Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019236.1 Corchorus olitorius cultivar O-4 contig19269, 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: 97311
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:9 original size:2 final size:2
Alignment explanation
Indices: 3--65 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
1 CT
3 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
45 TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC T
66 TTTCTCAAAT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:7594 original size:24 final size:24
Alignment explanation
Indices: 7567--7614 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
7557 CAATTGCAAA
7567 TAGGGCAAGTGCTGCTTTGAGTAG
1 TAGGGCAAGTGCTGCTTTGAGTAG
*
7591 TAGGGCGAGTGCTGCTTTGAGTAG
1 TAGGGCAAGTGCTGCTTTGAGTAG
7615 GTCGAATGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.19, C:0.12, G:0.40, T:0.29
Consensus pattern (24 bp):
TAGGGCAAGTGCTGCTTTGAGTAG
Found at i:7613 original size:21 final size:23
Alignment explanation
Indices: 7567--7628 Score: 74
Period size: 21 Copynumber: 2.7 Consensus size: 23
7557 CAATTGCAAA
*
7567 TAGGGCAAGTGCTGCTTTGAGTAG
1 TAGGGCGAGTGCTGCTTT-AGTAG
7591 TAGGGCGAGTGCTGCTTT-G-AG
1 TAGGGCGAGTGCTGCTTTAGTAG
* *
7612 TAGGTCGAATGCTGCTT
1 TAGGGCGAGTGCTGCTT
7629 CTCAAAGCTC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
21 17 0.49
22 1 0.03
24 17 0.49
ACGTcount: A:0.18, C:0.15, G:0.37, T:0.31
Consensus pattern (23 bp):
TAGGGCGAGTGCTGCTTTAGTAG
Found at i:21962 original size:29 final size:29
Alignment explanation
Indices: 21924--22021 Score: 81
Period size: 29 Copynumber: 3.3 Consensus size: 29
21914 CCAAAATGCT
* *
21924 CAAATGAGGGTTTAATCTTTTAATTTGGC
1 CAAATAAGGGTCTAATCTTTTAATTTGGC
* * **
21953 CAAATAAGGGTCTAATATTATCGAAAAT-GC
1 CAAATAAGGGTCTAATCTT-T-TAATTTGGC
** *
21983 TCAAATAAGGGTCCGATCTTTTAATTTGGT
1 -CAAATAAGGGTCTAATCTTTTAATTTGGC
22013 CAAATAAGG
1 CAAATAAGG
22022 ACCTAACGTT
Statistics
Matches: 52, Mismatches: 13, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
29 28 0.54
30 5 0.10
31 19 0.37
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34
Consensus pattern (29 bp):
CAAATAAGGGTCTAATCTTTTAATTTGGC
Found at i:22040 original size:60 final size:60
Alignment explanation
Indices: 21905--22053 Score: 192
Period size: 60 Copynumber: 2.5 Consensus size: 60
21895 AATAAGGGTT
* ** **
21905 TAACGTTTGCCAAAATGCTCAAATGAGGGTTTAATCTTTTAATTTGGCCAAATAAGGGTC
1 TAACGTTTGCCAAAATGCTCAAATAAGGGTCCAATCTTTTAATTTGGCCAAATAAGGACC
** * * *
21965 TAATATTAT-CGAAAATGCTCAAATAAGGGTCCGATCTTTTAATTTGGTCAAATAAGGACC
1 TAACGTT-TGCCAAAATGCTCAAATAAGGGTCCAATCTTTTAATTTGGCCAAATAAGGACC
22025 TAACGTTTGCCAAAATGCTCAAATAAGGG
1 TAACGTTTGCCAAAATGCTCAAATAAGGG
22054 CCTAGCGTCA
Statistics
Matches: 74, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
59 1 0.01
60 72 0.97
61 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (60 bp):
TAACGTTTGCCAAAATGCTCAAATAAGGGTCCAATCTTTTAATTTGGCCAAATAAGGACC
Found at i:22135 original size:31 final size:31
Alignment explanation
Indices: 22097--22233 Score: 118
Period size: 31 Copynumber: 4.5 Consensus size: 31
22087 TCGACGCTAG
22097 GCCCTTATTTGAGCATTTTGGCAAACATTAA
1 GCCCTTATTTGAGCATTTTGGCAAACATTAA
** * * ***
22128 GCCCTTATTTG-GCCAAATT--AAAAGATCGG
1 GCCCTTATTTGAG-CATTTTGGCAAACATTAA
* * *
22157 GTCCTTATTTGAGCATTTTGGCAAACGTTAG
1 GCCCTTATTTGAGCATTTTGGCAAACATTAA
* *
22188 GCCCTTATTTGAGCATTTTGACAAACGTTAA
1 GCCCTTATTTGAGCATTTTGGCAAACATTAA
* *
22219 ACCCTTATTTAAGCA
1 GCCCTTATTTGAGCA
22234 ATTAGCCTAT
Statistics
Matches: 82, Mismatches: 20, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
29 19 0.23
30 2 0.02
31 61 0.74
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (31 bp):
GCCCTTATTTGAGCATTTTGGCAAACATTAA
Found at i:30148 original size:31 final size:31
Alignment explanation
Indices: 30113--30221 Score: 100
Period size: 31 Copynumber: 3.6 Consensus size: 31
30103 TTAATTTGAC
*
30113 CAAATAAGGACCTAACGTTATCGAAAATGCT
1 CAAATAAGGGCCTAACGTTATCGAAAATGCT
* * * * **
30144 CAAATAAGTGCCCGATC-TT-T-TAATTTGGC-
1 CAAATAAG-GGCCTAACGTTATCGAAAAT-GCT
30173 CAAATAAGGGCCTAACGTTATCGAAAATGCT
1 CAAATAAGGGCCTAACGTTATCGAAAATGCT
*
30204 CAAATAAGGGCCTGACGT
1 CAAATAAGGGCCTAACGT
30222 CAGTTTGGAT
Statistics
Matches: 59, Mismatches: 13, Indels: 12
0.70 0.15 0.14
Matches are distributed among these distances:
28 5 0.08
29 13 0.22
30 6 0.10
31 30 0.51
32 5 0.08
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (31 bp):
CAAATAAGGGCCTAACGTTATCGAAAATGCT
Found at i:30211 original size:60 final size:59
Alignment explanation
Indices: 30053--30212 Score: 223
Period size: 60 Copynumber: 2.7 Consensus size: 59
30043 GCTAATTGCT
* * * **
30053 CAAATAAGGGTCTAACATT-TGCTAAAATGCTCAAATAAAGGTTCGATCTTTTAATTTGAC
1 CAAATAAGGGCCTAACGTTAT-CGAAAATGCTCAAAT-AAGGCCCGATCTTTTAATTTGAC
* *
30113 CAAATAAGGACCTAACGTTATCGAAAATGCTCAAATAAGTGCCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAG-GCCCGATCTTTTAATTTGAC
30173 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGG
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGG
30213 GCCTGACGTC
Statistics
Matches: 90, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
59 4 0.04
60 85 0.94
61 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (59 bp):
CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGCCCGATCTTTTAATTTGAC
Found at i:30296 original size:31 final size:30
Alignment explanation
Indices: 30258--30362 Score: 99
Period size: 31 Copynumber: 3.5 Consensus size: 30
30248 TTATGTCAGC
*
30258 CCCTTATTTGAGTATTTTGGCAAACGTTAGG
1 CCCTTATTTGAGCATTTT-GCAAACGTTAGG
** * *
30289 CCCTTATTTG-GCCAAATT--AAAAGATCAGG
1 CCCTTATTTGAG-CATTTTGCAAACG-TTAGG
*
30318 CCCTTATTTGAACATTTTGACAAACGTTAGG
1 CCCTTATTTGAGCATTTTG-CAAACGTTAGG
30349 CCCTTATTTGAGCA
1 CCCTTATTTGAGCA
30363 ATTAGCCCAA
Statistics
Matches: 57, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
28 4 0.07
29 18 0.32
30 1 0.02
31 30 0.53
32 4 0.07
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (30 bp):
CCCTTATTTGAGCATTTTGCAAACGTTAGG
Found at i:46462 original size:6 final size:7
Alignment explanation
Indices: 46444--46473 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
46434 TTAACCAAGC
46444 AAAAAAG
1 AAAAAAG
46451 AAAAAAAG
1 -AAAAAAG
46459 AAAAAAG
1 AAAAAAG
46466 AAAAAAG
1 AAAAAAG
46473 A
1 A
46474 TGAATGGGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:52877 original size:11 final size:11
Alignment explanation
Indices: 52834--52871 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
52824 TTCCTATATA
*
52834 AAATAAATTAT
1 AAATTAATTAT
52845 CAAA-TAATTAT
1 -AAATTAATTAT
52856 AAATTAATTAT
1 AAATTAATTAT
52867 AAATT
1 AAATT
52872 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:61114 original size:16 final size:15
Alignment explanation
Indices: 61093--61124 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
61083 TTTAGTTTGA
61093 TTTTTTCTTTTTCTTT
1 TTTTTTCTTTTT-TTT
61109 TTTTTTCTTTTTTTT
1 TTTTTTCTTTTTTTT
61124 T
1 T
61125 CACCAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (15 bp):
TTTTTTCTTTTTTTT
Found at i:61119 original size:9 final size:10
Alignment explanation
Indices: 61095--61125 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
61085 TAGTTTGATT
61095 TTTTCTTTTTC
1 TTTT-TTTTTC
61106 TTTTTTTTTC
1 TTTTTTTTTC
61116 TTTTTTTTTC
1 TTTTTTTTTC
61126 ACCAATTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 16 0.80
11 4 0.20
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:68103 original size:3 final size:3
Alignment explanation
Indices: 68095--68125 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
68085 ATACATTTTT
68095 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
68126 AAAAGTTGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:68981 original size:2 final size:2
Alignment explanation
Indices: 68974--68999 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
68964 TCTTTGATTG
68974 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
69000 GGTATAATGA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:69319 original size:20 final size:20
Alignment explanation
Indices: 69294--69331 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
69284 AATTCAAAAC
*
69294 AAAATAAAACTATCCATTTT
1 AAAATAAAACTACCCATTTT
69314 AAAATAAAACTACCCATT
1 AAAATAAAACTACCCATT
69332 AGACTATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.18, G:0.00, T:0.29
Consensus pattern (20 bp):
AAAATAAAACTACCCATTTT
Found at i:70527 original size:439 final size:440
Alignment explanation
Indices: 69676--70531 Score: 1041
Period size: 439 Copynumber: 1.9 Consensus size: 440
69666 CCCGCTCTTA
* *
69676 ATAAACAAATCATTTTTTTTCTGGATTATTTATCAAATGATTCCTATACTTTTATAATTTATGCT
1 ATAAACAAATCATTTTTTTACGGGATTATTTATCAAATGATTCCTATACTTTTATAATTTATGCT
* * * *
69741 ATTTAGTCCCTCATAAATTCTGGGTTGGACGATTGAATGTTTGGACTTTAATTCTTTTATTTTTT
66 ATTGAATCCCTCATAAATTATGGGTTGGACAATTGAATGTTTGGACTTTAATTCTTTTATTTTTT
*
69806 ATATTACTTATCCGATAAAGGTGATTCAAGTGTCTATTAAAAGATAATTTCATGATTTACAACTT
131 ATATTACTTATCCGATAAAGGTGATTCAAGTGTCTATTAAAAGATAATTTCATGATCTACAACTT
* ** * *
69871 CCATGACAGACTCAAAAGCCAATTCTAATGTTTTGATTCTGAGAAATGCTTCCGAAATTTTGTGG
196 CCATGACAGACTCAAAAACCAATTCTAATGTTTCAATTCTGAAAAATGCTTCCGAAATTTTGTGA
* * *
69936 TCTCGATTGCCGGTCTATCTAATATTGTATAATTTTCGGTCCACTTGTACGATTGAGGTTGTTCA
261 TCTCGATTGCCGGTCTATCTAATATTGTATAATTTTCGGTCCACTTATACGATTGAAGTTGCTCA
* ** * *
70001 AGGGTCGGTTAAAAGATTATTCTGTGATCTACGACTTTTGTTAAGGGCCTGAAAGCTGAATATGA
326 AAGGTCGGTTAAAAGATTATTCTGTGATCTACGACTTTCATTAAGGACCCGAAAGCTGAATATGA
* * *
70066 TTAATGAGTTTCGTGGAGGGTTCAAGAAGGAATTTTTATGTTTGGTCTCC
391 TTAATGAGATTCATGAAGGGTTCAAGAAGGAATTTTTATGTTTGGTCTCC
* ** *
70116 ATAAACTAAT-ATTTTTTTACGGGATTATTTATCAAATGA-TCCTCATACTTTTATGCTTTATGT
1 ATAAACAAATCATTTTTTTACGGGATTATTTATCAAATGATTCCT-ATACTTTTATAATTTATGC
* * * *
70179 TATTGAAT-CCT-TTACAATTATGGGTTGGACAATTTAATGCTTT-GCCTTTTATT-TTTGTATT
65 TATTGAATCCCTCATA-AATTATGGGTTGGACAATTGAATG-TTTGGACTTTAATTCTTT-TATT
* * * * *
70240 TTTTGT-TCTATTTGTCCGATTAAGGTGATTCAAGTGTCTATTAAAAGGTAAATTT-ATGATCTA
127 TTTTATAT-TACTTATCCGATAAAGGTGATTCAAGTGTCTATTAAAAGAT-AATTTCATGATCTA
* * * **
70303 CAACTTTCATGGATA-ACTCAAAAACCAATTTTTAATGTTTCAATTCT-AAACAATGCTTTTGAA
190 CAACTTCCAT-GACAGACTCAAAAACCAA-TTCTAATGTTTCAATTCTGAAA-AATGCTTCCGAA
* * * * * * * *
70366 ATTTTGTGATTTTGATTGCCGGTTTATTTACTATTGTATAATTTTTGGTGCACTTATCCGATTGA
252 ATTTTGTGATCTCGATTGCCGGTCTATCTAATATTGTATAATTTTCGGTCCACTTATACGATTGA
* * * *
70431 AGTTGCTCAAATGTTGGTTAAAATG-TTATTGTGTGATCTACGACTTTCATTAAGGACCCGAATG
317 AGTTGCTCAAAGGTCGGTTAAAA-GATTATTCTGTGATCTACGACTTTCATTAAGGACCCGAAAG
* * *
70495 TTGAATTTGATTCATGAGATTCATGAAGGGTTCAAGA
381 CTGAATATGATTAATGAGATTCATGAAGGGTTCAAGA
70532 GGTAATTAGT
Statistics
Matches: 350, Mismatches: 56, Indels: 21
0.82 0.13 0.05
Matches are distributed among these distances:
437 6 0.02
438 112 0.32
439 222 0.63
440 10 0.03
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.42
Consensus pattern (440 bp):
ATAAACAAATCATTTTTTTACGGGATTATTTATCAAATGATTCCTATACTTTTATAATTTATGCT
ATTGAATCCCTCATAAATTATGGGTTGGACAATTGAATGTTTGGACTTTAATTCTTTTATTTTTT
ATATTACTTATCCGATAAAGGTGATTCAAGTGTCTATTAAAAGATAATTTCATGATCTACAACTT
CCATGACAGACTCAAAAACCAATTCTAATGTTTCAATTCTGAAAAATGCTTCCGAAATTTTGTGA
TCTCGATTGCCGGTCTATCTAATATTGTATAATTTTCGGTCCACTTATACGATTGAAGTTGCTCA
AAGGTCGGTTAAAAGATTATTCTGTGATCTACGACTTTCATTAAGGACCCGAAAGCTGAATATGA
TTAATGAGATTCATGAAGGGTTCAAGAAGGAATTTTTATGTTTGGTCTCC
Found at i:70966 original size:40 final size:40
Alignment explanation
Indices: 70913--70997 Score: 118
Period size: 40 Copynumber: 2.1 Consensus size: 40
70903 AGTGTTTGAT
70913 TATTTGATCGGTGTTAATGATTAATTT-TTGATCAAACACC
1 TATTTGATCGGTGTTAATGATT-ATTTATTGATCAAACACC
* * * *
70953 TATTTGATTGGTGTTAGTTATTATTTATTGATCAAACACT
1 TATTTGATCGGTGTTAATGATTATTTATTGATCAAACACC
70993 TATTT
1 TATTT
70998 TAATTCTACA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
39 4 0.10
40 36 0.90
ACGTcount: A:0.28, C:0.09, G:0.14, T:0.48
Consensus pattern (40 bp):
TATTTGATCGGTGTTAATGATTATTTATTGATCAAACACC
Found at i:71720 original size:53 final size:53
Alignment explanation
Indices: 71648--71752 Score: 194
Period size: 53 Copynumber: 2.0 Consensus size: 53
71638 AAAATTTTCC
71648 AAATTTTCTCCACTATCAAACCGGTTTTATCCGGTCAGAA-CTCGGTCCAACCA
1 AAATTTTCTCCACTATCAAACCGGTTTTATCCGGTCAGAACCT-GGTCCAACCA
71701 AAATTTTCTCCACTATCAAACCGGTTTTATCCGGTCAGAACCTGGTCCAACC
1 AAATTTTCTCCACTATCAAACCGGTTTTATCCGGTCAGAACCTGGTCCAACC
71753 GGTTTTTACC
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
53 49 0.96
54 2 0.04
ACGTcount: A:0.28, C:0.30, G:0.13, T:0.29
Consensus pattern (53 bp):
AAATTTTCTCCACTATCAAACCGGTTTTATCCGGTCAGAACCTGGTCCAACCA
Found at i:72243 original size:128 final size:128
Alignment explanation
Indices: 72017--72274 Score: 344
Period size: 128 Copynumber: 2.0 Consensus size: 128
72007 TTTCCTGCTG
* * *
72017 TTTTCTTTGGATTTTCAGAGGTGAAGATGACACGGAGAAGGGGAAGCCGAGCTAATTTTATGGGT
1 TTTTCTTTGGATTTTCAGACGTGAAGATGACACGGAGAAGAGGAAGCCGAGCTAATTTGATGGGT
* * * * *
72082 ATTCTAATTTCATTCTTAATTTTTTCTTCCCTTGGTTGAAATTCAATGGGGTTTTTTAATTTCT
66 AATCTAATTTCAGTCTTAATATTTTCTCCCCTTGGTTGAAATTCAAT-GGGTTTTATAATTTCT
* * *
72146 TTTTCTTTGGATTTTTAGACGTGAAGAT-CCATGGAGAAGAGGAAGCCGAGCTAATTGATGGATG
1 TTTTCTTTGGATTTTCAGACGTGAAGATGACACGGAGAAGAGGAAGCCGAGCTAATT--T-GATG
*
72210 GGTAATCTAATTTTAGTC-TAA-ATTTTC-CCCCTTGGTTGAAATTCAATGGGTTTTATAATTTC
63 GGTAATCTAATTTCAGTCTTAATATTTTCTCCCCTTGGTTGAAATTCAATGGGTTTTATAATTTC
72272 T
128 T
72273 TT
1 TT
72275 CTTTATTTAA
Statistics
Matches: 114, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
127 17 0.15
128 44 0.39
129 31 0.27
130 4 0.04
131 18 0.16
ACGTcount: A:0.25, C:0.12, G:0.22, T:0.41
Consensus pattern (128 bp):
TTTTCTTTGGATTTTCAGACGTGAAGATGACACGGAGAAGAGGAAGCCGAGCTAATTTGATGGGT
AATCTAATTTCAGTCTTAATATTTTCTCCCCTTGGTTGAAATTCAATGGGTTTTATAATTTCT
Found at i:75445 original size:79 final size:79
Alignment explanation
Indices: 75322--75475 Score: 274
Period size: 79 Copynumber: 1.9 Consensus size: 79
75312 TATTTCGAAT
*
75322 AAATTGCTACATGTTTCTACTAGTCCCTTCAATACCACACTACATCGATCAATCCAAACTCCATA
1 AAATTGCTACATGTTTCTACTAGTCCCTTCAATACCACACTACATCGATCAATCCAAACTCCAAA
75387 GCCTCCATATTTCG
66 GCCTCCATATTTCG
*
75401 AAATTGCTACATGTTTCTACTAGTCCCTTC-ATCACCACACTACATCGATCAGTCCAAACTCCAA
1 AAATTGCTACATGTTTCTACTAGTCCCTTCAAT-ACCACACTACATCGATCAATCCAAACTCCAA
75465 AGCCTCCATAT
65 AGCCTCCATAT
75476 AATAGTGAAA
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
78 2 0.03
79 70 0.97
ACGTcount: A:0.31, C:0.32, G:0.08, T:0.29
Consensus pattern (79 bp):
AAATTGCTACATGTTTCTACTAGTCCCTTCAATACCACACTACATCGATCAATCCAAACTCCAAA
GCCTCCATATTTCG
Found at i:80845 original size:7 final size:7
Alignment explanation
Indices: 80791--80830 Score: 62
Period size: 7 Copynumber: 5.6 Consensus size: 7
80781 GAAGAGAGGA
80791 ATATATT
1 ATATATT
80798 ATATTATT
1 ATA-TATT
80806 ATATATT
1 ATATATT
80813 ATATATT
1 ATATATT
*
80820 ATATATC
1 ATATATT
80827 ATAT
1 ATAT
80831 CATAATATCA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
7 24 0.77
8 7 0.23
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (7 bp):
ATATATT
Found at i:82964 original size:19 final size:19
Alignment explanation
Indices: 82936--82976 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
82926 TTGCCCCTAT
* *
82936 TCTCTTTCTTCCCACTCAC
1 TCTCTCTCTTCACACTCAC
*
82955 TCTCTCTCTTCATACTCAC
1 TCTCTCTCTTCACACTCAC
82974 TCT
1 TCT
82977 TTTAACTAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.12, C:0.44, G:0.00, T:0.44
Consensus pattern (19 bp):
TCTCTCTCTTCACACTCAC
Found at i:83626 original size:21 final size:21
Alignment explanation
Indices: 83602--83644 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
83592 TTGTTATCGC
83602 TTAATTTATCGAACAAAGATA
1 TTAATTTATCGAACAAAGATA
83623 TTAATTTATCGAACAAAGATA
1 TTAATTTATCGAACAAAGATA
83644 T
1 T
83645 AGAAGGATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.35
Consensus pattern (21 bp):
TTAATTTATCGAACAAAGATA
Found at i:84850 original size:25 final size:25
Alignment explanation
Indices: 84807--84857 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 25
84797 TGATAAATTT
84807 TTATATATAGTTATAATTTCTTAAAAA
1 TTATATATAGTTATAA-TT-TTAAAAA
*
84834 TTATATGTA-TTAT-ATTTTAAAAA
1 TTATATATAGTTATAATTTTAAAAA
84857 T
1 T
84858 AATGTGGAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 8 0.35
24 2 0.09
25 1 0.04
26 4 0.17
27 8 0.35
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (25 bp):
TTATATATAGTTATAATTTTAAAAA
Found at i:86870 original size:71 final size:71
Alignment explanation
Indices: 86754--86894 Score: 273
Period size: 71 Copynumber: 2.0 Consensus size: 71
86744 CAAGTATAAA
86754 ACCTAATTATTAAATAACTTTATCCCAAAATTACCCCTATTAACTCCCCAAAGGGAGCCAACAAT
1 ACCTAATTATTAAATAACTTTATCCCAAAATTACCCCTATTAACTCCCCAAAGGGAGCCAACAAT
86819 ACATAT
66 ACATAT
*
86825 ACCTAATTATTAAATAACTTTATCCCAAAATTACCCCTATTAACTCCCCAAAGGGAGCCAAGAAT
1 ACCTAATTATTAAATAACTTTATCCCAAAATTACCCCTATTAACTCCCCAAAGGGAGCCAACAAT
86890 ACATA
66 ACATA
86895 CATATATATA
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 69 1.00
ACGTcount: A:0.41, C:0.26, G:0.06, T:0.26
Consensus pattern (71 bp):
ACCTAATTATTAAATAACTTTATCCCAAAATTACCCCTATTAACTCCCCAAAGGGAGCCAACAAT
ACATAT
Found at i:87361 original size:2 final size:2
Alignment explanation
Indices: 87354--87391 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
87344 ATTGGGTTTT
*
87354 TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
87392 GATTACAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:89035 original size:20 final size:20
Alignment explanation
Indices: 89010--89049 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
89000 ATTTAGGGTA
89010 TTACTAAATACCGCCCCCTT
1 TTACTAAATACCGCCCCCTT
**
89030 TTACTAGCTACCGCCCCCTT
1 TTACTAAATACCGCCCCCTT
89050 GGACTATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.20, C:0.42, G:0.07, T:0.30
Consensus pattern (20 bp):
TTACTAAATACCGCCCCCTT
Found at i:89055 original size:20 final size:20
Alignment explanation
Indices: 89018--89055 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
89008 TATTACTAAA
**
89018 TACCGCCCCCTTTTACTAGC
1 TACCGCCCCCTTGGACTAGC
89038 TACCGCCCCCTTGGACTA
1 TACCGCCCCCTTGGACTA
89056 TTTTGCCATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.16, C:0.45, G:0.13, T:0.26
Consensus pattern (20 bp):
TACCGCCCCCTTGGACTAGC
Found at i:94669 original size:14 final size:13
Alignment explanation
Indices: 94650--94688 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
94640 AAATTGTAAA
94650 ATTTAAAAAATTT
1 ATTTAAAAAATTT
* *
94663 CATTTAAGAAATAT
1 -ATTTAAAAAATTT
94677 ATTTAAAAAATT
1 ATTTAAAAAATT
94689 CTAATATATA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (13 bp):
ATTTAAAAAATTT
Found at i:94926 original size:131 final size:127
Alignment explanation
Indices: 94674--94918 Score: 381
Period size: 131 Copynumber: 1.9 Consensus size: 127
94664 ATTTAAGAAA
94674 TATATTTAAAAAATTCTAATATATATAAGTTTTTAAAATAAAATAGTAAAACGGTAAAAATAAAA
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTAAAATAAAATAGTAAAACGGTAAAAAT---A
*
94739 TAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAATTGTAAAA
63 CA-GTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAATTGTAAAA
94804 G
127 G
* * *
94805 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT-CA-
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTAAAATAAAATAGTAAAACGGTAAAAATACAG
*
94868 TA-AA-GATATTAGATTTAATTAAATAAAATTAGAGTTTTTAGTTGAGTAAAA
66 TATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAA
94919 CTATAAAAAT
Statistics
Matches: 109, Mismatches: 5, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
123 46 0.42
124 2 0.02
125 2 0.02
127 1 0.01
131 58 0.53
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.37
Consensus pattern (127 bp):
TATATTTAAAAAATTCTAATATATATAAGTTTTTAAAATAAAATAGTAAAACGGTAAAAATACAG
TATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAATTGTAAAAG
Found at i:95031 original size:2 final size:2
Alignment explanation
Indices: 95013--95055 Score: 50
Period size: 2 Copynumber: 20.5 Consensus size: 2
95003 GTACTTTTAA
* *
95013 AT AT AGT AT AG AT AT AT AT AT AT AT AT AT CT AT AT ACT AT AT A
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A
95056 AGTCTAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
2 31 0.89
3 4 0.11
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.44
Consensus pattern (2 bp):
AT
Found at i:95386 original size:30 final size:27
Alignment explanation
Indices: 95336--95418 Score: 112
Period size: 30 Copynumber: 3.0 Consensus size: 27
95326 GTTAATTTAG
95336 ACTTATTATTATTATAATAATTATTAA
1 ACTTATTATTATTATAATAATTATTAA
*
95363 ACTTATTATTAGTGGTATTATAATTATTAA
1 ACTTATTATTA-T--TATAATAATTATTAA
* *
95393 ACTTATTATTATAATAATTATTATTA
1 ACTTATTATTATTATAATAATTATTA
95419 TTAGTGGTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
27 22 0.45
28 1 0.02
29 1 0.02
30 25 0.51
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.52
Consensus pattern (27 bp):
ACTTATTATTATTATAATAATTATTAA
Done.