Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008981.1 Corchorus capsularis cultivar CVL-1 contig09002, 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: 78729
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:11065 original size:43 final size:43
Alignment explanation
Indices: 11017--11103 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 43
11007 TTATACTCAA
* *
11017 TACAACATAATTTTAATTGATTTACACTCTCCAAAACTGAAGC
1 TACAACAAAATTTTAATTGATTTACACTCTACAAAACTGAAGC
11060 TACAACAAAATTTTAATTGATTTACACTCTACAAAACTGAAGC
1 TACAACAAAATTTTAATTGATTTACACTCTACAAAACTGAAGC
11103 T
1 T
11104 TAAAATCTGA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.41, C:0.20, G:0.07, T:0.32
Consensus pattern (43 bp):
TACAACAAAATTTTAATTGATTTACACTCTACAAAACTGAAGC
Found at i:14756 original size:20 final size:20
Alignment explanation
Indices: 14731--14772 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
14721 ATTTACTGAA
14731 TTGCTAAATACCGCCCCCTT
1 TTGCTAAATACCGCCCCCTT
*
14751 TTGCTAAATACCGCCTCCTT
1 TTGCTAAATACCGCCCCCTT
14771 TT
1 TT
14773 TACAGTTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.19, C:0.36, G:0.10, T:0.36
Consensus pattern (20 bp):
TTGCTAAATACCGCCCCCTT
Found at i:14885 original size:25 final size:25
Alignment explanation
Indices: 14851--14934 Score: 127
Period size: 25 Copynumber: 3.4 Consensus size: 25
14841 TTCAAACCCT
*
14851 AAACTTCATTCCTAACAACTTCTTC
1 AAACTTCATTTCTAACAACTTCTTC
*
14876 AAACTTCATTTCTAACAACTTCTCC
1 AAACTTCATTTCTAACAACTTCTTC
*
14901 AAACTTCATTTCTAACAA-ATCTTC
1 AAACTTCATTTCTAACAACTTCTTC
14925 AAAC-TCATTT
1 AAACTTCATTT
14935 TCCTTCATTT
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
23 6 0.11
24 8 0.15
25 41 0.75
ACGTcount: A:0.35, C:0.29, G:0.00, T:0.37
Consensus pattern (25 bp):
AAACTTCATTTCTAACAACTTCTTC
Found at i:15213 original size:15 final size:15
Alignment explanation
Indices: 15180--15229 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
15170 AGTTTATTAA
15180 AATTAG-TT-TGTTT
1 AATTAGTTTATGTTT
15193 -ATTAGTTTATGTTT
1 AATTAGTTTATGTTT
**
15207 AATTAGTTTATAATT
1 AATTAGTTTATGTTT
15222 AATTAGTT
1 AATTAGTT
15230 CATTATTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
12 5 0.16
13 2 0.06
14 5 0.16
15 20 0.62
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (15 bp):
AATTAGTTTATGTTT
Found at i:15445 original size:15 final size:14
Alignment explanation
Indices: 15393--15472 Score: 71
Period size: 14 Copynumber: 5.9 Consensus size: 14
15383 TTGATGATTA
15393 ATTTTAATTAGTTT
1 ATTTTAATTAGTTT
**
15407 ATTAAAATTAGTTT
1 ATTTTAATTAGTTT
*
15421 -GTTT-ATTAGTTT
1 ATTTTAATTAGTTT
15433 ATGTTTAATTAG--T
1 AT-TTTAATTAGTTT
15446 A-TTTAATTAGTTT
1 ATTTTAATTAGTTT
*
15459 ATAATTAATTAGTT
1 AT-TTTAATTAGTT
15473 CATTATTTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
11 9 0.17
12 8 0.15
13 5 0.10
14 15 0.29
15 15 0.29
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (14 bp):
ATTTTAATTAGTTT
Found at i:15466 original size:26 final size:26
Alignment explanation
Indices: 15395--15471 Score: 86
Period size: 26 Copynumber: 3.0 Consensus size: 26
15385 GATGATTAAT
*
15395 TTTAATTAGTTTATTAA--AATTAGTT
1 TTTAATTAGTTTA-TAATTAATTAGTA
* **
15420 TGTTTATTAGTTTATGTTTAATTAGTA
1 T-TTAATTAGTTTATAATTAATTAGTA
15447 TTTAATTAGTTTATAATTAATTAGT
1 TTTAATTAGTTTATAATTAATTAGT
15472 TCATTATTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
25 2 0.05
26 32 0.76
27 8 0.19
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.57
Consensus pattern (26 bp):
TTTAATTAGTTTATAATTAATTAGTA
Found at i:15526 original size:18 final size:18
Alignment explanation
Indices: 15389--15526 Score: 76
Period size: 18 Copynumber: 7.9 Consensus size: 18
15379 AATTTTGATG
15389 ATTAATTTTAATTAGTTT
1 ATTAATTTTAATTAGTTT
** * *
15407 ATTAAAATTAGTTTGTTT
1 ATTAATTTTAATTAGTTT
*
15425 ATT-AGTTT-A-T-GTTT
1 ATTAATTTTAATTAGTTT
*
15439 AATTAGTATTTAATTAGTTT
1 -ATTAAT-TTTAATTAGTTT
*
15459 A-TAA--TTAATTAGTTC
1 ATTAATTTTAATTAGTTT
** **
15474 ATT-ATTTTTGTTTTTTT
1 ATTAATTTTAATTAGTTT
*
15491 ATTAATTATTACTTAGTTT
1 ATTAATT-TTAATTAGTTT
*
15510 ATTAGTTTTAATTAGTT
1 ATTAATTTTAATTAGTT
15527 AATTTATGAT
Statistics
Matches: 87, Mismatches: 22, Indels: 22
0.66 0.17 0.17
Matches are distributed among these distances:
14 4 0.05
15 16 0.18
16 1 0.01
17 15 0.17
18 32 0.37
19 15 0.17
20 4 0.05
ACGTcount: A:0.30, C:0.01, G:0.09, T:0.60
Consensus pattern (18 bp):
ATTAATTTTAATTAGTTT
Found at i:15572 original size:62 final size:58
Alignment explanation
Indices: 15263--15572 Score: 129
Period size: 62 Copynumber: 5.1 Consensus size: 58
15253 TTAGTACTTA
* *
15263 GTTTATTAGTTTTTTAATTAGTTAATTTATGATTAACTACTGTTAATTAATCTAAATTTTGATT
1 GTTTATTAG--TTTTAATTAGTTAATTTATAATT-A-TATTGTTAATTAAT-T-AATTTTGATT
* * *
15327 GTTTATTAGTTTTAATTAGTTTATACTTAAAAGTGGA-ATT-TTAATTAATATTAATTTTGA-T
1 GTTTATTAGTTTTAATTAG-TTA-ATTTATAA-T-TATATTGTTAATT-A-ATTAATTTTGATT
* * * * * * *
15388 G---ATTAATTTTAATTAGTTTA-TTAAAATTAGT-TTGTTTATTAGTTTATGTTTAATT
1 GTTTATTAGTTTTAATTAGTTAATTTATAATTA-TATTGTTAATTAATTAAT-TTTGATT
* * * * ** *
15443 AGTATTTAATTAGTTTATAATTAATTAGTTCATTATT-T-TTGTTTTTTTATTAATTATT-ACTT
1 -G--TTT-ATTAGTTT-TAATTAGTTAATTTATAATTATATTGTTAATTAATTAATT-TTGA-TT
*
15505 AGTTTATTAGTTTTAATTAGTTAATTTATGATTAACTATTGTTAATTAATCTAAATTTTGATT
1 -GTTTATTAGTTTTAATTAGTTAATTTATAATT-A-TATTGTTAATTAAT-T-AATTTTGATT
15568 GTTTA
1 GTTTA
15573 ATAATTTATT
Statistics
Matches: 187, Mismatches: 30, Indels: 60
0.68 0.11 0.22
Matches are distributed among these distances:
53 5 0.03
54 8 0.04
55 12 0.06
56 2 0.01
57 2 0.01
58 30 0.16
59 8 0.04
60 3 0.02
61 5 0.03
62 64 0.34
63 20 0.11
64 26 0.14
65 2 0.01
ACGTcount: A:0.32, C:0.03, G:0.10, T:0.56
Consensus pattern (58 bp):
GTTTATTAGTTTTAATTAGTTAATTTATAATTATATTGTTAATTAATTAATTTTGATT
Found at i:17751 original size:15 final size:15
Alignment explanation
Indices: 17733--17792 Score: 74
Period size: 15 Copynumber: 4.3 Consensus size: 15
17723 TATCATTAAT
17733 TAATTAATCATAAAC
1 TAATTAATCATAAAC
*
17748 TAATCAA--AT--AC
1 TAATTAATCATAAAC
17759 TAATTAATCATAAAC
1 TAATTAATCATAAAC
*
17774 TAATTAAACATAAAC
1 TAATTAATCATAAAC
17789 TAAT
1 TAAT
17793 AAACTAAGTA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
11 8 0.21
13 4 0.11
15 26 0.68
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (15 bp):
TAATTAATCATAAAC
Found at i:17792 original size:26 final size:26
Alignment explanation
Indices: 17737--17792 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
17727 ATTAATTAAT
* *
17737 TAATCATAAACTAATCAAATACTAAT
1 TAATCATAAACTAATCAAACACTAAC
*
17763 TAATCATAAACTAATTAAACA-TAAAC
1 TAATCATAAACTAATCAAACACT-AAC
17789 TAAT
1 TAAT
17793 AAACTAAGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 1 0.04
26 25 0.96
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.30
Consensus pattern (26 bp):
TAATCATAAACTAATCAAACACTAAC
Found at i:17816 original size:41 final size:41
Alignment explanation
Indices: 17727--17822 Score: 106
Period size: 41 Copynumber: 2.3 Consensus size: 41
17717 GACCAATATC
* * *
17727 ATTAATTAATTAATCATAAACTAATCAAATACTAATTAATC
1 ATTAACTAATTAAACATAAACTAATCAAATACTAATTAATA
* * *
17768 ATAAACTAATTAAACATAAACTAAT-AAACTAAGTAATT-TTA
1 ATTAACTAATTAAACATAAACTAATCAAA-T-ACTAATTAATA
17809 ATTAACTAATTAAA
1 ATTAACTAATTAAA
17823 ATTAATCATA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
40 3 0.07
41 37 0.80
42 6 0.13
ACGTcount: A:0.54, C:0.10, G:0.01, T:0.34
Consensus pattern (41 bp):
ATTAACTAATTAAACATAAACTAATCAAATACTAATTAATA
Found at i:18138 original size:21 final size:22
Alignment explanation
Indices: 18096--18141 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
18086 CAAAAATTAT
***
18096 AAAAAGGGGGGCGGTGTTTAGC
1 AAAAAGGGGGGCGGTAAATAGC
18118 AAAAA-GGGGGCGGTAAATAGC
1 AAAAAGGGGGGCGGTAAATAGC
18139 AAA
1 AAA
18142 CCCCTAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.39, C:0.09, G:0.39, T:0.13
Consensus pattern (22 bp):
AAAAAGGGGGGCGGTAAATAGC
Found at i:18360 original size:22 final size:21
Alignment explanation
Indices: 18291--18434 Score: 110
Period size: 22 Copynumber: 6.6 Consensus size: 21
18281 TGATCCAATT
*
18291 TCAAAATTTCA-AAGGCGGTTA
1 TCAAAATTTCATAA-GAGGTTA
* * *
18312 TCAAAATTACATAATGTGATTA
1 TCAAAATTTCATAA-GAGGTTA
*
18334 TCAAAATTTCATAGAGGGGTTA
1 TCAAAATTTCATA-AGAGGTTA
* * *
18356 ACAAAATTTTATAGAGAGGCTA
1 TCAAAATTTCATA-AGAGGTTA
18378 TCAAAATTTCATAAAGAGGTTA
1 TCAAAATTTCAT-AAGAGGTTA
* * * *
18400 TCAAATTTTCAAAATATGATTA
1 TCAAAATTTCATAAGA-GGTTA
*
18422 CCAAAATTTCATA
1 TCAAAATTTCATA
18435 GTGGTATTTC
Statistics
Matches: 98, Mismatches: 21, Indels: 7
0.78 0.17 0.06
Matches are distributed among these distances:
21 13 0.13
22 83 0.85
23 2 0.02
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (21 bp):
TCAAAATTTCATAAGAGGTTA
Found at i:18362 original size:44 final size:44
Alignment explanation
Indices: 18291--18435 Score: 143
Period size: 44 Copynumber: 3.3 Consensus size: 44
18281 TGATCCAATT
*
18291 TCAAAATTTCA-A-AGGCGGTTATCAAAATTACATAATGTGATTA
1 TCAAAATTTCATAGAGG-GGTTATCAAAATTTCATAATGTGATTA
* * * **
18334 TCAAAATTTCATAGAGGGGTTAACAAAATTTTATAGA-GAGGCTA
1 TCAAAATTTCATAGAGGGGTTATCAAAATTTCATA-ATGTGATTA
* * * * *
18378 TCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATATGATTA
1 TCAAAATTTCATAGAGGGGTTATCAAAATTTCATAATGTGATTA
*
18422 CCAAAATTTCATAG
1 TCAAAATTTCATAG
18436 TGGTATTTCT
Statistics
Matches: 80, Mismatches: 18, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
43 12 0.15
44 64 0.80
45 4 0.05
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (44 bp):
TCAAAATTTCATAGAGGGGTTATCAAAATTTCATAATGTGATTA
Found at i:18562 original size:22 final size:22
Alignment explanation
Indices: 18534--19092 Score: 175
Period size: 22 Copynumber: 25.7 Consensus size: 22
18524 CCAGAGAGGA
18534 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
**
18556 TATCAAAATTTCATAGTTTAGGT
1 TATCAAAATTTCATA-TGAAGGT
*
18579 T-TCAAAATTTCATAAGAAGGT
1 TATCAAAATTTCATATGAAGGT
* *
18600 TATCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATGAAGGT
* * * *
18621 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATATGAAGGT
*
18644 TAACAAAATTTCATAATG-AGGT
1 TATCAAAATTTCAT-ATGAAGGT
* * *
18666 TATCAAAAAATT-ATAGGGAGGT
1 TATC-AAAATTTCATATGAAGGT
*
18688 TATCAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* *
18704 TATCAAGATTTCAT-G--AGGT
1 TATCAAAATTTCATATGAAGGT
* * * * *
18723 TATCAAAATTTTACAGGGAGTTT
1 TATCAAAATTTCATATGAAG-GT
*
18746 TATCAAAATTTTAT-TGGAAGGTT
1 TATCAAAATTTCATAT-GAAGG-T
*
18769 TATCAAAATTTCATA-GCGAGGT
1 TATCAAAATTTCATATG-AAGGT
* *
18791 TATCAAAATTTCATA-GTATGAT
1 TATCAAAATTTCATATG-AAGGT
* * * *
18813 TATCAAAAATTCAGAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
*
18835 TA-CAGATAA-TTCATATGGAGGT
1 TATCA-A-AATTTCATATGAAGGT
* * ** * *
18857 TTTTAACTTTTCATAACG-TGGT
1 TATCAAAATTTCAT-ATGAAGGT
* * *
18879 TATCAATATATCATATGGAGGT
1 TATCAAAATTTCATATGAAGGT
* **
18901 TATCAACATCTT-ATAGTGTTGGT
1 TATCAAAAT-TTCATA-TGAAGGT
*
18924 TATCAAAATTTCATTTGGAA-GT
1 TATCAAAATTTCATAT-GAAGGT
*
18946 TATTAAAACTTT-ATAGTG-AGGT
1 TATCAAAA-TTTCATA-TGAAGGT
* * * *
18968 CT-TCAAAATTCCTTAGGGAGGT
1 -TATCAAAATTTCATATGAAGGT
* *
18990 TAAT-AAAATTTCATAAGATGGT
1 T-ATCAAAATTTCATATGAAGGT
** **
19012 TAAAAAAAATTT-ATAAAAAGGT
1 T-ATCAAAATTTCATATGAAGGT
* * **
19034 TCTCGAAATTTCATA-GTATCGT
1 TATCAAAATTTCATATG-AAGGT
** *
19056 TATTGAAATTTCATAGGAAGGT
1 TATCAAAATTTCATATGAAGGT
19078 TATCAAAATTTCATA
1 TATCAAAATTTCATA
19093 AAGACGTCAT
Statistics
Matches: 403, Mismatches: 89, Indels: 90
0.69 0.15 0.15
Matches are distributed among these distances:
16 9 0.02
17 2 0.00
18 3 0.01
19 14 0.03
20 2 0.00
21 32 0.08
22 253 0.63
23 87 0.22
24 1 0.00
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:18752 original size:23 final size:22
Alignment explanation
Indices: 18722--18806 Score: 89
Period size: 23 Copynumber: 3.8 Consensus size: 22
18712 TTTCATGAGG
*
18722 TTATCAAAATTTTACAGGGAGTT
1 TTATCAAAATTTTATAGGGAG-T
* *
18745 TTATCAAAATTTTATTGGAAGGT
1 TTATCAAAATTTTATAGGGA-GT
* * *
18768 TTATCAAAATTTCATAGCGAGG
1 TTATCAAAATTTTATAGGGAGT
*
18790 TTATCAAAATTTCATAG
1 TTATCAAAATTTTATAG
18807 TATGATTATC
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
22 18 0.34
23 34 0.64
24 1 0.02
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.39
Consensus pattern (22 bp):
TTATCAAAATTTTATAGGGAGT
Found at i:18960 original size:45 final size:45
Alignment explanation
Indices: 18875--18963 Score: 108
Period size: 45 Copynumber: 2.0 Consensus size: 45
18865 TTTCATAACG
* * *
18875 TGGTTATCAATATATCATATGGAGGTTATCAACATCTTATAGTGT
1 TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTTATAGTGT
* * *
18920 TGGTTATCAAAATTTCATTTGGAAGTTATTAAAA-CTTTATAGTG
1 TGGTTATCAAAATATCATATGGAAGTTATCAAAATC-TTATAGTG
18964 AGGTCTTCAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
44 1 0.03
45 36 0.97
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.42
Consensus pattern (45 bp):
TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTTATAGTGT
Found at i:19179 original size:40 final size:40
Alignment explanation
Indices: 19077--19184 Score: 153
Period size: 40 Copynumber: 2.7 Consensus size: 40
19067 CATAGGAAGG
* * * * *
19077 TTATCAAAATTTCATAAAGACGTCATAAAAAATAGTGTAA
1 TTATCATAATTTCATAAAAAGGTTATCAAAAATAGTGTAA
*
19117 TTATCATAATTTCATAAGAAGGTTATCAAAAATAGTGTAA
1 TTATCATAATTTCATAAAAAGGTTATCAAAAATAGTGTAA
*
19157 TTATCATAATTTAATAAAAAGGTTATCA
1 TTATCATAATTTCATAAAAAGGTTATCA
19185 TATTTCGTAT
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 60 1.00
ACGTcount: A:0.47, C:0.08, G:0.10, T:0.34
Consensus pattern (40 bp):
TTATCATAATTTCATAAAAAGGTTATCAAAAATAGTGTAA
Found at i:20104 original size:19 final size:19
Alignment explanation
Indices: 20080--20119 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
20070 CGACCATGAA
20080 TTCCGATGAATCTCTCCCC
1 TTCCGATGAATCTCTCCCC
20099 TTCCGATGAATCTCTCCCC
1 TTCCGATGAATCTCTCCCC
20118 TT
1 TT
20120 TTTAACTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.15, C:0.40, G:0.10, T:0.35
Consensus pattern (19 bp):
TTCCGATGAATCTCTCCCC
Found at i:23836 original size:19 final size:19
Alignment explanation
Indices: 23812--23851 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
23802 GAAAGTTAAA
23812 AAGGGGAGAGATTCATCGG
1 AAGGGGAGAGATTCATCGG
23831 AAGGGGAGAGATTCATCGG
1 AAGGGGAGAGATTCATCGG
23850 AA
1 AA
23852 TTCATGGTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.35, C:0.10, G:0.40, T:0.15
Consensus pattern (19 bp):
AAGGGGAGAGATTCATCGG
Found at i:24077 original size:12 final size:12
Alignment explanation
Indices: 24062--24099 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
24052 ATAATATTAA
24062 ATATATATAATT
1 ATATATATAATT
*
24074 ATATATATAATA
1 ATATATATAATT
24086 ATATATATAATT
1 ATATATATAATT
24098 AT
1 AT
24100 TCGACGGTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
ATATATATAATT
Found at i:24088 original size:24 final size:22
Alignment explanation
Indices: 24049--24099 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 22
24039 AACTTCACTC
*
24049 ATTATAATATTAAATATATATA
1 ATTATAATATAAAATATATATA
24071 ATTATATATATAATAATATATATA
1 ATTATA-ATATAA-AATATATATA
24095 ATTAT
1 ATTAT
24100 TCGACGGTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 6 0.23
23 5 0.19
24 15 0.58
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATTATAATATAAAATATATATA
Found at i:24491 original size:2 final size:2
Alignment explanation
Indices: 24484--24525 Score: 75
Period size: 2 Copynumber: 20.5 Consensus size: 2
24474 TCCGTGGATC
24484 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CTA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA T
24526 TATTTTTAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 37 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25379 original size:106 final size:104
Alignment explanation
Indices: 25182--25386 Score: 302
Period size: 106 Copynumber: 2.0 Consensus size: 104
25172 TGAAATAATT
* **
25182 AAATATTATTTAATAATGATAATTTAGAAATATATTTGAAAAAAGGGTATAATAAAAAAACATAA
1 AAATATTATTTAATAATGACAATTTAGAAATATATTTGAAAAAAGAATATAATAAAAAAACATAA
*
25247 AATTTCCCCTTATTCATACTTTTATATATAGTATAGATTA
66 AATTTCCCCTTATTCATACTTATATATATA-TATAGATTA
* *
25287 AAATATTATTTAATAATGACAATTTAGAAATATATTTGAAAAAAAGAATATAATCAGAAAACATA
1 AAATATTATTTAATAATGACAATTTAGAAATATATTTG-AAAAAAGAATATAATAAAAAAACATA
** * *
25352 AGGTTTTCCCTTATTCGTACTTATATATATATATA
65 AAATTTCCCCTTATTCATACTTATATATATATATA
25387 TATATATAAT
Statistics
Matches: 89, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
105 41 0.46
106 48 0.54
ACGTcount: A:0.47, C:0.07, G:0.08, T:0.38
Consensus pattern (104 bp):
AAATATTATTTAATAATGACAATTTAGAAATATATTTGAAAAAAGAATATAATAAAAAAACATAA
AATTTCCCCTTATTCATACTTATATATATATATAGATTA
Found at i:29241 original size:27 final size:27
Alignment explanation
Indices: 29208--29269 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
29198 ACTTTTTTTA
* *
29208 AAAATATATTTCTAAT-TTGTCATTATT
1 AAAATATACTT-TAATCATGTCATTATT
29235 AAAATATACTTTAATCATGTCATTATT
1 AAAATATACTTTAATCATGTCATTATT
29262 AAAATATA
1 AAAATATA
29270 ATTTTGTGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 4 0.12
27 28 0.88
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (27 bp):
AAAATATACTTTAATCATGTCATTATT
Found at i:29964 original size:1 final size:1
Alignment explanation
Indices: 29958--29982 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
29948 AAGTATCGTA
29958 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
29983 GCCTGTCCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:30445 original size:2 final size:2
Alignment explanation
Indices: 30438--30462 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
30428 CGTTTCAATT
30438 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 T
30463 CTCAAACACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:34144 original size:20 final size:20
Alignment explanation
Indices: 34119--34158 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
34109 TGCCATGCTT
* *
34119 TTGTCTCTGCCGCAATTATG
1 TTGTCTCTACCGCAACTATG
34139 TTGTCTCTACCGCAACTATG
1 TTGTCTCTACCGCAACTATG
34159 ATACTTCAAC
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:0.17, C:0.28, G:0.17, T:0.38
Consensus pattern (20 bp):
TTGTCTCTACCGCAACTATG
Found at i:35416 original size:72 final size:72
Alignment explanation
Indices: 35293--35927 Score: 760
Period size: 72 Copynumber: 8.8 Consensus size: 72
35283 GTAGTAGCAT
* * *
35293 GGATTGTGCAAAGGACTGCC-AATGTAGGAACTGCCTCGGCTACAATTGCAATGAGGAAGATAAT
1 GGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAGGAAGATAAT
*
35357 CACATAA
66 CATATAA
* * * *
35364 GGATTGTGCGAAGGACTGCCAAATGTGGGAATTGTCTCGGCTACAACCGCAAT-ATGGAAGATTA
1 GGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGA-GGAAGATAA
**
35428 TCATGGAA
65 TCATATAA
* *
35436 GGATTGTGCGAAGGACTGCCAAATGTGGGAACTGTCTCGGCTACAATCACAATGAAGGAAGATAA
1 GGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATG-AGGAAGATAA
*
35501 TCACATAA
65 TCATATAA
* * * * * *
35509 GGGTTGTGCGAAGGACTACCAAATGTGGGAATTGTCTCGACTACAATCGCAAT-ATGGAAGATTA
1 GGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGA-GGAAGATAA
* *
35573 TCATGTGA
65 TCATATAA
* * *
35581 GGATCGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACGATCGCAATGA-GAAGATGAT
1 GGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAGGAAGATAAT
*
35645 CATGTAA
66 CATATAA
35652 GGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAGGAAGATAAT
1 GGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAGGAAGATAAT
*
35717 CACATAA
66 CATATAA
* * * * * * *
35724 GGGTTGTGCGAAGGACTCCCATATGTGGGAACTGCCTCGGCTATAACCGCAAT-ATGGATGATGA
1 GGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGA-GGAAGATAA
* *
35788 TTATGTAA
65 TCATATAA
* * ** **
35796 GGATTATGCGAAGGGCTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAATAAGAGGAT
1 GGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAGGAAGATAAT
* *
35861 TA-AGTGA
66 CATA-TAA
* * * *
35868 GGATCGTGCGAAGGACTGCCAAATGTGGGAATTGCCTCGGCTACAATCGTAATGAAGAAG
1 GGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAGGAAG
35928 GTGACCATGT
Statistics
Matches: 485, Mismatches: 69, Indels: 19
0.85 0.12 0.03
Matches are distributed among these distances:
71 89 0.18
72 332 0.68
73 63 0.13
74 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.29, T:0.22
Consensus pattern (72 bp):
GGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAGGAAGATAAT
CATATAA
Found at i:36340 original size:35 final size:35
Alignment explanation
Indices: 36291--36375 Score: 93
Period size: 35 Copynumber: 2.4 Consensus size: 35
36281 TTATTGAAGC
*
36291 CCCCAAGTAG-TGAATGAAGAATGAGTTGCTGGAG-
1 CCCCAAGT-GTTGAATGAAGAAGGAGTTGCTGGAGT
* * * *
36325 CACCCAATTGTTGAATGATGAAGGGGTTGTTGGAGT
1 C-CCCAAGTGTTGAATGAAGAAGGAGTTGCTGGAGT
36361 CCCCAAGTGTTGAAT
1 CCCCAAGTGTTGAAT
36376 CTGATGAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
34 2 0.05
35 39 0.93
36 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.31, T:0.26
Consensus pattern (35 bp):
CCCCAAGTGTTGAATGAAGAAGGAGTTGCTGGAGT
Found at i:37754 original size:40 final size:40
Alignment explanation
Indices: 37691--37770 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
37681 GTTCTCCACC
* *
37691 ACCCATTGATTGAGAGAACCGTCGACTTCTGCAGCAGGAA
1 ACCCATTGATTGAAAGAACCGTCGACTTCTACAGCAGGAA
* *
37731 ACCCATTGATTGAAA-AGAGCGTCGACTTTTACAGCAGGAA
1 ACCCATTGATTGAAAGA-ACCGTCGACTTCTACAGCAGGAA
37771 GTTGGAGTGG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 1 0.03
40 34 0.97
ACGTcount: A:0.33, C:0.23, G:0.24, T:0.21
Consensus pattern (40 bp):
ACCCATTGATTGAAAGAACCGTCGACTTCTACAGCAGGAA
Found at i:40713 original size:20 final size:20
Alignment explanation
Indices: 40680--40718 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
40670 CATAGATGAA
*
40680 ATTTTCAGAAATTATTATTT
1 ATTTTCAGAAATTAGTATTT
40700 ATTTTCA-AATATTAGTATT
1 ATTTTCAGAA-ATTAGTATT
40719 GAATTCAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (20 bp):
ATTTTCAGAAATTAGTATTT
Found at i:40806 original size:16 final size:15
Alignment explanation
Indices: 40751--40808 Score: 55
Period size: 16 Copynumber: 3.7 Consensus size: 15
40741 GGGTACGGTT
*
40751 TTTTTCGAGTTTCAGA
1 TTTTTCGGGTTT-AGA
40767 TTTTTCGGGTTCT-GA
1 TTTTTCGGGTT-TAGA
* *
40782 TTTTCCGGGTTTAAGC
1 TTTTTCGGGTTT-AGA
40798 TTTTTCGGGTT
1 TTTTTCGGGTT
40809 CGGGTTTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
14 1 0.03
15 12 0.34
16 21 0.60
17 1 0.03
ACGTcount: A:0.10, C:0.14, G:0.24, T:0.52
Consensus pattern (15 bp):
TTTTTCGGGTTTAGA
Found at i:53482 original size:17 final size:16
Alignment explanation
Indices: 53456--53498 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
53446 CCCTTAGCTT
53456 AAAAACTAGAAGAATAAG
1 AAAAA-TAGAAGAA-AAG
* *
53474 AAAAATAGATGAAGAG
1 AAAAATAGAAGAAAAG
53490 AAAAATAGA
1 AAAAATAGA
53499 TCTAGATGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 11 0.48
17 7 0.30
18 5 0.22
ACGTcount: A:0.67, C:0.02, G:0.19, T:0.12
Consensus pattern (16 bp):
AAAAATAGAAGAAAAG
Found at i:63677 original size:33 final size:33
Alignment explanation
Indices: 63624--63696 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 33
63614 GTGTTTTAGA
* * *
63624 TGTTATTTGCGATAATACTAAACCTAATTTGAG
1 TGTTGTTTGCGATAACACTAAACCTAATTTAAG
* * **
63657 TGTTGTTTGCGATGACACTAAATCTGTTTTAAG
1 TGTTGTTTGCGATAACACTAAACCTAATTTAAG
63690 TGTTGTT
1 TGTTGTT
63697 AATGATGATA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.26, C:0.11, G:0.19, T:0.44
Consensus pattern (33 bp):
TGTTGTTTGCGATAACACTAAACCTAATTTAAG
Found at i:63772 original size:33 final size:33
Alignment explanation
Indices: 63723--63796 Score: 112
Period size: 33 Copynumber: 2.2 Consensus size: 33
63713 TCTTATTAGA
63723 TGAAAATAACTCTGTTTTAGTTGATCATAGCAT
1 TGAAAATAACTCTGTTTTAGTTGATCATAGCAT
* * * *
63756 TGCAAATAATTTTGTTTTGGTTGATCATAGCAT
1 TGAAAATAACTCTGTTTTAGTTGATCATAGCAT
63789 TGAAAATA
1 TGAAAATA
63797 GGAGTGTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.41
Consensus pattern (33 bp):
TGAAAATAACTCTGTTTTAGTTGATCATAGCAT
Found at i:63805 original size:33 final size:33
Alignment explanation
Indices: 63735--63808 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
63725 AAAATAACTC
* * ***
63735 TGTTTTAGTTGATCATAGCATTGCAAATAATTT
1 TGTTTTGGTTGATCATAGCATTGAAAATAAGAG
*
63768 TGTTTTGGTTGATCATAGCATTGAAAATAGGAG
1 TGTTTTGGTTGATCATAGCATTGAAAATAAGAG
63801 TGTTTTGG
1 TGTTTTGG
63809 GTGAAAACAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.27, C:0.07, G:0.23, T:0.43
Consensus pattern (33 bp):
TGTTTTGGTTGATCATAGCATTGAAAATAAGAG
Found at i:64216 original size:30 final size:30
Alignment explanation
Indices: 64180--64242 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
64170 TCTTCAAGGG
64180 GGAGGGAATGATGCGCCCAAAG-CTTATCAT
1 GGAGGGAATGATGCG-CCAAAGACTTATCAT
*
64210 GGAGGGAATGATGCGCCAATGACTTATCAT
1 GGAGGGAATGATGCGCCAAAGACTTATCAT
64240 GGA
1 GGA
64243 CTTGAAGATG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 5 0.16
30 26 0.84
ACGTcount: A:0.30, C:0.17, G:0.32, T:0.21
Consensus pattern (30 bp):
GGAGGGAATGATGCGCCAAAGACTTATCAT
Found at i:64372 original size:41 final size:41
Alignment explanation
Indices: 64311--64395 Score: 161
Period size: 41 Copynumber: 2.1 Consensus size: 41
64301 AGATGCATGG
*
64311 AGACCATGGAGATATTGATAATCATGTTCCAAGCACCAAGA
1 AGACCATGGAGATATCGATAATCATGTTCCAAGCACCAAGA
64352 AGACCATGGAGATATCGATAATCATGTTCCAAGCACCAAGA
1 AGACCATGGAGATATCGATAATCATGTTCCAAGCACCAAGA
64393 AGA
1 AGA
64396 TGTCATTCGA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (41 bp):
AGACCATGGAGATATCGATAATCATGTTCCAAGCACCAAGA
Found at i:77825 original size:22 final size:21
Alignment explanation
Indices: 77800--77858 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 21
77790 TATATTTATA
77800 TTATTAGTAAATTAGTAAATAT
1 TTATTAGTAAATTA-TAAATAT
* * *
77822 TTATTAGTATATATATTATTAT
1 TTATTAGTAAAT-TATAAATAT
77844 TTATTAGTAAATTAT
1 TTATTAGTAAATTAT
77859 CATAACATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 3 0.09
22 27 0.84
23 2 0.06
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.53
Consensus pattern (21 bp):
TTATTAGTAAATTATAAATAT
Found at i:77829 original size:14 final size:15
Alignment explanation
Indices: 77810--77842 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
77800 TTATTAGTAA
77810 ATTAGTAAATAT-TT
1 ATTAGTAAATATATT
*
77824 ATTAGTATATATATT
1 ATTAGTAAATATATT
77839 ATTA
1 ATTA
77843 TTTATTAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (15 bp):
ATTAGTAAATATATT
Found at i:77850 original size:44 final size:40
Alignment explanation
Indices: 77778--77857 Score: 115
Period size: 44 Copynumber: 1.9 Consensus size: 40
77768 ATAACAATAT
77778 ATATTTTTAATATATATTTATATTATTAGTAAATTAGTAA
1 ATATTTTTAATATATATTTATATTATTAGTAAATTAGTAA
*
77818 ATATTTATTAGTATATATATTATTATTTATTAGTAAATTA
1 ATATTT-TTAATATATAT-TTA-TA-TTATTAGTAAATTA
77858 TCATAACATA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
40 6 0.17
41 10 0.29
42 3 0.09
43 2 0.06
44 14 0.40
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (40 bp):
ATATTTTTAATATATATTTATATTATTAGTAAATTAGTAA
Done.