Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold890
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: 34897
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:1607 original size:82 final size:81
Alignment explanation
Indices: 1491--1646 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
1481 AAATTGTACA
* * * *
1491 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAGTG
1555 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
1572 GCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGTGTGCGAGTC-AACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
*
1637 TGCGAGTTGA
65 TGCGAATTGA
1647 TTGTATAGCA
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 18 0.28
82 47 0.72
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (81 bp):
GCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:1614 original size:55 final size:52
Alignment explanation
Indices: 1490--1643 Score: 175
Period size: 55 Copynumber: 2.9 Consensus size: 52
1480 TAAATTGTAC
* *
1490 AGCACTAAGTGTGCG-ATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATG
1 AGCACTAAGTGTGCGAATT-GACTATGTGGCACTAAGTGTGCG-AGTGAATATG
* * *
1543 ATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTCTAACTATG
1 A-GCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGT-GAA-TATG
* * *
1598 TAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTGTGCGAGT
1 -AGCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGT
1644 TGATTGTATA
Statistics
Matches: 86, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
53 3 0.03
54 36 0.42
55 46 0.53
56 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (52 bp):
AGCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGTGAATATG
Found at i:1648 original size:27 final size:27
Alignment explanation
Indices: 1491--1646 Score: 163
Period size: 27 Copynumber: 5.7 Consensus size: 27
1481 AAATTGTACA
*
1491 GCACTAAGTGTGCG-ATTCGACTATGTT
1 GCACTAAGTGTGCGAATT-GACTATGTG
* *
1518 GCACTAAGTGTGCGAAATGAATATGAT-
1 GCACTAAGTGTGCGAATTGACTATG-TG
* *
1545 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAATTGACTATGTG
* * *
1572 GCACTAAGTGTGCGAGTCTAACTATGTA
1 GCACTAAGTGTGCGAAT-TGACTATGTG
* * *
1600 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGAATTGACTATGTG
*
1627 GCACTAAGTGTGCGAGTTGA
1 GCACTAAGTGTGCGAATTGA
1647 TTGTATAGCA
Statistics
Matches: 108, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
27 83 0.77
28 25 0.23
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (27 bp):
GCACTAAGTGTGCGAATTGACTATGTG
Found at i:1657 original size:27 final size:27
Alignment explanation
Indices: 1483--1667 Score: 101
Period size: 27 Copynumber: 6.8 Consensus size: 27
1473 GCGGGATTAA
*
1483 ATTGTACAGCACTAAGTGTGCG-ATTCG
1 ATTGTATAGCACTAAGTGTGCGAATT-G
*
1510 ACTATGT-T-GCACTAAGTGTGCGAAATG
1 A-T-TGTATAGCACTAAGTGTGCGAATTG
1537 AATATG-AT-GCACTAAGTGTGCGAATTG
1 -AT-TGTATAGCACTAAGTGTGCGAATTG
*** *** * *
1564 ACCATGCGGCACTAAGTGTGCGAGTCTA
1 ATTGTATAGCACTAAGTGTGCGAAT-TG
* * * *
1592 ACTATGTAGCACTAAGTGTGCGATTTG
1 ATTGTATAGCACTAAGTGTGCGAATTG
*** * *
1619 ATTACGTGGCACTAAGTGTGCGAGTTG
1 ATTGTATAGCACTAAGTGTGCGAATTG
*
1646 ATTGTATAGCACTGAGTGTGCG
1 ATTGTATAGCACTAAGTGTGCG
1668 GGCTCAATAT
Statistics
Matches: 126, Mismatches: 24, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
26 1 0.01
27 96 0.76
28 26 0.21
29 3 0.02
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.29
Consensus pattern (27 bp):
ATTGTATAGCACTAAGTGTGCGAATTG
Found at i:1658 original size:82 final size:81
Alignment explanation
Indices: 1483--1667 Score: 210
Period size: 82 Copynumber: 2.3 Consensus size: 81
1473 GCGGGATTAA
* * * *
1483 ATTGTACAGCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCA
1 ATTGTACAGCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCA
1548 CTAAGTGTGCGAATTG
66 CTAAGTGTGCGAATTG
*** * * ** *
1564 ACCATGCGGCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGG
1 ATTGTACAGCACTAAGTGTGCGAGTC-AACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-G
*
1628 CACTAAGTGTGCGAGTTG
64 CACTAAGTGTGCGAATTG
* *
1646 ATTGTATAGCACTGAGTGTGCG
1 ATTGTACAGCACTAAGTGTGCG
1668 GGCTCAATAT
Statistics
Matches: 82, Mismatches: 20, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
81 21 0.26
82 61 0.74
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
ATTGTACAGCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCA
CTAAGTGTGCGAATTG
Found at i:9477 original size:82 final size:81
Alignment explanation
Indices: 9361--9516 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
9351 AAATTGTACA
* * * *
9361 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAGTG
9425 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
9442 GCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGTGTGCGAGTC-AACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
*
9507 TGCGAGTTGA
65 TGCGAATTGA
9517 TTGTATAGCA
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 18 0.28
82 47 0.72
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (81 bp):
GCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:9484 original size:55 final size:52
Alignment explanation
Indices: 9360--9513 Score: 175
Period size: 55 Copynumber: 2.9 Consensus size: 52
9350 TAAATTGTAC
* *
9360 AGCACTAAGTGTGCG-ATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATG
1 AGCACTAAGTGTGCGAATT-GACTATGTGGCACTAAGTGTGCG-AGTGAATATG
* * *
9413 ATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTCTAACTATG
1 A-GCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGT-GAA-TATG
* * *
9468 TAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTGTGCGAGT
1 -AGCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGT
9514 TGATTGTATA
Statistics
Matches: 86, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
53 3 0.03
54 36 0.42
55 46 0.53
56 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (52 bp):
AGCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGTGAATATG
Found at i:9518 original size:27 final size:27
Alignment explanation
Indices: 9361--9516 Score: 163
Period size: 27 Copynumber: 5.7 Consensus size: 27
9351 AAATTGTACA
*
9361 GCACTAAGTGTGCG-ATTCGACTATGTT
1 GCACTAAGTGTGCGAATT-GACTATGTG
* *
9388 GCACTAAGTGTGCGAAATGAATATGAT-
1 GCACTAAGTGTGCGAATTGACTATG-TG
* *
9415 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAATTGACTATGTG
* * *
9442 GCACTAAGTGTGCGAGTCTAACTATGTA
1 GCACTAAGTGTGCGAAT-TGACTATGTG
* * *
9470 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGAATTGACTATGTG
*
9497 GCACTAAGTGTGCGAGTTGA
1 GCACTAAGTGTGCGAATTGA
9517 TTGTATAGCA
Statistics
Matches: 108, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
27 83 0.77
28 25 0.23
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (27 bp):
GCACTAAGTGTGCGAATTGACTATGTG
Found at i:9527 original size:27 final size:27
Alignment explanation
Indices: 9353--9537 Score: 101
Period size: 27 Copynumber: 6.8 Consensus size: 27
9343 GCGGGATTAA
*
9353 ATTGTACAGCACTAAGTGTGCG-ATTCG
1 ATTGTATAGCACTAAGTGTGCGAATT-G
*
9380 ACTATGT-T-GCACTAAGTGTGCGAAATG
1 A-T-TGTATAGCACTAAGTGTGCGAATTG
9407 AATATG-AT-GCACTAAGTGTGCGAATTG
1 -AT-TGTATAGCACTAAGTGTGCGAATTG
*** *** * *
9434 ACCATGCGGCACTAAGTGTGCGAGTCTA
1 ATTGTATAGCACTAAGTGTGCGAAT-TG
* * * *
9462 ACTATGTAGCACTAAGTGTGCGATTTG
1 ATTGTATAGCACTAAGTGTGCGAATTG
*** * *
9489 ATTACGTGGCACTAAGTGTGCGAGTTG
1 ATTGTATAGCACTAAGTGTGCGAATTG
*
9516 ATTGTATAGCACTGAGTGTGCG
1 ATTGTATAGCACTAAGTGTGCG
9538 GGCTCAATAT
Statistics
Matches: 126, Mismatches: 24, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
26 1 0.01
27 96 0.76
28 26 0.21
29 3 0.02
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.29
Consensus pattern (27 bp):
ATTGTATAGCACTAAGTGTGCGAATTG
Found at i:9528 original size:82 final size:81
Alignment explanation
Indices: 9353--9537 Score: 210
Period size: 82 Copynumber: 2.3 Consensus size: 81
9343 GCGGGATTAA
* * * *
9353 ATTGTACAGCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCA
1 ATTGTACAGCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCA
9418 CTAAGTGTGCGAATTG
66 CTAAGTGTGCGAATTG
*** * * ** *
9434 ACCATGCGGCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGG
1 ATTGTACAGCACTAAGTGTGCGAGTC-AACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-G
*
9498 CACTAAGTGTGCGAGTTG
64 CACTAAGTGTGCGAATTG
* *
9516 ATTGTATAGCACTGAGTGTGCG
1 ATTGTACAGCACTAAGTGTGCG
9538 GGCTCAATAT
Statistics
Matches: 82, Mismatches: 20, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
81 21 0.26
82 61 0.74
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
ATTGTACAGCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCA
CTAAGTGTGCGAATTG
Found at i:10944 original size:40 final size:40
Alignment explanation
Indices: 10889--11031 Score: 182
Period size: 40 Copynumber: 3.6 Consensus size: 40
10879 GTTACAGTTG
* *
10889 CTATACCCGGGCTAAGTCTCGAAGGCATTTGTGCTAGTGA
1 CTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGA
* **
10929 CTATATTCGGGCTAAGTCCCGAAGGCATTCATGCTAGTGA
1 CTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGA
* *
10969 CTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGT-A
1 CTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGA
* *
11008 GCTATATCC-GGCTAAATCCTGAAG
1 -CTATATCCGGGCTAAGTCCCGAAG
11032 ATATTTGGGT
Statistics
Matches: 89, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
39 13 0.15
40 76 0.85
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (40 bp):
CTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGA
Found at i:19060 original size:40 final size:40
Alignment explanation
Indices: 19005--19188 Score: 194
Period size: 40 Copynumber: 4.5 Consensus size: 40
18995 TATTCGGATG
* *
19005 ATATCTGGGCTAAGTCCCGAGGGCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* *
19045 ATATCCAGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-A--AGTTACT
* ** * *
19088 ATA-CTCGGGCTAAGTCCCAAAGGCATTCATGCTAGTGACT
1 ATATC-CGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* *
19128 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-T
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTT-ACT
*
19168 ATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
19189 ATACTTGGGT
Statistics
Matches: 119, Mismatches: 19, Indels: 13
0.79 0.13 0.09
Matches are distributed among these distances:
39 13 0.11
40 70 0.59
41 3 0.03
42 1 0.01
43 32 0.27
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
Found at i:19150 original size:83 final size:83
Alignment explanation
Indices: 19011--19163 Score: 234
Period size: 83 Copynumber: 1.8 Consensus size: 83
19001 GATGATATCT
* * ** * *
19011 GGGCTAAGTCCCGAGGGCATTTGTGCAAGTTACTATATCCAGGCTAAGTCCCGAAGGCATTTGTG
1 GGGCTAAGTCCCAAAGGCATTCATGCAAGTGACTATATCCAGGCTAAGACCCGAAGGCATTTGTG
19076 CGAGTAGTTGCTATACTC
66 CGAGTAGTTGCTATACTC
* *
19094 GGGCTAAGTCCCAAAGGCATTCATGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCATTTGTG
1 GGGCTAAGTCCCAAAGGCATTCATGCAAGTGACTATATCCAGGCTAAGACCCGAAGGCATTTGTG
19159 CGAGT
66 CGAGT
19164 TGATATATCC
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
83 62 1.00
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (83 bp):
GGGCTAAGTCCCAAAGGCATTCATGCAAGTGACTATATCCAGGCTAAGACCCGAAGGCATTTGTG
CGAGTAGTTGCTATACTC
Found at i:25121 original size:38 final size:39
Alignment explanation
Indices: 25020--25171 Score: 234
Period size: 39 Copynumber: 3.9 Consensus size: 39
25010 ACATATTTCT
* * **
25020 AGCACGTAGCCTGCGGACCTTAAGTCCGGTTATAATTCC
1 AGCACATAGCCTGCGGACCCTAAGTCCGAATATAATTCC
* *
25059 AGCACATAGCCTGCGGACCTTAAGTCCGGATATAATTCC
1 AGCACATAGCCTGCGGACCCTAAGTCCGAATATAATTCC
25098 AGCACATAG-CTGCGGACCCTAAGTCCGAATATAATTCC
1 AGCACATAGCCTGCGGACCCTAAGTCCGAATATAATTCC
*
25136 AGCATATAGCCTGCGGACCCTAAGTCCGAATATAAT
1 AGCACATAGCCTGCGGACCCTAAGTCCGAATATAAT
25172 CATCACTGAA
Statistics
Matches: 107, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
38 35 0.33
39 72 0.67
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (39 bp):
AGCACATAGCCTGCGGACCCTAAGTCCGAATATAATTCC
Found at i:25121 original size:77 final size:78
Alignment explanation
Indices: 25020--25171 Score: 234
Period size: 77 Copynumber: 2.0 Consensus size: 78
25010 ACATATTTCT
* * ** *
25020 AGCACGTAGCCTGCGGACCTTAAGTCCGGTTATAATTCCAGCACATAGCCTGCGGACCTTAAGTC
1 AGCACATAGCCTGCGGACCCTAAGTCCGAATATAATTCCAGCACATAGCCTGCGGACCCTAAGTC
*
25085 CGGATATAATTCC
66 CGAATATAATTCC
*
25098 AGCACATAG-CTGCGGACCCTAAGTCCGAATATAATTCCAGCATATAGCCTGCGGACCCTAAGTC
1 AGCACATAGCCTGCGGACCCTAAGTCCGAATATAATTCCAGCACATAGCCTGCGGACCCTAAGTC
25162 CGAATATAAT
66 CGAATATAAT
25172 CATCACTGAA
Statistics
Matches: 67, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
77 59 0.88
78 8 0.12
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (78 bp):
AGCACATAGCCTGCGGACCCTAAGTCCGAATATAATTCCAGCACATAGCCTGCGGACCCTAAGTC
CGAATATAATTCC
Found at i:27596 original size:31 final size:31
Alignment explanation
Indices: 27559--27617 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
27549 TTTCATTAGA
27559 TCGATTACATTTTGTCCACTTAATTTATAGG
1 TCGATTACATTTTGTCCACTTAATTTATAGG
27590 TCGATTACATTTTGTCCACTTAATTTAT
1 TCGATTACATTTTGTCCACTTAATTTAT
27618 TAAAATTGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.47
Consensus pattern (31 bp):
TCGATTACATTTTGTCCACTTAATTTATAGG
Found at i:29321 original size:37 final size:37
Alignment explanation
Indices: 29271--29349 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
29261 TTATTACGAA
* * *
29271 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
29308 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
29345 GTCTT
1 GTCTT
29350 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:29553 original size:47 final size:47
Alignment explanation
Indices: 29466--29995 Score: 833
Period size: 47 Copynumber: 11.4 Consensus size: 47
29456 GCCTTCGGGA
* * * * * * * *
29466 CTTATCACATTTATGCACTTTCACATCCATTACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
29513 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29560 CTTATCAC--ATATACACTTTCACATTCATC-CATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29604 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
29651 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
29698 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
29745 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
29792 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29839 CTTAT-ACATATACATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATAT--ATACACTTTCACATTCATCACATCGGCCATTAGGC
29887 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
29934 CTTAT--CATACATACACTTTCACATTCATCACATC-GCCATTAGG-
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29977 CTTATCACATATATACACT
1 CTTATCACATATATACACT
29996 CTCTTGGCTG
Statistics
Matches: 457, Mismatches: 18, Indels: 18
0.93 0.04 0.04
Matches are distributed among these distances:
43 5 0.01
44 32 0.07
45 60 0.13
46 26 0.06
47 288 0.63
48 40 0.09
49 6 0.01
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:29923 original size:236 final size:228
Alignment explanation
Indices: 29517--29995 Score: 825
Period size: 236 Copynumber: 2.1 Consensus size: 228
29507 CTCGGCCCTG
29517 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATACACTTTCAC
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATACACTTTCAC
29582 ATTCATCCATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATT
66 ATTCATCCATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATT
*
29647 AGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACACATAT
131 AGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAC--AT
*
29712 ACACTTTCACATTCATCACATCGGCTATTAGGCCTTA
194 ACACTTTCACATTCATCACATC-GCCATTAGG-CTTA
* *
29749 TCACACATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACTTTC
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT--CACATATACACTTTC
29814 ACATTCATCACATCGGCCATTAGGCCTTAT-ACATATACATACACTTTCACATTCATCACATCGG
64 ACATTCATC-CATCGGCCATTAGGCCTTATCACATAT--ATACACTTTCACATTCATCACATCGG
*
29878 CCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCATA
126 CCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA
29943 CATACACTTTCACATTCATCACATCGCCATTAGGCTTA
191 CATACACTTTCACATTCATCACATCGCCATTAGGCTTA
29981 TCACATATATACACT
1 TCACATATATACACT
29996 CTCTTGGCTG
Statistics
Matches: 236, Mismatches: 6, Indels: 10
0.94 0.02 0.04
Matches are distributed among these distances:
232 64 0.27
233 8 0.03
234 54 0.23
235 20 0.08
236 90 0.38
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (228 bp):
TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATACACTTTCAC
ATTCATCCATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATT
AGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATAC
ACTTTCACATTCATCACATCGCCATTAGGCTTA
Found at i:33330 original size:24 final size:25
Alignment explanation
Indices: 33290--33339 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
33280 AAGGAATTCG
33290 CACACAACAGTGCCTC-TAATCATT
1 CACACAACAGTGCCTCTTAATCATT
* *
33314 CACACACATAGTG-CTCTTATTCATT
1 CACACA-ACAGTGCCTCTTAATCATT
33339 C
1 C
33340 GTTATTACAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.30, C:0.32, G:0.08, T:0.30
Consensus pattern (25 bp):
CACACAACAGTGCCTCTTAATCATT
Found at i:33601 original size:36 final size:39
Alignment explanation
Indices: 33504--33649 Score: 164
Period size: 36 Copynumber: 3.9 Consensus size: 39
33494 CGAATACACG
* * ** *
33504 TCACCAGCATGATTGCTCTTCGGGTTTAG-CCGGATATA
1 TCACTAGCATGAATGCTCTTCGGACTTAGCCCGGATACA
* *
33542 T--CTAG-ACGACTGCTCTTCGGGACTTAGCCCGG-TACA
1 TCACTAGCATGAATGCTCTTC-GGACTTAGCCCGGATACA
33578 TCACTAGCA-GAATGCTCTT-GGAC-TAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGACTTAGCCCGGATACA
33614 TCACTAGCATGAATGCTCTTCGGACTTAGCCCGGAT
1 TCACTAGCATGAATGCTCTTCGGACTTAGCCCGGAT
33650 TTAGTAACTC
Statistics
Matches: 92, Mismatches: 7, Indels: 17
0.79 0.06 0.15
Matches are distributed among these distances:
35 19 0.21
36 30 0.33
37 14 0.15
38 18 0.20
39 11 0.12
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (39 bp):
TCACTAGCATGAATGCTCTTCGGACTTAGCCCGGATACA
Found at i:34068 original size:29 final size:29
Alignment explanation
Indices: 34022--34099 Score: 97
Period size: 29 Copynumber: 2.7 Consensus size: 29
34012 CTTAATAATC
*
34022 AACCACGCACA-TTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
34051 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
34080 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
34100 ATCTCACAAC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
28 9 0.21
29 34 0.79
ACGTcount: A:0.28, C:0.32, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Done.