Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015139.1 Kokia drynarioides strain JFW-HI SEQ_130183, 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: 250268
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 299 characters in sequence are not A, C, G, or T
Found at i:4565 original size:26 final size:26
Alignment explanation
Indices: 4536--4589 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
4526 TTAGATAACA
** *
4536 TTGAATTTTGGAATATTTTTTATTTT
1 TTGAATTTTAAAATATTTTTAATTTT
*
4562 TTGAATTTTAAAATGTTTTTAATTTT
1 TTGAATTTTAAAATATTTTTAATTTT
4588 TT
1 TT
4590 TCATAATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.65
Consensus pattern (26 bp):
TTGAATTTTAAAATATTTTTAATTTT
Found at i:5758 original size:2 final size:2
Alignment explanation
Indices: 5751--5776 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5741 AGAAGGGATT
5751 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
5777 TGGCAGTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:17154 original size:15 final size:14
Alignment explanation
Indices: 17134--17174 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
17124 TAAAAAAGAA
17134 TTAAAAGTTATTTTT
1 TTAAAA-TTATTTTT
17149 TTAAAA-TATTGTTT
1 TTAAAATTATT-TTT
17163 TTAAAATTATTT
1 TTAAAATTATTT
17175 ATGAATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 4 0.17
14 10 0.42
15 10 0.42
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (14 bp):
TTAAAATTATTTTT
Found at i:17725 original size:18 final size:18
Alignment explanation
Indices: 17684--17725 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
17674 ATGTATGATA
*
17684 ATTTTTATATTTTTTATG
1 ATTTTTATATTTTTTATC
*
17702 AATTTTATATTTCTTTA-C
1 ATTTTTATATTT-TTTATC
17720 ATTTTT
1 ATTTTT
17726 TATAATCTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.69
Consensus pattern (18 bp):
ATTTTTATATTTTTTATC
Found at i:17804 original size:19 final size:19
Alignment explanation
Indices: 17684--17805 Score: 58
Period size: 19 Copynumber: 6.4 Consensus size: 19
17674 ATGTATGATA
*
17684 ATTTTTAT-ATTTTTTATG
1 ATTTTTATAATTTTTTACG
*
17702 AATTTTAT-ATTTCTTTAC-
1 ATTTTTATAATTT-TTTACG
*
17720 ATTTTTTATAATCTTCTTACG
1 A-TTTTTATAAT-TTTTTACG
* * * *
17741 ACTTTATAAAATTTTATA-A
1 A-TTTTTATAATTTTTTACG
* *
17760 ATTTTTTTTACA-TTTTTA-T
1 A-TTTTTATA-ATTTTTTACG
17779 ATATTTTATAATTTTTTACG
1 AT-TTTTATAATTTTTTACG
17799 ATTTTTA
1 ATTTTTA
17806 AAAAAATTTA
Statistics
Matches: 77, Mismatches: 18, Indels: 17
0.69 0.16 0.15
Matches are distributed among these distances:
18 14 0.18
19 39 0.51
20 13 0.17
21 11 0.14
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.62
Consensus pattern (19 bp):
ATTTTTATAATTTTTTACG
Found at i:21635 original size:15 final size:15
Alignment explanation
Indices: 21615--21644 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
21605 AATCCTCCTT
21615 CCAAAACCAACACTG
1 CCAAAACCAACACTG
21630 CCAAAACCAACACTG
1 CCAAAACCAACACTG
21645 TCACATCAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.40, G:0.07, T:0.07
Consensus pattern (15 bp):
CCAAAACCAACACTG
Found at i:26506 original size:19 final size:18
Alignment explanation
Indices: 26482--26519 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
26472 AATTTTAGAA
26482 ATTTTTATATATAAT-TTTT
1 ATTTTTA-A-ATAATATTTT
26501 ATTTTTAAATAATATTTT
1 ATTTTTAAATAATATTTT
26519 A
1 A
26520 ACATGATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.28
18 6 0.33
19 7 0.39
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
ATTTTTAAATAATATTTT
Found at i:26568 original size:29 final size:29
Alignment explanation
Indices: 26524--26583 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
26514 ATTTTAACAT
* * *
26524 GATTTTTAATAATTTATATTTATTTTTAA
1 GATTTTTAATAATTTAGAATTATTGTTAA
**
26553 GATTTTTAATTTTTTAGAATTATTGTTAA
1 GATTTTTAATAATTTAGAATTATTGTTAA
26582 GA
1 GA
26584 AAAAATTTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.58
Consensus pattern (29 bp):
GATTTTTAATAATTTAGAATTATTGTTAA
Found at i:41129 original size:2 final size:2
Alignment explanation
Indices: 41122--41154 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
41112 AATTTAAATA
41122 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
41155 AGACAATAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:43723 original size:27 final size:27
Alignment explanation
Indices: 43693--43744 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
43683 ATTTATTTTT
43693 TTATATAATT-AAAAAAAATAAAATTAA
1 TTATAT-ATTGAAAAAAAATAAAATTAA
* *
43720 TTATATATTGAATAAAAATAGAATT
1 TTATATATTGAAAAAAAATAAAATT
43745 CGATTTGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 3 0.14
27 19 0.86
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.37
Consensus pattern (27 bp):
TTATATATTGAAAAAAAATAAAATTAA
Found at i:57464 original size:20 final size:20
Alignment explanation
Indices: 57427--57472 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
57417 AATTCTCTTA
*
57427 AAAAATATATAAAATTATTT
1 AAAAATATATAAAATTATAT
*
57447 AAAAATATA-AAATTTTATAT
1 AAAAATATATAAA-ATTATAT
57467 AAAAAT
1 AAAAAT
57473 TTTAGAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAAATATATAAAATTATAT
Found at i:57476 original size:29 final size:30
Alignment explanation
Indices: 57432--57488 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
57422 TCTTAAAAAA
*
57432 TATATAAAATTATTTA-AAAATATAAAATTT
1 TATATAAAAATATTTAGAAAA-ATAAAATTT
57462 TATATAAAAAT-TTTAGAAAAATAAAAT
1 TATATAAAAATATTTAGAAAAATAAAAT
57489 CTTGAAAACG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (30 bp):
TATATAAAAATATTTAGAAAAATAAAATTT
Found at i:58657 original size:17 final size:14
Alignment explanation
Indices: 58628--58670 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
58618 TTATATTATC
*
58628 TTTAATTTAATATT
1 TTTATTTTAATATT
58642 TGTTGATTTTATATATT
1 T-TT-ATTTTA-ATATT
58659 TTTATTTTAATA
1 TTTATTTTAATA
58671 AAAGACTATC
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
14 4 0.16
15 8 0.32
16 7 0.28
17 6 0.24
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (14 bp):
TTTATTTTAATATT
Found at i:58665 original size:15 final size:15
Alignment explanation
Indices: 58617--58667 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
58607 TTTAAAAATA
* *
58617 TTTATATTATCTTTAA
1 TTTATA-TATTTTTAT
58633 TTTA-ATATTTGTTGAT
1 TTTATATATTT-TT-AT
58649 TTTATATATTTTTAT
1 TTTATATATTTTTAT
58664 TTTA
1 TTTA
58668 ATAAAAGACT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
14 4 0.13
15 9 0.30
16 11 0.37
17 6 0.20
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (15 bp):
TTTATATATTTTTAT
Found at i:59339 original size:2 final size:2
Alignment explanation
Indices: 59334--59362 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
59324 AAAGAAAAAC
59334 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
59363 AGATAAAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:66296 original size:17 final size:17
Alignment explanation
Indices: 66276--66309 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
66266 TGATTTTGTG
*
66276 CAATTTTTTAAATAACA
1 CAATTATTTAAATAACA
*
66293 CAATTATTTATATAACA
1 CAATTATTTAAATAACA
66310 TCATTTTATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (17 bp):
CAATTATTTAAATAACA
Found at i:68809 original size:21 final size:20
Alignment explanation
Indices: 68785--68824 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
68775 AATTATTTTT
* *
68785 AAATTTTTATAAATTTAAAAA
1 AAATTATTA-AAAGTTAAAAA
68806 AAATTATTAAAAGTTAAAA
1 AAATTATTAAAAGTTAAAA
68825 TATATTAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (20 bp):
AAATTATTAAAAGTTAAAAA
Found at i:85170 original size:15 final size:15
Alignment explanation
Indices: 85150--85182 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
85140 TTGAAATTTT
85150 AAAAAATCA-AAATTA
1 AAAAAATCATAAA-TA
85165 AAAAAATCATAAATA
1 AAAAAATCATAAATA
85180 AAA
1 AAA
85183 GGTTATATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 14 0.82
16 3 0.18
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (15 bp):
AAAAAATCATAAATA
Found at i:85918 original size:30 final size:30
Alignment explanation
Indices: 85878--85939 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
85868 AATTTTTCTA
85878 AAATTATTATAAAT-TTTTAAATAAATTTTG
1 AAATTATTATAAATATTTTAAAT-AATTTTG
* *
85908 AAATTTTTATAAATATTTTGAATAATTTTG
1 AAATTATTATAAATATTTTAAATAATTTTG
85938 AA
1 AA
85940 TTTCTTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 22 0.76
31 7 0.24
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (30 bp):
AAATTATTATAAATATTTTAAATAATTTTG
Found at i:85936 original size:22 final size:20
Alignment explanation
Indices: 85888--85929 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
85878 AAATTATTAT
85888 AAATTTTTAAATAAATTTTG
1 AAATTTTTAAATAAATTTTG
*
85908 AAATTTTTATAA-ATATTTTG
1 AAATTTTTA-AATAAATTTTG
85928 AA
1 AA
85930 TAATTTTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 18 0.90
21 2 0.10
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (20 bp):
AAATTTTTAAATAAATTTTG
Found at i:86815 original size:4 final size:4
Alignment explanation
Indices: 86808--86843 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
86798 TGCATGCATG
86808 CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA
86844 TATATATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:95621 original size:2 final size:2
Alignment explanation
Indices: 95614--95646 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
95604 ATATTTTTCT
95614 TA TA TA TA 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 TA TA TA TA T
95647 TGTGAATTCG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:97619 original size:18 final size:19
Alignment explanation
Indices: 97581--97619 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
97571 TATGATAAAC
*
97581 TAAAATTTCAGTTATTATT
1 TAAAAATTCAGTTATTATT
*
97600 TAAAAATTCA-TTATTTTT
1 TAAAAATTCAGTTATTATT
97618 TA
1 TA
97620 TTTGTCTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (19 bp):
TAAAAATTCAGTTATTATT
Found at i:119499 original size:32 final size:32
Alignment explanation
Indices: 119457--119517 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
119447 TTTTTGGGTC
119457 TAATTCGATACCCAAACTTGACACTTTTTTTT
1 TAATTCGATACCCAAACTTGACACTTTTTTTT
* *
119489 TAATTTGATACCTAAACTTGACACTTTTT
1 TAATTCGATACCCAAACTTGACACTTTTT
119518 CTTAAGTTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.44
Consensus pattern (32 bp):
TAATTCGATACCCAAACTTGACACTTTTTTTT
Found at i:119536 original size:31 final size:32
Alignment explanation
Indices: 119463--119538 Score: 100
Period size: 31 Copynumber: 2.4 Consensus size: 32
119453 GGTCTAATTC
* * *
119463 GATACCCAAACTTGACACTTTTTTTTTAATTT
1 GATACCTAAACTTGACACTTTTTTCTTAAGTT
119495 GATACCTAAACTTGACAC-TTTTTCTTAAGTT
1 GATACCTAAACTTGACACTTTTTTCTTAAGTT
* *
119526 GGTACTTAAACTT
1 GATACCTAAACTT
119539 TTTTTGGGTC
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
31 22 0.56
32 17 0.44
ACGTcount: A:0.29, C:0.18, G:0.09, T:0.43
Consensus pattern (32 bp):
GATACCTAAACTTGACACTTTTTTCTTAAGTT
Found at i:119554 original size:60 final size:62
Alignment explanation
Indices: 119490--119606 Score: 148
Period size: 62 Copynumber: 1.9 Consensus size: 62
119480 CTTTTTTTTT
* *
119490 AATTTGATACCTAAACTTGACAC-TTTTT-CTTAAGTTGGTACTTAAACTTTTTTTGGGTCC
1 AATTTGATACCTAAACTTGACACTTTTTTCCCTAAGTTGGTACCTAAACTTTTTTTGGGTCC
* * * * * *
119550 AATTTGGTACTTGAACTTGACTCTTTTTTCCCTAATTTGGTACCTAATCTTTTTTTG
1 AATTTGATACCTAAACTTGACACTTTTTTCCCTAAGTTGGTACCTAAACTTTTTTTG
119607 TTCGATTTGG
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
60 19 0.40
61 5 0.11
62 23 0.49
ACGTcount: A:0.22, C:0.17, G:0.13, T:0.48
Consensus pattern (62 bp):
AATTTGATACCTAAACTTGACACTTTTTTCCCTAAGTTGGTACCTAAACTTTTTTTGGGTCC
Found at i:119577 original size:91 final size:92
Alignment explanation
Indices: 119412--119596 Score: 219
Period size: 92 Copynumber: 2.0 Consensus size: 92
119402 TTGGTACTTG
* * * *
119412 AACTTGATATTTTTTCCTAATTTGGTACCTAAATTTTTTTGGGTCTAATTCGATACCCAAACTTG
1 AACTTGACACTTTTTCCTAAGTTGGTACCTAAATTTTTTTGGGTCCAATTCGATACCCAAACTTG
*
119477 ACACTTTTTTT-TTAATTTGATACCTA
66 ACACTTTTTTTCCTAATTTGATACCTA
* * * * ***
119503 AACTTGACACTTTTTCTTAAGTTGGTACTTAAACTTTTTTTGGGTCCAATTTGGTACTTGAACTT
1 AACTTGACACTTTTTCCTAAGTTGGTACCTAAA-TTTTTTTGGGTCCAATTCGATACCCAAACTT
* * *
119568 GACTCTTTTTTCCCTAATTTGGTACCTA
65 GACACTTTTTTTCCTAATTTGATACCTA
119596 A
1 A
119597 TCTTTTTTTG
Statistics
Matches: 77, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
91 28 0.36
92 35 0.45
93 14 0.18
ACGTcount: A:0.24, C:0.17, G:0.12, T:0.46
Consensus pattern (92 bp):
AACTTGACACTTTTTCCTAAGTTGGTACCTAAATTTTTTTGGGTCCAATTCGATACCCAAACTTG
ACACTTTTTTTCCTAATTTGATACCTA
Found at i:119615 original size:60 final size:59
Alignment explanation
Indices: 119503--119622 Score: 143
Period size: 60 Copynumber: 2.0 Consensus size: 59
119493 TTGATACCTA
* *
119503 AACTTGACACTTTTTCTTAAGTTGGTACTTAAACTTTTTTTGGGTCCAATTTGGTACTTG
1 AACTTGACACTTTTTCCTAAGTTGGTACCTAAACTTTTTTT-GGTCCAATTTGGTACTTG
* * * * *
119563 AACTTGACTCTTTTTTCCCTAATTTGGTACCTAATCTTTTTTT-GTTCGATTTGGTACTTG
1 AACTTGACAC-TTTTT-CCTAAGTTGGTACCTAAACTTTTTTTGGTCCAATTTGGTACTTG
119623 TCAAATGTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
60 24 0.47
61 5 0.10
62 22 0.43
ACGTcount: A:0.19, C:0.17, G:0.15, T:0.49
Consensus pattern (59 bp):
AACTTGACACTTTTTCCTAAGTTGGTACCTAAACTTTTTTTGGTCCAATTTGGTACTTG
Found at i:120109 original size:59 final size:60
Alignment explanation
Indices: 120001--120113 Score: 165
Period size: 60 Copynumber: 1.9 Consensus size: 60
119991 TAAACCTAAA
*
120001 AAAAAAGGTTAGGTTCCAAATTAAGAAAAAAGATGTCAAATTCAAGTATCAAATTGGGTC
1 AAAAAAGGTTAGGTACCAAATTAAGAAAAAAGATGTCAAATTCAAGTATCAAATTGGGTC
* * * * *
120061 AAAAAAGTTTAGGTACTAAATTAAGAAAAAA-ATGTTAAATTTAGGTATCAAAT
1 AAAAAAGGTTAGGTACCAAATTAAGAAAAAAGATGTCAAATTCAAGTATCAAAT
120114 GTTATATTAA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
59 19 0.40
60 28 0.60
ACGTcount: A:0.50, C:0.07, G:0.16, T:0.27
Consensus pattern (60 bp):
AAAAAAGGTTAGGTACCAAATTAAGAAAAAAGATGTCAAATTCAAGTATCAAATTGGGTC
Found at i:120685 original size:3 final size:3
Alignment explanation
Indices: 120670--120707 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
120660 AACATTTAAA
*
120670 ATT ATT GTT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
120708 GGAAATAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:147767 original size:18 final size:19
Alignment explanation
Indices: 147725--147768 Score: 67
Period size: 16 Copynumber: 2.5 Consensus size: 19
147715 GAAATTTTTA
147725 TCTAAATTTTATATAATTT
1 TCTAAATTTTATATAATTT
147744 T-T-AATTTT-TATAATTT
1 TCTAAATTTTATATAATTT
147760 TCTAAATTT
1 TCTAAATTT
147769 AACAAAAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 9 0.39
17 7 0.30
18 6 0.26
19 1 0.04
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (19 bp):
TCTAAATTTTATATAATTT
Found at i:157171 original size:29 final size:29
Alignment explanation
Indices: 157138--157329 Score: 133
Period size: 29 Copynumber: 6.6 Consensus size: 29
157128 TGGTTTTTAG
* * *
157138 AATGGTAATTTTGGGATGTTTGGGGGTGA
1 AATGGAAATTTTGGGAAGTTTGGGGGTAA
*
157167 AATGGAAATTTT-GGAAGTTTGAGGGTAA
1 AATGGAAATTTTGGGAAGTTTGGGGGTAA
* *
157195 AATGGAAATTTTTGGAAAGTTTGGGGTTAAA
1 AATGGAAA-TTTTGGGAAGTTTGGGGGT-AA
**
157226 AATGG-AATTTTTAGAAGATTT-GGGGT-A
1 AATGGAAATTTTGGGAAG-TTTGGGGGTAA
* * * *
157253 AATGGTAATTTTTGGAAATTT-AGGGTCAAA
1 AATGGAAATTTTGGGAAGTTTGGGGGT--AA
* * * * *
157283 AATAGAATTTTTTGCAAGTTTGAGGGTAA
1 AATGGAAATTTTGGGAAGTTTGGGGGTAA
* *
157312 AATGGTAATTTTTGGAAG
1 AATGGAAATTTTGGGAAG
157330 ATTCGAGGTC
Statistics
Matches: 131, Mismatches: 23, Indels: 18
0.76 0.13 0.10
Matches are distributed among these distances:
27 13 0.10
28 31 0.24
29 42 0.32
30 33 0.25
31 12 0.09
ACGTcount: A:0.33, C:0.01, G:0.30, T:0.36
Consensus pattern (29 bp):
AATGGAAATTTTGGGAAGTTTGGGGGTAA
Found at i:157235 original size:58 final size:58
Alignment explanation
Indices: 157166--157502 Score: 273
Period size: 58 Copynumber: 5.8 Consensus size: 58
157156 TTTGGGGGTG
* * * *
157166 AAATGGAAATTTTGGAAGTTTGAGGGTAAAATGGAAATTTTTGGAAAGTTTGGGGTTAA
1 AAATGGAATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTTGGAAA-TTTAGGGTCAA
*
157225 AAATGGAATTTTTAGAAGATTTG-GGGT-AAATGGTAATTTTTGGAAATTTAGGGTCAA
1 AAATGGAATTTTTGGAAG-TTTGAGGGTAAAATGGTAATTTTTGGAAATTTAGGGTCAA
* * *
157282 AAATAGAATTTTTTGCAAGTTTGAGGGTAAAATGGTAATTTTTGGAAGA-TTCGAGGTCAA
1 AAATGGAA-TTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTTGGAA-ATTTAG-GGTCAA
* * ** ***
157342 AAATAGTATTTTTGGATA-TCCG-GGGTAAAACCATAATTTTTGGAAAGTTTAGGGTCAA
1 AAATGGAATTTTTGGA-AGTTTGAGGGTAAAATGGTAATTTTTGGAAA-TTTAGGGTCAA
* * * * * * *
157400 AAATGAAAATTTT-GAAGGTTCGGGGGTAAAAAT-GTAATTTTTATGAAGTTCGAGGGTCAA
1 AAATGGAATTTTTGGAA-GTTTGAGGGT-AAAATGGTAATTTTT-GGAAATT-TAGGGTCAA
*
157460 ATTAT-G-ATTTTTGGAAGTTT-AGGGTTAAAAT-GTAATTTTTGGA
1 A-AATGGAATTTTTGGAAGTTTGAGGG-TAAAATGGTAATTTTTGGA
157503 CAGTTCAAGA
Statistics
Matches: 227, Mismatches: 33, Indels: 38
0.76 0.11 0.13
Matches are distributed among these distances:
56 1 0.00
57 25 0.11
58 85 0.37
59 76 0.33
60 38 0.17
61 2 0.01
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.36
Consensus pattern (58 bp):
AAATGGAATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTTGGAAATTTAGGGTCAA
Found at i:157353 original size:30 final size:30
Alignment explanation
Indices: 157175--157357 Score: 100
Period size: 30 Copynumber: 6.2 Consensus size: 30
157165 GAAATGGAAA
* * *
157175 TTTTGGAAGTTTGAGGGT--AAAATGGAAAT
1 TTTTGGAAGATTGAGGGTCAAAAATAG-TAT
* * * *
157204 TTTTGGAAAGTTTG-GGGTTAAAAATGGAAT
1 TTTTGG-AAGATTGAGGGTCAAAAATAGTAT
* *
157234 TTTTAGAAGATTTG-GGGT---AAATGGTAAT
1 TTTTGGAAGA-TTGAGGGTCAAAAATAGT-AT
* *
157262 TTTTGGAA-ATTTAGGGTCAAAAATAGAATT
1 TTTTGGAAGATTGAGGGTCAAAAATAGTA-T
* * *
157292 TTTTGCAAGTTTGAGGGT--AAAATGGTAAT
1 TTTTGGAAGATTGAGGGTCAAAAATAGT-AT
157321 TTTTGGAAGATTCGA-GGTCAAAAATAGTAT
1 TTTTGGAAGATT-GAGGGTCAAAAATAGTAT
157351 TTTTGGA
1 TTTTGGA
157358 TATCCGGGGT
Statistics
Matches: 124, Mismatches: 15, Indels: 29
0.74 0.09 0.17
Matches are distributed among these distances:
26 2 0.02
27 11 0.09
28 9 0.07
29 34 0.27
30 47 0.38
31 21 0.17
ACGTcount: A:0.34, C:0.02, G:0.27, T:0.37
Consensus pattern (30 bp):
TTTTGGAAGATTGAGGGTCAAAAATAGTAT
Found at i:157413 original size:117 final size:115
Alignment explanation
Indices: 157166--157460 Score: 301
Period size: 117 Copynumber: 2.5 Consensus size: 115
157156 TTTGGGGGTG
* * * * * *
157166 AAATGGAAATTTTGGAAGTTTGAGGGTAAAATGGAAATTTTTGGAA-AGTTTGGGGTTAAAAATG
1 AAATGAAAATTTT-GAAGTTTGAGGGTAAAATGGTAATTTTTGGAAGA-TTCGAGGTCAAAAATA
** ***
157230 GAATTTTTAGAAGATTTGGGGTAAATGGTAATTTTTGGAAATTTAGGGTCAA
64 GAATTTTTAGAAGATCCGGGGTAAACCATAATTTTTGGAAATTTAGGGTCAA
**
157282 AAATAGAATTTTTTGCAAGTTTGAGGGTAAAATGGTAATTTTTGGAAGATTCGAGGTCAAAAATA
1 AAAT-GAAAATTTTG-AAGTTTGAGGGTAAAATGGTAATTTTTGGAAGATTCGAGGTCAAAAATA
* * *
157347 GTATTTTT-GGATATCCGGGGTAAAACCATAATTTTTGGAAAGTTTAGGGTCAA
64 GAATTTTTAGAAGATCCGGGGT-AAACCATAATTTTTGGAAA-TTTAGGGTCAA
* * *
157400 AAATGAAAATTTTGAAGGTTCGGGGGTAAAAAT-GTAATTTTTATGAAG-TTCGAGGGTCAAA
1 AAATGAAAATTTTGAA-GTTTGAGGGT-AAAATGGTAATTTTT-GGAAGATTCGA-GGTCAAA
157461 TTATGATTTT
Statistics
Matches: 149, Mismatches: 21, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
116 16 0.11
117 101 0.68
118 32 0.21
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34
Consensus pattern (115 bp):
AAATGAAAATTTTGAAGTTTGAGGGTAAAATGGTAATTTTTGGAAGATTCGAGGTCAAAAATAGA
ATTTTTAGAAGATCCGGGGTAAACCATAATTTTTGGAAATTTAGGGTCAA
Found at i:157461 original size:29 final size:28
Alignment explanation
Indices: 157375--157507 Score: 88
Period size: 30 Copynumber: 4.5 Consensus size: 28
157365 GGTAAAACCA
* *
157375 TAATTTTTGGAAAGTTTAGGGTCAAAAATG
1 TAATTTTTGG-AAGTTGAGGGT-TAAAATG
* * * *
157405 AAAATTTT-GAAGGTTCGGGGGTAAAAATG
1 TAATTTTTGGAA-GTT-GAGGGTTAAAATG
* * * *
157434 TAATTTTTATGAAGTTCGAGGGTCAAATTA
1 TAATTTTT-GGAAGTT-GAGGGTTAAAATG
* *
157464 TGATTTTTGGAAGTTTAGGGTTAAAATG
1 TAATTTTTGGAAGTTGAGGGTTAAAATG
157492 TAATTTTTGGACAGTT
1 TAATTTTTGGA-AGTT
157508 CAAGAACCTT
Statistics
Matches: 81, Mismatches: 17, Indels: 11
0.74 0.16 0.10
Matches are distributed among these distances:
28 21 0.26
29 27 0.33
30 30 0.37
31 3 0.04
ACGTcount: A:0.33, C:0.04, G:0.25, T:0.38
Consensus pattern (28 bp):
TAATTTTTGGAAGTTGAGGGTTAAAATG
Found at i:157496 original size:117 final size:117
Alignment explanation
Indices: 157172--157507 Score: 287
Period size: 117 Copynumber: 2.9 Consensus size: 117
157162 GGTGAAATGG
* * * * * * * *
157172 AAATTTTGGAAGTTTGAGGGTAAAATGGAAATTTTTGGAA-AGTTTGGGGTTAAAAATGGAATTT
1 AAATTTTGCAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGA-TTCGAGGTCAAAAATAGTATTT
* * **
157236 TTAGAAGATTTGGGGT-AAATGGTAATTTTTGGAAA-TTTAGGGTCAAAAATAGA
65 TT-GGATATCAGGGGTAAAAT-GTAATTTTTGGAAAGTTTAGGGTCAAAAATAGA
** *
157289 ATTTTTTGCAAGTTTGAGGGTAAAATGGTAATTTTTGGAAGATTCGAGGTCAAAAATAGTATTTT
1 AAATTTTGCAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGATTCGAGGTCAAAAATAGTATTTT
* **
157354 TGGATATCCGGGGTAAAACCATAATTTTTGGAAAGTTTAGGGTCAAAAAT-GA
66 TGGATATCAGGGGTAAAA-TGTAATTTTTGGAAAGTTTAGGGTCAAAAATAGA
* * *
157406 AAATTTTG-AAGGTTCGGGGGTAAAAAT-GTAATTTTTATGAAG-TTCGAGGGTC-AAATTA-TG
1 AAATTTTGCAA-GTTCGAGGGT-AAAATGGTAATTTTT-GGAAGATTCGA-GGTCAAAAATAGT-
* * *
157466 ATTTTTGGA-AGTTTAGGGTTAAAATGTAATTTTTGGACAGTT
61 ATTTTTGGATA--TCAGGGGTAAAATGTAATTTTTGGAAAGTT
157508 CAAGAACCTT
Statistics
Matches: 181, Mismatches: 27, Indels: 22
0.79 0.12 0.10
Matches are distributed among these distances:
116 13 0.07
117 130 0.72
118 38 0.21
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.36
Consensus pattern (117 bp):
AAATTTTGCAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGATTCGAGGTCAAAAATAGTATTTT
TGGATATCAGGGGTAAAATGTAATTTTTGGAAAGTTTAGGGTCAAAAATAGA
Found at i:159341 original size:6 final size:6
Alignment explanation
Indices: 159332--159365 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
159322 GTATTTAGGA
**
159332 TAAATT TAAATT TATTTT TAAATT TAAATT TAAA
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAA
159366 AATAAATTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (6 bp):
TAAATT
Found at i:159371 original size:18 final size:18
Alignment explanation
Indices: 159331--159373 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
159321 TGTATTTAGG
***
159331 ATAAATTTAAATTTATTT
1 ATAAATTTAAATTTAAAA
*
159349 TTAAATTTAAATTTAAAA
1 ATAAATTTAAATTTAAAA
159367 ATAAATT
1 ATAAATT
159374 CAAACTTAAG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATAAATTTAAATTTAAAA
Found at i:165629 original size:29 final size:29
Alignment explanation
Indices: 165583--165643 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
165573 AAACAAAATT
*
165583 AAATAAAAGGATTGAATTGAAAATAAACA
1 AAATAAAAGGATTGAATTGAAAAGAAACA
* * *
165612 AAATAAAGAGGGTT-AATTTAAAAGAAATA
1 AAATAAA-AGGATTGAATTGAAAAGAAACA
165641 AAA
1 AAA
165644 GGATACAAGG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 22 0.81
30 5 0.19
ACGTcount: A:0.62, C:0.02, G:0.15, T:0.21
Consensus pattern (29 bp):
AAATAAAAGGATTGAATTGAAAAGAAACA
Found at i:167265 original size:24 final size:24
Alignment explanation
Indices: 167205--167371 Score: 192
Period size: 24 Copynumber: 6.9 Consensus size: 24
167195 TTTCAGAAAT
* ***
167205 TTAGCTCATACGAGCCCAGACAAAA
1 TTAGCTCTTACGAGCCCAGA-ATGG
*
167230 TTAGCTCATACGAGCCCAG-ATAGG
1 TTAGCTCTTACGAGCCCAGAAT-GG
167254 TTAGCTCTTACGAGCCCAGAATGG
1 TTAGCTCTTACGAGCCCAGAATGG
*
167278 TTAGCTTTTACGAGCCCAGAATGG
1 TTAGCTCTTACGAGCCCAGAATGG
* *
167302 TTAGCTCTTTCGATCCCAGAATGG
1 TTAGCTCTTACGAGCCCAGAATGG
* * * *
167326 TTAGCTCTTTCAAACCCAAAATGG
1 TTAGCTCTTACGAGCCCAGAATGG
*
167350 TTAGCTCTTACGAGACCAGAAT
1 TTAGCTCTTACGAGCCCAGAAT
167372 CAAAATAATG
Statistics
Matches: 124, Mismatches: 16, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
23 1 0.01
24 102 0.82
25 21 0.17
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (24 bp):
TTAGCTCTTACGAGCCCAGAATGG
Found at i:167405 original size:27 final size:28
Alignment explanation
Indices: 167353--167406 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
167343 AAAATGGTTA
167353 GCTCTTACGAGACCAGAATCAAAATAAT
1 GCTCTTACGAGACCAGAATCAAAATAAT
* *
167381 GCTCTTTCGAG-CCAGAATCAGAATAA
1 GCTCTTACGAGACCAGAATCAAAATAA
167407 CAAAGTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 14 0.58
28 10 0.42
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.22
Consensus pattern (28 bp):
GCTCTTACGAGACCAGAATCAAAATAAT
Found at i:170491 original size:12 final size:11
Alignment explanation
Indices: 170459--170492 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
170449 CAATTTTTTG
170459 ACCCAAACCAA
1 ACCCAAACCAA
*
170470 GCCCAAACCAA
1 ACCCAAACCAA
170481 ACCCTAAACCAA
1 ACCC-AAACCAA
170493 TTCAGGTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 13 0.65
12 7 0.35
ACGTcount: A:0.50, C:0.44, G:0.03, T:0.03
Consensus pattern (11 bp):
ACCCAAACCAA
Found at i:171773 original size:2 final size:2
Alignment explanation
Indices: 171766--171796 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
171756 TAAATTTTTG
*
171766 AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
171797 AAAATGTGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:175742 original size:43 final size:44
Alignment explanation
Indices: 175684--175769 Score: 147
Period size: 43 Copynumber: 2.0 Consensus size: 44
175674 GAGATAGTTC
*
175684 ATTTTCATAGGGTGCCTTTATTTATCATTTCTAATCGAGATCCT
1 ATTTTCATAGGGTGCCTTAATTTATCATTTCTAATCGAGATCCT
*
175728 ATTTT-ATGGGGTGCCTTAATTTATCATTTCTAATCGAGATCC
1 ATTTTCATAGGGTGCCTTAATTTATCATTTCTAATCGAGATCC
175770 GAGGTTTACT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
43 35 0.88
44 5 0.12
ACGTcount: A:0.23, C:0.17, G:0.15, T:0.44
Consensus pattern (44 bp):
ATTTTCATAGGGTGCCTTAATTTATCATTTCTAATCGAGATCCT
Found at i:177559 original size:13 final size:13
Alignment explanation
Indices: 177543--177567 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
177533 TGACCGTTAC
177543 CGTTGACTTTGAT
1 CGTTGACTTTGAT
177556 CGTTGACTTTGA
1 CGTTGACTTTGA
177568 CCATTGATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.16, G:0.24, T:0.44
Consensus pattern (13 bp):
CGTTGACTTTGAT
Found at i:179434 original size:16 final size:16
Alignment explanation
Indices: 179410--179447 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
179400 TATTTAGATA
*
179410 AATATTTAATTA-AAG
1 AATAATTAATTATAAG
179425 AGATAATTAATTATAAG
1 A-ATAATTAATTATAAG
179442 AATAAT
1 AATAAT
179448 AGGTACTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 15 0.75
17 4 0.20
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (16 bp):
AATAATTAATTATAAG
Found at i:181303 original size:18 final size:19
Alignment explanation
Indices: 181260--181305 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
181250 CCTTCAGGAT
* *
181260 CTTCTTCTTTCTCAAGATC
1 CTTCTTCTTCCTCAACATC
*
181279 C-TATTCTTCCTCAACA-C
1 CTTCTTCTTCCTCAACATC
181296 CTTCTTCTTC
1 CTTCTTCTTC
181306 TTTAACAGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
17 2 0.09
18 19 0.86
19 1 0.05
ACGTcount: A:0.15, C:0.37, G:0.02, T:0.46
Consensus pattern (19 bp):
CTTCTTCTTCCTCAACATC
Found at i:184113 original size:23 final size:23
Alignment explanation
Indices: 184087--184134 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
184077 AGCTTCTAAC
184087 ATAAGCTTACGCATCCTTGAACA
1 ATAAGCTTACGCATCCTTGAACA
184110 ATAAGCTTACGCATCCTTGAACA
1 ATAAGCTTACGCATCCTTGAACA
184133 AT
1 AT
184135 GTCGGCCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.35, C:0.25, G:0.12, T:0.27
Consensus pattern (23 bp):
ATAAGCTTACGCATCCTTGAACA
Found at i:197495 original size:21 final size:22
Alignment explanation
Indices: 197461--197505 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
197451 ATTTGTACCA
*
197461 TTATTTTCCCTTTTCCATT-TT
1 TTATTTTCCATTTTCCATTATT
* *
197482 TTATTTTTCATTTTCTATTATT
1 TTATTTTCCATTTTCCATTATT
197504 TT
1 TT
197506 TCCTTTATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.13, C:0.16, G:0.00, T:0.71
Consensus pattern (22 bp):
TTATTTTCCATTTTCCATTATT
Found at i:205099 original size:3 final size:3
Alignment explanation
Indices: 205091--205133 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
205081 AACACCCAGG
* *
205091 CTT CTT CTT CTT CTT CTT CTT CTT CTT ATT ATT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
205134 CTCCTCATGT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.05, C:0.30, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:225383 original size:24 final size:24
Alignment explanation
Indices: 225351--225414 Score: 101
Period size: 24 Copynumber: 2.7 Consensus size: 24
225341 CTCGTCACTT
*
225351 GCCAGCATGAATACGTTTACGCTC
1 GCCAGCATGAATACATTTACGCTC
*
225375 GCCAACATGAATACATTTACGCTC
1 GCCAGCATGAATACATTTACGCTC
*
225399 GTCAGCATGAATACAT
1 GCCAGCATGAATACAT
225415 ATTTCACATG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (24 bp):
GCCAGCATGAATACATTTACGCTC
Found at i:234868 original size:26 final size:25
Alignment explanation
Indices: 234839--234909 Score: 74
Period size: 25 Copynumber: 2.8 Consensus size: 25
234829 AAACTAAAAT
*
234839 AAAATCTAAAACTAAGAAAAAAGGGA
1 AAAATCT-AAACTAAGAAAAAAGAGA
234865 AAAA-CTAAACT-AGAATTAAAAGAGA
1 AAAATCTAAACTAAGAA--AAAAGAGA
* *
234890 AAACTCTAAACTAAGGAAAA
1 AAAATCTAAACTAAGAAAAA
234910 TGTTTCCATA
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
23 4 0.11
24 5 0.13
25 15 0.39
26 11 0.29
27 3 0.08
ACGTcount: A:0.63, C:0.10, G:0.13, T:0.14
Consensus pattern (25 bp):
AAAATCTAAACTAAGAAAAAAGAGA
Found at i:248167 original size:25 final size:23
Alignment explanation
Indices: 248137--248182 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
248127 GTTGGATCCA
248137 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
248162 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
248183 CTCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:249272 original size:69 final size:69
Alignment explanation
Indices: 249199--249413 Score: 322
Period size: 69 Copynumber: 3.1 Consensus size: 69
249189 CAATGCAAAT
* * * * * * *
249199 CAGTAGGCACACACAGTGCAAATCAGTAGGCACACACAATGCAAATCAATAAGCACAAACAGTGT
1 CAGTAAGCACACACAGTGCAAATCAGTAAGCACATATAGTGCAAATCAATAAGCACACACAGTGC
249264 TGAA
66 TGAA
* *
249268 CAGTAAGCACACACAGTGCAAATTAGTAAGCACATATAGTGCAAATCAATAAGCACACACAATGC
1 CAGTAAGCACACACAGTGCAAATCAGTAAGCACATATAGTGCAAATCAATAAGCACACACAGTGC
249333 TGAA
66 TGAA
* *
249337 CAGTAAGCACACACAGTGCAAATCGGTAAGCACATATAGTGCAAATCAGTAAGCACACACAGTGC
1 CAGTAAGCACACACAGTGCAAATCAGTAAGCACATATAGTGCAAATCAATAAGCACACACAGTGC
249402 TGAA
66 TGAA
*
249406 TAGTAAGC
1 CAGTAAGC
249414 GCGCTAATGT
Statistics
Matches: 132, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 132 1.00
ACGTcount: A:0.43, C:0.22, G:0.19, T:0.16
Consensus pattern (69 bp):
CAGTAAGCACACACAGTGCAAATCAGTAAGCACATATAGTGCAAATCAATAAGCACACACAGTGC
TGAA
Found at i:249413 original size:23 final size:23
Alignment explanation
Indices: 249176--249401 Score: 258
Period size: 23 Copynumber: 9.8 Consensus size: 23
249166 GCTAGGGAAA
* *
249176 CAGTAAGCAAACACAATGCAAAT
1 CAGTAAGCACACACAGTGCAAAT
*
249199 CAGTAGGCACACACAGTGCAAAT
1 CAGTAAGCACACACAGTGCAAAT
* *
249222 CAGTAGGCACACACAATGCAAAT
1 CAGTAAGCACACACAGTGCAAAT
* * **
249245 CAATAAGCACAAACAGTGTTGAA-
1 CAGTAAGCACACACAGTG-CAAAT
249268 CAGTAAGCACACACAGTGCAAAT
1 CAGTAAGCACACACAGTGCAAAT
* * *
249291 TAGTAAGCACATATAGTGCAAAT
1 CAGTAAGCACACACAGTGCAAAT
* * *
249314 CAATAAGCACACACAATGCTGAA-
1 CAGTAAGCACACACAGTGC-AAAT
249337 CAGTAAGCACACACAGTGCAAAT
1 CAGTAAGCACACACAGTGCAAAT
* * *
249360 CGGTAAGCACATATAGTGCAAAT
1 CAGTAAGCACACACAGTGCAAAT
249383 CAGTAAGCACACACAGTGC
1 CAGTAAGCACACACAGTGC
249402 TGAATAGTAA
Statistics
Matches: 167, Mismatches: 32, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
22 4 0.02
23 159 0.95
24 4 0.02
ACGTcount: A:0.44, C:0.23, G:0.18, T:0.15
Consensus pattern (23 bp):
CAGTAAGCACACACAGTGCAAAT
Done.