Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012394.1 Kokia drynarioides strain JFW-HI SEQ_127398, 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: 142516
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Warning! 143 characters in sequence are not A, C, G, or T
Found at i:1492 original size:30 final size:30
Alignment explanation
Indices: 1456--1747 Score: 334
Period size: 30 Copynumber: 9.9 Consensus size: 30
1446 GCCCAAGAGA
1456 CCTCGAAACTTCCAAAAATTCCATTTTTAC
1 CCTCGAAACTTCCAAAAATTCCATTTTTAC
* *
1486 CCTCGAAACTTCCAAAAATTTCATTTGT-C
1 CCTCGAAACTTCCAAAAATTCCATTTTTAC
* *
1515 CC-CG-AACTTTCAAAAATTCCATTTTGAC
1 CCTCGAAACTTCCAAAAATTCCATTTTTAC
* *
1543 CC-CGAAACTTTCAAAAATTCCATTTTTCC
1 CCTCGAAACTTCCAAAAATTCCATTTTTAC
** *
1572 CCTCG-AACTTTGAAAAATTCTATTTTTGA-
1 CCTCGAAACTTCCAAAAATTCCATTTTT-AC
1601 CCTCGAAACTTCCAAAAATTCCATTTTTAC
1 CCTCGAAACTTCCAAAAATTCCATTTTTAC
*
1631 CCTCG-AAC-TCCCAAAATTCCATTTTTGAC
1 CCTCGAAACTTCCAAAAATTCCATTTTT-AC
*
1660 CCT-GAAACTTCCAAAAATTCCATTTTTAA
1 CCTCGAAACTTCCAAAAATTCCATTTTTAC
* *
1689 CCTCAAAACTTCCAAAAACTCCATTTTTAAC
1 CCTCGAAACTTCCAAAAATTCCATTTTT-AC
** *
1720 CC-CGAATTTTCCCAAAATTACCATTTTT
1 CCTCGAAACTTCCAAAAATT-CCATTTTT
1748 CCCCCGAGCA
Statistics
Matches: 225, Mismatches: 25, Indels: 23
0.82 0.09 0.08
Matches are distributed among these distances:
27 18 0.08
28 25 0.11
29 68 0.30
30 103 0.46
31 11 0.05
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.34
Consensus pattern (30 bp):
CCTCGAAACTTCCAAAAATTCCATTTTTAC
Found at i:1647 original size:58 final size:59
Alignment explanation
Indices: 1456--1747 Score: 351
Period size: 58 Copynumber: 5.0 Consensus size: 59
1446 GCCCAAGAGA
* *
1456 CCTCGAAACTTCCAAAAATTCCATTTTT-ACCCTCGAAACTTCCAAAAATTTCATTTGT-C
1 CCTCG-AACTTCCAAAAATTCCATTTTTGACCC-CGAAACTTCCAAAAATTCCATTTTTAC
* * *
1515 CC-CGAACTTTCAAAAATTCCA-TTTTGACCCCGAAACTTTCAAAAATTCCATTTTTCC
1 CCTCGAACTTCCAAAAATTCCATTTTTGACCCCGAAACTTCCAAAAATTCCATTTTTAC
** * *
1572 CCTCGAACTTTGAAAAATTCTATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTAC
1 CCTCGAACTTCCAAAAATTCCATTTTTGACCCCGAAACTTCCAAAAATTCCATTTTTAC
* * *
1631 CCTCGAAC-TCCCAAAATTCCATTTTTGACCCTGAAACTTCCAAAAATTCCATTTTTAA
1 CCTCGAACTTCCAAAAATTCCATTTTTGACCCCGAAACTTCCAAAAATTCCATTTTTAC
* * * ** *
1689 CCTCAAAACTTCCAAAAACTCCATTTTTAACCCCGAATTTTCCCAAAATTACCATTTTT
1 CCTC-GAACTTCCAAAAATTCCATTTTTGACCCCGAAACTTCCAAAAATT-CCATTTTT
1748 CCCCCGAGCA
Statistics
Matches: 202, Mismatches: 24, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
56 26 0.13
57 23 0.11
58 66 0.33
59 46 0.23
60 33 0.16
61 8 0.04
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.34
Consensus pattern (59 bp):
CCTCGAACTTCCAAAAATTCCATTTTTGACCCCGAAACTTCCAAAAATTCCATTTTTAC
Found at i:2929 original size:21 final size:20
Alignment explanation
Indices: 2899--2967 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 20
2889 ATTCAAAAAA
2899 TAAA-AAATATAAACGAATT
1 TAAATAAATATAAACGAATT
**
2918 TAAAATAAATATAAATTAACCTT
1 T-AAATAAATATAAACGAA--TT
*
2941 T-TATAAATATAAACGAATT
1 TAAATAAATATAAACGAATT
2960 TAAATAAA
1 TAAATAAA
2968 ATTTTAAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
19 4 0.10
20 8 0.21
21 24 0.62
23 3 0.08
ACGTcount: A:0.59, C:0.06, G:0.03, T:0.32
Consensus pattern (20 bp):
TAAATAAATATAAACGAATT
Found at i:26330 original size:16 final size:16
Alignment explanation
Indices: 26311--26364 Score: 54
Period size: 18 Copynumber: 3.2 Consensus size: 16
26301 CAAAAAATAA
*
26311 TTTGTTTAAAAATGTT
1 TTTGTTTAAAAATATT
*
26327 TTTGTTTCAAAAATTTT
1 TTTGTTT-AAAAATATT
*
26344 ATTTATTCTAAAAATATT
1 -TTTGTT-TAAAAATATT
26362 TTT
1 TTT
26365 AAAAGTAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
16 7 0.22
17 11 0.34
18 13 0.41
19 1 0.03
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.57
Consensus pattern (16 bp):
TTTGTTTAAAAATATT
Found at i:26606 original size:17 final size:17
Alignment explanation
Indices: 26569--26615 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
26559 TCTCTTTTAG
* *
26569 TTAATAAATTATTAGAAA
1 TTAATAAAAT-TTAAAAA
26587 TTAATAAAATTTAAAAA
1 TTAATAAAATTTAAAAA
*
26604 TT-ATTAAATTTA
1 TTAATAAAATTTA
26616 GTTGAACAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 9 0.35
17 8 0.31
18 9 0.35
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (17 bp):
TTAATAAAATTTAAAAA
Found at i:32679 original size:21 final size:22
Alignment explanation
Indices: 32653--32693 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
32643 ATCACCAAGT
*
32653 ATTTTATTTTTA-AAATTTTAA
1 ATTTTATTTTAATAAATTTTAA
32674 ATTTTATTTTAATAAATTTT
1 ATTTTATTTTAATAAATTTT
32694 TTTTCATGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
ATTTTATTTTAATAAATTTTAA
Found at i:47892 original size:11 final size:11
Alignment explanation
Indices: 47876--47999 Score: 53
Period size: 11 Copynumber: 11.6 Consensus size: 11
47866 AATTATATCA
47876 TTGTTTTGATG
1 TTGTTTTGATG
** *
47887 TTGTTTTTTTA
1 TTGTTTTGATG
*
47898 TTGTTTTGGTG
1 TTGTTTTGATG
* *
47909 CTGATTTTGCTG
1 TTG-TTTTGATG
* *
47921 TTATTTTTGTTG
1 TT-GTTTTGATG
47933 TTGTTTT--TG
1 TTGTTTTGATG
* *
47942 TTATTTT-TTG
1 TTGTTTTGATG
*
47952 TTGTTTTGCTG
1 TTGTTTTGATG
*
47963 CTGTTTTGA--
1 TTGTTTTGATG
*
47972 TTGTTTGGATG
1 TTGTTTTGATG
* *
47983 TTATTTTTATG
1 TTGTTTTGATG
47994 TT-TTTT
1 TTGTTTT
48000 ACTATTGTTT
Statistics
Matches: 85, Mismatches: 22, Indels: 13
0.71 0.18 0.11
Matches are distributed among these distances:
9 15 0.18
10 12 0.14
11 41 0.48
12 17 0.20
ACGTcount: A:0.07, C:0.03, G:0.21, T:0.69
Consensus pattern (11 bp):
TTGTTTTGATG
Found at i:47900 original size:22 final size:22
Alignment explanation
Indices: 47879--47956 Score: 79
Period size: 22 Copynumber: 3.5 Consensus size: 22
47869 TATATCATTG
*
47879 TTTTGATGTTGTTTTT-TTATT
1 TTTTGTTGTTGTTTTTGTTATT
* *
47900 GTTTTGGTGCTGATTTTGCTGTTA-T
1 -TTTTGTTGTTG-TTTT--TGTTATT
47925 TTTTGTTGTTGTTTTTGTTATT
1 TTTTGTTGTTGTTTTTGTTATT
47947 TTTTGTTGTT
1 TTTTGTTGTT
47957 TTGCTGCTGT
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
21 5 0.11
22 20 0.43
23 8 0.17
24 9 0.19
25 2 0.04
26 3 0.06
ACGTcount: A:0.06, C:0.03, G:0.21, T:0.71
Consensus pattern (22 bp):
TTTTGTTGTTGTTTTTGTTATT
Found at i:47942 original size:12 final size:12
Alignment explanation
Indices: 47879--47956 Score: 56
Period size: 12 Copynumber: 6.8 Consensus size: 12
47869 TATATCATTG
*
47879 TTTTGATGTTGT
1 TTTTGTTGTTGT
*
47891 TTTT-TTATTG-
1 TTTTGTTGTTGT
* * *
47901 TTTTGGTGCTGA
1 TTTTGTTGTTGT
* *
47913 TTTTGCTGTTAT
1 TTTTGTTGTTGT
47925 TTTTGTTGTTGT
1 TTTTGTTGTTGT
*
47937 TTTTGTT-AT-T
1 TTTTGTTGTTGT
47947 TTTTGTTGTT
1 TTTTGTTGTT
47957 TTGCTGCTGT
Statistics
Matches: 50, Mismatches: 13, Indels: 7
0.71 0.19 0.10
Matches are distributed among these distances:
10 12 0.24
11 9 0.18
12 29 0.58
ACGTcount: A:0.06, C:0.03, G:0.21, T:0.71
Consensus pattern (12 bp):
TTTTGTTGTTGT
Found at i:74776 original size:16 final size:17
Alignment explanation
Indices: 74755--74791 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
74745 AATGGGATGA
74755 AAATAAATTT-TTAATT
1 AAATAAATTTATTAATT
74771 AAATAAATTTAATTAATT
1 AAATAAATTT-ATTAATT
74789 AAA
1 AAA
74792 ATTTTAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.53
18 9 0.47
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAATAAATTTATTAATT
Found at i:74797 original size:16 final size:16
Alignment explanation
Indices: 74755--74798 Score: 56
Period size: 14 Copynumber: 2.9 Consensus size: 16
74745 AATGGGATGA
*
74755 AAATAAATTTTTAATT
1 AAATAAAATTTTAATT
74771 AAAT-AAA-TTTAATT
1 AAATAAAATTTTAATT
*
74785 AATTAAAATTTTAA
1 AAATAAAATTTTAA
74799 AACCCTAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 10 0.42
15 5 0.21
16 9 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AAATAAAATTTTAATT
Found at i:79857 original size:23 final size:22
Alignment explanation
Indices: 79831--79882 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 22
79821 AATTTCAAAT
79831 AAAAAATTTAAAAAATAT-TTTTCAA
1 AAAAAATTT--AAAAT-TCTTTTC-A
79856 AAAAAATTTAAAATTCTTTTCA
1 AAAAAATTTAAAATTCTTTTCA
79878 AAAAA
1 AAAAA
79883 TATATTTTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
22 7 0.27
23 10 0.38
25 9 0.35
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.35
Consensus pattern (22 bp):
AAAAAATTTAAAATTCTTTTCA
Found at i:79882 original size:25 final size:26
Alignment explanation
Indices: 79823--79882 Score: 65
Period size: 25 Copynumber: 2.4 Consensus size: 26
79813 AACAGTCTAA
*
79823 TTTCAAATAAAAAATTTAAAAAATATT
1 TTTCAAAAAAAAAATTT-AAAAATATT
79850 TTTC--AAAAAAAATTT-AAAAT-TCT
1 TTTCAAAAAAAAAATTTAAAAATAT-T
79873 TTTCAAAAAA
1 TTTCAAAAAA
79883 TATATTTTGC
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
22 1 0.03
23 10 0.34
25 14 0.48
27 4 0.14
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.37
Consensus pattern (26 bp):
TTTCAAAAAAAAAATTTAAAAATATT
Found at i:85669 original size:7 final size:7
Alignment explanation
Indices: 85657--85681 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
85647 TTAAGTCCCT
85657 TTTTTTA
1 TTTTTTA
85664 TTTTTTA
1 TTTTTTA
85671 TTTTTTA
1 TTTTTTA
85678 TTTT
1 TTTT
85682 ATTTTGCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:85854 original size:10 final size:10
Alignment explanation
Indices: 85841--85883 Score: 61
Period size: 10 Copynumber: 4.3 Consensus size: 10
85831 AAATAAATAT
85841 AATTATTAAA
1 AATTATTAAA
*
85851 AATTATAAAA
1 AATTATTAAA
85861 AATTATT-AA
1 AATTATTAAA
85870 AATTATGTAAA
1 AATTAT-TAAA
85881 AAT
1 AAT
85884 ATTTTAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
9 8 0.28
10 16 0.55
11 5 0.17
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (10 bp):
AATTATTAAA
Found at i:85863 original size:29 final size:31
Alignment explanation
Indices: 85820--85883 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 31
85810 AAAAAAAGAT
*
85820 AAAA-TATAAATAAATAAATATAATTAT-TA
1 AAAATTATAAATAAATAAATAAAATTATGTA
* *
85849 AAAATTATAAA-AAATTATTAAAATTATGTA
1 AAAATTATAAATAAATAAATAAAATTATGTA
85879 AAAAT
1 AAAAT
85884 ATTTTAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 17 0.57
30 13 0.43
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (31 bp):
AAAATTATAAATAAATAAATAAAATTATGTA
Found at i:85881 original size:20 final size:19
Alignment explanation
Indices: 85841--85898 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 19
85831 AAATAAATAT
85841 AATTATTAAAAATTATAAAA
1 AATTATT-AAAATTATAAAA
85861 AATTATTAAAATTATGTAAAA
1 AATTATTAAAATTA--TAAAA
85882 ATATT-TTAAAA-TATAAA
1 A-ATTATTAAAATTATAAA
85899 CATATAGAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
18 4 0.11
19 7 0.20
20 9 0.26
21 12 0.34
22 3 0.09
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
AATTATTAAAATTATAAAA
Found at i:86089 original size:8 final size:8
Alignment explanation
Indices: 86076--86127 Score: 68
Period size: 9 Copynumber: 6.0 Consensus size: 8
86066 ATAAAATATT
86076 TTTTTATA
1 TTTTTATA
86084 TTTTTATAA
1 TTTTTAT-A
86093 TTTTTAATA
1 TTTTT-ATA
86102 TTTTTATA
1 TTTTTATA
86110 TTTTTCTATA
1 -TTTT-TATA
86120 TTTTTATA
1 TTTTTATA
86128 AATTTTATCG
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
8 14 0.35
9 20 0.50
10 6 0.15
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (8 bp):
TTTTTATA
Found at i:86096 original size:18 final size:18
Alignment explanation
Indices: 86075--86133 Score: 84
Period size: 18 Copynumber: 3.3 Consensus size: 18
86065 TATAAAATAT
86075 TTTTTTATATTTTTATAA
1 TTTTTTATATTTTTATAA
*
86093 TTTTTAATATTTTTAT-A
1 TTTTTTATATTTTTATAA
86110 TTTTTCTATATTTTTATAA
1 TTTTT-TATATTTTTATAA
*
86129 ATTTT
1 TTTTT
86134 ATCGTTTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
17 6 0.17
18 25 0.69
19 5 0.14
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTTTATATTTTTATAA
Found at i:86113 original size:36 final size:35
Alignment explanation
Indices: 86071--86160 Score: 110
Period size: 36 Copynumber: 2.5 Consensus size: 35
86061 TTATTATAAA
* *
86071 ATATTTTTTTATATTTTTATAATTTTTAATATTTTT
1 ATATTTTTTTATATTTTTATAAATTTT-ATAGTTTT
* *
86107 ATATTTTTCTATATTTTTATAAATTTTATCGTTTT
1 ATATTTTTTTATATTTTTATAAATTTTATAGTTTT
86142 A-ATTTATTTTAATATTTTT
1 ATATTT-TTTT-ATATTTTT
86161 TTTTATCATT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
34 4 0.09
35 10 0.21
36 33 0.70
ACGTcount: A:0.28, C:0.02, G:0.01, T:0.69
Consensus pattern (35 bp):
ATATTTTTTTATATTTTTATAAATTTTATAGTTTT
Found at i:86132 original size:10 final size:10
Alignment explanation
Indices: 86071--86133 Score: 71
Period size: 10 Copynumber: 6.7 Consensus size: 10
86061 TTATTATAAA
*
86071 ATATTTTTTT
1 ATATTTTTAT
86081 ATATTTTTAT
1 ATATTTTTAT
86091 A-ATTTTTA-
1 ATATTTTTAT
86099 ATA-TTTT-T
1 ATATTTTTAT
*
86107 ATATTTTTCT
1 ATATTTTTAT
86117 ATATTTTTAT
1 ATATTTTTAT
*
86127 AAATTTT
1 ATATTTT
86134 ATCGTTTTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
8 8 0.17
9 12 0.26
10 26 0.57
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.70
Consensus pattern (10 bp):
ATATTTTTAT
Found at i:86463 original size:23 final size:26
Alignment explanation
Indices: 86423--86474 Score: 74
Period size: 24 Copynumber: 2.1 Consensus size: 26
86413 AAATAACAAA
*
86423 TTAAATAAAAAAATTTTAAATAC-TT
1 TTAAATAAAAAAATTTTAAACACATT
86448 TTAAA-AAAAAAA-TTTAAACACATT
1 TTAAATAAAAAAATTTTAAACACATT
86472 TTA
1 TTA
86475 CACCCAAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 8 0.32
24 12 0.48
25 5 0.20
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.37
Consensus pattern (26 bp):
TTAAATAAAAAAATTTTAAACACATT
Found at i:89693 original size:31 final size:30
Alignment explanation
Indices: 89655--89755 Score: 111
Period size: 31 Copynumber: 3.4 Consensus size: 30
89645 TTAATATAAT
*
89655 ATTTGGTACCTGAACTTGATACTTTTTCCTA
1 ATTTGGTACCTAAACTTGATA-TTTTTCCTA
* *
89686 ATTTGGTACCTAAAC-T--T-TTTTACCCA
1 ATTTGGTACCTAAACTTGATATTTTTCCTA
*
89712 ATTCGGTACCTAAACTTGATATTTTTTCCTA
1 ATTTGGTACCTAAACTTGATA-TTTTTCCTA
*
89743 ATTTGGCACCTAA
1 ATTTGGTACCTAA
89756 CCTTTTTCTA
Statistics
Matches: 57, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
26 21 0.37
27 1 0.02
28 1 0.02
29 1 0.02
30 1 0.02
31 32 0.56
ACGTcount: A:0.26, C:0.21, G:0.11, T:0.43
Consensus pattern (30 bp):
ATTTGGTACCTAAACTTGATATTTTTCCTA
Found at i:89714 original size:26 final size:25
Alignment explanation
Indices: 89677--89728 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 25
89667 AACTTGATAC
* *
89677 TTTTTCCTAATTTGGTACCTAAACT
1 TTTTTCCCAATTCGGTACCTAAACT
89702 TTTTTACCCAATTCGGTACCTAAACT
1 TTTTT-CCCAATTCGGTACCTAAACT
89728 T
1 T
89729 GATATTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 5 0.21
26 19 0.79
ACGTcount: A:0.25, C:0.23, G:0.08, T:0.44
Consensus pattern (25 bp):
TTTTTCCCAATTCGGTACCTAAACT
Found at i:93824 original size:57 final size:57
Alignment explanation
Indices: 93762--93896 Score: 182
Period size: 57 Copynumber: 2.3 Consensus size: 57
93752 TTTTAATAAG
*
93762 ATTATTATTAAATATAATTTAATAAAATAATAAATAATTTAAT-TATATTTTAACATA
1 ATTATTATTAAATATAATTTAATAAAATAATAAATAATTTAATAAAT-TTTTAACATA
* * * * *
93819 TTTATTATTAAATACAATTTAATAAGATAATATATAATTTAATAAATTTTTAATATA
1 ATTATTATTAAATATAATTTAATAAAATAATAAATAATTTAATAAATTTTTAACATA
93876 ATTATTATTAAAATATGAATT
1 ATTATTATT-AAATAT-AATT
93897 AGTAAAAATC
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
57 56 0.84
58 7 0.10
59 4 0.06
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (57 bp):
ATTATTATTAAATATAATTTAATAAAATAATAAATAATTTAATAAATTTTTAACATA
Found at i:99859 original size:24 final size:24
Alignment explanation
Indices: 99823--99875 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
99813 TAAAATAACT
*
99823 AAAAAATAGATTT-TTATTTTAAA
1 AAAAAATAAATTTCTTATTTTAAA
*
99846 AAAAAATAAAATTTCTTTTTTTAAA
1 AAAAAAT-AAATTTCTTATTTTAAA
*
99871 GAAAA
1 AAAAA
99876 TAACTATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 7 0.28
24 5 0.20
25 13 0.52
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.40
Consensus pattern (24 bp):
AAAAAATAAATTTCTTATTTTAAA
Found at i:99865 original size:148 final size:148
Alignment explanation
Indices: 99584--99917 Score: 440
Period size: 150 Copynumber: 2.2 Consensus size: 148
99574 CAAAAATCAT
* * *
99584 TATTTTACTTAAAAATTCAAACTGTTATTTCGAAATAATTAAAAAAATAAAACTTTGTTAAAAAT
1 TATTTTGCTTAAAAATTCAAACTTTTATTTCGAAATAATTAAAAAAATAAAAATTTGTTAAAAAT
** ** *
99649 TTAAAATTTTTCTTTAAAACAACTAAAAAATAGATTTTTAATTTTTTAAAATCTAAATTTTCTCT
66 TTAAAATTTTTCTTTAAAACAACTAAAAAATAGATTTTTAATTTTAAAAAAAATAAATATTCTCT
* **
99714 TTTTTTAAAGGAAATCGC
131 TTTTTTAAAGAAAATAAC
* * *
99732 TATTTTGCTTAAAAATTCAAACTTTTATTTCGAAATAGTTAGAAAAAGTAAAAAATTTGTTAAAT
1 TATTTTGCTTAAAAATTCAAACTTTTATTTCGAAATAATTA-AAAAAAT-AAAAATTTGTTAAAA
* * *
99797 TTTTAAACTTTTTCTTTAAAATAACTAAAAAATAGATTTTT-ATTTTAAAAAAAAATAAA-ATT-
64 ATTTAAAATTTTTCTTTAAAACAACTAAAAAATAGATTTTTAATTTT-AAAAAAAATAAATATTC
99859 TCTTTTTTTAAAGAAAATAAC
128 TCTTTTTTTAAAGAAAATAAC
*
99880 TATTTTGCTTAAAAAAATCAAAACTTTTATTTCGAAAT
1 TATTTTGCTT-AAAAATTC-AAACTTTTATTTCGAAAT
99918 TGTTTAAAAA
Statistics
Matches: 163, Mismatches: 18, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
148 66 0.40
149 20 0.12
150 77 0.47
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (148 bp):
TATTTTGCTTAAAAATTCAAACTTTTATTTCGAAATAATTAAAAAAATAAAAATTTGTTAAAAAT
TTAAAATTTTTCTTTAAAACAACTAAAAAATAGATTTTTAATTTTAAAAAAAATAAATATTCTCT
TTTTTTAAAGAAAATAAC
Found at i:100385 original size:18 final size:18
Alignment explanation
Indices: 100362--100399 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
100352 TGAAACACAA
*
100362 AAAAATTAA-AATAATAAT
1 AAAAA-TAAGAATAAGAAT
100380 AAAAATAAGAATAAGAAT
1 AAAAATAAGAATAAGAAT
100398 AA
1 AA
100400 TAATGATGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (18 bp):
AAAAATAAGAATAAGAAT
Found at i:100386 original size:12 final size:12
Alignment explanation
Indices: 100369--100403 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
100359 CAAAAAAATT
100369 AAAATAATAATA
1 AAAATAATAATA
*
100381 AAAATAAGAATA
1 AAAATAATAATA
*
100393 AGAATAATAAT
1 AAAATAATAAT
100404 GATGATGATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (12 bp):
AAAATAATAATA
Found at i:102381 original size:24 final size:24
Alignment explanation
Indices: 102354--102402 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
102344 TGCCATTTAT
102354 TTATAGGGAGACATACGAGAATCC
1 TTATAGGGAGACATACGAGAATCC
102378 TTATAGGGAGACATACGAGAATCC
1 TTATAGGGAGACATACGAGAATCC
102402 T
1 T
102403 ACGTGAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.22
Consensus pattern (24 bp):
TTATAGGGAGACATACGAGAATCC
Found at i:102637 original size:29 final size:27
Alignment explanation
Indices: 102605--102658 Score: 63
Period size: 28 Copynumber: 1.9 Consensus size: 27
102595 GCATTTTATA
* *
102605 ATTTATTCCAATTTAATATATATTTTTCT
1 ATTT-TTCCAAATAAATAT-TATTTTTCT
*
102634 ATTTTTCGAAATAAATATTATTTTT
1 ATTTTTCCAAATAAATATTATTTTT
102659 AAATTAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 7 0.32
28 11 0.50
29 4 0.18
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.57
Consensus pattern (27 bp):
ATTTTTCCAAATAAATATTATTTTTCT
Found at i:109937 original size:14 final size:15
Alignment explanation
Indices: 109920--109948 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
109910 CATTATTATA
109920 AAAATA-AATAATTT
1 AAAATATAATAATTT
109934 AAAATATAATAATTT
1 AAAATATAATAATTT
109949 TTAATTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAAATATAATAATTT
Found at i:110135 original size:20 final size:21
Alignment explanation
Indices: 110107--110146 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
110097 TAATAAAAGT
110107 AATATTGATTCAATATTAATA
1 AATATTGATTCAATATTAATA
**
110128 AATA-TGATTGTATATTAAT
1 AATATTGATTCAATATTAAT
110147 GTACATGTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (21 bp):
AATATTGATTCAATATTAATA
Found at i:116442 original size:2 final size:2
Alignment explanation
Indices: 116437--116461 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
116427 AAAAAAAAAT
116437 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 T
116462 TTGGTGAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:118721 original size:13 final size:14
Alignment explanation
Indices: 118703--118731 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
118693 TTTTGTTTGG
118703 ATAAATAAAA-AAA
1 ATAAATAAAACAAA
118716 ATAAATAAAACAAA
1 ATAAATAAAACAAA
118730 AT
1 AT
118732 TTGATTATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.17
Consensus pattern (14 bp):
ATAAATAAAACAAA
Found at i:119843 original size:17 final size:17
Alignment explanation
Indices: 119813--119846 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
119803 CACAGACCGT
119813 TGATTCCTCAGCTCCCG
1 TGATTCCTCAGCTCCCG
* *
119830 TGATTGCTCGGCTCCCG
1 TGATTCCTCAGCTCCCG
119847 AAAACGCCGC
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:0.09, C:0.38, G:0.24, T:0.29
Consensus pattern (17 bp):
TGATTCCTCAGCTCCCG
Found at i:121875 original size:16 final size:18
Alignment explanation
Indices: 121854--121890 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
121844 GCTTTCTTTT
*
121854 AAAATAGAAT-AGAA-TA
1 AAAATAAAATAAGAAGTA
121870 AAAATAAAATAAGAAGTA
1 AAAATAAAATAAGAAGTA
121888 AAA
1 AAA
121891 TATACATCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 9 0.50
17 4 0.22
18 5 0.28
ACGTcount: A:0.73, C:0.00, G:0.11, T:0.16
Consensus pattern (18 bp):
AAAATAAAATAAGAAGTA
Found at i:122513 original size:14 final size:15
Alignment explanation
Indices: 122494--122526 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
122484 GGTAGGTTTT
*
122494 ATTTTG-ATCATTCA
1 ATTTTGAATAATTCA
122508 ATTTTGAATAATTCA
1 ATTTTGAATAATTCA
122523 ATTT
1 ATTT
122527 CATCATCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.33, C:0.09, G:0.06, T:0.52
Consensus pattern (15 bp):
ATTTTGAATAATTCA
Found at i:122711 original size:60 final size:61
Alignment explanation
Indices: 122600--122761 Score: 145
Period size: 60 Copynumber: 2.7 Consensus size: 61
122590 TTAGCCCTTT
* * * * * * *
122600 AATATTTATAAATTTTATCAATTTGATCCTAAATT--TAAAAGTTCAACAAATTTACCCCT-C
1 AATATTTACAAAATTTATCAATTTAATTCT-AATTCCAAAAATTTCAACAAATTTA-ACCTGC
* * *
122660 AATGA-TTACAAAATTTATC-ATTTAGTTCTAATTCCAAAAATTTCAATAAATTTAACCTGG
1 AAT-ATTTACAAAATTTATCAATTTAATTCTAATTCCAAAAATTTCAACAAATTTAACCTGC
* * *
122720 AATATTTACAAAGTTTTTCAATTTAATTCTAATTCTAAAAAT
1 AATATTTACAAAATTTATCAATTTAATTCTAATTCCAAAAAT
122762 AAAAAAGAGA
Statistics
Matches: 82, Mismatches: 14, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
58 4 0.05
59 11 0.13
60 46 0.56
61 21 0.26
ACGTcount: A:0.41, C:0.14, G:0.04, T:0.41
Consensus pattern (61 bp):
AATATTTACAAAATTTATCAATTTAATTCTAATTCCAAAAATTTCAACAAATTTAACCTGC
Found at i:125894 original size:13 final size:13
Alignment explanation
Indices: 125876--125902 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
125866 TAATTCATAT
125876 TTTATTATAAAAC
1 TTTATTATAAAAC
125889 TTTATTATAAAAC
1 TTTATTATAAAAC
125902 T
1 T
125903 AATGGAGCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTATTATAAAAC
Found at i:127488 original size:2 final size:2
Alignment explanation
Indices: 127465--127510 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
127455 TGAAGGGACA
* *
127465 AG AG A- AG AG AA AG AG GG 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 AG AG AG AG AG AG AG AG
127506 AG AG A
1 AG AG A
127511 AGGTGCCTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:130596 original size:6 final size:6
Alignment explanation
Indices: 130585--130627 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
130575 CCTCATTTTT
* * * *
130585 TTCATC TTCATC TTCACC TTGAGC TCCATC TTCATC TTCATC T
1 TTCATC TTCATC TTCATC TTCATC TTCATC TTCATC TTCATC T
130628 CATTCCTTCG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.16, C:0.35, G:0.05, T:0.44
Consensus pattern (6 bp):
TTCATC
Found at i:134144 original size:17 final size:18
Alignment explanation
Indices: 134112--134146 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
134102 GAGGTTTGTT
134112 AAATGAAATATTTTTAAA
1 AAATGAAATATTTTTAAA
134130 AAATGAAAT-TTTTTAAA
1 AAATGAAATATTTTTAAA
134147 TATATATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (18 bp):
AAATGAAATATTTTTAAA
Found at i:134833 original size:28 final size:29
Alignment explanation
Indices: 134761--134834 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 29
134751 ATTACAATTT
* *
134761 AAATTTATTTGATTCCTTTTAATAATATAA
1 AAATTAATTTGA-TCCATTTAATAATATAA
* * *
134791 AGATTAAATTAATCCATTTAATAATA-AA
1 AAATTAATTTGATCCATTTAATAATATAA
134819 AAATTAATTTGATCCA
1 AAATTAATTTGATCCA
134835 ATTATTATAA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
28 15 0.42
29 13 0.36
30 8 0.22
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (29 bp):
AAATTAATTTGATCCATTTAATAATATAA
Found at i:134977 original size:6 final size:6
Alignment explanation
Indices: 134966--135001 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
134956 CTTTTAAAGG
134966 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
135002 CCAGACATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:138812 original size:29 final size:29
Alignment explanation
Indices: 138780--138837 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
138770 AAACATAGAG
*
138780 CTATTACTAATCTCGAGTCAGATTACCAA
1 CTATTACTAATCTCGAGTCAAATTACCAA
138809 CTATTACTAATCTCGAGTCAAATTACCAA
1 CTATTACTAATCTCGAGTCAAATTACCAA
138838 AAAGCAAGCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.36, C:0.24, G:0.09, T:0.31
Consensus pattern (29 bp):
CTATTACTAATCTCGAGTCAAATTACCAA
Found at i:140953 original size:22 final size:24
Alignment explanation
Indices: 140900--140955 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 24
140890 GTGCTGGGGA
140900 AACAGAAGCACACACAGTGCTAGGT
1 AACAGAAGCACACACAGTGCTA-GT
*
140925 AACAGAAGCACACATAGTGCT-G-
1 AACAGAAGCACACACAGTGCTAGT
140947 AACAGAAGC
1 AACAGAAGC
140956 GCGCTAGCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 9 0.30
23 1 0.03
25 20 0.67
ACGTcount: A:0.43, C:0.23, G:0.23, T:0.11
Consensus pattern (24 bp):
AACAGAAGCACACACAGTGCTAGT
Found at i:141165 original size:21 final size:21
Alignment explanation
Indices: 141139--141179 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
141129 TGTCACAAAT
*
141139 TAATTACACA-ATCAATATTTA
1 TAATTAAACACAT-AATATTTA
141160 TAATTAAACACATAATATTT
1 TAATTAAACACATAATATTT
141180 CACATATACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (21 bp):
TAATTAAACACATAATATTTA
Done.