Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015910.1 Corchorus capsularis cultivar CVL-1 contig15931, 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: 31063
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:6525 original size:21 final size:22
Alignment explanation
Indices: 6499--6543 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
6489 TAGAAGGATG
*
6499 TTGCTAAACACCGTCCCA-TTT
1 TTGCTAAACACCGCCCCACTTT
**
6520 TTGCTATTCACCGCCCCACTTT
1 TTGCTAAACACCGCCCCACTTT
6542 TT
1 TT
6544 ACACTTTTAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.18, C:0.36, G:0.09, T:0.38
Consensus pattern (22 bp):
TTGCTAAACACCGCCCCACTTT
Found at i:6801 original size:33 final size:33
Alignment explanation
Indices: 6734--6804 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 33
6724 CATGGCACAA
* *
6734 CCGCCCTCCTAGGGCGGCATGAGCCATGGTATG
1 CCGCCCTCCTAGGGCGGCATAAGCCATGGCATG
*
6767 CCGCCCTCCTGGGGCGGCA-AATGCCACT-GCATG
1 CCGCCCTCCTAGGGCGGCATAA-GCCA-TGGCATG
6800 CCGCC
1 CCGCC
6805 ATAGGAGGGC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
32 1 0.03
33 31 0.94
34 1 0.03
ACGTcount: A:0.14, C:0.39, G:0.31, T:0.15
Consensus pattern (33 bp):
CCGCCCTCCTAGGGCGGCATAAGCCATGGCATG
Found at i:6940 original size:17 final size:18
Alignment explanation
Indices: 6918--6951 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
6908 GTATTGTTGT
6918 AATATTACTTA-AAAAAA
1 AATATTACTTACAAAAAA
6935 AATATTACTTACAAAAA
1 AATATTACTTACAAAAA
6952 TTACATACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (18 bp):
AATATTACTTACAAAAAA
Found at i:6960 original size:13 final size:13
Alignment explanation
Indices: 6933--7003 Score: 72
Period size: 13 Copynumber: 5.2 Consensus size: 13
6923 TACTTAAAAA
*
6933 AAAATATTACTTAC
1 AAAA-ATTACATAC
6947 AAAAATTACATAC
1 AAAAATTACATAC
6960 AATAATAATTAACATA-
1 -A-AA-AATT-ACATAC
*
6976 AAAAATTACTTAC
1 AAAAATTACATAC
6989 AAAAATTACATAC
1 AAAAATTACATAC
7002 AA
1 AA
7004 TAATAATTAC
Statistics
Matches: 49, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
12 4 0.08
13 26 0.53
14 7 0.14
15 3 0.06
16 4 0.08
17 5 0.10
ACGTcount: A:0.59, C:0.13, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAAATTACATAC
Found at i:6990 original size:42 final size:43
Alignment explanation
Indices: 6932--7012 Score: 155
Period size: 42 Copynumber: 1.9 Consensus size: 43
6922 TTACTTAAAA
6932 AAAAATATTACTTACAAAAATTACATACAATAATAATTAACAT
1 AAAAATATTACTTACAAAAATTACATACAATAATAATTAACAT
6975 AAAAA-ATTACTTACAAAAATTACATACAATAATAATTA
1 AAAAATATTACTTACAAAAATTACATACAATAATAATTA
7013 CAAACATGTC
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
42 33 0.87
43 5 0.13
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (43 bp):
AAAAATATTACTTACAAAAATTACATACAATAATAATTAACAT
Found at i:7240 original size:33 final size:33
Alignment explanation
Indices: 7163--7247 Score: 98
Period size: 33 Copynumber: 2.6 Consensus size: 33
7153 ATCTATGTCA
* *
7163 CCCTGTGAGGATGGTACGACCATGGGCGTGACG
1 CCCTGTGAGGATGGCACGACCATGGGCATGACG
* *** * *
7196 TCCTCACAGGATGGCATGACCATGGGCATGCCG
1 CCCTGTGAGGATGGCACGACCATGGGCATGACG
7229 CCCTGTGAGGATGGCACGA
1 CCCTGTGAGGATGGCACGA
7248 GGGCGGCATG
Statistics
Matches: 39, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.20, C:0.27, G:0.35, T:0.18
Consensus pattern (33 bp):
CCCTGTGAGGATGGCACGACCATGGGCATGACG
Found at i:12037 original size:32 final size:32
Alignment explanation
Indices: 11999--12062 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
11989 ATCAGACCTT
11999 GTTGGTGAATCCATCATCAAATACCCAGATGG
1 GTTGGTGAATCCATCATCAAATACCCAGATGG
12031 GTTGGTGAATCCATCATCAAATACCCAGATGG
1 GTTGGTGAATCCATCATCAAATACCCAGATGG
12063 TTTCTTAGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (32 bp):
GTTGGTGAATCCATCATCAAATACCCAGATGG
Found at i:13933 original size:26 final size:24
Alignment explanation
Indices: 13896--13944 Score: 80
Period size: 26 Copynumber: 2.0 Consensus size: 24
13886 CTCTACTGCC
13896 TTTGATTACAATTATTCGATTTTT
1 TTTGATTACAATTATTCGATTTTT
13920 TTTGAATTAACAATTATTCGATTTT
1 TTTG-ATT-ACAATTATTCGATTTT
13945 GATTGGATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 4 0.17
25 3 0.13
26 16 0.70
ACGTcount: A:0.29, C:0.08, G:0.08, T:0.55
Consensus pattern (24 bp):
TTTGATTACAATTATTCGATTTTT
Found at i:14321 original size:45 final size:44
Alignment explanation
Indices: 14250--14334 Score: 109
Period size: 45 Copynumber: 1.9 Consensus size: 44
14240 CTAAGGAATT
* *
14250 TTGATAACTTCCCAATGAAATTTTGATAACCAACATTATGAGATG
1 TTGATAACCTCCCAATGAAATATTGATAACC-ACATTATGAGATG
* *
14295 TTGATAACCT-CCATATGATATATTGATAACCACGTTATGA
1 TTGATAACCTCCCA-ATGAAATATTGATAACCACATTATGA
14335 AAATTTAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
44 11 0.31
45 24 0.69
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.34
Consensus pattern (44 bp):
TTGATAACCTCCCAATGAAATATTGATAACCACATTATGAGATG
Found at i:14447 original size:23 final size:23
Alignment explanation
Indices: 14376--14479 Score: 117
Period size: 23 Copynumber: 4.6 Consensus size: 23
14366 AATCACACTT
* *
14376 TAAAATTTTGAT-AATCACGCTA
1 TAAAATTTTGATAAACCTCGCTA
* *
14398 TGAAATTGTGAT-AACCTCGCTA
1 TAAAATTTTGATAAACCTCGCTA
*
14420 TAAAATTTTGATAAATCTTC-CTA
1 TAAAATTTTGATAAA-CCTCGCTA
14443 TAAAATTTTGATAAACCTC-CTTA
1 TAAAATTTTGATAAACCTCGC-TA
14466 TAAAATTTTGATAA
1 TAAAATTTTGATAA
14480 CTTTCTTATG
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
22 32 0.45
23 36 0.51
24 3 0.04
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
TAAAATTTTGATAAACCTCGCTA
Found at i:14493 original size:22 final size:22
Alignment explanation
Indices: 14132--14758 Score: 187
Period size: 22 Copynumber: 29.0 Consensus size: 22
14122 ATGATCCCAT
*
14132 TATGAAATTTTGATAACCTTTC
1 TATGAAATTTTGATAACCTTCC
* * *** *
14154 TATAAAATTTTAATAATGATAC
1 TATGAAATTTTGATAACCTTCC
* * * * **
14176 TATGGAATTTCGAGAACATTTT
1 TATGAAATTTTGATAACCTTCC
** *
14198 TAT-AAATTTTTTTAACCTTCT
1 TATGAAATTTTGATAACCTTCC
* * *
14219 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTTCC
* *
14241 TAAGGAATTTTGATAA-CTTCCC
1 TATGAAATTTTGATAACCTT-CC
* ** *
14263 AATGAAATTTTGATAACCAACAT
1 TATGAAATTTTGATAACCTTC-C
* *
14286 TATGAGATGTTGATAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* * * *
14307 ATATGATATATTGATAACC-ACGT
1 -TATGAAATTTTGATAACCTTC-C
* * * *
14330 TATGAAAATTTAAAAACCTTCA
1 TATGAAATTTTGATAACCTTCC
* *
14352 TATG-AATTGTT-AGTAATC-ACAC
1 TATGAAATT-TTGA-TAACCTTC-C
* * * *
14374 TTTAAAATTTTGATAATC-ACGC
1 TATGAAATTTTGATAACCTTC-C
*
14396 TATGAAATTGTGATAACC-TCGC
1 TATGAAATTTTGATAACCTTC-C
* *
14418 TATAAAATTTTGATAAATCTTCC
1 TATGAAATTTTGAT-AACCTTCC
*
14441 TATAAAATTTTGATAAACC-TCC
1 TATGAAATTTTGAT-AACCTTCC
* * *
14463 TTATAAAATTTTGATAACTTTCT
1 -TATGAAATTTTGATAACCTTCC
* *
14486 TATGAAATCTTGGTAA-----C
1 TATGAAATTTTGATAACCTTCC
* *
14503 TA-CAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTTCC
** * *
14524 TATGATTTTTTGAGAACC-TCAT
1 TATGAAATTTTGATAACCTTC-C
* * *
14546 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTTCC
* *
14568 TATGAAATTTTGATCTACAC--AC
1 TATGAAATTTTGAT-AAC-CTTCC
* *
14590 TATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAACCTTCC
* **
14612 TATGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-TCC
* *
14634 TATGAAACTTTGATAACCTTCA
1 TATGAAATTTTGATAACCTTCC
* *
14656 TATAAAATTTTGATATCC-TCC
1 TATGAAATTTTGATAACCTTCC
* *
14677 -CTGAAATTTTGATTA-C-TCC
1 TATGAAATTTTGATAACCTTCC
* * *
14696 ATAATAAAAGTTTAATAACCTTCC
1 -T-ATGAAATTTTGATAACCTTCC
* * *
14720 --T--AA-TTTGGTAACCATAC
1 TATGAAATTTTGATAACCTTCC
14737 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
14759 CAGAAATACC
Statistics
Matches: 436, Mismatches: 129, Indels: 80
0.68 0.20 0.12
Matches are distributed among these distances:
16 10 0.02
17 12 0.03
18 2 0.00
19 5 0.01
20 13 0.03
21 34 0.08
22 287 0.66
23 67 0.15
24 6 0.01
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:14826 original size:22 final size:22
Alignment explanation
Indices: 14771--14987 Score: 108
Period size: 22 Copynumber: 9.8 Consensus size: 22
14761 GAAATACCAC
*
14771 TATGAAATTTTTG-TAATCACATT
1 TATGAAA-TTTTGATAATCTC-TT
*
14794 T-TGGAAA-TTTGATAATCTTTT
1 TAT-GAAATTTTGATAATCTCTT
*
14815 TATGAAATTTTGATAACCTCTT
1 TATGAAATTTTGATAATCTCTT
* * * * * *
14837 TATAAAATTTTGTTGACCCCTC
1 TATGAAATTTTGATAATCTCTT
* * *
14859 TATGAAATTCTGATAATCAC-A
1 TATGAAATTTTGATAATCTCTT
* *
14880 CATGTAATTTTGATAA-C-CTT
1 TATGAAATTTTGATAATCTCTT
* * **
14900 GCTTTGAAATTTTGATAA-CAACAC
1 --TATGAAATTTTGATAATC-TCTT
*
14924 TATGAAATTTTGATAATCTTTT
1 TATGAAATTTTGATAATCTCTT
*
14946 TAT-AAATTTTGATAATCCGATCTC
1 TATGAAATTTTGATAAT-C--TCTT
*
14970 TATGAAATTTCGATAATC
1 TATGAAATTTTGATAATC
14988 AGTCCATGAG
Statistics
Matches: 147, Mismatches: 33, Indels: 27
0.71 0.16 0.13
Matches are distributed among these distances:
19 1 0.01
20 1 0.01
21 37 0.25
22 83 0.56
23 6 0.04
24 7 0.05
25 12 0.08
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (22 bp):
TATGAAATTTTGATAATCTCTT
Found at i:14866 original size:65 final size:64
Alignment explanation
Indices: 14797--14960 Score: 163
Period size: 65 Copynumber: 2.5 Consensus size: 64
14787 TCACATTTTG
* * ** *
14797 GAAATTTGATAATCTTTTTATGAAATTTTGATAACC-TCTTTATAAAATTTTGTTGACCCCTCTA
1 GAAATTTGATAATCTTTTTATGAAATTTTGATAACCTTC-TT-TAAAATTTTGATAACAACACTA
14861 T
64 T
**** * *
14862 GAAATTCTGATAATC-ACACATGTAATTTTGATAACCTTGCTTTGAAATTTTGATAACAACACTA
1 GAAATT-TGATAATCTTTTTATGAAATTTTGATAACCTT-CTTTAAAATTTTGATAACAACACTA
14926 T
64 T
14927 GAAATTTTGATAATCTTTTTAT-AAATTTTGATAA
1 GAAA-TTTGATAATCTTTTTATGAAATTTTGATAA
14961 TCCGATCTCT
Statistics
Matches: 78, Mismatches: 16, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
65 62 0.79
66 15 0.19
67 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (64 bp):
GAAATTTGATAATCTTTTTATGAAATTTTGATAACCTTCTTTAAAATTTTGATAACAACACTAT
Found at i:14953 original size:43 final size:45
Alignment explanation
Indices: 14771--14987 Score: 146
Period size: 44 Copynumber: 4.9 Consensus size: 45
14761 GAAATACCAC
* *
14771 TATGAAATTTTTG-TAATC-ACATTTTGGAAA-TTTGATAATCTTTT
1 TATGAAA-TTTTGATAATCAACACTAT-GAAATTTTGATAATCTTTT
** ** * * * * ** *
14815 TATGAAATTTTGATAA-CCTCTTTATAAAATTTTGTTGACCCCTC
1 TATGAAATTTTGATAATCAACACTATGAAATTTTGATAATCTTTT
* * * *
14859 TATGAAATTCTGATAATC-ACAC-ATGTAATTTTGATAACCTTGCT
1 TATGAAATTTTGATAATCAACACTATGAAATTTTGATAATCTT-TT
14903 T-TGAAATTTTGATAA-CAACACTATGAAATTTTGATAATCTTTT
1 TATGAAATTTTGATAATCAACACTATGAAATTTTGATAATCTTTT
* * *
14946 TAT-AAATTTTGATAATCCGATCTCTATGAAATTTCGATAATC
1 TATGAAATTTTGATAAT-C-AACACTATGAAATTTTGATAATC
14988 AGTCCATGAG
Statistics
Matches: 133, Mismatches: 29, Indels: 20
0.73 0.16 0.11
Matches are distributed among these distances:
42 1 0.01
43 53 0.40
44 57 0.43
45 2 0.02
46 20 0.15
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (45 bp):
TATGAAATTTTGATAATCAACACTATGAAATTTTGATAATCTTTT
Found at i:15023 original size:21 final size:22
Alignment explanation
Indices: 14797--15040 Score: 116
Period size: 22 Copynumber: 11.3 Consensus size: 22
14787 TCACATTTTG
* *
14797 GAAA-TTTGATAATCTTTTTAT
1 GAAATTTTGATAATCCTTCTAT
*
14818 GAAATTTTGATAA-CCTCTTTAT
1 GAAATTTTGATAATCCT-TCTAT
* * * * *
14840 AAAATTTTGTTGACCCCTCTAT
1 GAAATTTTGATAATCCTTCTAT
* *
14862 GAAATTCTGATAATCAC-AC-AT
1 GAAATTTTGATAATC-CTTCTAT
* *
14883 GTAATTTTGATAA-CCTTGCTTT
1 GAAATTTTGATAATCCTT-CTAT
*
14905 GAAATTTTGATAA-CAAC-ACTAT
1 GAAATTTTGATAATC--CTTCTAT
* *
14927 GAAATTTTGATAATCTTTTTAT
1 GAAATTTTGATAATCCTTCTAT
14949 -AAATTTTGATAATCCGATCTCTAT
1 GAAATTTTGATAATCC--T-TCTAT
* ** *
14973 GAAATTTCGATAATCAGTCCAT
1 GAAATTTTGATAATCCTTCTAT
**
14995 G-AGGTTTGATAA-CCTTCTAT
1 GAAATTTTGATAATCCTTCTAT
* * *
15015 CAAATTTTGGTACTCC-T-TAT
1 GAAATTTTGATAATCCTTCTAT
15035 GAAATT
1 GAAATT
15041 GAGACTTCTA
Statistics
Matches: 166, Mismatches: 40, Indels: 35
0.69 0.17 0.15
Matches are distributed among these distances:
19 1 0.01
20 14 0.08
21 50 0.30
22 78 0.47
23 5 0.03
24 5 0.03
25 13 0.08
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (22 bp):
GAAATTTTGATAATCCTTCTAT
Found at i:15185 original size:22 final size:22
Alignment explanation
Indices: 15061--15185 Score: 101
Period size: 22 Copynumber: 5.7 Consensus size: 22
15051 TAACCTTCAT
* *
15061 ATGAAATTTTGATAACCACACT
1 ATGAAATTTTGATAACCTCACC
* *
15083 ATAAAATTTTGATAACCTCCCC
1 ATGAAATTTTGATAACCTCACC
* *
15105 ATGAAATATT-AGTAACCTC-CTA
1 ATGAAATTTTGA-TAACCTCAC-C
* * *
15127 ATGAAATTTTGTTAACCACACT
1 ATGAAATTTTGATAACCTCACC
* * *
15149 ATGAAATTCTCATAACCTCGCC
1 ATGAAATTTTGATAACCTCACC
*
15171 ATGACATTTTGATAA
1 ATGAAATTTTGATAA
15186 TCTCTTTAAT
Statistics
Matches: 79, Mismatches: 20, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
21 2 0.03
22 76 0.96
23 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.33
Consensus pattern (22 bp):
ATGAAATTTTGATAACCTCACC
Found at i:15253 original size:22 final size:22
Alignment explanation
Indices: 15221--15360 Score: 83
Period size: 22 Copynumber: 6.3 Consensus size: 22
15211 TTGTGATAAT
* *
15221 TAACCACCCTATGAAATTTCAG
1 TAACCAACCTATGAAATTTTAG
* * *
15243 TAACCAACCTAAGAGATTTTAA
1 TAACCAACCTATGAAATTTTAG
* *
15265 TAACCTGATCCTATGAAATTTTGG
1 TAACC--AACCTATGAAATTTTAG
15289 TAACC-ACACTATGAAATTTT-G
1 TAACCAAC-CTATGAAATTTTAG
* *
15310 ATAACC-TCCTCATGAAATTAT-G
1 -TAACCAACCT-ATGAAATTTTAG
* *
15332 ATAACCATCTTATGAAATTTT-G
1 -TAACCAACCTATGAAATTTTAG
15354 ATAACCA
1 -TAACCA
15361 CATAGAGACA
Statistics
Matches: 97, Mismatches: 15, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
21 4 0.04
22 73 0.75
23 3 0.03
24 17 0.18
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.32
Consensus pattern (22 bp):
TAACCAACCTATGAAATTTTAG
Found at i:15278 original size:46 final size:46
Alignment explanation
Indices: 15228--15316 Score: 117
Period size: 46 Copynumber: 1.9 Consensus size: 46
15218 AATTAACCAC
*
15228 CCTATGAAATTTCAGTAACCA-ACCTAAGAGATTTTAATAACCTGAT
1 CCTATGAAATTTCAGTAACCACA-CTAAGAAATTTTAATAACCTGAT
** * *
15274 CCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCT
1 CCTATGAAATTTCAGTAACCACACTAAGAAATTTTAATAACCT
15317 CCTCATGAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
46 36 0.97
47 1 0.03
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (46 bp):
CCTATGAAATTTCAGTAACCACACTAAGAAATTTTAATAACCTGAT
Found at i:15346 original size:44 final size:43
Alignment explanation
Indices: 15273--15359 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 43
15263 AATAACCTGA
* *
15273 TCCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACC
1 TCCTATGAAATTATGATAACCACACTATGAAATTTTGATAACC
*
15316 TCCTCATGAAATTATGATAACCATC-TTATGAAATTTTGATAACC
1 TCCT-ATGAAATTATGATAACCA-CACTATGAAATTTTGATAACC
15360 ACATAGAGAC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
43 4 0.10
44 34 0.87
45 1 0.03
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (43 bp):
TCCTATGAAATTATGATAACCACACTATGAAATTTTGATAACC
Found at i:17227 original size:32 final size:31
Alignment explanation
Indices: 17191--17258 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
17181 TTTAGTAATG
*
17191 ACAATTTAGAAATATGTTTTTTAAAA-AAGGGT
1 ACAATTTAGAAATA--TATTTTAAAATAAGGGT
*
17223 ACAA-TTGGAAATATATTTTAAAATTAAGGGT
1 ACAATTTAGAAATATATTTTAAAA-TAAGGGT
17254 ACAAT
1 ACAAT
17259 CAGAAAACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
29 9 0.29
31 18 0.58
32 4 0.13
ACGTcount: A:0.46, C:0.04, G:0.15, T:0.35
Consensus pattern (31 bp):
ACAATTTAGAAATATATTTTAAAATAAGGGT
Found at i:19380 original size:40 final size:40
Alignment explanation
Indices: 19285--19400 Score: 146
Period size: 40 Copynumber: 2.9 Consensus size: 40
19275 CCCAATTTTA
** *
19285 TTATTTTCCAAAAGTCTTC-TCTTGGATTTTTTAAAA-CTT
1 TTATTTTCCAAAAGTCTTCTTC-TGGATTTGCTAAAATCAT
19324 TTATTTTCCAAAAGTCTTCTTCTGGATTTGCTAAAATCAT
1 TTATTTTCCAAAAGTCTTCTTCTGGATTTGCTAAAATCAT
* * * *
19364 TTATTTTCCAACAGTCTTCTCCTGGAATTGCTTAAAT
1 TTATTTTCCAAAAGTCTTCTTCTGGATTTGCTAAAAT
19401 TGAAAACGTT
Statistics
Matches: 68, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
39 31 0.46
40 37 0.54
ACGTcount: A:0.26, C:0.18, G:0.09, T:0.47
Consensus pattern (40 bp):
TTATTTTCCAAAAGTCTTCTTCTGGATTTGCTAAAATCAT
Found at i:19617 original size:13 final size:14
Alignment explanation
Indices: 19594--19622 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
19584 ACCTCTACTC
19594 AATGCATGAATGCA
1 AATGCATGAATGCA
19608 AATG-ATGAATGCA
1 AATGCATGAATGCA
19621 AA
1 AA
19623 GTCCAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.48, C:0.10, G:0.21, T:0.21
Consensus pattern (14 bp):
AATGCATGAATGCA
Found at i:26710 original size:78 final size:77
Alignment explanation
Indices: 26622--26857 Score: 316
Period size: 66 Copynumber: 3.2 Consensus size: 77
26612 ATTTTTTAAT
*
26622 TAAAATAGTAAAATGGTAAAATATAATAGTAATAAGGATATTAGATTTAATTATATAAAAATAGA
1 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTA-ATAAAAATAGA
26687 GTTTTTAGTTGAG
65 GTTTTTAGTTGAG
26700 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAG---------AT--AAATAGAG
1 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTAATAAAAATAGAG
26754 TTTTTAGTTGAG
66 TTTTTAGTTGAG
* * *
26766 TAAAATAGTAAAATGGTAAAATAAAATAGTTATAAAGATATTATATTTAATTAAATAAAAATTAG
1 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATT-AATAAAAA-TAG
26831 AGTTTTTAGTTGAG
64 AGTTTTTAGTTGAG
26845 TAAAACTA-TAAAA
1 TAAAA-TAGTAAAA
26858 ACCTAAACAA
Statistics
Matches: 140, Mismatches: 4, Indels: 27
0.82 0.02 0.16
Matches are distributed among these distances:
66 61 0.44
68 2 0.01
76 2 0.01
78 46 0.33
79 27 0.19
80 2 0.01
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.35
Consensus pattern (77 bp):
TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTAATAAAAATAGAG
TTTTTAGTTGAG
Found at i:28375 original size:3 final size:3
Alignment explanation
Indices: 28367--28413 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
28357 GTTCATTCCA
28367 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
28414 TCTTTTTAAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:29385 original size:8 final size:8
Alignment explanation
Indices: 29372--29397 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
29362 TAAAGCTAAA
29372 TTATATTT
1 TTATATTT
29380 TTATATTT
1 TTATATTT
29388 TTATATTT
1 TTATATTT
29396 TT
1 TT
29398 CAAATACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (8 bp):
TTATATTT
Found at i:29518 original size:22 final size:22
Alignment explanation
Indices: 29493--29540 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
29483 CATGGGGAGA
*
29493 TTATCGAAATTTCATAATGAGG
1 TTATCGAAATTTCAAAATGAGG
* *
29515 TTATCGAATTTTCAAAATGTGG
1 TTATCGAAATTTCAAAATGAGG
29537 TTAT
1 TTAT
29541 TAATATTTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.42
Consensus pattern (22 bp):
TTATCGAAATTTCAAAATGAGG
Found at i:29549 original size:22 final size:23
Alignment explanation
Indices: 29493--29549 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
29483 CATGGGGAGA
*
29493 TTATCGAA-ATTTCATAATGAGG
1 TTATCGAATATTTCAAAATGAGG
*
29515 TTATCGAAT-TTTCAAAATGTGG
1 TTATCGAATATTTCAAAATGAGG
*
29537 TTAT-TAATATTTC
1 TTATCGAATATTTC
29550 TATATTGGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 3 0.10
22 27 0.90
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.44
Consensus pattern (23 bp):
TTATCGAATATTTCAAAATGAGG
Found at i:31039 original size:2 final size:2
Alignment explanation
Indices: 31032--31061 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
31022 AATACTAGTG
31032 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31062 CT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.