Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012662.1 Kokia drynarioides strain JFW-HI SEQ_127673, 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: 335207
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 22 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:231516 original size:21 final size:21
Alignment explanation
Indices: 231492--231538 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
231482 ATAATAGCAT
*
231492 AATCCAAATATAAAGTTTAGA
1 AATCCAAACATAAAGTTTAGA
* *
231513 AATCGAAACATAAAGTTTATA
1 AATCCAAACATAAAGTTTAGA
231534 AATCC
1 AATCC
231539 GAATTACATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.51, C:0.13, G:0.09, T:0.28
Consensus pattern (21 bp):
AATCCAAACATAAAGTTTAGA
Found at i:232645 original size:80 final size:80
Alignment explanation
Indices: 232494--232645 Score: 243
Period size: 80 Copynumber: 1.9 Consensus size: 80
232484 CACTAATTTC
* *
232494 TTTTTAACTCTTGTAAGGAAGCTAATGAGTCATGTCTCTTCATTAGGATCTGATGTAGTTAAAAA
1 TTTTTAACTCTTGTAAGGAAGCCAATGAGTCATGTCTCTTCATTAGGATCTGATGTAGCTAAAAA
*
232559 GGCATGGTAATTTTG
66 GACATGGTAATTTTG
*
232574 TTTTTAACTCTTGT-AGGAAAGCCAATGAGTCATGTCTCTTCATTAGGATCTGATGTAGCTGAAA
1 TTTTTAACTCTTGTAAGG-AAGCCAATGAGTCATGTCTCTTCATTAGGATCTGATGTAGCTAAAA
*
232638 TGACATGG
65 AGACATGG
232646 CATTTCTCCT
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
79 3 0.05
80 63 0.95
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (80 bp):
TTTTTAACTCTTGTAAGGAAGCCAATGAGTCATGTCTCTTCATTAGGATCTGATGTAGCTAAAAA
GACATGGTAATTTTG
Found at i:233183 original size:48 final size:48
Alignment explanation
Indices: 233091--233259 Score: 241
Period size: 48 Copynumber: 3.5 Consensus size: 48
233081 CGAGGCATTT
* * *
233091 AACAAAGATGCATTTATCAAA-AAAATAGTTAATAATGCATATTACTA
1 AACAAAGATGCATTTAACAAACAAAACAGTTAATAATGCAGATTACTA
233138 AACAAAGATGCATTTAACAAACAAAACAGTTAATAATGCAGATTACTA
1 AACAAAGATGCATTTAACAAACAAAACAGTTAATAATGCAGATTACTA
* * * * *
233186 AAAAAAGATGCATTTAACAAACAAAACACTTAATGATGTAGATTATTA
1 AACAAAGATGCATTTAACAAACAAAACAGTTAATAATGCAGATTACTA
* *
233234 AACAAAGATGCATTTAAAAAAAAAAA
1 AACAAAGATGCATTTAACAAACAAAA
233260 ATACTTAATG
Statistics
Matches: 110, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
47 20 0.18
48 90 0.82
ACGTcount: A:0.54, C:0.11, G:0.09, T:0.25
Consensus pattern (48 bp):
AACAAAGATGCATTTAACAAACAAAACAGTTAATAATGCAGATTACTA
Found at i:236420 original size:21 final size:18
Alignment explanation
Indices: 236381--236429 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 18
236371 TTCTTTTATT
*
236381 TTTTTCTTTTTCTCTCTC
1 TTTTTCTTTTCCTCTCTC
236399 TTTTTCTTTTCCCTCATGCTC
1 TTTTTCTTTT-CCTC-T-CTC
236420 TTTTTCTTTT
1 TTTTTCTTTT
236430 TCTATTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 10 0.37
19 3 0.11
20 1 0.04
21 13 0.48
ACGTcount: A:0.02, C:0.27, G:0.02, T:0.69
Consensus pattern (18 bp):
TTTTTCTTTTCCTCTCTC
Found at i:236429 original size:6 final size:6
Alignment explanation
Indices: 236360--236408 Score: 53
Period size: 6 Copynumber: 8.0 Consensus size: 6
236350 TACCACAACC
* * * *
236360 TCTTTT TCTTGT TCTTTT ATTTTTT TCTTTT TCTCTC TCTTTT TCTTTT
1 TCTTTT TCTTTT TCTTTT -TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT
236409 CCCTCATGCT
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
6 29 0.85
7 5 0.15
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.78
Consensus pattern (6 bp):
TCTTTT
Found at i:239412 original size:48 final size:48
Alignment explanation
Indices: 239374--239557 Score: 221
Period size: 48 Copynumber: 3.9 Consensus size: 48
239364 CAAGGCATTT
* * *
239374 AACAAAGATGCATTTAACAAACAGAACAGTTAATAATGCATATTACTA
1 AACAAAGATGCATTTAACAAACAAAACAGTTAATAATGCATAGTATTA
* * * *
239422 AACAAAGATGCATTTAACAAACAAAATAGTTAATAATGCAGATTACTA
1 AACAAAGATGCATTTAACAAACAAAACAGTTAATAATGCATAGTATTA
* * * *
239470 AATAAAGATGCATTTAACAAACAAAACACTTAATGATGCATATTATTA
1 AACAAAGATGCATTTAACAAACAAAACAGTTAATAATGCATAGTATTA
* *
239518 AACAAAGATGCATTTTA-AAA-AAAACACTTAATGAA-GCATA
1 AACAAAGATGCATTTAACAAACAAAACAGTTAAT-AATGCATA
239558 AAAAAACAAC
Statistics
Matches: 123, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
46 17 0.14
47 4 0.03
48 102 0.83
ACGTcount: A:0.52, C:0.13, G:0.10, T:0.26
Consensus pattern (48 bp):
AACAAAGATGCATTTAACAAACAAAACAGTTAATAATGCATAGTATTA
Found at i:241402 original size:118 final size:118
Alignment explanation
Indices: 241194--241429 Score: 463
Period size: 118 Copynumber: 2.0 Consensus size: 118
241184 AGACTACTAT
*
241194 GATTAGTGAAATGAGAATTATGGTTACATAAAATGATTTTTATGGTATGAGTTCACGTTATGGTA
1 GATTAGTGAAATGAGAATTATGGTTACATAAAATGATTTTTAGGGTATGAGTTCACGTTATGGTA
241259 TAGTACACCCTATAACAATTATGGCCTCGTGCCAGTTAATTTATAAGTTAAGC
66 TAGTACACCCTATAACAATTATGGCCTCGTGCCAGTTAATTTATAAGTTAAGC
241312 GATTAGTGAAATGAGAATTATGGTTACATAAAATGATTTTTAGGGTATGAGTTCACGTTATGGTA
1 GATTAGTGAAATGAGAATTATGGTTACATAAAATGATTTTTAGGGTATGAGTTCACGTTATGGTA
241377 TAGTACACCCTATAACAATTATGGCCTCGTGCCAGTTAATTTATAAGTTAAGC
66 TAGTACACCCTATAACAATTATGGCCTCGTGCCAGTTAATTTATAAGTTAAGC
241430 TTATTAGGAA
Statistics
Matches: 117, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
118 117 1.00
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (118 bp):
GATTAGTGAAATGAGAATTATGGTTACATAAAATGATTTTTAGGGTATGAGTTCACGTTATGGTA
TAGTACACCCTATAACAATTATGGCCTCGTGCCAGTTAATTTATAAGTTAAGC
Found at i:242580 original size:28 final size:28
Alignment explanation
Indices: 242486--242584 Score: 101
Period size: 28 Copynumber: 3.5 Consensus size: 28
242476 GGCAATTCGT
* *
242486 AAAGTAAAACCTTTGTGGCA-AACCTCTG
1 AAAGGAAAGCCTTTGTGG-AGAACCTCTG
* * *
242514 AAAAGAAAGCATTAGTGGAGAACCTCTG
1 AAAGGAAAGCCTTTGTGGAGAACCTCTG
* * * *
242542 AAAGGGAAGCCTTTTTGGTGAACCTATG
1 AAAGGAAAGCCTTTGTGGAGAACCTCTG
242570 AAAGGAAAGCCTTTG
1 AAAGGAAAGCCTTTG
242585 AGGCAACCCC
Statistics
Matches: 56, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
27 1 0.02
28 55 0.98
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.23
Consensus pattern (28 bp):
AAAGGAAAGCCTTTGTGGAGAACCTCTG
Found at i:242592 original size:27 final size:28
Alignment explanation
Indices: 242534--242592 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
242524 ATTAGTGGAG
* * ** *
242534 AACCTCTGAAAGGGAAGCCTTTTTGGTG
1 AACCTATGAAAGGAAAGCCTTTGAGGTC
242562 AACCTATGAAAGGAAAGCCTTTGAGG-C
1 AACCTATGAAAGGAAAGCCTTTGAGGTC
242589 AACC
1 AACC
242593 CCCGAACATG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 4 0.15
28 22 0.85
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.22
Consensus pattern (28 bp):
AACCTATGAAAGGAAAGCCTTTGAGGTC
Found at i:242661 original size:27 final size:27
Alignment explanation
Indices: 242630--242689 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
242620 TTTGAAATGA
**
242630 AAGCCTTAGTGGCTAACCATGTAAAAG
1 AAGCCTTAGTGGAAAACCATGTAAAAG
* *
242657 AAGCCTTTGTGGAAAACCATGTAAAGG
1 AAGCCTTAGTGGAAAACCATGTAAAAG
242684 AAGCCT
1 AAGCCT
242690 CTATGCCAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.22
Consensus pattern (27 bp):
AAGCCTTAGTGGAAAACCATGTAAAAG
Found at i:242713 original size:27 final size:27
Alignment explanation
Indices: 242683--242740 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
242673 CCATGTAAAG
242683 GAAGCCTCTATGCCAATCTCTATAATA
1 GAAGCCTCTATGCCAATCTCTATAATA
* * * *
242710 GAAGCCTCTGTGGCAATCTCTGTAATG
1 GAAGCCTCTATGCCAATCTCTATAATA
242737 GAAG
1 GAAG
242741 TATCTATGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (27 bp):
GAAGCCTCTATGCCAATCTCTATAATA
Found at i:250383 original size:68 final size:68
Alignment explanation
Indices: 250274--250415 Score: 284
Period size: 68 Copynumber: 2.1 Consensus size: 68
250264 AGTTACTGAA
250274 ATGATTTTCAATGACCGATAAGAAGTCGAGTGCCCAACCGACTACATTAGGTTTTCATCTTTCTT
1 ATGATTTTCAATGACCGATAAGAAGTCGAGTGCCCAACCGACTACATTAGGTTTTCATCTTTCTT
250339 TAG
66 TAG
250342 ATGATTTTCAATGACCGATAAGAAGTCGAGTGCCCAACCGACTACATTAGGTTTTCATCTTTCTT
1 ATGATTTTCAATGACCGATAAGAAGTCGAGTGCCCAACCGACTACATTAGGTTTTCATCTTTCTT
250407 TAG
66 TAG
250410 ATGATT
1 ATGATT
250416 GTCCAAAGTC
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 74 1.00
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.35
Consensus pattern (68 bp):
ATGATTTTCAATGACCGATAAGAAGTCGAGTGCCCAACCGACTACATTAGGTTTTCATCTTTCTT
TAG
Found at i:251702 original size:17 final size:18
Alignment explanation
Indices: 251653--251704 Score: 63
Period size: 17 Copynumber: 2.8 Consensus size: 18
251643 ATTTCAAAAA
251653 TAATATTATTTTAATTGTT
1 TAATATTATTTTAA-TGTT
251672 TAATATTATATTTAA-G-T
1 TAATATTAT-TTTAATGTT
251689 TAATATTTATTTTAAT
1 TAATA-TTATTTTAAT
251705 AGAATTTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
17 11 0.37
18 5 0.17
19 9 0.30
20 5 0.17
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.60
Consensus pattern (18 bp):
TAATATTATTTTAATGTT
Found at i:267585 original size:38 final size:38
Alignment explanation
Indices: 267505--267631 Score: 132
Period size: 38 Copynumber: 3.4 Consensus size: 38
267495 TGCAATAGTA
** * * *
267505 GAAT-CTTGCTCAAGTGAGCGAATCCACTAATTATACT
1 GAATGCTTGCTCAAGAAAGCGAATCCATTGATTATATT
* * *
267542 AAATGCCTGCTCAAGCAAGCGAATCCATTGATTATATT
1 GAATGCTTGCTCAAGAAAGCGAATCCATTGATTATATT
* *
267580 GAATGCTTGTTCAA-AAGAGTGAATCCATTGATTATATT
1 GAATGCTTGCTCAAGAA-AGCGAATCCATTGATTATATT
*
267618 GAATGTTTGCTCAA
1 GAATGCTTGCTCAA
267632 ACGAACAATA
Statistics
Matches: 74, Mismatches: 14, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
37 4 0.05
38 70 0.95
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Consensus pattern (38 bp):
GAATGCTTGCTCAAGAAAGCGAATCCATTGATTATATT
Found at i:267670 original size:77 final size:77
Alignment explanation
Indices: 267524--267968 Score: 423
Period size: 77 Copynumber: 5.8 Consensus size: 77
267514 TCAAGTGAGC
* ** * * * *
267524 GAATCCACTAATTATACTAAATGCCTGCTCAAGCAAGCGAAT--CCATTGATTATATTGAATGCT
1 GAATCCACTGATTATACTAAATGTTTGCTCAAACGAGC-AATAACTACTGATTATATTGAATGCT
*
267587 TGTTCAAAAGAGT
65 TGTTCAAACGAGT
* * * * *
267600 GAATCCATTGATTATATTGAATGTTTGCTCAAACGAACAATAACTACTAATTATATTGAATGCTT
1 GAATCCACTGATTATACTAAATGTTTGCTCAAACGAGCAATAACTACTGATTATATTGAATGCTT
* *
267665 TTTCAAACGAGC
66 GTTCAAACGAGT
* * * * * * *
267677 AAAGCCATTTATTATAC-AAATGTTTACTCAAACGAGCGATAACTACTGATTATACTGAATGCTT
1 GAATCCACTGATTATACTAAATGTTTGCTCAAACGAGCAATAACTACTGATTATATTGAATGCTT
267741 GTTCAAACGAGT
66 GTTCAAACGAGT
* * * * *
267753 GAATCCACTGATTATACTAAATGCTTGCTCAAATGAGCGATAACTACCGATTATATTGTATGCTT
1 GAATCCACTGATTATACTAAATGTTTGCTCAAACGAGCAATAACTACTGATTATATTGAATGCTT
* * *
267818 ATTTAAACGAGC
66 GTTCAAACGAGT
* * * * * * *
267830 GAATCCACTAATCATACTAAATGTTTGCTCAAACGAGCATTACCCACTGATTATACTAAATGCTT
1 GAATCCACTGATTATACTAAATGTTTGCTCAAACGAGCAATAACTACTGATTATATTGAATGCTT
* *
267895 GCTCAAAAGAGCAT
66 GTTCAAACGAG--T
* * * * *
267909 -AATCCACTGATTATACTAAATGCTTACTCAAACGAGC-ATTATTCACTGATTATACTGAAT
1 GAATCCACTGATTATACTAAATGTTTGCTCAAACGAGCAATAACT-ACTGATTATATTGAAT
267969 AAGATTTTTT
Statistics
Matches: 296, Mismatches: 67, Indels: 10
0.79 0.18 0.03
Matches are distributed among these distances:
75 3 0.01
76 93 0.31
77 152 0.51
78 48 0.16
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.32
Consensus pattern (77 bp):
GAATCCACTGATTATACTAAATGTTTGCTCAAACGAGCAATAACTACTGATTATATTGAATGCTT
GTTCAAACGAGT
Found at i:267816 original size:153 final size:154
Alignment explanation
Indices: 267570--267946 Score: 483
Period size: 153 Copynumber: 2.4 Consensus size: 154
267560 GCGAATCCAT
* * * * *
267570 TGATTATATTGAATGCTTGTTCAAAAGAGTGAATCCATTGATTATATTGAATGTTTGCTCAAACG
1 TGATTATACTGAATGCTTGTTCAAAAGAGTGAATCCACTGATTATACTAAATGCTTGCTCAAACG
* * * * *
267635 AACAATAACTACTAATTATATTGAATGCTT-TTTCAAACGAGCAAAGCCATTTATTATAC-AAAT
66 AGCAATAACTACCAATTATATTGAATGCTTATTT-AAACGAGCAAAGCCACTAATCATACTAAAT
*
267698 GTTTACTCAAACGAGCGA-TAACTAC
130 GTTTACTCAAACGAGC-ATTAACCAC
* *
267723 TGATTATACTGAATGCTTGTTCAAACGAGTGAATCCACTGATTATACTAAATGCTTGCTCAAATG
1 TGATTATACTGAATGCTTGTTCAAAAGAGTGAATCCACTGATTATACTAAATGCTTGCTCAAACG
* * * * *
267788 AGCGATAACTACCGATTATATTGTATGCTTATTTAAACGAGCGAATCCACTAATCATACTAAATG
66 AGCAATAACTACCAATTATATTGAATGCTTATTTAAACGAGCAAAGCCACTAATCATACTAAATG
* *
267853 TTTGCTCAAACGAGCATTACCCAC
131 TTTACTCAAACGAGCATTAACCAC
* * *
267877 TGATTATACTAAATGCTTGCTCAAAAGAGCAT-AATCCACTGATTATACTAAATGCTTACTCAAA
1 TGATTATACTGAATGCTTGTTCAAAAGAG--TGAATCCACTGATTATACTAAATGCTTGCTCAAA
267941 CGAGCA
64 CGAGCA
267947 TTATTCACTG
Statistics
Matches: 193, Mismatches: 26, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
153 104 0.54
154 53 0.27
155 35 0.18
156 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (154 bp):
TGATTATACTGAATGCTTGTTCAAAAGAGTGAATCCACTGATTATACTAAATGCTTGCTCAAACG
AGCAATAACTACCAATTATATTGAATGCTTATTTAAACGAGCAAAGCCACTAATCATACTAAATG
TTTACTCAAACGAGCATTAACCAC
Found at i:267947 original size:39 final size:39
Alignment explanation
Indices: 267525--267964 Score: 326
Period size: 39 Copynumber: 11.4 Consensus size: 39
267515 CAAGTGAGCG
* * * * *
267525 AATCCACTAATTATACTAAATGCCTGCTCAAGCAAGC-G
1 AATCCACTGATTATACTAAATGCTTGCTCAAACGAGCAT
* * * * *
267563 AATCCATTGATTATATTGAATGCTTGTTCAAAAGAG--T
1 AATCCACTGATTATACTAAATGCTTGCTCAAACGAGCAT
* * * * *
267600 GAATCCATTGATTATATTGAATGTTTGCTCAAACGAACAAT
1 -AATCCACTGATTATACTAAATGCTTGCTCAAACGAGC-AT
* * * * **
267641 AA-CTACTAATTATATTGAATGCTTTTTCAAACGAGCA-
1 AATCCACTGATTATACTAAATGCTTGCTCAAACGAGCAT
* * * * *
267678 AAGCCATTTATTATAC-AAATGTTTACTCAAACGAGCGAT
1 AATCCACTGATTATACTAAATGCTTGCTCAAACGAGC-AT
* * *
267717 AA-CTACTGATTATACTGAATGCTTGTTCAAACGAG--T
1 AATCCACTGATTATACTAAATGCTTGCTCAAACGAGCAT
*
267753 GAATCCACTGATTATACTAAATGCTTGCTCAAATGAGCGAT
1 -AATCCACTGATTATACTAAATGCTTGCTCAAACGAGC-AT
* * * ** ** * *
267794 AA-CTACCGATTATATTGTATGCTTATTTAAACGAGC-G
1 AATCCACTGATTATACTAAATGCTTGCTCAAACGAGCAT
* * *
267831 AATCCACTAATCATACTAAATGTTTGCTCAAACGAGCAT
1 AATCCACTGATTATACTAAATGCTTGCTCAAACGAGCAT
* * *
267870 TACCCACTGATTATACTAAATGCTTGCTCAAAAGAGCAT
1 AATCCACTGATTATACTAAATGCTTGCTCAAACGAGCAT
*
267909 AATCCACTGATTATACTAAATGCTTACTCAAACGAGCAT
1 AATCCACTGATTATACTAAATGCTTGCTCAAACGAGCAT
* *
267948 TATTCACTGATTATACT
1 AATCCACTGATTATACT
267965 GAATAAGATT
Statistics
Matches: 313, Mismatches: 74, Indels: 29
0.75 0.18 0.07
Matches are distributed among these distances:
36 1 0.00
37 22 0.07
38 132 0.42
39 152 0.49
40 4 0.01
41 2 0.01
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.32
Consensus pattern (39 bp):
AATCCACTGATTATACTAAATGCTTGCTCAAACGAGCAT
Found at i:268112 original size:19 final size:19
Alignment explanation
Indices: 268090--268127 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
268080 TATATCATGT
268090 TTGAGTTAGTAA-AAACTTA
1 TTGA-TTAGTAACAAACTTA
*
268109 TTGATTATTAACAAACTTA
1 TTGATTAGTAACAAACTTA
268128 CTAAGCTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (19 bp):
TTGATTAGTAACAAACTTA
Found at i:270054 original size:24 final size:24
Alignment explanation
Indices: 270022--270095 Score: 85
Period size: 24 Copynumber: 3.1 Consensus size: 24
270012 AATTCATCAT
*
270022 GTTTACGCTCGTCAGCATGAATAC
1 GTTTACGCTCGCCAGCATGAATAC
*
270046 GTTTACGCTCGCCAGCATGGATAC
1 GTTTACGCTCGCCAGCATGAATAC
* * * * *
270070 ATTTACGTTCACCTGGATGAATAC
1 GTTTACGCTCGCCAGCATGAATAC
270094 GT
1 GT
270096 GAAACATTAC
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (24 bp):
GTTTACGCTCGCCAGCATGAATAC
Found at i:273808 original size:23 final size:23
Alignment explanation
Indices: 273777--273950 Score: 130
Period size: 23 Copynumber: 7.8 Consensus size: 23
273767 GAGAGTACTG
*
273777 AAGTACTAAACAGAGAGCACACA
1 AAGTGCTAAACAGAGAGCACACA
* *
273800 AAGTGCTAAACAGTGAGTACACA
1 AAGTGCTAAACAGAGAGCACACA
* *
273823 AA--G-T--AC--TGAGCACACG
1 AAGTGCTAAACAGAGAGCACACA
* * *
273839 AAGTACTAATCAGAGAGCACACG
1 AAGTGCTAAACAGAGAGCACACA
* *
273862 AAGTGCTAATAACAGATAGCACGA-G
1 AAGTGCT-A-AACAGAGAGCAC-ACA
* *
273887 ACGTGCTAAACGGAGAGCACACA
1 AAGTGCTAAACAGAGAGCACACA
*
273910 TAGTGCTAAACAGAGAGCACACA
1 AAGTGCTAAACAGAGAGCACACA
* *
273933 TAGTGCTAATCAGAGAGC
1 AAGTGCTAAACAGAGAGC
273951 GTCTAGTGTT
Statistics
Matches: 121, Mismatches: 19, Indels: 22
0.75 0.12 0.14
Matches are distributed among these distances:
16 10 0.08
18 2 0.02
19 1 0.01
20 1 0.01
21 2 0.02
22 1 0.01
23 84 0.69
24 2 0.02
25 17 0.14
26 1 0.01
ACGTcount: A:0.43, C:0.21, G:0.23, T:0.14
Consensus pattern (23 bp):
AAGTGCTAAACAGAGAGCACACA
Found at i:282771 original size:9 final size:9
Alignment explanation
Indices: 282752--282794 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
282742 ATTTTATGTA
282752 AATATATATT
1 AATA-ATATT
282762 AATAATATT
1 AATAATATT
*
282771 AATAATAAT
1 AATAATATT
* *
282780 AATAAAATA
1 AATAATATT
282789 AATAAT
1 AATAAT
282795 TATATATATA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
9 24 0.86
10 4 0.14
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
AATAATATT
Found at i:283177 original size:24 final size:25
Alignment explanation
Indices: 283150--283229 Score: 75
Period size: 24 Copynumber: 3.4 Consensus size: 25
283140 GATTTTGCAC
283150 ATTG-TTAAAATTTTATAAACACTT
1 ATTGATTAAAATTTTATAAACACTT
**
283174 ATTGATT-AAATTGATT-T-TGCAC--
1 ATTGATTAAAATT--TTATAAACACTT
283196 ATTG-TTAAAATTTTATAAACACTT
1 ATTGATTAAAATTTTATAAACACTT
283220 ATTGATTAAA
1 ATTGATTAAA
283230 TCGAGTAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 17
0.67 0.06 0.27
Matches are distributed among these distances:
20 2 0.05
21 3 0.07
22 12 0.28
24 16 0.37
25 8 0.19
26 2 0.05
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.45
Consensus pattern (25 bp):
ATTGATTAAAATTTTATAAACACTT
Found at i:283205 original size:46 final size:46
Alignment explanation
Indices: 283138--283230 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
283128 AGTGAAATGG
283138 TTGATTTTGCACATTGTTAAAATTTTATAAACACTTATTGATTAAA
1 TTGATTTTGCACATTGTTAAAATTTTATAAACACTTATTGATTAAA
283184 TTGATTTTGCACATTGTTAAAATTTTATAAACACTTATTGATTAAA
1 TTGATTTTGCACATTGTTAAAATTTTATAAACACTTATTGATTAAA
283230 T
1 T
283231 CGAGTAAATT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.46
Consensus pattern (46 bp):
TTGATTTTGCACATTGTTAAAATTTTATAAACACTTATTGATTAAA
Found at i:284332 original size:13 final size:13
Alignment explanation
Indices: 284314--284342 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
284304 AGCCATATTC
284314 GGGACTTGTTGAT
1 GGGACTTGTTGAT
284327 GGGACTTGTTGAT
1 GGGACTTGTTGAT
284340 GGG
1 GGG
284343 CTCACTCACC
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:0.14, C:0.07, G:0.45, T:0.34
Consensus pattern (13 bp):
GGGACTTGTTGAT
Found at i:288340 original size:66 final size:66
Alignment explanation
Indices: 288252--288383 Score: 201
Period size: 66 Copynumber: 2.0 Consensus size: 66
288242 AGAGAGGACT
* *
288252 ATCTTGCATCTCTTCGAAGGTGTGTGTGAACTTTTGAAGTTCGTATTCCAATTTAGAGTTGTTTA
1 ATCTTGCATCTCTTCGAAGGTGTGTGTGAACTTTAGAAGTTCGAATTCCAATTTAGAGTTGTTTA
288317 C
66 C
* * * * *
288318 ATCTTGCATGTTTTCGAGGGTGTGTGTGAACTTTAGAAGTTTGAATTCTAATTTAGAGTTGTTTA
1 ATCTTGCATCTCTTCGAAGGTGTGTGTGAACTTTAGAAGTTCGAATTCCAATTTAGAGTTGTTTA
288383 C
66 C
288384 TTATAATTGT
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
66 59 1.00
ACGTcount: A:0.22, C:0.12, G:0.23, T:0.43
Consensus pattern (66 bp):
ATCTTGCATCTCTTCGAAGGTGTGTGTGAACTTTAGAAGTTCGAATTCCAATTTAGAGTTGTTTA
C
Found at i:291827 original size:22 final size:20
Alignment explanation
Indices: 291797--291851 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
291787 TTTTCTATTG
*
291797 AGTTAATTTTTTTAGATAATTA
1 AGTTTATTTTTTT-GA-AATTA
*
291819 AGTTTATTTTTTTTAAATTA
1 AGTTTATTTTTTTGAAATTA
291839 AGGTTTATTTTTT
1 A-GTTTATTTTTT
291852 AAATTTAATG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
20 6 0.20
21 12 0.40
22 12 0.40
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.62
Consensus pattern (20 bp):
AGTTTATTTTTTTGAAATTA
Found at i:291851 original size:19 final size:19
Alignment explanation
Indices: 291814--291856 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 19
291804 TTTTTTAGAT
291814 AATTAAGTTTATTTTTTTTA
1 AATTAAGTTTA-TTTTTTTA
291834 AATTAAGGTTTA-TTTTTTA
1 AATTAA-GTTTATTTTTTTA
291853 AATT
1 AATT
291857 TAATGTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 11 0.50
20 6 0.27
21 5 0.23
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (19 bp):
AATTAAGTTTATTTTTTTA
Found at i:291867 original size:21 final size:20
Alignment explanation
Indices: 291823--291868 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
291813 TAATTAAGTT
291823 TATT-TTTTTTAAATTAAGG
1 TATTATTTTTTAAATTAAGG
*
291842 T-TTATTTTTTAAATTTAATG
1 TATTATTTTTTAAA-TTAAGG
291862 TATTATT
1 TATTATT
291869 ATTATTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 2 0.09
19 10 0.43
20 6 0.26
21 5 0.22
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (20 bp):
TATTATTTTTTAAATTAAGG
Found at i:292082 original size:15 final size:16
Alignment explanation
Indices: 292047--292084 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
292037 CAATTTTTAT
*
292047 TTTTTAATTAAATGTA
1 TTTTTAATTAAATATA
*
292063 ATTTTAA-TAAATATA
1 TTTTTAATTAAATATA
292078 TTTTTAA
1 TTTTTAA
292085 GCTAAAAACT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
TTTTTAATTAAATATA
Found at i:293587 original size:21 final size:21
Alignment explanation
Indices: 293563--293620 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
293553 TCTATGCTAG
*
293563 TTCTACCGATACAAGTATGAT
1 TTCTATCGATACAAGTATGAT
*
293584 TTCTATCGATACAAGTATGGT
1 TTCTATCGATACAAGTATGAT
293605 TTCTATCGATACAAGT
1 TTCTATCGATACAAGT
293621 CATACAACTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (21 bp):
TTCTATCGATACAAGTATGAT
Found at i:306033 original size:20 final size:21
Alignment explanation
Indices: 305948--306040 Score: 82
Period size: 21 Copynumber: 4.5 Consensus size: 21
305938 CCATAACTCT
* *
305948 TAATTTAAAATACCCTACACCC
1 TAATTTAAAA-AACCTAAACCC
* * * *
305970 TTATTTAAAATATCAAAACCC
1 TAATTTAAAAAACCTAAACCC
* * *
305991 TAATTTTAATAACATAAACCC
1 TAATTTAAAAAACCTAAACCC
306012 TAATTTAAAAAACCTAAA-CC
1 TAATTTAAAAAACCTAAACCC
306032 TAA-TTAAAA
1 TAATTTAAAA
306041 CAAAAAAAAA
Statistics
Matches: 55, Mismatches: 16, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
19 6 0.11
20 5 0.09
21 35 0.64
22 9 0.16
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.30
Consensus pattern (21 bp):
TAATTTAAAAAACCTAAACCC
Found at i:307782 original size:21 final size:21
Alignment explanation
Indices: 307758--307799 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
307748 TTTGTTGATT
*
307758 AGAAAAAAATATGCATCTAAA
1 AGAAAAAAATATGAATCTAAA
* *
307779 AGAAATAATTATGAATCTAAA
1 AGAAAAAAATATGAATCTAAA
307800 GTATTCAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.60, C:0.07, G:0.10, T:0.24
Consensus pattern (21 bp):
AGAAAAAAATATGAATCTAAA
Found at i:319756 original size:31 final size:31
Alignment explanation
Indices: 319712--319830 Score: 118
Period size: 31 Copynumber: 3.8 Consensus size: 31
319702 AAATGGGCCC
*
319712 AAAATATTATTTTTTAATTTTTAAGGGGTCCAA
1 AAAATA-TATTTTTTAACTTTTAA-GGGTCCAA
*
319745 AAAATAT-TTTTTTAGCTTTTAAGGGTCCAA
1 AAAATATATTTTTTAACTTTTAAGGGTCCAA
* * * *
319775 AAATTTTATTTTTTAACTTTTAAAGGACCTAA
1 AAAATATATTTTTTAACTTTTAAGGGTCC-AA
*
319807 AAAA-AT-TTTCTTCAACTTTTAAGG
1 AAAATATATTT-TTTAACTTTTAAGG
319831 ACTCTAAAAC
Statistics
Matches: 72, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
30 16 0.22
31 44 0.61
32 6 0.08
33 6 0.08
ACGTcount: A:0.36, C:0.09, G:0.10, T:0.45
Consensus pattern (31 bp):
AAAATATATTTTTTAACTTTTAAGGGTCCAA
Found at i:319809 original size:62 final size:62
Alignment explanation
Indices: 319712--319830 Score: 152
Period size: 62 Copynumber: 1.9 Consensus size: 62
319702 AAATGGGCCC
* * * * *
319712 AAAATATTATTTTTTAATTTTTAAGGGGTCCAAAAAATATTTT-TTTAGCTTTTAAGGGTCCA
1 AAAATATTATTTTTTAACTTTTAAGAGGACCAAAAAA-ATTTTCTTCAACTTTTAAGGGTCCA
*
319774 AAAATTTTATTTTTTAACTTTTAA-AGGACCTAAAAAAATTTTCTTCAACTTTTAAGG
1 AAAATATTATTTTTTAACTTTTAAGAGGACC-AAAAAAATTTTCTTCAACTTTTAAGG
319831 ACTCTAAAAC
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
61 9 0.18
62 40 0.82
ACGTcount: A:0.36, C:0.09, G:0.10, T:0.45
Consensus pattern (62 bp):
AAAATATTATTTTTTAACTTTTAAGAGGACCAAAAAAATTTTCTTCAACTTTTAAGGGTCCA
Found at i:319838 original size:31 final size:29
Alignment explanation
Indices: 319782--319839 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 29
319772 CAAAAATTTT
319782 ATTTTTTAACTTTTAAAGGACCTAAAAAA
1 ATTTTTTAACTTTTAAAGGACCTAAAAAA
319811 ATTTTCTTCAACTTTT-AAGGACTCTAAAA
1 ATTTT-TT-AACTTTTAAAGGAC-CTAAAA
319840 CCCTATTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 5 0.19
30 8 0.31
31 13 0.50
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.40
Consensus pattern (29 bp):
ATTTTTTAACTTTTAAAGGACCTAAAAAA
Found at i:321499 original size:3 final size:3
Alignment explanation
Indices: 321482--321570 Score: 69
Period size: 3 Copynumber: 30.7 Consensus size: 3
321472 ATAACATTCA
* * * *
321482 AAC AACC AA- AAC AAC AAC AAA AAT AAC AGC AA- AAC AAC AAC AAA
1 AAC AA-C AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
* * * *
321526 AAC AAC AAC AAA AAC AAC AA- AA- AAT AGC AAC AAA AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
321571 AAATAACAGC
Statistics
Matches: 68, Mismatches: 14, Indels: 8
0.76 0.16 0.09
Matches are distributed among these distances:
2 8 0.12
3 57 0.84
4 3 0.04
ACGTcount: A:0.72, C:0.24, G:0.02, T:0.02
Consensus pattern (3 bp):
AAC
Found at i:321597 original size:36 final size:36
Alignment explanation
Indices: 321484--321678 Score: 208
Period size: 35 Copynumber: 5.6 Consensus size: 36
321474 AACATTCAAA
*
321484 CAACCAAAACAACAACAAAAATAACAGCAAAACA-A-
1 CAACAAAAACAACAACAAAAATAACAGCAAAA-ATAG
*
321519 CAACAAAAACAACAACAAAAACAACA--AAAAATAG
1 CAACAAAAACAACAACAAAAATAACAGCAAAAATAG
321553 CAACAAAAACAACAACAAAAATAACAGCAAAAATAG
1 CAACAAAAACAACAACAAAAATAACAGCAAAAATAG
* * *
321589 CAATAAAAACAGCAACAAAAATAACATCAAAAATAG
1 CAACAAAAACAACAACAAAAATAACAGCAAAAATAG
* * * *
321625 C-ACCAAAACAGCAATC-AAAATAATA--AAAAATAA
1 CAACAAAAACAACAA-CAAAAATAACAGCAAAAATAG
* *
321658 CACCAAAAATAACAATCAAAA
1 CAACAAAAACAACAA-CAAAA
321679 CAATAAAAAA
Statistics
Matches: 139, Mismatches: 14, Indels: 14
0.83 0.08 0.08
Matches are distributed among these distances:
32 1 0.01
33 13 0.09
34 36 0.26
35 46 0.33
36 43 0.31
ACGTcount: A:0.69, C:0.21, G:0.04, T:0.07
Consensus pattern (36 bp):
CAACAAAAACAACAACAAAAATAACAGCAAAAATAG
Found at i:321622 original size:12 final size:12
Alignment explanation
Indices: 321482--321678 Score: 147
Period size: 12 Copynumber: 16.8 Consensus size: 12
321472 ATAACATTCA
* *
321482 AACAACCAAAAC
1 AACAACAAAAAT
321494 AACAACAAAAAT
1 AACAACAAAAAT
* *
321506 AACAGC-AAAAC
1 AACAACAAAAAT
*
321517 AACAACAAAAAC
1 AACAACAAAAAT
*
321529 AACAACAAAAAC
1 AACAACAAAAAT
321541 AAC-A-AAAAAT
1 AACAACAAAAAT
* *
321551 AGCAACAAAAAC
1 AACAACAAAAAT
321563 AACAACAAAAAT
1 AACAACAAAAAT
*
321575 AACAGCAAAAAT
1 AACAACAAAAAT
* * *
321587 AGCAATAAAAAC
1 AACAACAAAAAT
*
321599 AGCAACAAAAAT
1 AACAACAAAAAT
*
321611 AACATCAAAAAT
1 AACAACAAAAAT
* * *
321623 AGC-ACCAAAAC
1 AACAACAAAAAT
*
321634 AGCAATC-AAAAT
1 AACAA-CAAAAAT
*
321646 AA-TA-AAAAAT
1 AACAACAAAAAT
*
321656 AACACCAAAAAT
1 AACAACAAAAAT
321668 AACAATCAAAA
1 AACAA-CAAAA
321679 CAATAAAAAA
Statistics
Matches: 147, Mismatches: 29, Indels: 17
0.76 0.15 0.09
Matches are distributed among these distances:
10 14 0.10
11 20 0.14
12 107 0.73
13 6 0.04
ACGTcount: A:0.69, C:0.20, G:0.04, T:0.07
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:321633 original size:105 final size:106
Alignment explanation
Indices: 321489--321678 Score: 244
Period size: 105 Copynumber: 1.8 Consensus size: 106
321479 TCAAACAACC
*
321489 AAAACAACAACAAAAATAACAGCAAAACAACAACAAAAACAACAA-CAAAAACAACAAAAAATAG
1 AAAACAACAACAAAAATAACAGCAAAACAACAACAAAAACAACAATC-AAAACAACAAAAAATAA
321553 CAACAAAAACAACAA-CAAAAATAACAGCAAAAATAGCAATA
65 CAACAAAAACAACAATCAAAAATAACAGCAAAAATAGCAATA
* * * * * *
321594 AAAACAGCAACAAAAATAACATCAAAA-ATAGC-ACCAAAACAGCAATCAAAATAATAAAAAATA
1 AAAACAACAACAAAAATAACAGCAAAACA-A-CAACAAAAACAACAATCAAAACAACAAAAAATA
* *
321657 ACACCAAAAATAACAATCAAAA
64 ACAACAAAAACAACAATCAAAA
321679 CAATAAAAAA
Statistics
Matches: 72, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
104 1 0.01
105 64 0.89
106 7 0.10
ACGTcount: A:0.69, C:0.19, G:0.04, T:0.07
Consensus pattern (106 bp):
AAAACAACAACAAAAATAACAGCAAAACAACAACAAAAACAACAATCAAAACAACAAAAAATAAC
AACAAAAACAACAATCAAAAATAACAGCAAAAATAGCAATA
Found at i:325276 original size:30 final size:29
Alignment explanation
Indices: 325183--325293 Score: 95
Period size: 30 Copynumber: 3.8 Consensus size: 29
325173 AATTTAGATG
325183 AAAATGGAATTTTTGG-AAGTTCGAGGGT-
1 AAAATGGAATTTTTGGAAAGTTCGA-GGTC
* * *
325211 AAAATGGTAATTTTTGGAAAAATTAG-GGAC
1 AAAATGG-AATTTTTGG-AAAGTTCGAGGTC
325241 AAAAATGGAATTTTTGGAAAGTTCGGAGGTC
1 -AAAATGGAATTTTTGGAAAGTTC-GAGGTC
* *
325272 AAAATATG-ATTTTTGGACAGTT
1 AAAAT-GGAATTTTTGGAAAGTT
325294 TAAGGATCTT
Statistics
Matches: 67, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
28 7 0.10
29 16 0.24
30 28 0.42
31 16 0.24
ACGTcount: A:0.37, C:0.05, G:0.26, T:0.32
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAAGTTCGAGGTC
Found at i:326427 original size:16 final size:16
Alignment explanation
Indices: 326401--326443 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
326391 CAAATTCTTT
326401 TTTATTTATTAGAAAATA
1 TTTA-TTATTA-AAAATA
*
326419 -TTATTATTAAAGATA
1 TTTATTATTAAAAATA
326434 TTTATTATTA
1 TTTATTATTA
326444 TTATTATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 5 0.22
16 15 0.65
17 3 0.13
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (16 bp):
TTTATTATTAAAAATA
Found at i:327241 original size:6 final size:6
Alignment explanation
Indices: 327230--327290 Score: 54
Period size: 6 Copynumber: 10.0 Consensus size: 6
327220 TATTTCAAAT
* * *
327230 TTTAAA TTTAAA -ATAAA TTTAAA CTTAATAGA TTTAAA TTTAAA -ATAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA -TT--TAAA TTTAAA TTTAAA TTTAAA
327279 TTTAAA TTTAAA
1 TTTAAA TTTAAA
327291 ATAATTCTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
5 8 0.18
6 29 0.66
7 2 0.05
8 2 0.05
9 3 0.07
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:327252 original size:17 final size:17
Alignment explanation
Indices: 327230--327318 Score: 112
Period size: 17 Copynumber: 5.4 Consensus size: 17
327220 TATTTCAAAT
327230 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
* *
327247 TTTAAACTT--AATAGA
1 TTTAAATTTAAAATAAA
327262 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
327279 TTTAAATTTAAAAT-AA
1 TTTAAATTTAAAATAAA
* *
327295 TTCTAAACTTAGAATAAA
1 TT-TAAATTTAAAATAAA
327313 TTTAAA
1 TTTAAA
327319 ATAAAGATTT
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
15 13 0.21
16 4 0.06
17 41 0.66
18 4 0.06
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.40
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:327880 original size:49 final size:48
Alignment explanation
Indices: 327827--328307 Score: 376
Period size: 49 Copynumber: 9.9 Consensus size: 48
327817 TATTTTCGCA
*
327827 GTACTGGATTCGCCGTTGCTGCTTAAATCTTTCCCTTCATGTCTCTGAG
1 GTACTGGATTCGCCGTTGCTGCTTAAATCTTTCCCTTCATGTCT-TGTG
* * * * **
327876 GTACTAGG-TTTGTCATTG-TGACTTAAACCTTTCCCTTTGTGTCTTTGTG
1 GTACT-GGATTCGCCGTTGCTG-CTTAAATCTTTCCCTTCATGTC-TTGTG
* * * *
327925 GTATTGGATTCGCCGTTACGGCTTAAATCTTTCCCTTCATGTCTCTGAG
1 GTACTGGATTCGCCGTTGCTGCTTAAATCTTTCCCTTCATGTCT-TGTG
* * *
327974 GTACTAGG-TTCGTCATTGC-GACTTAAACCTTTCCCTT--TGTCTTCGTG
1 GTACT-GGATTCGCCGTTGCTG-CTTAAATCTTTCCCTTCATGTCTT-GTG
**
328021 GTACTGGATTCGTTGTTG-TGGCTTAAATCTTTCCCTTCATGTCTTCGTG
1 GTACTGGATTCGCCGTTGCT-GCTTAAATCTTTCCCTTCATGTCTT-GTG
* *
328070 GTACTGGATTCGTCGTTGC-GACTTAAATCTTTCCCTTCATGTCTTCATG
1 GTACTGGATTCGCCGTTGCTG-CTTAAATCTTTCCCTTCATGTCTT-GTG
* * * * * * *
328119 GTACTGGATTTGTCATTTCGGCTTAAATATTTCCCTTCACGTCTTTGTG
1 GTACTGGATTCGCCGTTGCTGCTTAAATCTTTCCCTTCATGTC-TTGTG
* * * *
328168 GAACAGGATTCGCCGTTG-TGGCTTAAATCTTTCCCTTTATG-CTTCTAAG
1 GTACTGGATTCGCCGTTGCT-GCTTAAATCTTTCCCTTCATGTCTTGT--G
* * * *
328217 GTACACGG-TTCGCCGTTGC-GACAT-AATCCTTTCCCTCCATATCTTCGTG
1 GTAC-TGGATTCGCCGTTGCTG-CTTAAAT-CTTTCCCTTCATGTCTT-GTG
* *
328266 GTACTGGATTCGCCATTGCGGCTTAAATCTTTCCCTTCATGT
1 GTACTGGATTCGCCGTTGCTGCTTAAATCTTTCCCTTCATGT
328308 TTCATGGTAC
Statistics
Matches: 345, Mismatches: 57, Indels: 60
0.75 0.12 0.13
Matches are distributed among these distances:
46 3 0.01
47 38 0.11
48 15 0.04
49 270 0.78
50 18 0.05
51 1 0.00
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (48 bp):
GTACTGGATTCGCCGTTGCTGCTTAAATCTTTCCCTTCATGTCTTGTG
Found at i:327933 original size:98 final size:97
Alignment explanation
Indices: 327758--328319 Score: 448
Period size: 98 Copynumber: 5.8 Consensus size: 97
327748 GTTGCTTGAA
* * * * * * * *
327758 TTTCCTTTCATG-CTTCTGAGGTA-TAGGGTTCGCCGTTGCGACTTCAACCTTTCTCTTCGTATT
1 TTTCCCTTCATGTC-TCTGAGGTACTA-GGTTCGTCATTGCGACTTAAACCTTTCCCTT-TTGTC
** *
327821 TTCGCAGTACTGGATTCGCCGTTGCTGCTTAAATC
63 TTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATC
* *
327856 TTTCCCTTCATGTCTCTGAGGTACTAGGTTTGTCATTGTGACTTAAACCTTTCCCTTTGTGTCTT
1 TTTCCCTTCATGTCTCTGAGGTACTAGGTTCGTCATTGCGACTTAAACCTTTCCCTTT-TGTCTT
* * *
327921 TGTGGTATTGGATTCGCCGTTACGGCTTAAATC
65 CGTGGTACTGGATTCGCCGTTGCGGCTTAAATC
327954 TTTCCCTTCATGTCTCTGAGGTACTAGGTTCGTCATTGCGACTTAAACCTTTCCC-TTTGTCTTC
1 TTTCCCTTCATGTCTCTGAGGTACTAGGTTCGTCATTGCGACTTAAACCTTTCCCTTTTGTCTTC
** *
328018 GTGGTACTGGATTCGTTGTTGTGGCTTAAATC
66 GTGGTACTGGATTCGCCGTTGCGGCTTAAATC
* * * *
328050 TTTCCCTTCATGTCT-TCGTGGTACT-GGATTCGTCGTTGCGACTTAAATCTTTCCCTTCATGTC
1 TTTCCCTTCATGTCTCT-GAGGTACTAGG-TTCGTCATTGCGACTTAAACCTTTCCCTT-TTGTC
* * * * * *
328113 TTCATGGTACTGGATTTGTCATTTCGGCTTAAATA
63 TTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATC
* * * * * * * * *
328148 TTTCCCTTCACGTCTTTGTGGAAC-AGGATTCGCCGTTGTGGCTTAAATCTTTCCCTTTATG-CT
1 TTTCCCTTCATGTCTCTGAGGTACTAGG-TTCGTCATTGCGACTTAAACCTTTCCCTTT-TGTCT
* * *
328211 TC-TAAGGTACACGG-TTCGCCGTTGCGACAT-AATCC
64 TCGT--GGTAC-TGGATTCGCCGTTGCGGCTTAAAT-C
* * * * * * *
328246 TTTCCCTCCATATCT-TCGTGGTACT-GGATTCGCCATTGCGGCTTAAATCTTTCCCTTCATGT-
1 TTTCCCTTCATGTCTCT-GAGGTACTAGG-TTCGTCATTGCGACTTAAACCTTTCCCTT-TTGTC
*
328308 TTCATGGTACTG
63 TTCGTGGTACTG
328320 AGACCTGTAG
Statistics
Matches: 388, Mismatches: 57, Indels: 40
0.80 0.12 0.08
Matches are distributed among these distances:
95 3 0.01
96 82 0.21
97 16 0.04
98 280 0.72
99 7 0.02
ACGTcount: A:0.15, C:0.24, G:0.20, T:0.41
Consensus pattern (97 bp):
TTTCCCTTCATGTCTCTGAGGTACTAGGTTCGTCATTGCGACTTAAACCTTTCCCTTTTGTCTTC
GTGGTACTGGATTCGCCGTTGCGGCTTAAATC
Found at i:328238 original size:147 final size:147
Alignment explanation
Indices: 327786--328304 Score: 473
Period size: 147 Copynumber: 3.5 Consensus size: 147
327776 AGGTATAGGG
* * * * * * *** * * *
327786 TTCGCCGTTGCGACTTCAACCTTTCTCTTCGTATTTTCGCAGTACTGGATTCGCCGTTGCTGCTT
1 TTCGCCGTTGCGACTTAAATCTTTCCCTTCATGTCTTCATGGTACTGGATTCGTCATTGCGGCTT
* * * * * * * * *
327851 AAATCTTTCCCTTCATGTC-TCTGAGGTACTAGG-TTTGTCATTGTGACTTAAACCTTTCCCTTT
66 AAATCTTTCCCTTCACGTCTTC-GTGGAAC-AGGATTCGCCGTTGTGGCTTAAATCTTTCCCTTC
* * **
327914 GTGTCTTTGTGGTATTGGA
129 ATGTCTTCGTGGTACCGGA
* * * *
327933 TTCGCCGTTACGGCTTAAATCTTTCCCTTCATGTCTCTGA-GGTACTAGG-TTCGTCATTGCGAC
1 TTCGCCGTTGCGACTTAAATCTTTCCCTTCATGTCT-TCATGGTACT-GGATTCGTCATTGCGGC
* * * * **
327996 TTAAACCTTTCCCTT--TGTCTTCGTGGTACTGGATTCGTTGTTGTGGCTTAAATCTTTCCCTTC
64 TTAAATCTTTCCCTTCACGTCTTCGTGGAACAGGATTCGCCGTTGTGGCTTAAATCTTTCCCTTC
*
328059 ATGTCTTCGTGGTACTGGA
129 ATGTCTTCGTGGTACCGGA
* * *
328078 TTCGTCGTTGCGACTTAAATCTTTCCCTTCATGTCTTCATGGTACTGGATTTGTCATTTCGGCTT
1 TTCGCCGTTGCGACTTAAATCTTTCCCTTCATGTCTTCATGGTACTGGATTCGTCATTGCGGCTT
* * *
328143 AAATATTTCCCTTCACGTCTTTGTGGAACAGGATTCGCCGTTGTGGCTTAAATCTTTCCCTTTAT
66 AAATCTTTCCCTTCACGTCTTCGTGGAACAGGATTCGCCGTTGTGGCTTAAATCTTTCCCTTCAT
328208 G-CTTC-TAAGGTACACGG-
131 GTCTTCGT--GGTAC-CGGA
* * * * *
328225 TTCGCCGTTGCGACAT-AATCCTTTCCCTCCATATCTTCGTGGTACTGGATTCGCCATTGCGGCT
1 TTCGCCGTTGCGACTTAAAT-CTTTCCCTTCATGTCTTCATGGTACTGGATTCGTCATTGCGGCT
328289 TAAATCTTTCCCTTCA
65 TAAATCTTTCCCTTCA
328305 TGTTTCATGG
Statistics
Matches: 307, Mismatches: 53, Indels: 24
0.80 0.14 0.06
Matches are distributed among these distances:
144 6 0.02
145 114 0.37
146 9 0.03
147 173 0.56
148 5 0.02
ACGTcount: A:0.16, C:0.25, G:0.19, T:0.40
Consensus pattern (147 bp):
TTCGCCGTTGCGACTTAAATCTTTCCCTTCATGTCTTCATGGTACTGGATTCGTCATTGCGGCTT
AAATCTTTCCCTTCACGTCTTCGTGGAACAGGATTCGCCGTTGTGGCTTAAATCTTTCCCTTCAT
GTCTTCGTGGTACCGGA
Found at i:328755 original size:18 final size:18
Alignment explanation
Indices: 328734--328769 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
328724 CAAACTACCG
*
328734 AATATTTACAAGGAACAA
1 AATAATTACAAGGAACAA
328752 AATAATTACAAGGAACAA
1 AATAATTACAAGGAACAA
328770 TATTAGATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.58, C:0.11, G:0.11, T:0.19
Consensus pattern (18 bp):
AATAATTACAAGGAACAA
Done.