Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014421.1 Kokia drynarioides strain JFW-HI SEQ_129459, 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: 66239
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 42 characters in sequence are not A, C, G, or T
Found at i:3442 original size:25 final size:25
Alignment explanation
Indices: 3414--3465 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
3404 TTACAACAAC
3414 TTCTAAAAAAAAAACTC-AAGAGCAA
1 TTCTAAAAAAAAAACTCAAAGAG-AA
** *
3439 TTCTTGAAGAAAAACTCAAAGAGAA
1 TTCTAAAAAAAAAACTCAAAGAGAA
3464 TT
1 TT
3466 ATTATTAACT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.54, C:0.13, G:0.12, T:0.21
Consensus pattern (25 bp):
TTCTAAAAAAAAAACTCAAAGAGAA
Found at i:22113 original size:25 final size:25
Alignment explanation
Indices: 22085--22135 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
22075 TGGGTCAAAT
*
22085 TAATTAAATTAACACAATTAATTAA
1 TAATTAAATAAACACAATTAATTAA
* * *
22110 TAATTTAATAAACTCAATTTATTAA
1 TAATTAAATAAACACAATTAATTAA
22135 T
1 T
22136 GAAATAATTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (25 bp):
TAATTAAATAAACACAATTAATTAA
Found at i:24633 original size:17 final size:17
Alignment explanation
Indices: 24601--24634 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
24591 TTGTTAGTAA
* *
24601 TCATTGTCGTTGCATTT
1 TCATTGTCATTACATTT
24618 TCATTGTCATTACATTT
1 TCATTGTCATTACATTT
24635 AAATGTTAGT
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:0.18, C:0.18, G:0.12, T:0.53
Consensus pattern (17 bp):
TCATTGTCATTACATTT
Found at i:30457 original size:20 final size:20
Alignment explanation
Indices: 30421--30470 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
30411 ATTAACATGA
30421 TTTATATTAAGTATAAATAG-G
1 TTTA-ATTAAGTATAAA-AGTG
30442 TTTAATTAAG-ATTAAAAGTG
1 TTTAATTAAGTA-TAAAAGTG
*
30462 ATTAATTAA
1 TTTAATTAA
30471 ATCTTAATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 3 0.12
20 19 0.73
21 4 0.15
ACGTcount: A:0.46, C:0.00, G:0.12, T:0.42
Consensus pattern (20 bp):
TTTAATTAAGTATAAAAGTG
Found at i:35759 original size:13 final size:13
Alignment explanation
Indices: 35741--35770 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
35731 TTATATGAGT
*
35741 AATAAATACATAA
1 AATAAATAAATAA
35754 AATAAATAAATAA
1 AATAAATAAATAA
35767 AATA
1 AATA
35771 CGAAAGAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.23
Consensus pattern (13 bp):
AATAAATAAATAA
Found at i:37812 original size:18 final size:18
Alignment explanation
Indices: 37789--37853 Score: 103
Period size: 18 Copynumber: 3.6 Consensus size: 18
37779 CATTGAGCTT
37789 CACTTCATTGTTTTGGTC
1 CACTTCATTGTTTTGGTC
37807 CACTTCATTGTTTTGGTC
1 CACTTCATTGTTTTGGTC
* *
37825 CACTTCTTTGTATTGGTC
1 CACTTCATTGTTTTGGTC
*
37843 CACTTCTTTGT
1 CACTTCATTGT
37854 ATCTCATCAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.11, C:0.23, G:0.15, T:0.51
Consensus pattern (18 bp):
CACTTCATTGTTTTGGTC
Found at i:38002 original size:48 final size:48
Alignment explanation
Indices: 37948--38041 Score: 125
Period size: 48 Copynumber: 2.0 Consensus size: 48
37938 CATTGAGCTT
** * * * *
37948 CGCTTCATTGTTTTGGTCCACTTCTCTGTATCTCATTAGGAAGATGAC
1 CGCTTCATCATTTTGATCCACTTCTCTATATCTCATCAAGAAGATGAC
*
37996 CGCTTCATCATTTTGATTCACTTCTCTATATCTCATCAAGAAGATG
1 CGCTTCATCATTTTGATCCACTTCTCTATATCTCATCAAGAAGATG
38042 GGGGTTTGAA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.22, C:0.23, G:0.15, T:0.39
Consensus pattern (48 bp):
CGCTTCATCATTTTGATCCACTTCTCTATATCTCATCAAGAAGATGAC
Found at i:38056 original size:124 final size:123
Alignment explanation
Indices: 37827--38117 Score: 422
Period size: 124 Copynumber: 2.4 Consensus size: 123
37817 TTTTGGTCCA
* * * * *
37827 CTTCTTTGTATTGGTCCACTTCTTTGTATCTCATCATGAAGATGAACATTTCATTGTTTGATCCA
1 CTTCATTGTTTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGAACACTTCATTGTTTGATCCA
* * * *
37892 CTTCTCTGTATCTCATTAGGAAGATGGGGGTTTGAAGTTTCACTCACATTGAGCTTCG
66 CTTCTCTATATCTCATCAAGAAGATGGGGGTTTGAAGTTTCAATCACATTGAGCTTCG
* * * *
37950 CTTCATTGTTTTGGTCCACTTCTCTGTATCTCATTAGGAAGATGACCGCTTCATCAT-TTTGATT
1 CTTCATTGTTTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGAACACTTCAT--TGTTTGATC
38014 CACTTCTCTATATCTCATCAAGAAGATGGGGGTTTGAAGTTTCAATCACATTGAGCTTCG
64 CACTTCTCTATATCTCATCAAGAAGATGGGGGTTTGAAGTTTCAATCACATTGAGCTTCG
* *
38074 ATTCATTGTTTTGATCCACTTCTCTGTATCTCATCAGGAAGATG
1 CTTCATTGTTTTGGTCCACTTCTCTGTATCTCATCAGGAAGATG
38118 GGGGTTTGAA
Statistics
Matches: 150, Mismatches: 16, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
123 46 0.31
124 103 0.69
125 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.40
Consensus pattern (123 bp):
CTTCATTGTTTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGAACACTTCATTGTTTGATCCA
CTTCTCTATATCTCATCAAGAAGATGGGGGTTTGAAGTTTCAATCACATTGAGCTTCG
Found at i:38338 original size:144 final size:145
Alignment explanation
Indices: 38082--38350 Score: 434
Period size: 144 Copynumber: 1.9 Consensus size: 145
38072 CGATTCATTG
* * *
38082 TTTTGATCCACTTCTCTGTATCTCATCAGGAAGATGGGGGTTTGAAGTTTCACTCTACTCTACTA
1 TTTTGATCCACTTCTCTATATCTCATCAAGAAGATGGGGGTTTGAAGTTTCACTCTACTCCACTA
*
38147 TAACCTCAGGAATGTTGAGCTCTGCTTCATTATTTTGGTTCACTTCTCTGTATCTCATCATAAAG
66 TAACCTCAGGAATGTTGAGCTCTGCTTCATTATTTTGATTCACTTCTCTGTATCTCATCATAAAG
38212 ATGACCTTTTCATCA
131 ATGACCTTTTCATCA
* *
38227 TTTTGATCCACTTCTCTATATCTCATCAAGAAGAT-GGGGTTTGAAGTTTCACTTTACTCCACTG
1 TTTTGATCCACTTCTCTATATCTCATCAAGAAGATGGGGGTTTGAAGTTTCACTCTACTCCACTA
* * *
38291 TAATCTCAAGG-ATGTTGAGCTCTGCTTCATTGTTTTGATTCATTTCTCTGTATCTCATCA
66 TAACCTC-AGGAATGTTGAGCTCTGCTTCATTATTTTGATTCACTTCTCTGTATCTCATCA
38351 GGAAGATGGG
Statistics
Matches: 114, Mismatches: 9, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
144 78 0.68
145 36 0.32
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.41
Consensus pattern (145 bp):
TTTTGATCCACTTCTCTATATCTCATCAAGAAGATGGGGGTTTGAAGTTTCACTCTACTCCACTA
TAACCTCAGGAATGTTGAGCTCTGCTTCATTATTTTGATTCACTTCTCTGTATCTCATCATAAAG
ATGACCTTTTCATCA
Found at i:49973 original size:3 final size:3
Alignment explanation
Indices: 49965--49996 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
49955 TAACCAAATA
49965 TGT TGT TGT TGT TGT TGT TGT TGT TGT T-T TGT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
49997 AGATATTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TGT
Found at i:51976 original size:281 final size:281
Alignment explanation
Indices: 51473--52035 Score: 1108
Period size: 281 Copynumber: 2.0 Consensus size: 281
51463 ACTTGCAACG
51473 ACGACTACCTTGCGATGGCAAGGGTGGTGCGATGGCGATGAAGTGTAACAGTAATAGCAGCGTGC
1 ACGACTACCTTGCGATGGCAAGGGTGGTGCGATGGCGATGAAGTGTAACAGTAATAGCAGCGTGC
*
51538 GATGACGACAATAGCACTCTGGCAACCACCTTACAGAAGCGATGGGTGGTTTCGAAGACAAGGGA
66 GACGACGACAATAGCACTCTGGCAACCACCTTACAGAAGCGATGGGTGGTTTCGAAGACAAGGGA
*
51603 AGAAAAACTAGGGTTTTCTTCAGGATTTGAGGCTAACAACATAAGGGAAAATTAGGGGTGGCTAG
131 AGAAAAACTAGGGTTTTCTTCAGGATTTGAGGCTAACAACATAAGGGAAAATTAAGGGTGGCTAG
51668 GGTTTAAGCTACTTGATTTGAGGGATGTGAAAAATTGTGTGATGGAGAGGGGTTTATACAGGAAA
196 GGTTTAAGCTACTTGATTTGAGGGATGTGAAAAATTGTGTGATGGAGAGGGGTTTATACAGGAAA
51733 GAATTAGGGAAACATGTAGCA
261 GAATTAGGGAAACATGTAGCA
51754 ACGACTACCTTGCGATGGCAAGGGTGGTGCGATGGCGATGAAGTGTAACAGTAATAGCAGCGTGC
1 ACGACTACCTTGCGATGGCAAGGGTGGTGCGATGGCGATGAAGTGTAACAGTAATAGCAGCGTGC
51819 GACGACGACAATAGCACTCTGGCAACCACCTTACAGAAGCGATGGGTGGTTTCGAAGACAAGGGA
66 GACGACGACAATAGCACTCTGGCAACCACCTTACAGAAGCGATGGGTGGTTTCGAAGACAAGGGA
51884 AGAAAAACTAGGGTTTTCTTCAGGATTTGAGGCTAACAACATAAGGGAAAATTAAGGGTGGCTAG
131 AGAAAAACTAGGGTTTTCTTCAGGATTTGAGGCTAACAACATAAGGGAAAATTAAGGGTGGCTAG
51949 GGTTTAAGCTACTTGATTTGAGGGATGTGAAAAATTGTGTGATGGAGAGGGGTTTATACAGGAAA
196 GGTTTAAGCTACTTGATTTGAGGGATGTGAAAAATTGTGTGATGGAGAGGGGTTTATACAGGAAA
52014 GAATTAGGGAAACATGTAGCA
261 GAATTAGGGAAACATGTAGCA
52035 A
1 A
52036 AATTTTGGCT
Statistics
Matches: 280, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
281 280 1.00
ACGTcount: A:0.32, C:0.14, G:0.31, T:0.23
Consensus pattern (281 bp):
ACGACTACCTTGCGATGGCAAGGGTGGTGCGATGGCGATGAAGTGTAACAGTAATAGCAGCGTGC
GACGACGACAATAGCACTCTGGCAACCACCTTACAGAAGCGATGGGTGGTTTCGAAGACAAGGGA
AGAAAAACTAGGGTTTTCTTCAGGATTTGAGGCTAACAACATAAGGGAAAATTAAGGGTGGCTAG
GGTTTAAGCTACTTGATTTGAGGGATGTGAAAAATTGTGTGATGGAGAGGGGTTTATACAGGAAA
GAATTAGGGAAACATGTAGCA
Found at i:55593 original size:17 final size:16
Alignment explanation
Indices: 55566--55600 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
55556 AATATTTATT
*
55566 TATAAAAATAATTAAA
1 TATAAAAATAATAAAA
55582 TATAACAAATAATAAAA
1 TATAA-AAATAATAAAA
55599 TA
1 TA
55601 AACCCAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (16 bp):
TATAAAAATAATAAAA
Found at i:56448 original size:36 final size:35
Alignment explanation
Indices: 56419--56486 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
56409 AAAATGACGT
56419 CGTCTTGGCCTAATTGCATAGGCCCCAAAACAACG
1 CGTCTTGGCCTAATTGCATAGGCCCCAAAACAACG
* * *
56454 CTTTTTTGCCTAATTGCATAGGCCCCAAAACAA
1 CGTCTTGGCCTAATTGCATAGGCCCCAAAACAA
56487 TACCGTTTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.25
Consensus pattern (35 bp):
CGTCTTGGCCTAATTGCATAGGCCCCAAAACAACG
Found at i:56496 original size:35 final size:35
Alignment explanation
Indices: 56426--56496 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
56416 CGTCGTCTTG
* **
56426 GCCTAATTGCATAGGCCCCAAAACAACGCTTTTTT
1 GCCTAATTGCATAGGCCCCAAAACAACACCGTTTT
*
56461 GCCTAATTGCATAGGCCCCAAAACAATACCGTTTT
1 GCCTAATTGCATAGGCCCCAAAACAACACCGTTTT
56496 G
1 G
56497 GCATATGACC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (35 bp):
GCCTAATTGCATAGGCCCCAAAACAACACCGTTTT
Found at i:56756 original size:5 final size:5
Alignment explanation
Indices: 56746--56784 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
56736 TCCCTGTAAT
**
56746 TTTTA TTTTA TTTTA TTTTA GTTAAA TTTTA TTTTA TTT
1 TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA TTTTA TTT
56785 CTGTTTTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 26 0.90
6 3 0.10
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (5 bp):
TTTTA
Found at i:56942 original size:14 final size:15
Alignment explanation
Indices: 56923--56953 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
56913 CATTTATTCT
56923 TTATTTTATTT-GTA
1 TTATTTTATTTAGTA
56937 TTATTTTATTTAGTA
1 TTATTTTATTTAGTA
56952 TT
1 TT
56954 TAATTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (15 bp):
TTATTTTATTTAGTA
Found at i:56982 original size:17 final size:16
Alignment explanation
Indices: 56956--56990 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
56946 TTAGTATTTA
56956 ATTTTTATTTATTGTT
1 ATTTTTATTTATTGTT
*
56972 ATTTATTATTTATTTTT
1 ATTT-TTATTTATTGTT
56989 AT
1 AT
56991 GCTATTTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (16 bp):
ATTTTTATTTATTGTT
Found at i:56996 original size:28 final size:27
Alignment explanation
Indices: 56924--56997 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 27
56914 ATTTATTCTT
* *
56924 TATTTTATTTGTAT-TATTTTATTTAG
1 TATTTAATTTTTATCTATTTTATTTAG
* *
56950 TATTTAATTTTTATTTATTGTTATTTAT
1 TATTTAATTTTTATCTATT-TTATTTAG
56978 TATTT-ATTTTTATGCTATTT
1 TATTTAATTTTTAT-CTATTT
56998 ACATTCTTGC
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
26 12 0.29
27 13 0.32
28 16 0.39
ACGTcount: A:0.23, C:0.01, G:0.05, T:0.70
Consensus pattern (27 bp):
TATTTAATTTTTATCTATTTTATTTAG
Found at i:56997 original size:32 final size:29
Alignment explanation
Indices: 56914--56998 Score: 77
Period size: 28 Copynumber: 2.9 Consensus size: 29
56904 ATTTGGTCCC
*
56914 ATTTATTCTTTATTTTATTTGTA-TTATTTT
1 ATTTATTATTTA-TTT-TTTGTATTTATTTT
* *
56944 ATTTAGTATTTA-ATTTT-TATTTATTGTT
1 ATTTATTATTTATTTTTTGTATTTATT-TT
56972 ATTTATTATTTATTTTTATGCTATTTA
1 ATTTATTATTTATTTTT-TG-TATTTA
56999 CATTCTTGCC
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
26 2 0.05
27 8 0.18
28 14 0.32
29 3 0.07
30 11 0.25
32 6 0.14
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.69
Consensus pattern (29 bp):
ATTTATTATTTATTTTTTGTATTTATTTT
Found at i:57117 original size:74 final size:74
Alignment explanation
Indices: 56939--57164 Score: 259
Period size: 70 Copynumber: 3.0 Consensus size: 74
56929 TATTTGTATT
*
56939 ATTTTATTTAGTATTTAATTTTTATTTATTGTTATTTATTATTTATTTTTATGCTATTTACATTC
1 ATTTTATTTA--A-TTAATTTTTATTTATT-TTATTTATTATTTATTTTTATGCTATTTACATTT
*
57004 TTGCCTTTATTTA
62 TTTCCTTTATTTA
* *
57017 ATTTTA--T--TTAATTTTTATGTATTTTATTTATT-TGTTATTTTTATGCTATTTATATTTTTT
1 ATTTTATTTAATTAATTTTTATTTATTTTATTTATTAT-TTATTTTTATGCTATTTACATTTTTT
57077 CCTTTATTTA
65 CCTTTATTTA
* * *
57087 ATTTTATTTAATTAATTTTTATTT-TATTTATTTGTTATTTAATTATATG-TCATTTACATTTTT
1 ATTTTATTTAATTAATTTTTATTTAT-TTTATTTATTATTTATTTTTATGCT-ATTTACATTTTT
*
57150 GTCTTTTATTTA
64 -TCCTTTATTTA
57162 ATT
1 ATT
57165 ACACATTTTA
Statistics
Matches: 129, Mismatches: 10, Indels: 21
0.81 0.06 0.13
Matches are distributed among these distances:
69 1 0.01
70 48 0.37
71 15 0.12
72 1 0.01
73 2 0.02
74 41 0.32
75 14 0.11
76 1 0.01
78 6 0.05
ACGTcount: A:0.23, C:0.05, G:0.04, T:0.67
Consensus pattern (74 bp):
ATTTTATTTAATTAATTTTTATTTATTTTATTTATTATTTATTTTTATGCTATTTACATTTTTTC
CTTTATTTA
Found at i:57127 original size:20 final size:21
Alignment explanation
Indices: 57079--57130 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 21
57069 TATTTTTTCC
57079 TTTATTTAATTTTATTTAATT
1 TTTATTTAATTTTATTTAATT
*
57100 AATT-TTT-ATTTTATTT-ATT
1 -TTTATTTAATTTTATTTAATT
57119 TGTTATTTAATT
1 T-TTATTTAATT
57131 ATATGTCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
19 5 0.20
20 12 0.48
21 6 0.24
22 2 0.08
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (21 bp):
TTTATTTAATTTTATTTAATT
Found at i:57132 original size:15 final size:15
Alignment explanation
Indices: 57090--57151 Score: 56
Period size: 15 Copynumber: 4.1 Consensus size: 15
57080 TTATTTAATT
57090 TTATTTAATTAATTT-
1 TTATTTAATT-ATTTG
*
57105 TTATTTTATTTATTTG
1 TTA-TTTAATTATTTG
*
57121 TTATTTAATTATATG
1 TTATTTAATTATTTG
*
57136 TCATTTACATT-TTTG
1 TTATTTA-ATTATTTG
57151 T
1 T
57152 CTTTTATTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
15 27 0.69
16 12 0.31
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.66
Consensus pattern (15 bp):
TTATTTAATTATTTG
Found at i:57258 original size:154 final size:154
Alignment explanation
Indices: 57094--57417 Score: 639
Period size: 154 Copynumber: 2.1 Consensus size: 154
57084 TTAATTTTAT
57094 TTAATTAATTTTTATTTTATTTATTTGTTATTTAATTATATGTCATTTACATTTTTGTCTTTTAT
1 TTAATTAATTTTTATTTTATTTATTTGTTATTTAATTATATGTCATTTACATTTTTGTCTTTTAT
57159 TTAATTACACATTTTATTGTGTCCTTGACTTAATCATTTTAGAGTTTTCCCGTGATTGTGTTTTT
66 TTAATTACACATTTTATTGTGTCCTTGACTTAATCATTTTAGAGTTTTCCCGTGATTGTGTTTTT
57224 ATATATTTGTTATTACTTGTATTA
131 ATATATTTGTTATTACTTGTATTA
57248 TTAATTAATTTTTATTTTATTTATTTGTTATTTAATTATATGTCATTTACATTTTTGTCTTTTAT
1 TTAATTAATTTTTATTTTATTTATTTGTTATTTAATTATATGTCATTTACATTTTTGTCTTTTAT
*
57313 TTAATTACATATTTTATTGTGTCCTTGACTTAATCATTTTAGAGTTTTCCCGTGATTGTGTTTTT
66 TTAATTACACATTTTATTGTGTCCTTGACTTAATCATTTTAGAGTTTTCCCGTGATTGTGTTTTT
57378 ATATATTTGTTATTACTTGTATTA
131 ATATATTTGTTATTACTTGTATTA
57402 TTAATTAATTTTTATT
1 TTAATTAATTTTTATT
57418 GCCATCATTA
Statistics
Matches: 169, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
154 169 1.00
ACGTcount: A:0.24, C:0.08, G:0.09, T:0.60
Consensus pattern (154 bp):
TTAATTAATTTTTATTTTATTTATTTGTTATTTAATTATATGTCATTTACATTTTTGTCTTTTAT
TTAATTACACATTTTATTGTGTCCTTGACTTAATCATTTTAGAGTTTTCCCGTGATTGTGTTTTT
ATATATTTGTTATTACTTGTATTA
Done.