Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022702.1 Corchorus olitorius cultivar O-4 contig22735, 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: 109429
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:797 original size:98 final size:99
Alignment explanation
Indices: 507--810 Score: 450
Period size: 99 Copynumber: 3.1 Consensus size: 99
497 AGATGAGTGC
* *
507 TAAATTCTATAAACAATTTTTTTTTATTTCATTTGGAAACGGAATTTAACACGGAAACTACATAT
1 TAAATTCTATAAATAA--TTTTTCTATTTCATTTGGAAACGGAATTTAACACGGAAACTACATAT
*
572 TCGTGTCTAAATCCGCTTTCAAATGATAATATGTAA
64 TCGTGTCTAAATCCGCTTCCAAATGATAATATGTAA
* * *
608 TAAATTCCATAGATAAATTTTTC-ATTTCATTTGGAAACGGAATTTAATACGGAAACTACATATT
1 TAAATTCTATAAAT-AATTTTTCTATTTCATTTGGAAACGGAATTTAACACGGAAACTACATATT
** *
672 CGTGTCTAAATCCGCTTCCAACCGATAATAAGTAA
65 CGTGTCTAAATCCGCTTCCAAATGATAATATGTAA
* * * *
707 TAAATTCTATAAATAATTTTTCTACTTCATTTGGAAACGGAACTTAGCACGG-AACTACATATCC
1 TAAATTCTATAAATAATTTTTCTATTTCATTTGGAAACGGAATTTAACACGGAAACTACATATTC
771 GTGTCTAAATCCGCTTCCAAATGATAATATGTAA
66 GTGTCTAAATCCGCTTCCAAATGATAATATGTAA
805 TAAATT
1 TAAATT
811 TTTATCGTAA
Statistics
Matches: 182, Mismatches: 19, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
98 56 0.31
99 108 0.59
100 5 0.03
101 11 0.06
102 2 0.01
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.36
Consensus pattern (99 bp):
TAAATTCTATAAATAATTTTTCTATTTCATTTGGAAACGGAATTTAACACGGAAACTACATATTC
GTGTCTAAATCCGCTTCCAAATGATAATATGTAA
Found at i:1246 original size:98 final size:98
Alignment explanation
Indices: 979--1264 Score: 380
Period size: 97 Copynumber: 2.9 Consensus size: 98
969 AAGTACTATC
* * * *
979 TTCTATAAATTAATTTTCTATTTCACTTGGAAACGGAATTTAACACGGAAACTGCATATCTGTGT
1 TTCTATAAATAAATTTTTTATTTCA-TTGGAAACGGAATTTAACACGGAAACTACATATCCGTGT
* * * *
1044 CTAAATCCGATTCAAATTGATAATGATAAAATAA
65 CTAAATCCGCTTCAAACTAATAATAATAAAATAA
* *
1078 TTCTATAAATAAA--TTTTATTTCATATGGAAACGGAATTTAACACAGAAACTACATATTCGTGT
1 TTCTATAAATAAATTTTTTATTTCAT-TGGAAACGGAATTTAACACGGAAACTACATATCCGTGT
* *
1141 CTAAATCCGCTTCTAACTAATAATAATAAAATTA
65 CTAAATCCGCTTCAAACTAATAATAATAAAATAA
* * *
1175 TTCTATAAATAAATTTTTTATTTCATTTGAAACGGAATTTAACACGGAAATTACATATCCATGTC
1 TTCTATAAATAAATTTTTTATTTCATTGGAAACGGAATTTAACACGGAAACTACATATCCGTGTC
*
1240 TAAATCCGCTTCCAAA-TGATAATAA
66 TAAATCCGCTT-CAAACTAATAATAA
1265 ATTTAATAAA
Statistics
Matches: 164, Mismatches: 19, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
96 1 0.01
97 84 0.51
98 53 0.32
99 26 0.16
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.36
Consensus pattern (98 bp):
TTCTATAAATAAATTTTTTATTTCATTGGAAACGGAATTTAACACGGAAACTACATATCCGTGTC
TAAATCCGCTTCAAACTAATAATAATAAAATAA
Found at i:3520 original size:45 final size:45
Alignment explanation
Indices: 3466--3569 Score: 122
Period size: 45 Copynumber: 2.3 Consensus size: 45
3456 AGGCAGCCTC
* * **
3466 TTATTTTGTATAGGTC-CTTAA-TTTGACATTATCTAGAGGAGGCAT
1 TTATTTTGTATAGGTCAC-TAACTTTCA-ATGATCTAGAAAAGGCAT
* *
3511 TTATTTTGTATAGATCACTAACTTTCAATGATCTAGAAAAGGCCT
1 TTATTTTGTATAGGTCACTAACTTTCAATGATCTAGAAAAGGCAT
3556 TTATTTTGTATAGG
1 TTATTTTGTATAGG
3570 GTTTAGTTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
45 45 0.90
46 5 0.10
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42
Consensus pattern (45 bp):
TTATTTTGTATAGGTCACTAACTTTCAATGATCTAGAAAAGGCAT
Found at i:3874 original size:24 final size:24
Alignment explanation
Indices: 3842--3893 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
3832 TGTCAGATAG
*
3842 AATTCCGTTTCTGATTCTGTTGCA
1 AATTCCGTTTCTGATTCCGTTGCA
*
3866 AATTCCGTTTTTGATTCCGTTGCA
1 AATTCCGTTTCTGATTCCGTTGCA
3890 AATT
1 AATT
3894 ACTCATAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.15, T:0.46
Consensus pattern (24 bp):
AATTCCGTTTCTGATTCCGTTGCA
Found at i:6153 original size:60 final size:61
Alignment explanation
Indices: 6052--6173 Score: 210
Period size: 60 Copynumber: 2.0 Consensus size: 61
6042 TGACCCGCGC
*
6052 TTCGCTGCAGGTTTTTTTTTTTTTTTTGAGTAGTAGATTCATTTAATTAAAGAGTTCGGAT
1 TTCGCTGCAGGTTTTTTTTTTTTTTTTGAGTAGTAGATTCATTCAATTAAAGAGTTCGGAT
* *
6113 TTCGCTGTAGG-TTTTTTTTTTTTTTTGAGTAGTAGGTTCATTCAATTAAAGAGTTCGGAT
1 TTCGCTGCAGGTTTTTTTTTTTTTTTTGAGTAGTAGATTCATTCAATTAAAGAGTTCGGAT
6173 T
1 T
6174 ACAAACACAA
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
60 48 0.83
61 10 0.17
ACGTcount: A:0.20, C:0.08, G:0.20, T:0.51
Consensus pattern (61 bp):
TTCGCTGCAGGTTTTTTTTTTTTTTTTGAGTAGTAGATTCATTCAATTAAAGAGTTCGGAT
Found at i:6221 original size:31 final size:31
Alignment explanation
Indices: 6186--6247 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
6176 AAACACAAAC
6186 ACCGGGAGTAAACCCCCGTACCGCACATAGT
1 ACCGGGAGTAAACCCCCGTACCGCACATAGT
*
6217 ACCGGGAGTAAACCCTCGTACCGCACATAGT
1 ACCGGGAGTAAACCCCCGTACCGCACATAGT
6248 TAGCAAACAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.29, C:0.34, G:0.23, T:0.15
Consensus pattern (31 bp):
ACCGGGAGTAAACCCCCGTACCGCACATAGT
Found at i:7961 original size:70 final size:70
Alignment explanation
Indices: 7839--7971 Score: 223
Period size: 70 Copynumber: 1.9 Consensus size: 70
7829 GATTCTTGTG
* *
7839 CCGTTACCCAATGTGCATTTAACATGATGACATTAACAGATTAAGTTGGGTTCATGATACCAATA
1 CCGTTACCCAATGTACATTTAACATGATGACAATAACAGATTAAGTTGGGTTCATGATACCAATA
7904 CCAAA
66 CCAAA
*
7909 CCGTTAACCCAATGTACATTTAACATGATGATAAT-ACAGATTAAGTTGGGTTCATGATACCAA
1 CCGTT-ACCCAATGTACATTTAACATGATGACAATAACAGATTAAGTTGGGTTCATGATACCAA
7972 ATAAGCTTTA
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
70 33 0.56
71 26 0.44
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (70 bp):
CCGTTACCCAATGTACATTTAACATGATGACAATAACAGATTAAGTTGGGTTCATGATACCAATA
CCAAA
Found at i:14478 original size:22 final size:23
Alignment explanation
Indices: 14450--14492 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
14440 TAGAAGGAGT
14450 AGGTTTTACT-TTCCTACCAGAA
1 AGGTTTTACTATTCCTACCAGAA
14472 AGGTTTTACTATTCCTACCAG
1 AGGTTTTACTATTCCTACCAG
14493 GATTAGGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (23 bp):
AGGTTTTACTATTCCTACCAGAA
Found at i:17209 original size:2 final size:2
Alignment explanation
Indices: 17202--17233 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
17192 CACCTGTTGA
17202 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
17234 CAGATGAAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:21925 original size:30 final size:31
Alignment explanation
Indices: 21870--21927 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
21860 GTCATTAATG
21870 AATATTGTGATTATTCATGAATCAAGAGATA
1 AATATTGTGATTATTCATGAATCAAGAGATA
21901 AATATTGTGATTATTCAT-AATCAAGAG
1 AATATTGTGATTATTCATGAATCAAGAG
21928 CTCTCCTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
30 9 0.33
31 18 0.67
ACGTcount: A:0.41, C:0.07, G:0.16, T:0.36
Consensus pattern (31 bp):
AATATTGTGATTATTCATGAATCAAGAGATA
Found at i:22014 original size:13 final size:13
Alignment explanation
Indices: 21996--22023 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
21986 CATGTATCCA
21996 TTAAAAGTTGTGT
1 TTAAAAGTTGTGT
22009 TTAAAAGTTGTGT
1 TTAAAAGTTGTGT
22022 TT
1 TT
22024 TTTGAGAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (13 bp):
TTAAAAGTTGTGT
Found at i:23024 original size:2 final size:2
Alignment explanation
Indices: 23017--23051 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
23007 ATGTTCATGC
23017 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
23052 TTCTTTGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:26488 original size:11 final size:11
Alignment explanation
Indices: 26472--26501 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
26462 CTCATTCGAC
26472 AAACTCTCTTA
1 AAACTCTCTTA
26483 AAACTCTCTTA
1 AAACTCTCTTA
26494 AAACTCTC
1 AAACTCTC
26502 GTTACTCTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.37, C:0.30, G:0.00, T:0.33
Consensus pattern (11 bp):
AAACTCTCTTA
Found at i:29581 original size:29 final size:29
Alignment explanation
Indices: 29548--29805 Score: 304
Period size: 29 Copynumber: 8.9 Consensus size: 29
29538 TTCGCACGTT
*
29548 CAGGGGCATTTTGGTCATTTTTTCATATC
1 CAGGGGCATTTTGGTCATTTTTGCATATC
* *
29577 CAGGGGTATTTCGGTCATTTTTGCATATC
1 CAGGGGCATTTTGGTCATTTTTGCATATC
*
29606 CAGGGGCATTTTGGTCATTTTTGCACATC
1 CAGGGGCATTTTGGTCATTTTTGCATATC
*
29635 CAGTGGGCATTTTGGTCATTTTTGCATATT
1 CAG-GGGCATTTTGGTCATTTTTGCATATC
* *
29665 CAGGGGCATTTTGGTCATTTTTGCATGTT
1 CAGGGGCATTTTGGTCATTTTTGCATATC
* * *
29694 TAGGTGCATTTTGGTCATTTTTGCACATC
1 CAGGGGCATTTTGGTCATTTTTGCATATC
* * * * *
29723 TAGGGGTATTATAGTCATTTTTGCGTATC
1 CAGGGGCATTTTGGTCATTTTTGCATATC
** *
29752 CAAAGGCATTTTGGTCATCTTTGCAT-TC
1 CAGGGGCATTTTGGTCATTTTTGCATATC
* * *
29780 TA-CGGCAGTTTGGTCATTTTTGCATA
1 CAGGGGCATTTTGGTCATTTTTGCATA
29806 CTTTAGGTTC
Statistics
Matches: 195, Mismatches: 32, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
27 20 0.10
28 3 0.02
29 145 0.74
30 27 0.14
ACGTcount: A:0.18, C:0.16, G:0.23, T:0.43
Consensus pattern (29 bp):
CAGGGGCATTTTGGTCATTTTTGCATATC
Found at i:29703 original size:88 final size:85
Alignment explanation
Indices: 29548--29803 Score: 323
Period size: 88 Copynumber: 3.0 Consensus size: 85
29538 TTCGCACGTT
* * * *
29548 CAGGGGCATTTTGGTCATTTTTTCATATCCAGGGGTATTTCGGTCATTTTTGCATATCCAGGGGC
1 CAGGGGCATTTTGGTCATTTTTGCATATCCAGGGGCATTTTGGTCATTTTTGCAT-TCTA-GGGC
29613 ATTTTGGTCATTTTTGCACATC
64 ATTTTGGTCATTTTTGCACATC
* *
29635 CAGTGGGCATTTTGGTCATTTTTGCATATTCAGGGGCATTTTGGTCATTTTTGCATGTTTAGGTG
1 CAG-GGGCATTTTGGTCATTTTTGCATATCCAGGGGCATTTTGGTCATTTTTGCAT-TCTAGG-G
29700 CATTTTGGTCATTTTTGCACATC
63 CATTTTGGTCATTTTTGCACATC
* * * * * ** * * *
29723 TAGGGGTATTATAGTCATTTTTGCGTATCCAAAGGCATTTTGGTCATCTTTGCATTCTACGGCAG
1 CAGGGGCATTTTGGTCATTTTTGCATATCCAGGGGCATTTTGGTCATTTTTGCATTCTAGGGCAT
29788 TTTGGTCATTTTTGCA
66 TTTGGTCATTTTTGCA
29804 TACTTTAGGT
Statistics
Matches: 148, Mismatches: 19, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
85 19 0.13
86 4 0.03
87 49 0.33
88 76 0.51
ACGTcount: A:0.18, C:0.16, G:0.23, T:0.43
Consensus pattern (85 bp):
CAGGGGCATTTTGGTCATTTTTGCATATCCAGGGGCATTTTGGTCATTTTTGCATTCTAGGGCAT
TTTGGTCATTTTTGCACATC
Found at i:41821 original size:19 final size:21
Alignment explanation
Indices: 41793--41840 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
41783 CCAATTCAAG
*
41793 TTGAACCCTA-GTT-TACCAC
1 TTGAATCCTATGTTGTACCAC
*
41812 TTGAATCCTATTTTGTACCAC
1 TTGAATCCTATGTTGTACCAC
41833 TTGAATCC
1 TTGAATCC
41841 AATAGGGTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 9 0.36
20 2 0.08
21 14 0.56
ACGTcount: A:0.25, C:0.27, G:0.10, T:0.38
Consensus pattern (21 bp):
TTGAATCCTATGTTGTACCAC
Found at i:42120 original size:10 final size:10
Alignment explanation
Indices: 42105--42138 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
42095 GATCGGAAAA
*
42105 TTTTTTAACT
1 TTTTTTAAAT
42115 TTTTTTAAAT
1 TTTTTTAAAT
*
42125 TTTTTTATAT
1 TTTTTTAAAT
42135 TTTT
1 TTTT
42139 CAATTAAACC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTTTTAAAT
Found at i:43946 original size:129 final size:128
Alignment explanation
Indices: 43708--43966 Score: 448
Period size: 129 Copynumber: 2.0 Consensus size: 128
43698 TAGAATGAAT
*
43708 ATCTATACTAATTATAATGCGAGAACTTGAGTTTGTCTCCGAGTCAACTCGGAGACAAATTCAGT
1 ATCTATACTAATTATAATGCGAGAACCTGAGTTTGTCTCCGAGTCAACTCGGAGACAAATTCAGT
43773 TTTTAAAAAACAAAACAAAATAAAATCTACCCATTTTAAATAAAACTACCCATTAGAGGATAA
66 TTTTAAAAAACAAAACAAAATAAAATCTACCCATTTTAAATAAAACTACCCATTAGAGGATAA
* **
43836 ATCTATACTAATTATAATGCGAGAACCTGAGTTTGTCTCACGGGTTGACTCGGAGACAAATTCAG
1 ATCTATACTAATTATAATGCGAGAACCTGAGTTTGTCTC-CGAGTCAACTCGGAGACAAATTCAG
*
43901 TTTTTAAAAAATCAAAACAAAATGAAA-CTACCCATTTTAAATAAAACTACCCATTAGAGGATAA
65 TTTTTAAAAAA-CAAAACAAAATAAAATCTACCCATTTTAAATAAAACTACCCATTAGAGGATAA
43965 AT
1 AT
43967 ATAATAGAGT
Statistics
Matches: 124, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
128 38 0.31
129 72 0.58
130 14 0.11
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.28
Consensus pattern (128 bp):
ATCTATACTAATTATAATGCGAGAACCTGAGTTTGTCTCCGAGTCAACTCGGAGACAAATTCAGT
TTTTAAAAAACAAAACAAAATAAAATCTACCCATTTTAAATAAAACTACCCATTAGAGGATAA
Found at i:45995 original size:3 final size:3
Alignment explanation
Indices: 45987--46016 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
45977 GAAAGGAAAA
45987 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
46017 CTTTGAACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:46693 original size:13 final size:13
Alignment explanation
Indices: 46667--46700 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
46657 TATAAACGGA
46667 AATATATA-TAAT
1 AATATATATTAAT
46679 AATATATATTAAT
1 AATATATATTAAT
46692 AATATATAT
1 AATATATAT
46701 ATATATTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.38
13 13 0.62
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AATATATATTAAT
Found at i:52841 original size:2 final size:2
Alignment explanation
Indices: 52834--52860 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
52824 CGCATCCCAA
52834 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
52861 ATAGAACTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:55628 original size:42 final size:43
Alignment explanation
Indices: 55577--55671 Score: 149
Period size: 45 Copynumber: 2.2 Consensus size: 43
55567 AGTGCATTAC
*
55577 CTAA-ATTCTACT-CCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACTCCCATCTCTAGATAATTCATCAAAATAAAG
55618 CTAATATTCTACTCCCCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTACT--CCCATCTCTAGATAATTCATCAAAATAAAG
55663 CTAATATTC
1 CTAATATTC
55672 ATTGTTGCTT
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
41 4 0.08
42 8 0.16
45 37 0.76
ACGTcount: A:0.38, C:0.24, G:0.05, T:0.33
Consensus pattern (43 bp):
CTAATATTCTACTCCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:66262 original size:16 final size:18
Alignment explanation
Indices: 66230--66313 Score: 97
Period size: 18 Copynumber: 4.9 Consensus size: 18
66220 GCAATTGTGC
*
66230 TTCTTGCTCCCTAAGAGT
1 TTCTTGCTCCGTAAGAGT
66248 TTCTTG-T-CGTAAGAGT
1 TTCTTGCTCCGTAAGAGT
*
66264 TTCTT--TTCGTAAG-GTT
1 TTCTTGCTCCGTAAGAG-T
*
66280 TTCTTGCTCCGTAAGGGT
1 TTCTTGCTCCGTAAGAGT
66298 TTCTTGCTCCGTAAGA
1 TTCTTGCTCCGTAAGA
66314 TTTGTCGAAC
Statistics
Matches: 58, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
15 2 0.03
16 25 0.43
17 1 0.02
18 29 0.50
19 1 0.02
ACGTcount: A:0.15, C:0.20, G:0.21, T:0.43
Consensus pattern (18 bp):
TTCTTGCTCCGTAAGAGT
Found at i:67158 original size:10 final size:11
Alignment explanation
Indices: 67138--67166 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
67128 AATCTAAAAT
67138 TAAAGCTAAAC
1 TAAAGCTAAAC
67149 TAAA-CTAAAC
1 TAAAGCTAAAC
67159 TAAAGCTA
1 TAAAGCTA
67167 TGATAATTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.55, C:0.17, G:0.07, T:0.21
Consensus pattern (11 bp):
TAAAGCTAAAC
Found at i:68772 original size:14 final size:14
Alignment explanation
Indices: 68753--68780 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
68743 CAAACCTCTT
68753 CACCAAGTTGCTGC
1 CACCAAGTTGCTGC
68767 CACCAAGTTGCTGC
1 CACCAAGTTGCTGC
68781 AAAACAAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.36, G:0.21, T:0.21
Consensus pattern (14 bp):
CACCAAGTTGCTGC
Found at i:70012 original size:21 final size:21
Alignment explanation
Indices: 69988--70027 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
69978 CTCTTGTCAT
*
69988 TGGACCTAATGGCATCTTTAA
1 TGGACCAAATGGCATCTTTAA
*
70009 TGGATCAAATGGCATCTTT
1 TGGACCAAATGGCATCTTT
70028 GGTAATTCCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (21 bp):
TGGACCAAATGGCATCTTTAA
Found at i:76778 original size:35 final size:35
Alignment explanation
Indices: 76511--76766 Score: 442
Period size: 35 Copynumber: 7.3 Consensus size: 35
76501 CAAGAAACAA
*
76511 AATTAAGGAAATTGGTATTCAACTTAATTCGGTGT
1 AATTAAGGAAATTGGTAATCAACTTAATTCGGTGT
*
76546 AATTAAGGAAATTGGTATTCAACTTAATTCGGTGT
1 AATTAAGGAAATTGGTAATCAACTTAATTCGGTGT
76581 AATTAAGGAAATTGGTAATCAACTTAATTCGGTGT
1 AATTAAGGAAATTGGTAATCAACTTAATTCGGTGT
*
76616 AATTAAGGAAATTGGT-ATCCAACTTAATTCGATGT
1 AATTAAGGAAATTGGTAAT-CAACTTAATTCGGTGT
76651 AATTAAGGAAATTGGTAATCAACTTAATTCGGTGT
1 AATTAAGGAAATTGGTAATCAACTTAATTCGGTGT
76686 AATTAAGGAAATTGGTAATCAACTTAATTCGGTGT
1 AATTAAGGAAATTGGTAATCAACTTAATTCGGTGT
* **
76721 AATTAAGGAGATTGGTGGTCAACTTAATTCGGTGT
1 AATTAAGGAAATTGGTAATCAACTTAATTCGGTGT
76756 AATTAAGGAAA
1 AATTAAGGAAA
76767 CCAGCAATCA
Statistics
Matches: 212, Mismatches: 7, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
34 2 0.01
35 208 0.98
36 2 0.01
ACGTcount: A:0.36, C:0.09, G:0.21, T:0.34
Consensus pattern (35 bp):
AATTAAGGAAATTGGTAATCAACTTAATTCGGTGT
Found at i:85486 original size:21 final size:21
Alignment explanation
Indices: 85460--85530 Score: 108
Period size: 21 Copynumber: 3.4 Consensus size: 21
85450 TACTAGGAGT
85460 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
85481 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
85502 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
85523 TTATTGGA
1 TCATTGGA
85531 ATTGGCTAAG
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
20 2 0.04
21 45 0.96
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:85949 original size:11 final size:11
Alignment explanation
Indices: 85909--85945 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
85899 AGGAGTAGGA
85909 TCTTTCCTAGC
1 TCTTTCCTAGC
85920 TCTTTCCTAGC
1 TCTTTCCTAGC
*
85931 TCCTTCCTAGC
1 TCTTTCCTAGC
85942 -CTTT
1 TCTTT
85946 TCCTTTACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 3 0.12
11 21 0.88
ACGTcount: A:0.08, C:0.38, G:0.08, T:0.46
Consensus pattern (11 bp):
TCTTTCCTAGC
Found at i:91336 original size:76 final size:76
Alignment explanation
Indices: 91210--91361 Score: 189
Period size: 76 Copynumber: 2.0 Consensus size: 76
91200 ACAAGGACCC
* * *
91210 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAACACCCATGTGGTTTGCCTGAGAACCCAGAT
91275 GGGCAGTGTCA
66 GGGCAGTGTCA
** * * * **
91286 CGACTCCAGTTGGGTGCCCACATGGTTTGTC-TGAACACCCATGTGTTTTGCCTGATCACCCAGA
1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTGAACACCCATGTGGTTTGCCTGAGAACCCAGA
*
91350 TGGGCTGTGTCA
65 TGGGCAGTGTCA
91362 TAGCTCATCA
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
76 60 0.94
77 4 0.06
ACGTcount: A:0.17, C:0.29, G:0.28, T:0.26
Consensus pattern (76 bp):
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAACACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA
Found at i:92243 original size:26 final size:25
Alignment explanation
Indices: 92201--92249 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
92191 ATGATTTAGG
*
92201 GGTTACTAACTCCCTTTTTCTTTTGA
1 GGTTACTAACACCCTTTTT-TTTTGA
*
92227 GGTTACTAACACTCTTTTTTTTT
1 GGTTACTAACACCCTTTTTTTTT
92250 CAGAGGGACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.16, C:0.20, G:0.10, T:0.53
Consensus pattern (25 bp):
GGTTACTAACACCCTTTTTTTTTGA
Found at i:92315 original size:3 final size:3
Alignment explanation
Indices: 92307--92353 Score: 76
Period size: 3 Copynumber: 15.0 Consensus size: 3
92297 GTTACTAACC
92307 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TATA TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA T-TA TTA
92354 ATTAAAGAGT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 36 0.84
4 7 0.16
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:97215 original size:21 final size:21
Alignment explanation
Indices: 97182--97230 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
97172 AAGAATTGTA
**
97182 GCTT-CTTGGAAATGGCTCTT
1 GCTTCCTTGGAAATCCCTCTT
*
97202 GCTTCCTTTGAAATCCCTCTT
1 GCTTCCTTGGAAATCCCTCTT
97223 GCATTCCT
1 GC-TTCCT
97231 AAAGCATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.17
21 15 0.62
22 5 0.21
ACGTcount: A:0.14, C:0.29, G:0.16, T:0.41
Consensus pattern (21 bp):
GCTTCCTTGGAAATCCCTCTT
Found at i:103173 original size:15 final size:16
Alignment explanation
Indices: 103142--103181 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
103132 TTACTTTGTT
103142 TTGTTTTCTAGTTTAA
1 TTGTTTTCTAGTTTAA
103158 TTGTTTTCTA-TTTAA
1 TTGTTTTCTAGTTTAA
*
103173 TTGCTTTCT
1 TTGTTTTCT
103182 GTCAATCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.15, C:0.10, G:0.10, T:0.65
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Found at i:106789 original size:21 final size:21
Alignment explanation
Indices: 106734--106800 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
106724 CCAAGCCATT
*
106734 ACCGGCCATTCACCGTGCCACC
1 ACCGGCCATGC-CCGTGCCACC
* ** *
106756 ACTGGTTAAGCCCGTGCCACC
1 ACCGGCCATGCCCGTGCCACC
*
106777 ACCGGCCATGCCCGTGCCATC
1 ACCGGCCATGCCCGTGCCACC
106798 ACC
1 ACC
106801 ATTCCAAGCC
Statistics
Matches: 35, Mismatches: 10, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
21 29 0.83
22 6 0.17
ACGTcount: A:0.18, C:0.46, G:0.21, T:0.15
Consensus pattern (21 bp):
ACCGGCCATGCCCGTGCCACC
Done.