGGCGTCCTTTAACAAAGA-TC
1 GCCACAAAGGCATCCTTT-ATAAAGATTT
* * ** * *
79554 GCAACAAAGGCTTTCCCGTCTAAAGTTTT
1 GCCACAAAGGC-ATCCTTTATAAAGATTT
*
79583 GCCACAAAGGCGTCCTT
1 GCCACAAAGGCATCCTT
79600 CAACAGAGAT
Statistics
Matches: 151, Mismatches: 54, Indels: 24
0.66 0.24 0.10
Matches are distributed among these distances:
28 77 0.51
29 71 0.47
30 3 0.02
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.30
Consensus pattern (28 bp):
GCCACAAAGGCATCCTTTATAAAGATTT
Found at i:79453 original size:57 final size:56
Alignment explanation
Indices: 79384--79628 Score: 222
Period size: 57 Copynumber: 4.3 Consensus size: 56
79374 TAAAGATTTG
* ** *
79384 CCACTAAGGCTTTCCTTATAGAGGTTTGCCACAAAGATTATCCTTTAACAGATATCA
1 CCACAAAGGCTTTCCTTATAGAGGTTTGCCACAAAG-GCATCCTTTAACAGAGATCA
* * * * *
79441 CCACAAAGGCTTTCCTGTCTAGTGTTTTGCCACAAAGGCATCCTTTAATAGAGATCT
1 CCACAAAGGCTTTCCT-TATAGAGGTTTGCCACAAAGGCATCCTTTAACAGAGATCA
* * * * * *
79498 CCACAAAGGCTTT-CTTATCTAAAGTTTTTCCACAAAGGCGTCCTTTAACAAAGATCG
1 CCACAAAGGCTTTCCTTA--TAGAGGTTTGCCACAAAGGCATCCTTTAACAGAGATCA
* * * * * * * *
79555 CAACAAAGGCTTTCCCGTCTAAAGTTTTGCCACAAAGGCGTCCTTCAACAGAGATCG
1 CCACAAAGGCTTT-CCTTATAGAGGTTTGCCACAAAGGCATCCTTTAACAGAGATCA
*
79612 CCATAAAGGCTTTCCTT
1 CCACAAAGGCTTTCCTT
79629 TAATAGAGAT
Statistics
Matches: 157, Mismatches: 26, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
55 1 0.01
56 5 0.03
57 132 0.84
58 17 0.11
59 2 0.01
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (56 bp):
CCACAAAGGCTTTCCTTATAGAGGTTTGCCACAAAGGCATCCTTTAACAGAGATCA
Found at i:79482 original size:114 final size:113
Alignment explanation
Indices: 79355--79625 Score: 285
Period size: 114 Copynumber: 2.4 Consensus size: 113
79345 TACAAAGGCA
* * * *
79355 GCCACAAAGGCATCCTTT-TTAAAGATTTGCCACTAAGGCTTTCCTTA-TAGAGGTTTGCCACAA
1 GCCACAAAGGCATCCTTTAATAAAGATCT-CCACAAAGGCTTT-CTTACTAAAGGTTTGCCACAA
** * * * * **
79418 AGATTATCCTTTAACAGATATCACCACAAAGGCTTTCCTGTCTAGTGTTTT
64 AG-GCATCCTTTAACAAAGATCACAACAAAGGCTTTCCCGTCTAAAGTTTT
* * *
79469 GCCACAAAGGCATCCTTTAATAGAGATCTCCACAAAGGCTTTCTTATCTAAAGTTTTTCCACAAA
1 GCCACAAAGGCATCCTTTAATAAAGATCTCCACAAAGGCTTTCTTA-CTAAAGGTTTGCCACAAA
* *
79534 GGCGTCCTTTAACAAAGATCGCAACAAAGGCTTTCCCGTCTAAAGTTTT
65 GGCATCCTTTAACAAAGATCACAACAAAGGCTTTCCCGTCTAAAGTTTT
* * * * * *
79583 GCCACAAAGGCGTCCTTCAACAGAGATCGCCATAAAGGCTTTC
1 GCCACAAAGGCATCCTTTAATAAAGATCTCCACAAAGGCTTTC
79626 CTTTAATAGA
Statistics
Matches: 132, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
113 4 0.03
114 106 0.80
115 22 0.17
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (113 bp):
GCCACAAAGGCATCCTTTAATAAAGATCTCCACAAAGGCTTTCTTACTAAAGGTTTGCCACAAAG
GCATCCTTTAACAAAGATCACAACAAAGGCTTTCCCGTCTAAAGTTTT
Found at i:79550 original size:29 final size:29
Alignment explanation
Indices: 79464--79550 Score: 70
Period size: 29 Copynumber: 3.0 Consensus size: 29
79454 CCTGTCTAGT
* * *
79464 GTTTTGCCACAAAGGCATCCTTTAATAGA
1 GTTTTTCCACAAAGGCATCCTTTAACAAA
* * * * *
79493 G-ATCTCCACAAAGGCTTTC-TTATCTAAA
1 GTTTTTCCACAAAGGCATCCTTTAAC-AAA
*
79521 GTTTTTCCACAAAGGCGTCCTTTAACAAA
1 GTTTTTCCACAAAGGCATCCTTTAACAAA
79550 G
1 G
79551 ATCGCAACAA
Statistics
Matches: 42, Mismatches: 13, Indels: 6
0.69 0.21 0.10
Matches are distributed among these distances:
27 3 0.07
28 16 0.38
29 19 0.45
30 4 0.10
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (29 bp):
GTTTTTCCACAAAGGCATCCTTTAACAAA
Found at i:79619 original size:28 final size:29
Alignment explanation
Indices: 79583--79651 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
79573 CTAAAGTTTT
* *
79583 GCCACAAAGGC-GTCCTTCAACAGAGATC
1 GCCATAAAGGCTGTCCTTCAACAGAGATA
* * *
79611 GCCATAAAGGCTTTCCTTTAATAGAGATA
1 GCCATAAAGGCTGTCCTTCAACAGAGATA
*
79640 GCCATAAGGGCT
1 GCCATAAAGGCT
79652 TCCCACTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
28 10 0.29
29 24 0.71
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.22
Consensus pattern (29 bp):
GCCATAAAGGCTGTCCTTCAACAGAGATA
Found at i:79637 original size:29 final size:29
Alignment explanation
Indices: 79595--79652 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
79585 CACAAAGGCG
*
79595 TCCTTCAACAGAGATCGCCATAAAGGCTT
1 TCCTTCAACAGAGATAGCCATAAAGGCTT
* * *
79624 TCCTTTAATAGAGATAGCCATAAGGGCTT
1 TCCTTCAACAGAGATAGCCATAAAGGCTT
79653 CCCACTTTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (29 bp):
TCCTTCAACAGAGATAGCCATAAAGGCTT
Done.