Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010182.1 Corchorus capsularis cultivar CVL-1 contig10203, 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: 53153
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:826 original size:14 final size:13
Alignment explanation
Indices: 807--850 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
797 TTCAAAATAT
807 TTTTCAAGAAAAGG
1 TTTTCAA-AAAAGG
*
821 TTTTCAAAAATGG
1 TTTTCAAAAAAGG
834 ATTTTC-AAAAAGG
1 -TTTTCAAAAAAGG
847 TTTT
1 TTTT
851 GAGTCTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 4 0.15
13 11 0.41
14 12 0.44
ACGTcount: A:0.39, C:0.07, G:0.16, T:0.39
Consensus pattern (13 bp):
TTTTCAAAAAAGG
Found at i:3733 original size:69 final size:68
Alignment explanation
Indices: 3573--4023 Score: 514
Period size: 68 Copynumber: 6.6 Consensus size: 68
3563 AATGCTTCAA
* * * *
3573 CTTTTCCATAAGTCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCACCCAAGCATTC
1 CTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTT-AAGCCTTGGTTCCATCCAAGCA-AC
*
3638 AAGGG
64 AGGGG
* * * * *
3643 CTTTTCCATAAGCCAATCTCGTTTCCATACGAGGT-AGATTAAG-CTTTGTTCCGTCCAACCATT
1 CTTTTCCATAAGCCAAACTCGTTTCCATACGA-GTCAG-TTAAGCCTTGGTTCCATCCAAGCA-A
3706 CAGGGG
63 CAGGGG
* * * *
3712 CTTTTCCACAAGCTAAACTCGTTTCCATACGAGTCAGTTTAGCCTTGGTTCCATCCAAGCAGCAG
1 CTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTTAAGCCTTGGTTCCATCCAAGCAACAG
*
3777 GGT
66 GGG
* * * *
3780 CTTTTCCATAAGCC-AACTTCGTTTCCATACGACTCAGTTTAGCCTTGGTTCTATCCAAGTAACA
1 CTTTTCCATAAGCCAAAC-TCGTTTCCATACGAGTCAGTTAAGCCTTGGTTCCATCCAAGCAACA
3844 GGGG
65 GGGG
* * * * *
3848 CTTTTCCACAAGCCAATCTCGTTTCCATACAAGTCAGTCAAGCCTTGGTTCCATCCAAGCAACAA
1 CTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTTAAGCCTTGGTTCCATCCAAGCAACAG
3913 GGG
66 GGG
* * *
3916 CTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAACTTTGGTTCCAT-CAAGCAGCA
1 CTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTT-AAGCCTTGGTTCCATCCAAGCAAC-
3980 AGGGG
64 AGGGG
** * *
3985 CTTTTCCATAAGCCAAGTTCATTTCCATATGAAGTCAGT
1 CTTTTCCATAAGCCAAACTCGTTTCCATACG-AGTCAGT
4024 CTTCCAAGAC
Statistics
Matches: 327, Mismatches: 45, Indels: 18
0.84 0.12 0.05
Matches are distributed among these distances:
67 3 0.01
68 166 0.51
69 112 0.34
70 42 0.13
71 4 0.01
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (68 bp):
CTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTTAAGCCTTGGTTCCATCCAAGCAACAG
GGG
Found at i:5072 original size:20 final size:20
Alignment explanation
Indices: 5036--5074 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5026 AAATACAAGG
*
5036 CATTTGATTTACGAATTGGA
1 CATTTGATTTACAAATTGGA
*
5056 CATTTGATTTGCAAATTGG
1 CATTTGATTTACAAATTGG
5075 TGCTCTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (20 bp):
CATTTGATTTACAAATTGGA
Found at i:8102 original size:21 final size:22
Alignment explanation
Indices: 8074--8506 Score: 83
Period size: 22 Copynumber: 20.4 Consensus size: 22
8064 GCAATCATTA
*
8074 AAAG-GTAAAATGGTAATTAGT
1 AAAGAGTAAAATGATAATTAGT
*
8095 -AAGAGTAAAGTGATAATTAGT
1 AAAGAGTAAAATGATAATTAGT
*
8116 AAAGAGT--AAT-AGAATTCAGT
1 AAAGAGTAAAATGATAATT-AGT
* *
8136 -AAGAAGTAATA-G-TACA-CAGT
1 AAAG-AGTAAAATGATA-ATTAGT
* * * *
8156 AAAAAAGTAAAAAGGTAATCAGT
1 -AAAGAGTAAAATGATAATTAGT
* * *
8179 AAAAAGTAAAAAGGT-ATCT-G-
1 AAAGAGTAAAATGATAAT-TAGT
* * *
8199 AAAGGGTAAAATGGTAATTAAT
1 AAAGAGTAAAATGATAATTAGT
* *
8221 AAAGAGTAAAGTGATAATCAGT
1 AAAGAGTAAAATGATAATTAGT
* *
8243 AAAGAGTAATA-GA-AATCAGT
1 AAAGAGTAAAATGATAATTAGT
* ** *
8263 -AAGAAGTAATA-G-TAAACAGCA
1 AAAG-AGTAAAATGATAATTAG-T
* * * * *
8284 AAAAAGTAAAAAGGTAATCAAT
1 AAAGAGTAAAATGATAATTAGT
* * * *
8306 AAAAAGTAAAGA-GGT-A-TCGG
1 AAAGAGTAAA-ATGATAATTAGT
* *
8326 AAAGGGTAAAATGGTAATTAGT
1 AAAGAGTAAAATGATAATTAGT
* * *
8348 AAAGAGTAAAGTAATAATCAGT
1 AAAGAGTAAAATGATAATTAGT
* *
8370 AAAGAGTAATA-GA-AATCAGT
1 AAAGAGTAAAATGATAATTAGT
* **
8390 -AAGAAGTAATA-G-TAAACAGT
1 AAAG-AGTAAAATGATAATTAGT
* * * * *
8410 AAAAAGTAAAAAGGTAATCAAT
1 AAAGAGTAAAATGATAATTAGT
* * *
8432 AAAAAGTAAAAAGGGT-ATCT-GT
1 AAAGAGT-AAAATGATAAT-TAGT
* *
8454 AAAGGGTAAAATGGTAATTAGT
1 AAAGAGTAAAATGATAATTAGT
* *
8476 AAAGAGTAAAGTGATAATCAGT
1 AAAGAGTAAAATGATAATTAGT
*
8498 AAAGCGTAA
1 AAAGAGTAA
8507 TAGTAATCAG
Statistics
Matches: 316, Mismatches: 60, Indels: 71
0.71 0.13 0.16
Matches are distributed among these distances:
19 15 0.05
20 85 0.27
21 49 0.16
22 148 0.47
23 19 0.06
ACGTcount: A:0.53, C:0.04, G:0.21, T:0.22
Consensus pattern (22 bp):
AAAGAGTAAAATGATAATTAGT
Found at i:8185 original size:22 final size:22
Alignment explanation
Indices: 8152--8558 Score: 188
Period size: 22 Copynumber: 19.1 Consensus size: 22
8142 TAATAGTACA
8152 CAGTAAAAAAGTAAAAAGGTAAT
1 CAGT-AAAAAGTAAAAAGGTAAT
8175 CAGTAAAAAGTAAAAAGGT-AT
1 CAGTAAAAAGTAAAAAGGTAAT
* ** *
8196 CTG-AAAGGGTAAAATGGTAAT
1 CAGTAAAAAGTAAAAAGGTAAT
* * * ** *
8217 TAATAAAGAGTAAAGTGATAAT
1 CAGTAAAAAGTAAAAAGGTAAT
* * *
8239 CAGTAAAGAGT-AATA-GAAAT
1 CAGTAAAAAGTAAAAAGGTAAT
* * *
8259 CAGTAAGAAGT-AATA-GTAAA
1 CAGTAAAAAGTAAAAAGGTAAT
*
8279 CAGCAAAAAAGTAAAAAGGTAAT
1 CAG-TAAAAAGTAAAAAGGTAAT
* *
8302 CAATAAAAAGTAAAGAGGT-AT
1 CAGTAAAAAGTAAAAAGGTAAT
* ** *
8323 C-GGAAAGGGTAAAATGGTAAT
1 CAGTAAAAAGTAAAAAGGTAAT
* *
8344 TAGTAAAGAGTAAAGTAA--TAAT
1 CAGTAAAAAGTAAA--AAGGTAAT
* * *
8366 CAGTAAAGAGT-AATA-GAAAT
1 CAGTAAAAAGTAAAAAGGTAAT
* * *
8386 CAGTAAGAAGT-AATA-GTAAA
1 CAGTAAAAAGTAAAAAGGTAAT
8406 CAGTAAAAAGTAAAAAGGTAAT
1 CAGTAAAAAGTAAAAAGGTAAT
*
8428 CAATAAAAAGTAAAAAGGGT-AT
1 CAGTAAAAAGTAAAAA-GGTAAT
* ** *
8450 CTGTAAAGGGTAAAATGGTAAT
1 CAGTAAAAAGTAAAAAGGTAAT
* * ** *
8472 TAGTAAAGAGTAAAGTGATAAT
1 CAGTAAAAAGTAAAAAGGTAAT
** *
8494 CAGTAAAGCGT-AATA-GTAAT
1 CAGTAAAAAGTAAAAAGGTAAT
* ** *
8514 CAGTAAGAAGT-ATTA-GTAAA
1 CAGTAAAAAGTAAAAAGGTAAT
8534 CAGT-AAAAGTAAAAAGGGTAAT
1 CAGTAAAAAGTAAAAA-GGTAAT
8556 CAG
1 CAG
8559 AAATCAAGGT
Statistics
Matches: 295, Mismatches: 72, Indels: 35
0.73 0.18 0.09
Matches are distributed among these distances:
19 6 0.02
20 99 0.34
21 29 0.10
22 147 0.50
23 13 0.04
24 1 0.00
ACGTcount: A:0.53, C:0.05, G:0.21, T:0.21
Consensus pattern (22 bp):
CAGTAAAAAGTAAAAAGGTAAT
Found at i:8237 original size:127 final size:126
Alignment explanation
Indices: 8077--8557 Score: 795
Period size: 127 Copynumber: 3.8 Consensus size: 126
8067 ATCATTAAAA
* *
8077 GGTAAAATGGTAATTAGT-AAGAGTAAAGTGATAATTAGTAAAGAGTAATAGAATTCAGTAAGAA
1 GGTAAAATGGTAATTAGTAAAGAGTAAAGTGATAATCAGTAAAGAGTAATAGAAATCAGTAAGAA
* *
8141 GTAATAGTACACAGTAAAAAAGTAAAAAGGTAATCAGTAAAAAGTAAAAAGGTATCTGAAAG
66 GTAATAGTAAACAGT-AAAAAGTAAAAAGGTAATCAATAAAAAGTAAAAAGGTATCTGAAAG
*
8203 GGTAAAATGGTAATTAATAAAGAGTAAAGTGATAATCAGTAAAGAGTAATAGAAATCAGTAAGAA
1 GGTAAAATGGTAATTAGTAAAGAGTAAAGTGATAATCAGTAAAGAGTAATAGAAATCAGTAAGAA
* * *
8268 GTAATAGTAAACAGCAAAAAAGTAAAAAGGTAATCAATAAAAAGTAAAGAGGTATCGGAAAG
66 GTAATAGTAAACAG-TAAAAAGTAAAAAGGTAATCAATAAAAAGTAAAAAGGTATCTGAAAG
*
8330 GGTAAAATGGTAATTAGTAAAGAGTAAAGTAATAATCAGTAAAGAGTAATAGAAATCAGTAAGAA
1 GGTAAAATGGTAATTAGTAAAGAGTAAAGTGATAATCAGTAAAGAGTAATAGAAATCAGTAAGAA
8395 GTAATAGTAAACAGTAAAAAGTAAAAAGGTAATCAATAAAAAGTAAAAAGGGTATCTGTAAAG
66 GTAATAGTAAACAGTAAAAAGTAAAAAGGTAATCAATAAAAAGTAAAAA-GGTATCTG-AAAG
* *
8458 GGTAAAATGGTAATTAGTAAAGAGTAAAGTGATAATCAGTAAAGCGTAATAGTAATCAGTAAGAA
1 GGTAAAATGGTAATTAGTAAAGAGTAAAGTGATAATCAGTAAAGAGTAATAGAAATCAGTAAGAA
*
8523 GTATTAGTAAACAGT-AAAAGTAAAAAGGGTAATCA
66 GTAATAGTAAACAGTAAAAAGTAAAAA-GGTAATCA
8558 GAAATCAAGG
Statistics
Matches: 333, Mismatches: 17, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
126 50 0.15
127 195 0.59
128 88 0.26
ACGTcount: A:0.52, C:0.04, G:0.21, T:0.22
Consensus pattern (126 bp):
GGTAAAATGGTAATTAGTAAAGAGTAAAGTGATAATCAGTAAAGAGTAATAGAAATCAGTAAGAA
GTAATAGTAAACAGTAAAAAGTAAAAAGGTAATCAATAAAAAGTAAAAAGGTATCTGAAAG
Found at i:8261 original size:20 final size:20
Alignment explanation
Indices: 8236--8418 Score: 74
Period size: 20 Copynumber: 8.8 Consensus size: 20
8226 GTAAAGTGAT
8236 AATCAGTAAAGAGTAATAGA
1 AATCAGTAAAGAGTAATAGA
8256 AATCAGT-AAGAAGTAATAGTA
1 AATCAGTAAAG-AGTAATAG-A
* * * *
8277 AA-CAGCAAAAAAGTAAAAAGGT
1 AATCAG-TAAAGAGT-AATA-GA
* *
8299 AATCAATAAAAAGTAA-AGA
1 AATCAGTAAAGAGTAATAGA
* * * * *
8318 GGTATC-GGAAAGGGTAAAATGGT
1 --AATCAGTAAAGAGT--AATAGA
*
8341 AATTAGTAAAGAGTAA-AGTAA
1 AATCAGTAAAGAGTAATAG--A
8362 TAATCAGTAAAGAGTAATAGA
1 -AATCAGTAAAGAGTAATAGA
8383 AATCAGT-AAGAAGTAATAGTA
1 AATCAGTAAAG-AGTAATAG-A
*
8404 AA-CAGTAAAAAGTAA
1 AATCAGTAAAGAGTAA
8419 AAAGGTAATC
Statistics
Matches: 121, Mismatches: 22, Indels: 40
0.66 0.12 0.22
Matches are distributed among these distances:
19 8 0.07
20 50 0.41
21 19 0.16
22 38 0.31
23 6 0.05
ACGTcount: A:0.55, C:0.05, G:0.20, T:0.20
Consensus pattern (20 bp):
AATCAGTAAAGAGTAATAGA
Found at i:8530 original size:20 final size:19
Alignment explanation
Indices: 8507--8544 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
8497 TAAAGCGTAA
*
8507 TAGTAATCAGTAAGAAGTAT
1 TAGTAAACAGTAA-AAGTAT
8527 TAGTAAACAGTAAAAGTA
1 TAGTAAACAGTAAAAGTA
8545 AAAAGGGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.50, C:0.05, G:0.18, T:0.26
Consensus pattern (19 bp):
TAGTAAACAGTAAAAGTAT
Found at i:8727 original size:39 final size:37
Alignment explanation
Indices: 8667--8787 Score: 120
Period size: 38 Copynumber: 3.2 Consensus size: 37
8657 AATTAAATTC
* *
8667 AAAGAGT-AAAATGGTAGTCAGTAAAAGAGAAAAAGA
1 AAAGAGTAAAAATGGTAATCAGTAAAAAAGAAAAAGA
**
8703 AGAAGAGTAAAAAGTGGTAATCAGTAAAAAAGAGTAAGA
1 A-AAGAGTAAAAA-TGGTAATCAGTAAAAAAGAAAAAGA
* * * **
8742 AATGAGTAAAAAATGGTGATCAATAAAAAAGAGTAA-A
1 AAAGAGT-AAAAATGGTAATCAGTAAAAAAGAAAAAGA
8779 AAAGAGTAA
1 AAAGAGTAA
8788 TTAGTAATAA
Statistics
Matches: 73, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
36 3 0.04
37 13 0.18
38 30 0.41
39 27 0.37
ACGTcount: A:0.59, C:0.02, G:0.23, T:0.16
Consensus pattern (37 bp):
AAAGAGTAAAAATGGTAATCAGTAAAAAAGAAAAAGA
Found at i:8769 original size:38 final size:37
Alignment explanation
Indices: 8705--8787 Score: 121
Period size: 38 Copynumber: 2.2 Consensus size: 37
8695 GAAAAAGAAG
* *
8705 AAGAGTAAAAAGTGGTAATCAGTAAAAAAGAGTAAGAA
1 AAGAGTAAAAAATGGTAATCAATAAAAAAGAGTAA-AA
* *
8743 ATGAGTAAAAAATGGTGATCAATAAAAAAGAGTAAAA
1 AAGAGTAAAAAATGGTAATCAATAAAAAAGAGTAAAA
8780 AAGAGTAA
1 AAGAGTAA
8788 TTAGTAATAA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
37 9 0.22
38 31 0.77
ACGTcount: A:0.59, C:0.02, G:0.22, T:0.17
Consensus pattern (37 bp):
AAGAGTAAAAAATGGTAATCAATAAAAAAGAGTAAAA
Found at i:8839 original size:27 final size:27
Alignment explanation
Indices: 8735--8833 Score: 119
Period size: 27 Copynumber: 3.6 Consensus size: 27
8725 AGTAAAAAAG
*
8735 AGTAAGAAATGAGTAAAAAATGGTGATC
1 AGTAA-AAAAGAGTAAAAAATGGTGATC
* * *
8763 AATAAAAAAGAGTAAAAAA-GAGTAATT
1 AGTAAAAAAGAGTAAAAAATG-GTGATC
* *
8790 AGTAATAAAGAGTAAGAAATGGTGATC
1 AGTAAAAAAGAGTAAAAAATGGTGATC
8817 AGTAAAAAAGAGTAAAA
1 AGTAAAAAAGAGTAAAA
8834 TGTGGTATTC
Statistics
Matches: 58, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
26 1 0.02
27 52 0.90
28 5 0.09
ACGTcount: A:0.58, C:0.02, G:0.21, T:0.19
Consensus pattern (27 bp):
AGTAAAAAAGAGTAAAAAATGGTGATC
Found at i:8845 original size:27 final size:27
Alignment explanation
Indices: 8765--8854 Score: 78
Period size: 27 Copynumber: 3.3 Consensus size: 27
8755 TGGTGATCAA
**
8765 TAAAAAAGAGTAAAAAAGAGTAATT-AG
1 TAAAAAAGAGTAAAAGTG-GTAATTCAG
* * *
8792 TAATAAAGAGTAAGAAATGGTGA-TCAG
1 TAAAAAAGAGTAA-AAGTGGTAATTCAG
8819 TAAAAAAGAGTAAAATGTGGT-ATTCAG
1 TAAAAAAGAGTAAAA-GTGGTAATTCAG
8846 TAAGAAAAG
1 TAA-AAAAG
8855 GGGTAATTAG
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
26 4 0.08
27 40 0.75
28 9 0.17
ACGTcount: A:0.54, C:0.02, G:0.22, T:0.21
Consensus pattern (27 bp):
TAAAAAAGAGTAAAAGTGGTAATTCAG
Found at i:8891 original size:31 final size:28
Alignment explanation
Indices: 8856--8924 Score: 79
Period size: 26 Copynumber: 2.4 Consensus size: 28
8846 TAAGAAAAGG
8856 GGTAATTAGTAAAAAAAGAGAGTAAAAATAT
1 GGTAATTAGT-AAAAAA-AGAGTAAAAA-AT
* *
8887 GGTAATCAGT--ACAAAGAGTAAAAAAT
1 GGTAATTAGTAAAAAAAGAGTAAAAAAT
8913 GGTAATTAGTAA
1 GGTAATTAGTAA
8925 TCAAGAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
26 11 0.33
27 10 0.30
28 3 0.09
31 9 0.27
ACGTcount: A:0.54, C:0.03, G:0.20, T:0.23
Consensus pattern (28 bp):
GGTAATTAGTAAAAAAAGAGTAAAAAAT
Found at i:10927 original size:13 final size:13
Alignment explanation
Indices: 10909--10935 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
10899 CTCTATAACC
10909 TCATAAATCATAT
1 TCATAAATCATAT
10922 TCATAAATCATAT
1 TCATAAATCATAT
10935 T
1 T
10936 TATTATATTT
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:0.15, G:0.00, T:0.41
Consensus pattern (13 bp):
TCATAAATCATAT
Found at i:11078 original size:19 final size:18
Alignment explanation
Indices: 11045--11086 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
11035 TAAATAGTTT
*
11045 TTAAGTAAAAATATAATA
1 TTAAATAAAAATATAATA
*
11063 TATAAATAAAAGTATAATA
1 T-TAAATAAAAATATAATA
11082 TTAAA
1 TTAAA
11087 ATAATTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (18 bp):
TTAAATAAAAATATAATA
Found at i:11090 original size:19 final size:19
Alignment explanation
Indices: 11050--11086 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
11040 AGTTTTTAAG
11050 TAAAAATATAATATATAAA
1 TAAAAATATAATATATAAA
*
11069 TAAAAGTATAATAT-TAAA
1 TAAAAATATAATATATAAA
11087 ATAATTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:18071 original size:20 final size:20
Alignment explanation
Indices: 18046--18086 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
18036 CCCTCGATTC
18046 ACTTATGAGTCCTCATCTTA
1 ACTTATGAGTCCTCATCTTA
18066 ACTTATGAGTCCTCATCTTA
1 ACTTATGAGTCCTCATCTTA
18086 A
1 A
18087 GCCAATTATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.27, C:0.24, G:0.10, T:0.39
Consensus pattern (20 bp):
ACTTATGAGTCCTCATCTTA
Found at i:18303 original size:26 final size:26
Alignment explanation
Indices: 18267--18320 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
18257 TAGACTGATG
18267 GTTTCTTGGGTCCTTCATGTATATAT
1 GTTTCTTGGGTCCTTCATGTATATAT
18293 GTTTCTTGGGTCCTTCATGTATATAT
1 GTTTCTTGGGTCCTTCATGTATATAT
18319 GT
1 GT
18321 CACTCAAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.15, C:0.15, G:0.20, T:0.50
Consensus pattern (26 bp):
GTTTCTTGGGTCCTTCATGTATATAT
Found at i:18344 original size:34 final size:34
Alignment explanation
Indices: 18301--18367 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
18291 ATGTTTCTTG
18301 GGTCCTTCATGTATATATGTCACTCAAACAACCC
1 GGTCCTTCATGTATATATGTCACTCAAACAACCC
18335 GGTCCTTCATGTATATATGTCACTCAAACAACC
1 GGTCCTTCATGTATATATGTCACTCAAACAACC
18368 AATCTCTTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.30, C:0.28, G:0.12, T:0.30
Consensus pattern (34 bp):
GGTCCTTCATGTATATATGTCACTCAAACAACCC
Found at i:18377 original size:34 final size:34
Alignment explanation
Indices: 18303--18379 Score: 120
Period size: 34 Copynumber: 2.3 Consensus size: 34
18293 GTTTCTTGGG
**
18303 TCCTTCATGTATATATGTCACTCAAACAACCCGG
1 TCCTTCATGTATATATGTCACTCAAACAACCCAA
18337 TCCTTCATGTATATATGTCACTCAAACAA-CCAA
1 TCCTTCATGTATATATGTCACTCAAACAACCCAA
18370 TCTCTTCATG
1 TC-CTTCATG
18380 ATGTGGGATG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
33 4 0.10
34 36 0.90
ACGTcount: A:0.30, C:0.29, G:0.09, T:0.32
Consensus pattern (34 bp):
TCCTTCATGTATATATGTCACTCAAACAACCCAA
Found at i:18423 original size:19 final size:19
Alignment explanation
Indices: 18399--18437 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
18389 GTTTCCCTCA
18399 CATGTGAATCCCTAACAAT
1 CATGTGAATCCCTAACAAT
18418 CATGTGAATCCCTAACAAT
1 CATGTGAATCCCTAACAAT
18437 C
1 C
18438 TCCCCCGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.28, G:0.10, T:0.26
Consensus pattern (19 bp):
CATGTGAATCCCTAACAAT
Found at i:21771 original size:155 final size:155
Alignment explanation
Indices: 21489--22054 Score: 766
Period size: 155 Copynumber: 3.7 Consensus size: 155
21479 ATGTGGACCA
* * * *
21489 TCTTGGCTAAATTTCATCTCAAACGGACTTA-AGATGAAAAACTTATGCAAGTTTTTCAGTTAAG
1 TCTTGGCCAAGTTTCATCTCAAACAGACTTAGA-ATGAAAAACTTATGCAAGTTTTTCATTTAAG
* * * *
21553 GACAATTTGGGGTGAGAAACC-ACTTCACCATGATA-GGGAGTTTGGTTTTACTTAGAATTTTTT
65 GACAATTTGGGGAGAGAAACCGAGTTCACCATCA-AGGGGAGTTCGGTTTTACTTAGAATTTTTT
21616 CCATAAGTTTGTGGAGATAATCTAAGTC
129 CCATAAGTTT-TGGAGATAATCTAAGTC
*
21644 TCTTGGCCAAGTTTCATCTCAAACAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGG
1 TCTTGGCCAAGTTTCATCTCAAACAGACTTAGAATGAAAAACTTATGCAAGTTTTTCATTTAAGG
*
21709 ACAATTT-GGGAGAGAAACCGAGTTCACCATCAAGGGGAGTTCGGTTTTACTTAGAATTTTTTCT
66 ACAATTTGGGGAGAGAAACCGAGTTCACCATCAAGGGGAGTTCGGTTTTACTTAGAATTTTTTCC
21773 ATAAGTTTTCGGAGATAATCTAAGTC
131 ATAAGTTTT-GGAGATAATCTAAGTC
*
21799 TCTTGGCCAAGTTTCATCTCAAACAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGG
1 TCTTGGCCAAGTTTCATCTCAAACAGACTTAGAATGAAAAACTTATGCAAGTTTTTCATTTAAGG
* * * * * *
21864 ACAATTT-TGGAGAGAAACCGAGTTCACCATCAAGAGGAGGTCGGTTTTACTTGGGATTTTTTAC
66 ACAATTTGGGGAGAGAAACCGAGTTCACCATCAAGGGGAGTTCGGTTTTACTTAGAATTTTTTCC
* * *
21928 AT-AGTCTCATGGAAATATTCTAAGTC
131 ATAAGT-T-TTGGAGATAATCTAAGTC
* * * **
21954 CCTTGGCAAAGTTTCAGCTCATTCAGACTTAGAATGAAAAACTTATGCAAGTTTTTCATTTAAGG
1 TCTTGGCCAAGTTTCATCTCAAACAGACTTAGAATGAAAAACTTATGCAAGTTTTTCATTTAAGG
* * * * *
22019 ACAGTTTGGGGTGTGAAACCTAGTTCACCATGAAGG
66 ACAATTTGGGGAGAGAAACCGAGTTCACCATCAAGG
22055 AGGGCTCGAA
Statistics
Matches: 371, Mismatches: 33, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
154 16 0.04
155 331 0.89
156 24 0.06
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.34
Consensus pattern (155 bp):
TCTTGGCCAAGTTTCATCTCAAACAGACTTAGAATGAAAAACTTATGCAAGTTTTTCATTTAAGG
ACAATTTGGGGAGAGAAACCGAGTTCACCATCAAGGGGAGTTCGGTTTTACTTAGAATTTTTTCC
ATAAGTTTTGGAGATAATCTAAGTC
Found at i:23196 original size:15 final size:16
Alignment explanation
Indices: 23172--23213 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
23162 CTTCTTCTTC
*
23172 TTCTTATTTCTTTCT-
1 TTCTTTTTTCTTTCTA
*
23187 TTCTTTTTTCTCTCTA
1 TTCTTTTTTCTTTCTA
23203 TT-TTTTTTCTT
1 TTCTTTTTTCTT
23214 CTTCTTCTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 21 0.91
16 2 0.09
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.76
Consensus pattern (16 bp):
TTCTTTTTTCTTTCTA
Found at i:23225 original size:42 final size:43
Alignment explanation
Indices: 23139--23225 Score: 108
Period size: 42 Copynumber: 2.0 Consensus size: 43
23129 CCCCACTTAT
*
23139 TTTCATTTCTTTTTTTACTCTATCTTCTTCTTCTTCTTATTTC
1 TTTCATTTCTTTTTTTACTCTATCTTCTTCTTCTTCTTACTTC
* *
23182 TTTC-TTTCTTTTTTCT-CTCTATTTTTTTTCTTCTTCTT-CTTC
1 TTTCATTTCTTTTTT-TACTCTA-TCTTCTTCTTCTTCTTACTTC
23224 TT
1 TT
23226 CTCTACTCAT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
42 20 0.51
43 19 0.49
ACGTcount: A:0.06, C:0.23, G:0.00, T:0.71
Consensus pattern (43 bp):
TTTCATTTCTTTTTTTACTCTATCTTCTTCTTCTTCTTACTTC
Found at i:24359 original size:54 final size:51
Alignment explanation
Indices: 24278--24382 Score: 174
Period size: 54 Copynumber: 2.0 Consensus size: 51
24268 AAATTGCCTT
*
24278 GCTGTTAATAGGGTATTTAATACTGAGTAATAGGCCTTCAATTCATATAAGTG
1 GCTGTTAATAGAGTATTTAATACTGAGTAATAGGCCTTCAATT--TATAAGTG
24331 GCTGTTAATAGAAGTATTTAATACTGAGTAATAGGCCTTCAATTTATAAGTG
1 GCTGTTAATAG-AGTATTTAATACTGAGTAATAGGCCTTCAATTTATAAGTG
24383 TACAAGTATC
Statistics
Matches: 50, Mismatches: 1, Indels: 3
0.93 0.02 0.06
Matches are distributed among these distances:
52 8 0.16
53 11 0.22
54 31 0.62
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.36
Consensus pattern (51 bp):
GCTGTTAATAGAGTATTTAATACTGAGTAATAGGCCTTCAATTTATAAGTG
Found at i:28432 original size:22 final size:21
Alignment explanation
Indices: 28392--28432 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
28382 GCCTCTTCTC
*
28392 CTCTTCTCTCGATACCCCACT
1 CTCTTCTCTCGATAACCCACT
*
28413 CTCTCTCTCTCGTTAACCCA
1 CTCT-TCTCTCGATAACCCA
28433 TAATTTTGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.15, C:0.46, G:0.05, T:0.34
Consensus pattern (21 bp):
CTCTTCTCTCGATAACCCACT
Found at i:29397 original size:12 final size:12
Alignment explanation
Indices: 29355--29400 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
29345 TGAATGTTTG
*
29355 ATTATTAATATT
1 ATTATTTATATT
29367 ATTATTTATATT
1 ATTATTTATATT
29379 ATTTATTTATAATT
1 A-TTATTTAT-ATT
29393 A-TATTTAT
1 ATTATTTAT
29401 TGATTATTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 19 0.61
13 8 0.26
14 4 0.13
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
ATTATTTATATT
Found at i:29409 original size:16 final size:16
Alignment explanation
Indices: 29352--29409 Score: 50
Period size: 16 Copynumber: 3.6 Consensus size: 16
29342 CCGTGAATGT
29352 TTGATTATTA-ATATTA
1 TTGATTATTATAT-TTA
29368 TT-ATT-TATATTATTTA
1 TTGATTAT-TA-TATTTA
* *
29384 TTTATAATTATATTTA
1 TTGATTATTATATTTA
29400 TTGATTATTA
1 TTGATTATTA
29410 GTCTTTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
14 1 0.03
15 5 0.15
16 21 0.62
17 6 0.18
18 1 0.03
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (16 bp):
TTGATTATTATATTTA
Found at i:33421 original size:5 final size:5
Alignment explanation
Indices: 33411--33486 Score: 68
Period size: 5 Copynumber: 14.8 Consensus size: 5
33401 GAGAAGAGGA
* *
33411 AAAAG AAAAG AAAA- TAAGG AAAAG AAAAAG AAAA- AAAGAGG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG -AAAAG AAAAG AAA-A-G AAAAG
33457 AAAAG AAAAG AAAAGG AAAAAG AAAA- AAAA
1 AAAAG AAAAG AAAA-G -AAAAG AAAAG AAAA
33487 AACCACGTCA
Statistics
Matches: 60, Mismatches: 4, Indels: 15
0.76 0.05 0.19
Matches are distributed among these distances:
4 9 0.15
5 36 0.60
6 8 0.13
7 7 0.12
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.01
Consensus pattern (5 bp):
AAAAG
Found at i:33452 original size:22 final size:21
Alignment explanation
Indices: 33411--33488 Score: 92
Period size: 22 Copynumber: 3.8 Consensus size: 21
33401 GAGAAGAGGA
*
33411 AAAAG-AAAAG-AAAATAAGG
1 AAAAGAAAAAGAAAAAAAAGG
33430 AAAAGAAAAAGAAAAAAAGAGG
1 AAAAGAAAAAGAAAAAAA-AGG
33452 AAAAG-AAAAGAAAAGAAAAGG
1 AAAAGAAAAAGAAAA-AAAAGG
33473 AAAAAGAAAAA-AAAAA
1 -AAAAGAAAAAGAAAAA
33489 CCACGTCAGG
Statistics
Matches: 52, Mismatches: 1, Indels: 10
0.83 0.02 0.16
Matches are distributed among these distances:
19 5 0.10
20 5 0.10
21 18 0.35
22 20 0.38
23 4 0.08
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.01
Consensus pattern (21 bp):
AAAAGAAAAAGAAAAAAAAGG
Found at i:33457 original size:16 final size:14
Alignment explanation
Indices: 33410--33486 Score: 68
Period size: 14 Copynumber: 5.4 Consensus size: 14
33400 GGAGAAGAGG
33410 AAAAAGAAAAGAAA
1 AAAAAGAAAAGAAA
* *
33424 ATAAGGAAAAGAAA
1 AAAAAGAAAAGAAA
*
33438 AAGAAA-AAAAG-AG
1 AA-AAAGAAAAGAAA
*
33451 GAAAAGAAAAGAAA
1 AAAAAGAAAAGAAA
33465 AGAAAAGGAAAAAGAAA
1 A-AAAA-G-AAAAGAAA
33482 AAAAA
1 AAAAA
33487 AACCACGTCA
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
12 3 0.06
13 7 0.14
14 19 0.39
15 6 0.12
16 5 0.10
17 9 0.18
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.01
Consensus pattern (14 bp):
AAAAAGAAAAGAAA
Found at i:33632 original size:31 final size:30
Alignment explanation
Indices: 33555--33632 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 30
33545 GTCCAAAAAA
*
33555 ACCCCGAATTGAGCAGTCCCGAAAACGTTTG
1 ACCCCAAATTGAGCA-TCCCGAAAACGTTTG
* ** * *
33586 GCCCCAAATCAAGCATCACGGCAAACGTTTG
1 ACCCCAAATTGAGCATC-CCGAAAACGTTTG
33617 ACCCCAAATTGAGCAT
1 ACCCCAAATTGAGCAT
33633 TTTGCCAAGA
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
30 2 0.05
31 35 0.95
ACGTcount: A:0.32, C:0.31, G:0.19, T:0.18
Consensus pattern (30 bp):
ACCCCAAATTGAGCATCCCGAAAACGTTTG
Found at i:44258 original size:18 final size:18
Alignment explanation
Indices: 44235--44272 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
44225 AGAAACTTAT
*
44235 ACTTTCAATATTACAGAA
1 ACTTTCAATATTAAAGAA
44253 ACTTTCAATATTAAAGAA
1 ACTTTCAATATTAAAGAA
44271 AC
1 AC
44273 CCATCATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.47, C:0.16, G:0.05, T:0.32
Consensus pattern (18 bp):
ACTTTCAATATTAAAGAA
Found at i:44397 original size:43 final size:43
Alignment explanation
Indices: 44349--44439 Score: 155
Period size: 43 Copynumber: 2.1 Consensus size: 43
44339 AAAGGTTTTC
44349 AAACACAAAAACAGTGGCCTAGATAACAAAAAGAAACCCTTTG
1 AAACACAAAAACAGTGGCCTAGATAACAAAAAGAAACCCTTTG
* *
44392 AAACACAAAAACAGTGGCTTAGATAACAAAAAGAATCCCTTTG
1 AAACACAAAAACAGTGGCCTAGATAACAAAAAGAAACCCTTTG
*
44435 CAACA
1 AAACA
44440 GAAACCTTGA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.51, C:0.21, G:0.13, T:0.15
Consensus pattern (43 bp):
AAACACAAAAACAGTGGCCTAGATAACAAAAAGAAACCCTTTG
Found at i:44420 original size:21 final size:21
Alignment explanation
Indices: 44353--44423 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
44343 GTTTTCAAAC
*
44353 ACAAAAACAGTGGCCTAGATA
1 ACAAAAACAGTGGCTTAGATA
* **** * *
44374 ACAAAAAGAAACCCTTTGAAA
1 ACAAAAACAGTGGCTTAGATA
44395 CACAAAAACAGTGGCTTAGATA
1 -ACAAAAACAGTGGCTTAGATA
44417 ACAAAAA
1 ACAAAAA
44424 GAATCCCTTT
Statistics
Matches: 34, Mismatches: 15, Indels: 2
0.67 0.29 0.04
Matches are distributed among these distances:
21 20 0.59
22 14 0.41
ACGTcount: A:0.54, C:0.18, G:0.14, T:0.14
Consensus pattern (21 bp):
ACAAAAACAGTGGCTTAGATA
Found at i:44423 original size:22 final size:23
Alignment explanation
Indices: 44350--44423 Score: 59
Period size: 22 Copynumber: 3.4 Consensus size: 23
44340 AAGGTTTTCA
*
44350 AACACAAAAACAGTGGCCTAGAT
1 AACACAAAAACAGTGGCTTAGAT
*** *
44373 AACA-AAAAGA-A-ACCCTTTGA-
1 AACACAAAA-ACAGTGGCTTAGAT
44393 AACACAAAAACAGTGGCTTAGAT
1 AACACAAAAACAGTGGCTTAGAT
44416 AACA-AAAA
1 AACACAAAA
44424 GAATCCCTTT
Statistics
Matches: 37, Mismatches: 9, Indels: 11
0.65 0.16 0.19
Matches are distributed among these distances:
20 5 0.14
21 9 0.24
22 14 0.38
23 9 0.24
ACGTcount: A:0.54, C:0.19, G:0.14, T:0.14
Consensus pattern (23 bp):
AACACAAAAACAGTGGCTTAGAT
Found at i:50475 original size:24 final size:24
Alignment explanation
Indices: 50443--50493 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
50433 TGAATTGTTT
*
50443 TAATGCAAGAGCCAAAATAAAACA
1 TAATGCAAGAACCAAAATAAAACA
50467 TAATGCAAGAACCAAAATAAAACA
1 TAATGCAAGAACCAAAATAAAACA
50491 TAA
1 TAA
50494 CGTTCCATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.61, C:0.16, G:0.10, T:0.14
Consensus pattern (24 bp):
TAATGCAAGAACCAAAATAAAACA
Found at i:52661 original size:5 final size:5
Alignment explanation
Indices: 52651--52684 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
52641 TGGAGTTTAC
*
52651 TTTCT TTTCT TTTCT TTTCTT TTTTT TTTCT TTT
1 TTTCT TTTCT TTTCT TTTC-T TTTCT TTTCT TTT
52685 ACAAGTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 22 0.85
6 4 0.15
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (5 bp):
TTTCT
Found at i:53009 original size:21 final size:22
Alignment explanation
Indices: 52969--53009 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
52959 TTAATTTGAC
* *
52969 TTTATTTATATTTTTAATTATG
1 TTTATTTATATATGTAATTATG
52991 TTTATTT-TATATGTAATTA
1 TTTATTTATATATGTAATTA
53010 AAAAAGTCAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (22 bp):
TTTATTTATATATGTAATTATG
Done.