Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001621.1 Kokia drynarioides strain JFW-HI SEQ_113255, 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: 122843
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 44 characters in sequence are not A, C, G, or T
Found at i:676 original size:13 final size:13
Alignment explanation
Indices: 658--683 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
648 TTAGGCTTGA
658 TTTGTAATTGGAC
1 TTTGTAATTGGAC
671 TTTGTAATTGGAC
1 TTTGTAATTGGAC
684 ATTATTTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (13 bp):
TTTGTAATTGGAC
Found at i:705 original size:6 final size:6
Alignment explanation
Indices: 694--744 Score: 54
Period size: 6 Copynumber: 9.0 Consensus size: 6
684 ATTATTTAAA
* * *
694 TAAATT TAAATT TAAATT TAAA-A TAAACT TAATTT TAAA-- TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
739 TAAATT
1 TAAATT
745 CTGCTGGACC
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
4 4 0.11
5 4 0.11
6 29 0.78
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (6 bp):
TAAATT
Found at i:720 original size:23 final size:22
Alignment explanation
Indices: 687--733 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
677 ATTGGACATT
*
687 ATTTAAATAAATTTAAATTTAA
1 ATTTAAATAAACTTAAATTTAA
*
709 ATTTAAAATAAACTTAATTTTAA
1 ATTT-AAATAAACTTAAATTTAA
732 AT
1 AT
734 AAATTTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
ATTTAAATAAACTTAAATTTAA
Found at i:725 original size:17 final size:17
Alignment explanation
Indices: 700--744 Score: 65
Period size: 16 Copynumber: 2.7 Consensus size: 17
690 TAAATAAATT
700 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
* *
717 TAAACTT-AATTTTAAA
1 TAAATTTAAATTTAAAA
733 TAAATTTAAATT
1 TAAATTTAAATT
745 CTGCTGGACC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:738 original size:11 final size:10
Alignment explanation
Indices: 687--743 Score: 50
Period size: 10 Copynumber: 5.8 Consensus size: 10
677 ATTGGACATT
687 ATTTAAATAA
1 ATTTAAATAA
697 ATTTAAATTTAA
1 ATTTAAA--TAA
709 ATTTAAAATAA
1 ATTT-AAATAA
*
720 ACTT-AAT--
1 ATTTAAATAA
727 -TTTAAATAA
1 ATTTAAATAA
736 ATTTAAAT
1 ATTTAAAT
744 TCTGCTGGAC
Statistics
Matches: 38, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
6 2 0.05
7 3 0.08
9 3 0.08
10 14 0.37
11 6 0.16
12 7 0.18
13 3 0.08
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (10 bp):
ATTTAAATAA
Found at i:1604 original size:3 final size:3
Alignment explanation
Indices: 1596--1628 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1586 ATCTATATGC
1596 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1629 CCTTGATATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2330 original size:29 final size:28
Alignment explanation
Indices: 2256--2343 Score: 88
Period size: 29 Copynumber: 3.0 Consensus size: 28
2246 TATTGCAACG
* **
2256 ATATTACGTTTAATGATAAAAATTCGAATT
1 ATATTACG-TTAATGAT-AAATTTTTAATT
*
2286 ATA-TACATTAATTGATAAATTTTTAATT
1 ATATTACGTTAA-TGATAAATTTTTAATT
2314 ATATTACGTTGAATGATAAATTTTTTAATT
1 ATATTACGTT-AATGATAAA-TTTTTAATT
2344 TTCCTACTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
28 16 0.33
29 19 0.39
30 14 0.29
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.47
Consensus pattern (28 bp):
ATATTACGTTAATGATAAATTTTTAATT
Found at i:2854 original size:29 final size:30
Alignment explanation
Indices: 2818--2888 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
2808 AATTCAAAAT
* *
2818 TTCATGTATAAAATTATACA-AAATCA-AA
1 TTCATGTATAAAATTACACATAAACCATAA
*
2846 GTTCATGTATACAATTACACATTAAACCATAA
1 -TTCATGTATAAAATTACACA-TAAACCATAA
2878 TTCATGTATAA
1 TTCATGTATAA
2889 TTTTGAGATT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
29 18 0.51
31 15 0.43
32 2 0.06
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.34
Consensus pattern (30 bp):
TTCATGTATAAAATTACACATAAACCATAA
Found at i:3386 original size:10 final size:12
Alignment explanation
Indices: 3362--3410 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
3352 AACTAAATTA
3362 TATAATATTTAT
1 TATAATATTTAT
3374 TATAAT-TTT-T
1 TATAATATTTAT
* *
3384 TATACTAAATT-T
1 TATAAT-ATTTAT
3396 TATAATATTTAT
1 TATAATATTTAT
3408 TAT
1 TAT
3411 TAATTATTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
10 6 0.20
11 6 0.20
12 18 0.60
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (12 bp):
TATAATATTTAT
Found at i:3400 original size:34 final size:35
Alignment explanation
Indices: 3353--3424 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 35
3343 TACATAATTA
* *
3353 ACTAAATTATATAATATTTATTA-TAATTTTTTAT
1 ACTAAATTATATAATATTTATTATTAATTATTGAT
*
3387 ACTAAATTTTATAATATTTATTATTAATTATTGAT
1 ACTAAATTATATAATATTTATTATTAATTATTGAT
3422 ACT
1 ACT
3425 CGATTAAGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
34 22 0.65
35 12 0.35
ACGTcount: A:0.40, C:0.04, G:0.01, T:0.54
Consensus pattern (35 bp):
ACTAAATTATATAATATTTATTATTAATTATTGAT
Found at i:16617 original size:22 final size:21
Alignment explanation
Indices: 16584--16632 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 21
16574 GTATTTTCGA
*
16584 TTTTTTTCATGTAATTTTAAG
1 TTTTTTTCATGTAATTTAAAG
* **
16605 TTTTTTTAGATGTTGTTTAAAG
1 TTTTTTT-CATGTAATTTAAAG
16627 TTTTTT
1 TTTTTT
16633 ATTTTTAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.20, C:0.02, G:0.12, T:0.65
Consensus pattern (21 bp):
TTTTTTTCATGTAATTTAAAG
Found at i:17433 original size:22 final size:22
Alignment explanation
Indices: 17405--17451 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
17395 ATGTCATGAT
17405 AAAAAATAACTT-AAAAATTATA
1 AAAAAAT-ACTTCAAAAATTATA
* *
17427 AAAAAATATTTCAAAAATTTTA
1 AAAAAATACTTCAAAAATTATA
17449 AAA
1 AAA
17452 TATAAAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 3 0.14
22 19 0.86
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (22 bp):
AAAAAATACTTCAAAAATTATA
Found at i:23130 original size:38 final size:38
Alignment explanation
Indices: 23082--23157 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
23072 CCCCAAAGAA
23082 ACTTACGTTTTTTCCTATTCAGACTACCATAAACAAAG
1 ACTTACGTTTTTTCCTATTCAGACTACCATAAACAAAG
* *
23120 ACTTATGTTTTTTCCTATTCAGACTACCATAAATAAAG
1 ACTTACGTTTTTTCCTATTCAGACTACCATAAACAAAG
23158 GAAATATATA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.34, C:0.21, G:0.08, T:0.37
Consensus pattern (38 bp):
ACTTACGTTTTTTCCTATTCAGACTACCATAAACAAAG
Found at i:33695 original size:58 final size:59
Alignment explanation
Indices: 33630--33810 Score: 231
Period size: 59 Copynumber: 3.1 Consensus size: 59
33620 ATATTTGAAT
* *
33630 ATTTGGTACCTCAATTTGACACTTTTTCTTAATTTGGTACTTAAAC-TTTTTAGATTCA
1 ATTTGGTACCTGAACTTGACACTTTTTCTTAATTTGGTACTTAAACTTTTTTAGATTCA
* * *
33688 ATTTGGTACTTGAACTTGACACTTTTTCTTAATTTGGTA-TCTAAACTTTTTTGGACTCA
1 ATTTGGTACCTGAACTTGACACTTTTTCTTAATTTGGTACT-TAAACTTTTTTAGATTCA
* * * * * *
33747 ATTTGATACCTGAACTTGATATTTTTTCCTAATTTAGTACCTAAACTTTTGTTAGATTCA
1 ATTTGGTACCTGAACTTGACACTTTTTCTTAATTTGGTACTTAAACTTTT-TTAGATTCA
33807 ATTT
1 ATTT
33811 AGGACCTAAA
Statistics
Matches: 105, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
57 1 0.01
58 41 0.39
59 52 0.50
60 11 0.10
ACGTcount: A:0.26, C:0.15, G:0.11, T:0.48
Consensus pattern (59 bp):
ATTTGGTACCTGAACTTGACACTTTTTCTTAATTTGGTACTTAAACTTTTTTAGATTCA
Found at i:34066 original size:58 final size:58
Alignment explanation
Indices: 33971--34104 Score: 162
Period size: 57 Copynumber: 2.3 Consensus size: 58
33961 AAAAGATTAG
* * * *
33971 ATATCAAATTAAGAAAAATAGTCAAGTTCAGATATCAAATTGAATCTCAAAAAATTTAA
1 ATATCAAATTAAAAAAAATAGTCAAATTCAAATATCAAATTGAATC-AAAAAAATTTAA
* * * *
34030 GTATCAACTTAAAAAAAAT-GTCAAATTTAAATATCAAATTGAGTCAAAAAAATTTAA
1 ATATCAAATTAAAAAAAATAGTCAAATTCAAATATCAAATTGAATCAAAAAAATTTAA
* *
34087 ATACCAAATTAATAAAAA
1 ATATCAAATTAAAAAAAA
34105 GTATCAAGTT
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
57 25 0.40
58 22 0.35
59 16 0.25
ACGTcount: A:0.55, C:0.10, G:0.07, T:0.28
Consensus pattern (58 bp):
ATATCAAATTAAAAAAAATAGTCAAATTCAAATATCAAATTGAATCAAAAAAATTTAA
Found at i:41725 original size:23 final size:23
Alignment explanation
Indices: 41692--41801 Score: 123
Period size: 23 Copynumber: 4.8 Consensus size: 23
41682 GTTCAATTCT
* * *
41692 ATGTTCATGAATATGTTCGTTTA
1 ATGTTCGTGAACATGTTCGATTA
*
41715 ATGTTCGTGAACATATTCGATTA
1 ATGTTCGTGAACATGTTCGATTA
41738 ATGTTCGTGAACATGTTCGATTA
1 ATGTTCGTGAACATGTTCGATTA
* * *
41761 ATGTTTGTGATCATGTTTGATTA
1 ATGTTCGTGAACATGTTCGATTA
**
41784 A-GTTAAATGAACATGTTC
1 ATGTT-CGTGAACATGTTC
41802 ATGAACATTA
Statistics
Matches: 74, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
22 3 0.04
23 71 0.96
ACGTcount: A:0.28, C:0.10, G:0.19, T:0.43
Consensus pattern (23 bp):
ATGTTCGTGAACATGTTCGATTA
Found at i:45435 original size:24 final size:23
Alignment explanation
Indices: 45408--45453 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
45398 AACCTTCCAG
* *
45408 TTAAACTTTGTTTATTTGTTTCAA
1 TTAAACTCTATTTATTT-TTTCAA
45432 TTAAACTCTATTTATTTTTTCA
1 TTAAACTCTATTTATTTTTTCA
45454 GTCTAACTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.26, C:0.11, G:0.04, T:0.59
Consensus pattern (23 bp):
TTAAACTCTATTTATTTTTTCAA
Found at i:58585 original size:15 final size:15
Alignment explanation
Indices: 58565--58595 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
58555 AGATTCGTTA
58565 ACTTGACTCGATTTG
1 ACTTGACTCGATTTG
*
58580 ACTTGATTCGATTTG
1 ACTTGACTCGATTTG
58595 A
1 A
58596 TTAAAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.16, G:0.19, T:0.42
Consensus pattern (15 bp):
ACTTGACTCGATTTG
Found at i:59086 original size:20 final size:19
Alignment explanation
Indices: 59046--59118 Score: 76
Period size: 20 Copynumber: 3.8 Consensus size: 19
59036 AAAAAAATTT
* *
59046 AAATAATAAATAA-TATAA
1 AAATTATAAAAAATTATAA
* *
59064 AAATTATAAATATTTATTAA
1 AAATTATAAAAAATTA-TAA
59084 AAATTATAAAAAAATTATAA
1 AAATTAT-AAAAAATTATAA
*
59104 AAATTATAAACAATT
1 AAATTATAAAAAATT
59119 CCAAAAAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
18 11 0.23
19 9 0.19
20 20 0.43
21 7 0.15
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (19 bp):
AAATTATAAAAAATTATAA
Found at i:59096 original size:11 final size:11
Alignment explanation
Indices: 59082--59106 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
59072 AATATTTATT
59082 AAAAATTATAA
1 AAAAATTATAA
59093 AAAAATTATAA
1 AAAAATTATAA
59104 AAA
1 AAA
59107 TTATAAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AAAAATTATAA
Found at i:59105 original size:8 final size:9
Alignment explanation
Indices: 59046--59118 Score: 67
Period size: 9 Copynumber: 7.6 Consensus size: 9
59036 AAAAAAATTT
*
59046 AAATAATAA
1 AAATTATAA
59055 ATAA-TATAA
1 A-AATTATAA
59064 AAATTATAA
1 AAATTATAA
*
59073 ATATTTATTAA
1 A-AATTA-TAA
59084 AAATTATAAAA
1 AAATTAT--AA
59095 AAATTATAA
1 AAATTATAA
59104 AAATTATAA
1 AAATTATAA
59113 ACAATT
1 A-AATT
59119 CCAAAAAAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 13
0.77 0.04 0.19
Matches are distributed among these distances:
8 2 0.04
9 25 0.46
10 14 0.26
11 13 0.24
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (9 bp):
AAATTATAA
Found at i:59126 original size:31 final size:31
Alignment explanation
Indices: 59062--59128 Score: 66
Period size: 30 Copynumber: 2.2 Consensus size: 31
59052 TAAATAATAT
* * *
59062 AAAAATTATAAATATTTATTAAAAATTATAA
1 AAAAAATATAAATAATTATTAAAAATTACAA
* *
59093 AAAAATTATAAA-AATTA-TAAACAATTCCAA
1 AAAAAATATAAATAATTATTAAA-AATTACAA
59123 AAAAAA
1 AAAAAA
59129 AAAAAAACAC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
29 4 0.13
30 15 0.48
31 12 0.39
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (31 bp):
AAAAAATATAAATAATTATTAAAAATTACAA
Found at i:63538 original size:27 final size:27
Alignment explanation
Indices: 63508--63691 Score: 224
Period size: 27 Copynumber: 6.8 Consensus size: 27
63498 AGTCTGACTG
*
63508 GCTCGAATGAGCGATATTCTGTATCTT
1 GCTCGAATGAGCGATATTCTGTATCTA
* * *
63535 GCTCGAATGAGCAATATTCTGTATTTG
1 GCTCGAATGAGCGATATTCTGTATCTA
* * *
63562 GCTCGACTGAGAGATATTTTGTATCTA
1 GCTCGAATGAGCGATATTCTGTATCTA
* *
63589 GCTCGAATGAGTGATATTCTATATCTA
1 GCTCGAATGAGCGATATTCTGTATCTA
* *
63616 GCTCGAATGAGTGATATTCTATATCTA
1 GCTCGAATGAGCGATATTCTGTATCTA
* * *
63643 GCTCGAATGAGCGATATTCTATATTTG
1 GCTCGAATGAGCGATATTCTGTATCTA
* *
63670 GCTCGAACGAGTGATATTCTGT
1 GCTCGAATGAGCGATATTCTGT
63692 TATTGTTGAA
Statistics
Matches: 138, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 138 1.00
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.36
Consensus pattern (27 bp):
GCTCGAATGAGCGATATTCTGTATCTA
Found at i:63593 original size:54 final size:54
Alignment explanation
Indices: 63506--63691 Score: 255
Period size: 54 Copynumber: 3.4 Consensus size: 54
63496 AAAGTCTGAC
* * * *
63506 TGGCTCGAATGAGCGATATTCTGTATCTTGCTCGAATGAGCAATATTCTGTATT
1 TGGCTCGAATGAGAGATATTCTGTATCTAGCTCGAATGAGCGATATTCTATATT
* * * *
63560 TGGCTCGACTGAGAGATATTTTGTATCTAGCTCGAATGAGTGATATTCTATATC
1 TGGCTCGAATGAGAGATATTCTGTATCTAGCTCGAATGAGCGATATTCTATATT
* * *
63614 TAGCTCGAATGAGTGATATTCTATATCTAGCTCGAATGAGCGATATTCTATATT
1 TGGCTCGAATGAGAGATATTCTGTATCTAGCTCGAATGAGCGATATTCTATATT
* *
63668 TGGCTCGAACGAGTGATATTCTGT
1 TGGCTCGAATGAGAGATATTCTGT
63692 TATTGTTGAA
Statistics
Matches: 114, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 114 1.00
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.37
Consensus pattern (54 bp):
TGGCTCGAATGAGAGATATTCTGTATCTAGCTCGAATGAGCGATATTCTATATT
Found at i:78814 original size:18 final size:18
Alignment explanation
Indices: 78781--78815 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
78771 GTAATTTCTT
**
78781 TCAAGCAAATTTGTTTTA
1 TCAAGCAAATGAGTTTTA
78799 TCAAGCAAATGAGTTTT
1 TCAAGCAAATGAGTTTT
78816 TGATTTTGAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.40
Consensus pattern (18 bp):
TCAAGCAAATGAGTTTTA
Found at i:78980 original size:20 final size:19
Alignment explanation
Indices: 78955--79021 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 19
78945 AAAATTATTT
78955 AATAATTTTATATTTCAAAA
1 AATAATTTTATATTT-AAAA
*
78975 AATAA---TATA-ATAAATA
1 AATAATTTTATATTTAAA-A
78991 TAATAATTTTATATTTTAAAA
1 -AATAATTTTATA-TTTAAAA
79012 AATAATTTTA
1 AATAATTTTA
79022 AATTAATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
15 3 0.08
16 2 0.05
17 9 0.24
20 19 0.50
21 1 0.03
22 4 0.11
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (19 bp):
AATAATTTTATATTTAAAA
Found at i:79030 original size:11 final size:11
Alignment explanation
Indices: 79010--79052 Score: 77
Period size: 11 Copynumber: 3.9 Consensus size: 11
79000 TATATTTTAA
79010 AAAATAATTTT
1 AAAATAATTTT
*
79021 AAATTAATTTT
1 AAAATAATTTT
79032 AAAATAATTTT
1 AAAATAATTTT
79043 AAAATAATTT
1 AAAATAATTT
79053 ATTGACGTGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
AAAATAATTTT
Found at i:83895 original size:15 final size:15
Alignment explanation
Indices: 83875--83911 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
83865 ACTCTTGCAG
83875 AGATAGCCTTTGGCT
1 AGATAGCCTTTGGCT
83890 AGATAGCCTTTGGCT
1 AGATAGCCTTTGGCT
83905 AGATAGC
1 AGATAGC
83912 TTTTCTAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (15 bp):
AGATAGCCTTTGGCT
Found at i:84401 original size:17 final size:17
Alignment explanation
Indices: 84367--84403 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
84357 AATGTGACAG
*
84367 CAATTAAAATGCAGTGA
1 CAATTAAAATGCAATGA
*
84384 CAATTAAAATGTAATGA
1 CAATTAAAATGCAATGA
84401 CAA
1 CAA
84404 CTAGAGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.51, C:0.11, G:0.14, T:0.24
Consensus pattern (17 bp):
CAATTAAAATGCAATGA
Found at i:93779 original size:337 final size:329
Alignment explanation
Indices: 93171--93837 Score: 1131
Period size: 337 Copynumber: 2.0 Consensus size: 329
93161 TAAAAGATAA
* *
93171 ATTGAAGCATGCTATTCCTAGTCTACTAGAATCTTTCCATAATCGCTCCTCTTGCATCGCACATA
1 ATTGAAGCATGCTATTCCTAGTCTACTAGAATCTTCCCATAATCGCTCCTCTTGCATCACACATA
93236 GGCACTCCTCGTCAGGAGTAGTGCGTCAACTTACCCTCCATGGAATCAAGCTTCCATGGCAGCTA
66 GGCACTCCTCGTCAGGAGTAGT-CGTCAACTTACCCTCCATGGAATCAAGCTTCCATGGCAGCTA
*
93301 ACTTTGAGAAAATATGTGGAATTGAATTCTTCACAGCTTGATATCGATCTCCTCTTACTTCCCTC
130 ACTTTGAGAAAATATGTGGAATTGAATTCTTCACAACTTGATATCGATCTCCTCTTACTTCCCTC
* * *
93366 TATTTATAATCATTCCACAACACAAGTCTATCCCTTTTCTCAGATTTAACTTCCTTTTTTGTAGC
195 TATTTATAATCATTCCACAACACAAGTCTATCCCTTTTCTCAAATTTAACTTCCCTTTTTGCAGC
* *
93431 TGTACAAGTTTGTTATTGCCAGCTATGCACTCACGCATATTTGGTTTGTGCATTAGGCAGTTGCA
260 TATACAAGTTTGTTATTGCCAGCTATGCACTCACGCAGATTTGGTTTGTGCATTAGGCAGTTGCA
93496 GATTG
325 GATTG
93501 ATTGAAGCATGCTATTCCTAGTCTACTAGAATCTTCCCATAATCGCTCCTCTTGCATCACACATA
1 ATTGAAGCATGCTATTCCTAGTCTACTAGAATCTTCCCATAATCGCTCCTCTTGCATCACACATA
*
93566 GGCACTCCTCGTCAGGAGTA-T-GTCAACTTACCCTCCATGGAATCAAGCTTCCATGGCAGCTGA
66 GGCACTCCTCGTCAGGAGTAGTCGTCAACTTACCCTCCATGGAATCAAGCTTCCATGGCAGCTAA
93629 CTTTGAGAAAATATGAGAAAATATGTGGAATTGAATTCTTCACAACTTGATATCGATCTCCTCTT
131 C--T-------T-TGAGAAAATATGTGGAATTGAATTCTTCACAACTTGATATCGATCTCCTCTT
93694 ACTTCCCTCTATTTATAATCATTCCACAACACAAGTCTATCCCTTTTCTCAAATTTAACTTCCCT
186 ACTTCCCTCTATTTATAATCATTCCACAACACAAGTCTATCCCTTTTCTCAAATTTAACTTCCCT
93759 TTTTGCAGCTATACAAGTTTGTTATTGCCAGCTATGCACTCACGCAGATTTGGTTTGTGCATTAG
251 TTTTGCAGCTATACAAGTTTGTTATTGCCAGCTATGCACTCACGCAGATTTGGTTTGTGCATTAG
*
93824 GCAGTTGTAGATTG
316 GCAGTTGCAGATTG
93838 TCGTGACATC
Statistics
Matches: 317, Mismatches: 10, Indels: 13
0.93 0.03 0.04
Matches are distributed among these distances:
327 42 0.13
329 2 0.01
330 83 0.26
336 1 0.00
337 189 0.60
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (329 bp):
ATTGAAGCATGCTATTCCTAGTCTACTAGAATCTTCCCATAATCGCTCCTCTTGCATCACACATA
GGCACTCCTCGTCAGGAGTAGTCGTCAACTTACCCTCCATGGAATCAAGCTTCCATGGCAGCTAA
CTTTGAGAAAATATGTGGAATTGAATTCTTCACAACTTGATATCGATCTCCTCTTACTTCCCTCT
ATTTATAATCATTCCACAACACAAGTCTATCCCTTTTCTCAAATTTAACTTCCCTTTTTGCAGCT
ATACAAGTTTGTTATTGCCAGCTATGCACTCACGCAGATTTGGTTTGTGCATTAGGCAGTTGCAG
ATTG
Found at i:106230 original size:49 final size:49
Alignment explanation
Indices: 106151--106898 Score: 498
Period size: 49 Copynumber: 15.3 Consensus size: 49
106141 TCTTCTTTGT
* * * *
106151 GGCTTCAATCTTTCCCT-TCACATTTATAGGGTATAAGGTTCACCGTTGC
1 GGCTTCAACCTTTCCCTCT-ACATCTCTAGGGTATAAGATTCACCGTTGC
* * * ** *
106200 GGTTTCAACCTTTCCCTCTACGTCTCTAGGGTATAATATTCGTCGTTGT
1 GGCTTCAACCTTTCCCTCTACATCTCTAGGGTATAAGATTCACCGTTGC
* * *
106249 GGCTTCAACCTTTCCCTCAATATCTCTAGGGTATAAGATTCACCGTTGT
1 GGCTTCAACCTTTCCCTCTACATCTCTAGGGTATAAGATTCACCGTTGC
** * * *
106298 GGCTTCAATATTTCTCT-TCACATCTCTAGGGTATAAGGTTCGCCGTTGC
1 GGCTTCAACCTTTCCCTCT-ACATCTCTAGGGTATAAGATTCACCGTTGC
* * * * *
106347 AGCTTCAACCTTTCCCTCCACATCTCTAGGGTATAAGGTTCATCGTTAC
1 GGCTTCAACCTTTCCCTCTACATCTCTAGGGTATAAGATTCACCGTTGC
* * * * * *
106396 GGCTTCAACCATTCCCTCCATATCTCTAAGGTATAAGATTCATCGCTGC
1 GGCTTCAACCTTTCCCTCTACATCTCTAGGGTATAAGATTCACCGTTGC
* * * * * ** *
106445 GACATCAATCTTTCCCT-TCAGATCTTTAGGGTATAAGATTCGTCGTTGT
1 GGCTTCAACCTTTCCCTCT-ACATCTCTAGGGTATAAGATTCACCGTTGC
* * * * *
106494 GGCTTCAATCTTTCCCT-TCAAATCTCTAGGGTATAAGGTTCGCCGTTGT
1 GGCTTCAACCTTTCCCTCT-ACATCTCTAGGGTATAAGATTCACCGTTGC
* * * * * *
106543 GGCTTAAAGCTTTCCCTCCACA--TCTAAGGTACAAGATTCGCCGTTGC
1 GGCTTCAACCTTTCCCTCTACATCTCTAGGGTATAAGATTCACCGTTGC
* * * * * * *
106590 GACTTCAATCTTGCCCATC-ACATCTCTATGGTACAAGATTCATCATTGC
1 GGCTTCAACCTTTCCC-TCTACATCTCTAGGGTATAAGATTCACCGTTGC
* * * * **
106639 GGCTTCAATC-TTCCCTATCATATCTCTAAGGTATAAGATTCGTCGTTGC
1 GGCTTCAACCTTTCCCTCT-ACATCTCTAGGGTATAAGATTCACCGTTGC
* * * * * * *
106688 GACTTCATATCTTTCCCT-TCACATCTTTACGGTACAAGATTCACCATTCC
1 GGCTTCA-ACCTTTCCCTCT-ACATCTCTAGGGTATAAGATTCACCGTTGC
* * * * * ** *
106738 GACTTCAATCTTTCCCATCATA-A-CTCTAAGGTACAGGATTCACTATTAC
1 GGCTTCAACCTTTCCC-TC-TACATCTCTAGGGTATAAGATTCACCGTTGC
* * * * *
106787 GGCTTCAATCTTTCCCATC-ACATCTCTAAGGTACAAGATTCGCTGTTGC
1 GGCTTCAACCTTTCCC-TCTACATCTCTAGGGTATAAGATTCACCGTTGC
* * * *
106836 AGTTTCATATCTTTCCCATC-ACATCTCTA-TGTATAAGATTCACCGTTGC
1 GGCTTCA-ACCTTTCCC-TCTACATCTCTAGGGTATAAGATTCACCGTTGC
* *
106885 GACTTCAATCTTTC
1 GGCTTCAACCTTTC
106899 TCTTCACATC
Statistics
Matches: 572, Mismatches: 109, Indels: 37
0.80 0.15 0.05
Matches are distributed among these distances:
47 38 0.07
48 14 0.02
49 454 0.79
50 58 0.10
51 7 0.01
52 1 0.00
ACGTcount: A:0.23, C:0.27, G:0.15, T:0.35
Consensus pattern (49 bp):
GGCTTCAACCTTTCCCTCTACATCTCTAGGGTATAAGATTCACCGTTGC
Found at i:106404 original size:147 final size:146
Alignment explanation
Indices: 106153--106918 Score: 720
Period size: 147 Copynumber: 5.2 Consensus size: 146
106143 TTCTTTGTGG
* * * *
106153 CTTCAATCTTTCCCTTCACATTTATAGGGTATAAGGTTCACCGTTGCGGTTTCAACCTTTCCCTC
1 CTTCAATCTTTCCCTTCACATCTCTAGGGTATAAGGTTCACCGTTGCGGCTTCAATCTTTCCCTC
* * * * * *
106218 TACGTCTCTAGGGTATAATATTCGTCGTTGTGGCTTCAACCTTTCCCTCAATATCTCTAGGGTAT
66 CACATCTCTAGGGTATAAGATTCGTCGTTGCGGCTTCAACCTTTCCCTC-ACATCTCTAAGGTAT
* *
106283 AAGATTCACCGTTGTGG
130 AAGATTCACCGTTGCGA
* * * * *
106300 CTTCAATATTTCTCTTCACATCTCTAGGGTATAAGGTTCGCCGTTGCAGCTTCAACCTTTCCCTC
1 CTTCAATCTTTCCCTTCACATCTCTAGGGTATAAGGTTCACCGTTGCGGCTTCAATCTTTCCCTC
* * * * *
106365 CACATCTCTAGGGTATAAGGTTCATCGTTACGGCTTCAACCATTCCCTCCATATCTCTAAGGTAT
66 CACATCTCTAGGGTATAAGATTCGTCGTTGCGGCTTCAACCTTTCCCT-CACATCTCTAAGGTAT
* *
106430 AAGATTCATCGCTGCGA
130 AAGATTCACCGTTGCGA
* * * * ** * *
106447 CATCAATCTTTCCCTTCAGATCTTTAGGGTATAAGATTCGTCGTTGTGGCTTCAATCTTTCCCTT
1 CTTCAATCTTTCCCTTCACATCTCTAGGGTATAAGGTTCACCGTTGCGGCTTCAATCTTTCCCTC
* * * * * * *
106512 CAAATCTCTAGGGTATAAGGTTCGCCGTTGTGGCTTAAAGCTTTCCCTC-CA-CATCTAAGGTAC
66 CACATCTCTAGGGTATAAGATTCGTCGTTGCGGCTTCAACCTTTCCCTCACATC-TCTAAGGTAT
*
106575 AAGATTCGCCGTTGCGA
130 AAGATTCACCGTTGCGA
* * * * * * *
106592 CTTCAATCTTGCCCATCACATCTCTATGGTACAAGATTCATCATTGCGGCTTCAATC-TTCCCTA
1 CTTCAATCTTTCCCTTCACATCTCTAGGGTATAAGGTTCACCGTTGCGGCTTCAATCTTTCCCT-
* * * * * * *
106656 TCATATCTCTAAGGTATAAGATTCGTCGTTGCGACTTCATATCTTTCCCTTCACATCTTTACGGT
65 CCACATCTCTAGGGTATAAGATTCGTCGTTGCGGCTTCA-ACCTTTCCC-TCACATCTCTAAGGT
* * *
106721 ACAAGATTCACCATTCCGA
128 ATAAGATTCACCGTTGCGA
* * * * * ** *
106740 CTTCAATCTTTCCCATCATAACTCTAAGGTA-CAGGATTCACTATTACGGCTTCAATCTTTCCCA
1 CTTCAATCTTTCCCTTCACATCTCTAGGGTATAAGG-TTCACCGTTGCGGCTTCAATCTTTCCC-
* * * * * *
106804 T-CACATCTCTAAGGTACAAGATTCG-CTGTTGCAGTTTCATATCTTTCCCATCACATCTCT-AT
64 TCCACATCTCTAGGGTATAAGATTCGTC-GTTGCGGCTTCA-ACCTTTCCC-TCACATCTCTAAG
106866 GTATAAGATTCACCGTTGCGA
126 GTATAAGATTCACCGTTGCGA
*
106887 CTTCAATCTTTCTCTTCACATCT-TCAGGGTAT
1 CTTCAATCTTTCCCTTCACATCTCT-AGGGTAT
106919 GAATTCAATG
Statistics
Matches: 513, Mismatches: 93, Indels: 25
0.81 0.15 0.04
Matches are distributed among these distances:
144 7 0.01
145 103 0.20
146 10 0.02
147 266 0.52
148 120 0.23
149 6 0.01
150 1 0.00
ACGTcount: A:0.23, C:0.27, G:0.15, T:0.35
Consensus pattern (146 bp):
CTTCAATCTTTCCCTTCACATCTCTAGGGTATAAGGTTCACCGTTGCGGCTTCAATCTTTCCCTC
CACATCTCTAGGGTATAAGATTCGTCGTTGCGGCTTCAACCTTTCCCTCACATCTCTAAGGTATA
AGATTCACCGTTGCGA
Found at i:106906 original size:98 final size:97
Alignment explanation
Indices: 106152--106909 Score: 596
Period size: 98 Copynumber: 7.7 Consensus size: 97
106142 CTTCTTTGTG
* * * * * *
106152 GCTTCAATCTTTCCCTTCACATTTATAGGGTATAAGGTTCACCGTTGCGGTTTCAACCTTTCCC-
1 GCTTCAATCTTTCCCATCACATCTCTA-GGTATAAGATTCACCGTTGCGGCTTCAATCTTTCCCT
* * * * * **
106216 TCTACGTCTCTAGGGTATAATATTCGTCGTTGTG
65 TC-ACATCTCTAAGGTACAAGATTCGCCGTTGCA
* * * * *
106250 GCTTCAACCTTTCCC-TCAATATCTCTAGGGTATAAGATTCACCGTTGTGGCTTCAATATTTCTC
1 GCTTCAATCTTTCCCATC-ACATCTCTA-GGTATAAGATTCACCGTTGCGGCTTCAATCTTTCCC
* * *
106314 TTCACATCTCTAGGGTATAAGGTTCGCCGTTGCA
64 TTCACATCTCTAAGGTACAAGATTCGCCGTTGCA
* * * * * *
106348 GCTTCAACCTTTCCC-TCCACATCTCTAGGGTATAAGGTTCATCGTTACGGCTTCAACCATTCCC
1 GCTTCAATCTTTCCCAT-CACATCTCTA-GGTATAAGATTCACCGTTGCGGCTTCAATCTTTCCC
* * * ** *
106412 TCCATATCTCTAAGGTATAAGATTCATCGCTGC-
64 TTCACATCTCTAAGGTACAAGATTCGCCGTTGCA
* * * * ** *
106445 GACATCAATCTTTCCCTTCAGATCTTTAGGGTATAAGATTCGTCGTTGTGGCTTCAATCTTTCCC
1 G-CTTCAATCTTTCCCATCACATCTCTA-GGTATAAGATTCACCGTTGCGGCTTCAATCTTTCCC
* * * * **
106510 TTCAAATCTCTAGGGTATAAGGTTCGCCGTTGTG
64 TTCACATCTCTAAGGTACAAGATTCGCCGTTGCA
* * * * * * * *
106544 GCTTAAAGCTTTCCC-TCCACATCT-AAGGTACAAGATTCGCCGTTGCGACTTCAATCTTGCCCA
1 GCTTCAATCTTTCCCAT-CACATCTCTAGGTATAAGATTCACCGTTGCGGCTTCAATCTTTCCCT
* ** * *
106607 TCACATCTCTATGGTACAAGATTCATCATTGCG
65 TCACATCTCTAAGGTACAAGATTCGCCGTTGCA
* ** *
106640 GCTTCAATC-TTCCCTATCATATCTCTAAGGTATAAGATTCGTCGTTGCGACTTCATATCTTTCC
1 GCTTCAATCTTTCCC-ATCACATCTCT-AGGTATAAGATTCACCGTTGCGGCTTCA-ATCTTTCC
* * * * *
106704 CTTCACATCTTTACGGTACAAGATTCACCATT-CC
63 CTTCACATCTCTAAGGTACAAGATTCGCCGTTGCA
* * * * ** *
106738 GACTTCAATCTTTCCCATCATAACTCTAAGGTACAGGATTCACTATTACGGCTTCAATCTTTCCC
1 G-CTTCAATCTTTCCCATCACATCTCT-AGGTATAAGATTCACCGTTGCGGCTTCAATCTTTCCC
* *
106803 ATCACATCTCTAAGGTACAAGATTCGCTGTTGCA
64 TTCACATCTCTAAGGTACAAGATTCGCCGTTGCA
* * * *
106837 GTTTCATATCTTTCCCATCACATCTCTATGTATAAGATTCACCGTTGCGACTTCAATCTTTCTCT
1 GCTTCA-ATCTTTCCCATCACATCTCTAGGTATAAGATTCACCGTTGCGGCTTCAATCTTTCCCT
106902 TCACATCT
65 TCACATCT
106910 TCAGGGTATG
Statistics
Matches: 535, Mismatches: 109, Indels: 32
0.79 0.16 0.05
Matches are distributed among these distances:
95 5 0.01
96 69 0.13
97 6 0.01
98 351 0.66
99 99 0.19
100 5 0.01
ACGTcount: A:0.23, C:0.27, G:0.15, T:0.35
Consensus pattern (97 bp):
GCTTCAATCTTTCCCATCACATCTCTAGGTATAAGATTCACCGTTGCGGCTTCAATCTTTCCCTT
CACATCTCTAAGGTACAAGATTCGCCGTTGCA
Found at i:107753 original size:1 final size:1
Alignment explanation
Indices: 107743--107826 Score: 51
Period size: 1 Copynumber: 84.0 Consensus size: 1
107733 TGACCTCTCC
* * * * * * * * * * * *
107743 TTTTTCTTTTTTTCTCTTCTTTTTTCTTTTATTTTTCTTTTCTTTTCTTTTCTTTCTTTTTCTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
107808 TTTTTTTTTCTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTT
107827 GGTTTCAAGA
Statistics
Matches: 57, Mismatches: 26, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
1 57 1.00
ACGTcount: A:0.01, C:0.14, G:0.00, T:0.85
Consensus pattern (1 bp):
T
Found at i:107772 original size:5 final size:5
Alignment explanation
Indices: 107744--107825 Score: 77
Period size: 5 Copynumber: 16.8 Consensus size: 5
107734 GACCTCTCCT
*
107744 TTTTC TTTT- TTTCTC TTCTT- TTTTC TTTTAT TTTTC TTTTC TTTTC
1 TTTTC TTTTC TTT-TC TT-TTC TTTTC TTTT-C TTTTC TTTTC TTTTC
107790 TTTTC -TTTC TTTTTC TTTT- TTTT- TTTTC TTTT- TTTT
1 TTTTC TTTTC -TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
107826 TGGTTTCAAG
Statistics
Matches: 67, Mismatches: 2, Indels: 17
0.78 0.02 0.20
Matches are distributed among these distances:
4 21 0.31
5 34 0.51
6 11 0.16
7 1 0.01
ACGTcount: A:0.01, C:0.15, G:0.00, T:0.84
Consensus pattern (5 bp):
TTTTC
Found at i:107784 original size:36 final size:32
Alignment explanation
Indices: 107743--107825 Score: 105
Period size: 36 Copynumber: 2.4 Consensus size: 32
107733 TGACCTCTCC
107743 TTTTTC-TTTTTTTCTCTTCTTTTTTCTTTTATTTT
1 TTTTTCTTTTTTTTCT-TTC-TTTTTC-TTT-TTTT
107778 TCTTTTCTTTTCTTTTCTTTCTTTTTCTTTTTTT
1 T-TTTTCTTTT-TTTTCTTTCTTTTTCTTTTTTT
107812 TTTTTCTTTTTTTT
1 TTTTTCTTTTTTTT
107826 TGGTTTCAAG
Statistics
Matches: 45, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
32 4 0.09
33 9 0.20
34 5 0.11
35 4 0.09
36 11 0.24
37 6 0.13
38 6 0.13
ACGTcount: A:0.01, C:0.14, G:0.00, T:0.84
Consensus pattern (32 bp):
TTTTTCTTTTTTTTCTTTCTTTTTCTTTTTTT
Found at i:107822 original size:10 final size:10
Alignment explanation
Indices: 107743--107826 Score: 100
Period size: 10 Copynumber: 8.5 Consensus size: 10
107733 TGACCTCTCC
107743 TTTTTCTTTT
1 TTTTTCTTTT
* *
107753 TTTCTCTTCT
1 TTTTTCTTTT
107763 TTTTTCTTTT
1 TTTTTCTTTT
107773 ATTTTTCTTTT
1 -TTTTTCTTTT
*
107784 CTTTTC-TTT
1 TTTTTCTTTT
*
107793 TCTTTCTTTT
1 TTTTTCTTTT
*
107803 TCTTT-TTTT
1 TTTTTCTTTT
107812 TTTTTCTTTT
1 TTTTTCTTTT
107822 TTTTT
1 TTTTT
107827 GGTTTCAAGA
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
9 15 0.24
10 38 0.60
11 10 0.16
ACGTcount: A:0.01, C:0.14, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:108045 original size:5 final size:5
Alignment explanation
Indices: 108016--108095 Score: 69
Period size: 5 Copynumber: 15.8 Consensus size: 5
108006 GACCTCTCAT
*
108016 TTTTC TTTT- TTTTC TCTTCTT TTTTC TTTTC TTTTTC TTTTTC TTTTC
1 TTTTC TTTTC TTTTC T-TT-TC TTTTC TTTTC -TTTTC -TTTTC TTTTC
*
108064 TTTTC -TTTC TTTTTC TTTT- TTTT- TTCTC TTTT
1 TTTTC TTTTC -TTTTC TTTTC TTTTC TTTTC TTTT
108096 TTGGGTTTCA
Statistics
Matches: 64, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
4 15 0.23
5 28 0.44
6 19 0.30
7 2 0.03
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:108045 original size:26 final size:25
Alignment explanation
Indices: 108016--108097 Score: 93
Period size: 22 Copynumber: 3.4 Consensus size: 25
108006 GACCTCTCAT
108016 TTTTCTTTTTTTTCTCTTCTTTTTTC
1 TTTTCTTTTTTTT-TCTTCTTTTTTC
*
108042 TTTTCTTTTTCTTT-TTC--TTTTC
1 TTTTCTTTTTTTTTCTTCTTTTTTC
*
108064 TTTTCTTTCTTTTTCTT-TTTTTT-
1 TTTTCTTTTTTTTTCTTCTTTTTTC
*
108087 TTCTCTTTTTT
1 TTTTCTTTTTT
108098 GGGTTTCAAG
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
22 17 0.35
23 11 0.23
24 7 0.15
25 1 0.02
26 12 0.25
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (25 bp):
TTTTCTTTTTTTTTCTTCTTTTTTC
Found at i:108047 original size:17 final size:16
Alignment explanation
Indices: 108017--108090 Score: 66
Period size: 17 Copynumber: 4.8 Consensus size: 16
108007 ACCTCTCATT
*
108017 TTTCTTTTTT-TTCTC
1 TTTCTTTTTTCTTTTC
108032 -TTCTTTTTTCTTTTC
1 TTTCTTTTTTCTTTTC
*
108047 TTTTTCTTTTTCTTTTC
1 TTTCT-TTTTTCTTTTC
*
108064 -TT-TTCTTTCTTTTTC
1 TTTCTTTTTTC-TTTTC
*
108079 TTTTTTTTTTCT
1 TTTCTTTTTTCT
108091 CTTTTTTGGG
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
14 14 0.29
15 10 0.20
16 8 0.16
17 17 0.35
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTCTTTTTTCTTTTC
Found at i:108054 original size:32 final size:32
Alignment explanation
Indices: 108015--108090 Score: 104
Period size: 32 Copynumber: 2.4 Consensus size: 32
108005 TGACCTCTCA
*
108015 TTTTTCTTTTT-TTTCTCTTCTTTTTTC-TTTTC
1 TTTTTCTTTTTCTTT-TCTT-TTCTTTCTTTTTC
108047 TTTTTCTTTTTCTTTTCTTTTCTTTCTTTTTC
1 TTTTTCTTTTTCTTTTCTTTTCTTTCTTTTTC
108079 TTTTT-TTTTTCT
1 TTTTTCTTTTTCT
108091 CTTTTTTGGG
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
31 13 0.32
32 25 0.61
33 3 0.07
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (32 bp):
TTTTTCTTTTTCTTTTCTTTTCTTTCTTTTTC
Found at i:108085 original size:272 final size:271
Alignment explanation
Indices: 107589--108130 Score: 951
Period size: 272 Copynumber: 2.0 Consensus size: 271
107579 GTCAATGCCC
*
107589 CAAGATGTAAAGTTTCTTCGTGTTGTTATGTTTGAGGGAAACGATCATTTCAAGTCCATTCTTTG
1 CAAGATGTAAAGTTTCTTCGTGTTGTTATGTTTGAAGGAAACGATCATTTCAAGTCCATTCTTTG
*
107654 CTCCAAATTTGAGTCGCTCTTTCGGGTTTTTAACTCAAAATCCCTTTGGTTTCAAGACACCTTTT
66 CTCCAAATTTGAGTCGCCCTTTCGGGTTTTTAACTCAAAATCCCTTTGGTTTCAAGACACCTTTT
* *
107719 ACGTGTTTTCATCTTGACCTCTCCTTTTTCTTTTTTTCTCTTCTTTTTTCTTTTATTTTTCTTTT
131 ACATGTTTTCATCTTGACCTCTCATTTTTCTTTTTTTCTCTTCTTTTTTCTTTTATTTTTCTTTT
* * *
107784 CTTTTCTTTTCTTTCTTTTTCTTTTTTTTTTTTCTTTTTTTTTGGTTTCAAGACGTCTTTTGCGG
196 CTTTTCTTTTCTTTCTTTTTC-TTTTTTTTTTTCTCTTTTTTGGGTTTCAAGACGCCTTTTGCGG
107849 GTTTTTGTCTTG
260 GTTTTTGTCTTG
107861 CAAGATGTAAAGTTTCTTCGTGTTGTTATGTTTGAAGGAAACGATCATTTCAAGTCCATTCTTTG
1 CAAGATGTAAAGTTTCTTCGTGTTGTTATGTTTGAAGGAAACGATCATTTCAAGTCCATTCTTTG
***
107926 CTCCAAATTTGAGTCGCCCTTTCGGGTTTTTAACTCAAAATCCCTTTGGTTTCAAGATGTCTTTT
66 CTCCAAATTTGAGTCGCCCTTTCGGGTTTTTAACTCAAAATCCCTTTGGTTTCAAGACACCTTTT
*
107991 ACATGTTTTCATCTTGACCTCTCATTTTTCTTTTTTTTCTCTTCTTTTTTCTTTTCTTTTTCTTT
131 ACATGTTTTCATCTTGACCTCTCATTTTTC-TTTTTTTCTCTTCTTTTTTCTTTTATTTTTC-TT
108056 TTCTTTTCTTTTCTTTCTTTTTC-TTTTTTTTTTCTCTTTTTTGGGTTTCAAGACGCCTTTTGCG
194 TTCTTTTCTTTTCTTTCTTTTTCTTTTTTTTTTTCTCTTTTTTGGGTTTCAAGACGCCTTTTGCG
108120 GGTTTTTGTCT
259 GGTTTTTGTCT
108131 CGACCTTTTT
Statistics
Matches: 257, Mismatches: 11, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
272 202 0.79
273 30 0.12
274 25 0.10
ACGTcount: A:0.14, C:0.19, G:0.13, T:0.54
Consensus pattern (271 bp):
CAAGATGTAAAGTTTCTTCGTGTTGTTATGTTTGAAGGAAACGATCATTTCAAGTCCATTCTTTG
CTCCAAATTTGAGTCGCCCTTTCGGGTTTTTAACTCAAAATCCCTTTGGTTTCAAGACACCTTTT
ACATGTTTTCATCTTGACCTCTCATTTTTCTTTTTTTCTCTTCTTTTTTCTTTTATTTTTCTTTT
CTTTTCTTTTCTTTCTTTTTCTTTTTTTTTTTCTCTTTTTTGGGTTTCAAGACGCCTTTTGCGGG
TTTTTGTCTTG
Found at i:108097 original size:11 final size:11
Alignment explanation
Indices: 108015--108097 Score: 73
Period size: 11 Copynumber: 7.2 Consensus size: 11
108005 TGACCTCTCA
108015 TTTT-TCTTTT
1 TTTTCTCTTTT
108025 TTTTCTCTTCTT
1 TTTTCTCTT-TT
108037 TTTTCT-TTTCT
1 TTTTCTCTTT-T
108048 TTTTCT-TTTT
1 TTTTCTCTTTT
108058 CTTTTCTTTTCTTTCT
1 -TTTTC---TCTTT-T
*
108074 TTTTCTTTTTT
1 TTTTCTCTTTT
108085 TTTTCTCTTTT
1 TTTTCTCTTTT
108096 TT
1 TT
108098 GGGTTTCAAG
Statistics
Matches: 62, Mismatches: 2, Indels: 17
0.77 0.02 0.21
Matches are distributed among these distances:
10 6 0.10
11 34 0.55
12 12 0.19
14 1 0.02
15 8 0.13
16 1 0.02
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTCTCTTTT
Found at i:108104 original size:26 final size:26
Alignment explanation
Indices: 108049--108104 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
108039 TTCTTTTCTT
**
108049 TTTCTTTTTCTTTTCTTTTCTTTCTT
1 TTTCTTTTTCTTTTCTTTTCTTTCGG
* *
108075 TTTCTTTTTTTTTTCTCTTT-TTTGGG
1 TTTCTTTTTCTTTTCT-TTTCTTTCGG
108101 TTTC
1 TTTC
108105 AAGACGCCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 22 0.88
27 3 0.12
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.79
Consensus pattern (26 bp):
TTTCTTTTTCTTTTCTTTTCTTTCGG
Found at i:110981 original size:23 final size:23
Alignment explanation
Indices: 110951--111006 Score: 112
Period size: 23 Copynumber: 2.4 Consensus size: 23
110941 ACATTTACCA
110951 ATTTCACATTACTTAAAGTCTAT
1 ATTTCACATTACTTAAAGTCTAT
110974 ATTTCACATTACTTAAAGTCTAT
1 ATTTCACATTACTTAAAGTCTAT
110997 ATTTCACATT
1 ATTTCACATT
111007 GAACAAGCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.34, C:0.18, G:0.04, T:0.45
Consensus pattern (23 bp):
ATTTCACATTACTTAAAGTCTAT
Found at i:117724 original size:16 final size:17
Alignment explanation
Indices: 117703--117735 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
117693 GGATATTGCC
*
117703 TCATTT-TTTTTTGAAA
1 TCATTTATTTTATGAAA
117719 TCATTTATTTTATGAAA
1 TCATTTATTTTATGAAA
117736 CAACACATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.30, C:0.06, G:0.06, T:0.58
Consensus pattern (17 bp):
TCATTTATTTTATGAAA
Found at i:117865 original size:20 final size:19
Alignment explanation
Indices: 117836--117887 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
117826 ATGCATGGCA
*
117836 TAAATTAAATGACAACAAT
1 TAAATTAAATGACAAAAAT
*
117855 TAAATTTAAATTACAAAAAT
1 TAAA-TTAAATGACAAAAAT
*
117875 AAAAATTAAATGA
1 -TAAATTAAATGA
117888 ATAAACAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 4 0.15
20 20 0.74
21 3 0.11
ACGTcount: A:0.62, C:0.06, G:0.04, T:0.29
Consensus pattern (19 bp):
TAAATTAAATGACAAAAAT
Found at i:118029 original size:15 final size:16
Alignment explanation
Indices: 117995--118048 Score: 90
Period size: 16 Copynumber: 3.4 Consensus size: 16
117985 AAAAAATTCT
117995 AAAAGGATTAAATTTA
1 AAAAGGATTAAATTTA
*
118011 AAAAGGACTAAATTTA
1 AAAAGGATTAAATTTA
*
118027 AAAAGGATTAATTTTA
1 AAAAGGATTAAATTTA
118043 AAAAGG
1 AAAAGG
118049 GTTTAACTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.56, C:0.02, G:0.15, T:0.28
Consensus pattern (16 bp):
AAAAGGATTAAATTTA
Found at i:121575 original size:34 final size:32
Alignment explanation
Indices: 121502--121575 Score: 87
Period size: 32 Copynumber: 2.2 Consensus size: 32
121492 TATGGGATAT
* * *
121502 TATCTTTTAGGGATATATTGTATATTATTGTA
1 TATCTTTTAGGCATATATTGAATATTATTATA
121534 TATCTTTTAGGCATATATTTAGGAATA-TATTATA
1 TATCTTTTAGGCATATA-TT--GAATATTATTATA
121568 TATCTTTT
1 TATCTTTT
121576 CTATTCTTAC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
32 16 0.44
33 2 0.06
34 14 0.39
35 4 0.11
ACGTcount: A:0.30, C:0.05, G:0.12, T:0.53
Consensus pattern (32 bp):
TATCTTTTAGGCATATATTGAATATTATTATA
Done.