Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010776.1 Corchorus capsularis cultivar CVL-1 contig10797, 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: 41691
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Found at i:2044 original size:72 final size:72
Alignment explanation
Indices: 1918--2054 Score: 179
Period size: 72 Copynumber: 1.9 Consensus size: 72
1908 CCCATCAATA
* * * * *
1918 TCAATTTTTTACAATCTAAAATTTTCAGTAGAAAATTTTGCATACAAACCAGAATTCCACAAACC
1 TCAATTTTTGACAATCTAAAACTTTCAGCAAAAAAATTTGCATACAAACCAGAATTCCACAAACC
1983 TTCAAAG
66 TTCAAAG
* *
1990 TCAATTTTTGACAATCTCAAGACTTT-AGCAAAAAAATTTGCAT-CAAAACTAGAATTCCACAAA
1 TCAATTTTTGACAATCT-AAAACTTTCAGCAAAAAAATTTGCATAC-AAACCAGAATTCCACAAA
2053 CC
64 CC
2055 AAGATCTTCG
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
71 1 0.02
72 49 0.88
73 6 0.11
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.30
Consensus pattern (72 bp):
TCAATTTTTGACAATCTAAAACTTTCAGCAAAAAAATTTGCATACAAACCAGAATTCCACAAACC
TTCAAAG
Found at i:3614 original size:11 final size:11
Alignment explanation
Indices: 3598--3640 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
3588 TATACTATAT
3598 CTAATTAATAG
1 CTAATTAATAG
*
3609 CTAATTAATAT
1 CTAATTAATAG
3620 CTAATTAATAG
1 CTAATTAATAG
*
3631 TTAATTAATA
1 CTAATTAATA
3641 ATGAATATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.42
Consensus pattern (11 bp):
CTAATTAATAG
Found at i:3622 original size:22 final size:22
Alignment explanation
Indices: 3594--3640 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
3584 CCATTATACT
3594 ATATCTAATTAATAGCTAATTA
1 ATATCTAATTAATAGCTAATTA
*
3616 ATATCTAATTAATAGTTAATTA
1 ATATCTAATTAATAGCTAATTA
3638 ATA
1 ATA
3641 ATGAATATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (22 bp):
ATATCTAATTAATAGCTAATTA
Found at i:4474 original size:13 final size:13
Alignment explanation
Indices: 4456--4482 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4446 CACGGAGAGT
4456 AAAAAAAATAAAA
1 AAAAAAAATAAAA
4469 AAAAAAAATAAAA
1 AAAAAAAATAAAA
4482 A
1 A
4483 GACGCCTGAC
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:0.93, C:0.00, G:0.00, T:0.07
Consensus pattern (13 bp):
AAAAAAAATAAAA
Found at i:6687 original size:64 final size:65
Alignment explanation
Indices: 6571--6727 Score: 187
Period size: 64 Copynumber: 2.4 Consensus size: 65
6561 TAAACCCATT
* * *
6571 TATTAATCAATC--AATAAACGTCTCATCAAATATCTTATCAATCAATGCATGTTATTATTATCC
1 TATTAATCCATCAAAATAAATGTCTCATCAAATATCCTATCAATCAATGCATGTTATTATTATCC
* * *
6634 TATT-ATCCATCAATATAAATGTCTCATCAACTATCCTATCAATCTAA-GTATGTTATTATTATC
1 TATTAATCCATCAAAATAAATGTCTCATCAAATATCCTATCAATC-AATGCATGTTATTATTATC
*
6697 T
65 C
* *
6698 TATTAATCGATCAAAATAAATAGTTTCATC
1 TATTAATCCATCAAAATAAAT-GTCTCATC
6728 TTAACATGAC
Statistics
Matches: 79, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
62 6 0.08
63 4 0.05
64 46 0.58
65 16 0.20
66 7 0.09
ACGTcount: A:0.38, C:0.18, G:0.05, T:0.39
Consensus pattern (65 bp):
TATTAATCCATCAAAATAAATGTCTCATCAAATATCCTATCAATCAATGCATGTTATTATTATCC
Found at i:8286 original size:69 final size:67
Alignment explanation
Indices: 8116--8295 Score: 224
Period size: 68 Copynumber: 2.6 Consensus size: 67
8106 TTGGTCATGT
*
8116 ATGTTATTA-CTATCCTATTAATCAATTGATATAAATGTCTCATCACTATCTATATTATCAATCT
1 ATGTTATTATC-ATCCTATTAATCAATCGATATAAATGTCTCATCAC-ATCTATATTATCAATCT
8180 ATGC
64 ATGC
*
8184 ATGTTATTATCATCCTATTAATCAATCGATATAAATGTCTCATCA-A-CTATCTTATCAAT-TCA
1 ATGTTATTATCATCCTATTAATCAATCGATATAAATGTCTCATCACATCTATATTATCAATCT-A
8246 TGC
65 TGC
* * *
8249 ATGTTATTATTATCTTATTAGTTAATCAATCGATATAAACGTCTCAT
1 ATGTTATTATCATC---CTA-TTAATCAATCGATATAAATGTCTCAT
8296 GTTTAGGAGA
Statistics
Matches: 101, Mismatches: 5, Indels: 11
0.86 0.04 0.09
Matches are distributed among these distances:
64 1 0.01
65 29 0.29
66 1 0.01
68 44 0.44
69 26 0.26
ACGTcount: A:0.34, C:0.17, G:0.07, T:0.42
Consensus pattern (67 bp):
ATGTTATTATCATCCTATTAATCAATCGATATAAATGTCTCATCACATCTATATTATCAATCTAT
GC
Found at i:8333 original size:2 final size:2
Alignment explanation
Indices: 8326--8360 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
8316 CAAATTGCAT
8326 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
8361 TAATAATATC
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:11411 original size:22 final size:22
Alignment explanation
Indices: 11381--11483 Score: 93
Period size: 22 Copynumber: 4.6 Consensus size: 22
11371 TCCAAGGTAT
*
11381 AAATATTGATAACCACACTGTGA
1 AAAT-TTGATAACCACACTATGA
* * *
11404 AAATTTGATAAACTCATTATG-
1 AAATTTGATAACCACACTATGA
*
11425 AAATTTCGATAA-CATCTCTATGA
1 AAATTT-GATAACCA-CACTATGA
* *
11448 AAATTTGATAATCACACTGTGA
1 AAATTTGATAACCACACTATGA
*
11470 AATTTTGATAACCA
1 AAATTTGATAACCA
11484 TAATCTTTTG
Statistics
Matches: 65, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
21 7 0.11
22 46 0.71
23 12 0.18
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.33
Consensus pattern (22 bp):
AAATTTGATAACCACACTATGA
Found at i:11581 original size:22 final size:22
Alignment explanation
Indices: 11549--11810 Score: 148
Period size: 22 Copynumber: 12.0 Consensus size: 22
11539 AACCTAATCC
11549 CTAT-AAATTTTGATAACCACT
1 CTATGAAATTTTGATAACCACT
* *
11570 CTATGAAATTTTGGTAA-CATT
1 CTATGAAATTTTGATAACCACT
* *
11591 CATAAGAAATTTTGGTAACCACT
1 C-TATGAAATTTTGATAACCACT
*
11614 CTATGAAATTTTGATAACC-TT
1 CTATGAAATTTTGATAACCACT
* *** *
11635 CATATGAAATTTTGGTAATTGCA
1 C-TATGAAATTTTGATAACCACT
* *
11658 CTATGAAATTTTGGTAATCA-T
1 CTATGAAATTTTGATAACCACT
* * * * *
11679 AGTATGAATTTTTTATAACCTCC
1 -CTATGAAATTTTGATAACCACT
* * **
11702 CTAT-AAAATTTGGTAACCAGA
1 CTATGAAATTTTGATAACCACT
*
11723 CTATGAGATTTTGATAATCTC-CT
1 CTATGAAATTTTGATAA-C-CACT
* *
11746 -TATGAAAATTTTCATAACCTC-
1 CTATG-AAATTTTGATAACCACT
11767 CTTATGAAATTTTGATAATCTCA-T
1 C-TATGAAATTTTGATAA-C-CACT
*
11791 -TATGAAATTTTGATTACCAC
1 CTATGAAATTTTGATAACCAC
11811 ACAAAGACAA
Statistics
Matches: 183, Mismatches: 40, Indels: 36
0.71 0.15 0.14
Matches are distributed among these distances:
20 2 0.01
21 26 0.14
22 132 0.72
23 21 0.11
24 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.40
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCACT
Found at i:11610 original size:44 final size:44
Alignment explanation
Indices: 11553--11674 Score: 172
Period size: 44 Copynumber: 2.8 Consensus size: 44
11543 TAATCCCTAT
*
11553 AAATTTTGATAACCACTCTATGAAATTTTGGTAACATTCATAAG
1 AAATTTTGGTAACCACTCTATGAAATTTTGGTAACATTCATAAG
* * *
11597 AAATTTTGGTAACCACTCTATGAAATTTTGATAACCTTCATATG
1 AAATTTTGGTAACCACTCTATGAAATTTTGGTAACATTCATAAG
*** *
11641 AAATTTTGGTAATTGCACTATGAAATTTTGGTAA
1 AAATTTTGGTAACCACTCTATGAAATTTTGGTAA
11675 TCATAGTATG
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 69 1.00
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.39
Consensus pattern (44 bp):
AAATTTTGGTAACCACTCTATGAAATTTTGGTAACATTCATAAG
Found at i:11641 original size:66 final size:67
Alignment explanation
Indices: 11549--11718 Score: 183
Period size: 66 Copynumber: 2.6 Consensus size: 67
11539 AACCTAATCC
*
11549 CTAT-AAATTTTGATAACCACTCTATGAAATTTTGGTAACATT-CA-TAAGAAATTTTGGTAACC
1 CTATGAAATTTTGATAACC-TTCTATGAAATTTTGGTAACATTGCACTAAGAAATTTTGGTAACC
11611 ACT-
65 A-TA
* *
11614 CTATGAAATTTTGATAACCTTCATATGAAATTTTGGT-A-ATTGCACTATGAAATTTTGGTAATC
1 CTATGAAATTTTGATAACCTTC-TATGAAATTTTGGTAACATTGCACTAAGAAATTTTGGTAACC
11677 ATA
65 ATA
* * * * *
11680 GTATGAATTTTTTATAACCTCCCTAT-AAAATTTGGTAAC
1 CTATGAAATTTTGATAACCT-TCTATGAAATTTTGGTAAC
11719 CAGACTATGA
Statistics
Matches: 89, Mismatches: 8, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
64 3 0.03
65 19 0.21
66 66 0.74
67 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (67 bp):
CTATGAAATTTTGATAACCTTCTATGAAATTTTGGTAACATTGCACTAAGAAATTTTGGTAACCA
TA
Found at i:11728 original size:43 final size:44
Alignment explanation
Indices: 11658--11756 Score: 112
Period size: 43 Copynumber: 2.3 Consensus size: 44
11648 GGTAATTGCA
* * * * *
11658 CTATGAAATTTTGGTAATCATAGTATGA-ATTTTTTATAACCTCC
1 CTATGAAAATTTGGTAACCAGACTATGAGA-TTTTGATAACCTCC
*
11702 CTAT-AAAATTTGGTAACCAGACTATGAGATTTTGATAATCTCC
1 CTATGAAAATTTGGTAACCAGACTATGAGATTTTGATAACCTCC
*
11745 TTATGAAAATTT
1 CTATGAAAATTT
11757 TCATAACCTC
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
43 34 0.74
44 12 0.26
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.40
Consensus pattern (44 bp):
CTATGAAAATTTGGTAACCAGACTATGAGATTTTGATAACCTCC
Found at i:11905 original size:22 final size:22
Alignment explanation
Indices: 11879--11929 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
11869 TAATTTTCCT
11879 CATGAAAGCTTGATAATCTCAC
1 CATGAAAGCTTGATAATCTCAC
*
11901 CATGAAAGTTTGATAATCTCAC
1 CATGAAAGCTTGATAATCTCAC
*
11923 TATGAAA
1 CATGAAA
11930 TTTTTTGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (22 bp):
CATGAAAGCTTGATAATCTCAC
Found at i:12745 original size:22 final size:22
Alignment explanation
Indices: 12499--13079 Score: 255
Period size: 22 Copynumber: 26.0 Consensus size: 22
12489 ATATAACAAT
* *
12499 ATAGTGTGATTATCAAAATTTC
1 ATAGTGAGGTTATCAAAATTTC
* * *
12521 ACACTGAGGTAATCAAAATTTC
1 ATAGTGAGGTTATCAAAATTTC
* * *
12543 ATAATGTGGTTTTCAAAATTTC
1 ATAGTGAGGTTATCAAAATTTC
* *
12565 ATA-TG-GATTA--AAAATTTT
1 ATAGTGAGGTTATCAAAATTTC
*
12583 ATAG-GAAAGTTATCAAAATTTC
1 ATAGTG-AGGTTATCAAAATTTC
* * *
12605 ACAATGTGGTTATCAAAATTTC
1 ATAGTGAGGTTATCAAAATTTC
*
12627 ATAAG-GAGGTTATCAAAATTCCAC
1 AT-AGTGAGGTTATCAAAATT--TC
*
12651 AACTAGCGAGGTTATCAAAATTTC
1 -A-TAGTGAGGTTATCAAAATTTC
* *
12675 ATAGTGTGGTTATCAAAATTTT
1 ATAGTGAGGTTATCAAAATTTC
12697 ATAAG-GAGGTTATCAAAGATTTC
1 AT-AGTGAGGTTATCAAA-ATTTC
* *
12720 ATAGTGTGGTTACCAAAATTTC
1 ATAGTGAGGTTATCAAAATTTC
* ** *
12742 ATAGTAATATTAGAAAAATCTAAATTTC
1 ATAGTGAGGTT------ATCAAAATTTC
* *
12770 ATACG-AAGGTTATTAAAATTT-
1 ATA-GTGAGGTTATCAAAATTTC
*
12791 ATAGT-ATAGTTATCAAAATTTC
1 ATAGTGA-GGTTATCAAAATTTC
* **
12813 ATCAG-GAAGCAATCAAAATCTT-
1 AT-AGTGAGGTTATCAAAAT-TTC
* * *
12835 ATAGAGTA-GTTGGTCAAAAATTC
1 ATAGTG-AGGTT-ATCAAAATTTC
* * *
12858 ATAGAGATCAGATTACCAAAATTTC
1 AT--AG-TGAGGTTATCAAAATTTC
*
12883 ATAG-GAAGGTTATCAAAATTTT
1 ATAGTG-AGGTTATCAAAATTTC
*
12905 AAAGTGAGGTTATCAAAATTTC
1 ATAGTGAGGTTATCAAAATTTC
* *
12927 CTAGTGAGGTTATGAAAAATTTTC
1 ATAGTGAGGTTAT-CAAAA-TTTC
* *** * *
12951 ATATTGTTATTATTAAAATTTG
1 ATAGTGAGGTTATCAAAATTTC
12973 ATA-TGGAGGTT-TC-AAATTTC
1 ATAGT-GAGGTTATCAAAATTTC
*
12993 ATAGT-ATGATTATCAAAATTTC
1 ATAGTGA-GGTTATCAAAATTTC
** * *
13015 ATAAAGAGATTAGCAAAATTTC
1 ATAGTGAGGTTATCAAAATTTC
* * **
13037 ATTAG-AATGTTATTGAAATTTC
1 A-TAGTGAGGTTATCAAAATTTC
* *
13059 ATAGGGAGGTTATCGAAATTT
1 ATAGTGAGGTTATCAAAATTT
13080 TATAATGTTA
Statistics
Matches: 420, Mismatches: 91, Indels: 96
0.69 0.15 0.16
Matches are distributed among these distances:
18 11 0.03
19 1 0.00
20 20 0.05
21 27 0.06
22 247 0.59
23 49 0.12
24 14 0.03
25 16 0.04
26 18 0.04
28 16 0.04
29 1 0.00
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.36
Consensus pattern (22 bp):
ATAGTGAGGTTATCAAAATTTC
Found at i:12760 original size:115 final size:110
Alignment explanation
Indices: 12550--12760 Score: 246
Period size: 115 Copynumber: 1.9 Consensus size: 110
12540 TTCATAATGT
*
12550 GGTTTTCAAAATTTCATATGGATTAAAAATTTTATAGGAAAGTTATCAAAATTTCACAATGTGGT
1 GGTTATCAAAATTTCATATGGATTAAAAATTTTATAGGAAAGTTATCAAAATTTCACAATGTGGT
* * * **
12615 TATCAAAATTTCATAAGGAGGTTATCAAAATTCCACAACTAGCGA
66 TACCAAAATTTCATAAGAAGATTAGAAAAATTCCACAACTAGCGA
* * * *
12660 GGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTTATAAGG-AGGTTATCAAAGATTTCATAG
1 GGTTATCAAAATTTCATA-TG-GATTA--AAAATTTTAT-AGGAAAGTTATCAAA-ATTTCACAA
*
12724 TGTGGTTACCAAAATTTCAT-AGTAATATTAGAAAAAT
60 TGTGGTTACCAAAATTTCATAAG-AAGATTAGAAAAAT
12761 CTAAATTTCA
Statistics
Matches: 83, Mismatches: 11, Indels: 9
0.81 0.11 0.09
Matches are distributed among these distances:
110 17 0.20
111 2 0.02
112 4 0.05
114 22 0.27
115 38 0.46
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (110 bp):
GGTTATCAAAATTTCATATGGATTAAAAATTTTATAGGAAAGTTATCAAAATTTCACAATGTGGT
TACCAAAATTTCATAAGAAGATTAGAAAAATTCCACAACTAGCGA
Found at i:15169 original size:22 final size:21
Alignment explanation
Indices: 15128--15352 Score: 142
Period size: 22 Copynumber: 10.6 Consensus size: 21
15118 TTGTATGAAG
* * *
15128 GTTATTAAAATTTCAAAGGGG
1 GTTATCAAAATTTCATAGGGA
*
15149 GATTATCAAAATTGCATAGGGA
1 G-TTATCAAAATTTCATAGGGA
**
15171 GTATATCAAAATTTCATAGTTTA
1 GT-TATCAAAATTTCATAG-GGA
* *
15194 GTTTTCAAAATTTTATA-GGA
1 GTTATCAAAATTTCATAGGGA
15214 GTTATCAAAATTTCATAGGGA
1 GTTATCAAAATTTCATAGGGA
* * *
15235 GGTTAAC-AAATTTCATAATGAA
1 -GTTATCAAAATTTCAT-AGGGA
*
15257 GTTATCGAAAA-ATCATAGGGA
1 GTTATC-AAAATTTCATAGGGA
*
15278 GGTTATCAAAA-TT--T-GTGA
1 -GTTATCAAAATTTCATAGGGA
* *
15296 -ATATCAAAATTTCATAAGGA
1 GTTATCAAAATTTCATAGGGA
* * *
15316 GGTTATCAAAATTTTATAAGAA
1 -GTTATCAAAATTTCATAGGGA
15338 GGTTTATCAAAATTT
1 -G-TTATCAAAATTT
15353 TATGGCTAAA
Statistics
Matches: 160, Mismatches: 28, Indels: 30
0.73 0.13 0.14
Matches are distributed among these distances:
16 8 0.05
17 2 0.01
18 3 0.02
19 2 0.01
20 18 0.11
21 27 0.17
22 82 0.51
23 18 0.11
ACGTcount: A:0.40, C:0.08, G:0.17, T:0.35
Consensus pattern (21 bp):
GTTATCAAAATTTCATAGGGA
Found at i:15317 original size:38 final size:40
Alignment explanation
Indices: 15174--15329 Score: 131
Period size: 43 Copynumber: 3.8 Consensus size: 40
15164 ATAGGGAGTA
** * * *
15174 TATCAAAATTTCATAGTTTA-GTTTTCAAAATTTTATAGGAG
1 TATCAAAATTTCATAG-GGAGGTTATCAAAATTTAAT-GAAG
* *
15215 TTATCAAAATTTCATAGGGAGGTTAACAAATTTCATAATGAAG
1 -TATCAAAATTTCATAGGGAGGTTATCAAAATT--TAATGAAG
* *
15258 TTATCGAAAA-ATCATAGGGAGGTTATCAAAATTT-GTGAA-
1 -TATC-AAAATTTCATAGGGAGGTTATCAAAATTTAATGAAG
*
15297 TATCAAAATTTCATAAGGAGGTTATCAAAATTT
1 TATCAAAATTTCATAGGGAGGTTATCAAAATTT
15330 TATAAGAAGG
Statistics
Matches: 96, Mismatches: 13, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
37 4 0.04
38 26 0.27
40 4 0.04
41 2 0.02
42 25 0.26
43 28 0.29
44 7 0.07
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.36
Consensus pattern (40 bp):
TATCAAAATTTCATAGGGAGGTTATCAAAATTTAATGAAG
Found at i:16748 original size:29 final size:31
Alignment explanation
Indices: 16696--16760 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 31
16686 AACGGTTTGG
*
16696 ACTTATTTAACCTAAATTGAAAAGGTTGGGC
1 ACTTATTTAACCTAAATTGAAAAGGTTAGGC
* *
16727 ACTTATTTGACCT-TATTG-AAAGGTTAGGC
1 ACTTATTTAACCTAAATTGAAAAGGTTAGGC
*
16756 CCTTA
1 ACTTA
16761 AATGGCCTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 14 0.47
30 4 0.13
31 12 0.40
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.35
Consensus pattern (31 bp):
ACTTATTTAACCTAAATTGAAAAGGTTAGGC
Found at i:16878 original size:22 final size:22
Alignment explanation
Indices: 16824--17083 Score: 119
Period size: 22 Copynumber: 11.8 Consensus size: 22
16814 ATATGAATGT
** *
16824 TTATCAAAATTTCATACCGAGA
1 TTATCAAAATTTCATAGTGTGA
* * *
16846 TCATTACAATTTCATAGTGTGA
1 TTATCAAAATTTCATAGTGTGA
*
16868 TTATCAAAATTTCACAGTGTGA
1 TTATCAAAATTTCATAGTGTGA
* * * *
16890 TCA-CTAAGATTTCATAAG-GAGG
1 TTATC-AAAATTTCAT-AGTGTGA
* * *
16912 TTATAAAAAATATCATAGTGTATGC
1 TTAT-CAAAATTTCATAGTG--TGA
* * * *
16937 TTACCAACATTTCACA-TGGAGA
1 TTATCAAAATTTCATAGT-GTGA
16959 TTATCAAAATTTCATAGTGTGA
1 TTATCAAAATTTCATAGTGTGA
16981 TTATCAAAATTT-A-AGTGGATGA
1 TTATCAAAATTTCATAGT-G-TGA
* *
17003 TTATCAAAATTTCATTAG-GAGG
1 TTATCAAAATTTCA-TAGTGTGA
* * *
17025 TCATCAAAATTTTATAGTAATG-
1 TTATCAAAATTTCATAGT-GTGA
*
17047 TTTTCAAAA-TTCTATAG-G-GA
1 TTATCAAAATTTC-ATAGTGTGA
17067 GTTA-CAAAATTTCATAG
1 -TTATCAAAATTTCATAG
17084 GGAAGTTCTT
Statistics
Matches: 175, Mismatches: 43, Indels: 42
0.67 0.17 0.16
Matches are distributed among these distances:
19 1 0.01
20 12 0.07
21 13 0.07
22 118 0.67
23 16 0.09
24 9 0.05
25 6 0.03
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGTGA
Found at i:16892 original size:44 final size:46
Alignment explanation
Indices: 16824--17017 Score: 138
Period size: 44 Copynumber: 4.3 Consensus size: 46
16814 ATATGAATGT
** * *
16824 TTATCAAAATTTCATACCGAGATCATTACA-ATTTCATAGT-GTGA
1 TTATCAAAATTTCATAGTGTGATCATTACACATTTCATAGTGGAGA
* * * * *
16868 TTATCAAAATTTCACAGTGTGATCACTA-AGATTTCATA-AGGAGG
1 TTATCAAAATTTCATAGTGTGATCATTACACATTTCATAGTGGAGA
* * *
16912 TTATAAAAAATATCATAGTGT-ATGC-TTACCAACATTTCACA-TGGAGA
1 TTAT-CAAAATTTCATAGTGTGAT-CATTA-C-ACATTTCATAGTGGAGA
* * *
16959 TTATCAAAATTTCATAGTGTGATTATCA-AAATTT-A-AGTGGATGA
1 TTATCAAAATTTCATAGTGTGATCATTACACATTTCATAGTGGA-GA
17003 TTATCAAAATTTCAT
1 TTATCAAAATTTCAT
17018 TAGGAGGTCA
Statistics
Matches: 118, Mismatches: 21, Indels: 22
0.73 0.13 0.14
Matches are distributed among these distances:
42 1 0.01
43 6 0.05
44 63 0.53
45 14 0.12
46 14 0.12
47 20 0.17
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (46 bp):
TTATCAAAATTTCATAGTGTGATCATTACACATTTCATAGTGGAGA
Found at i:17156 original size:22 final size:22
Alignment explanation
Indices: 16959--17162 Score: 97
Period size: 22 Copynumber: 9.4 Consensus size: 22
16949 CACATGGAGA
16959 TTATCAAAATTTCATAGTG--TG
1 TTATCAAAATTTCATAG-GAATG
*
16980 ATTATCAAAATTT-A-AGTGGATG
1 -TTATCAAAATTTCATAG-GAATG
*
17002 ATTATCAAAATTTCATTAGG-AGG
1 -TTATCAAAATTTCA-TAGGAATG
* * *
17025 TCATCAAAATTTTATAGTAATG
1 TTATCAAAATTTCATAGGAATG
* *
17047 TTTTCAAAA-TTCTATAGGGA-G
1 TTATCAAAATTTC-ATAGGAATG
17068 TTA-CAAAATTTCATAGGGAA-G
1 TTATCAAAATTTCATA-GGAATG
* ** * *
17089 TTCTTGAAATTTGATTGGAATG
1 TTATCAAAATTTCATAGGAATG
* ** * * *
17111 TTTTTGAAATGT-A-AAGTATCG
1 TTATCAAAATTTCATAGGAAT-G
17132 TTATCAAAATTTCATAGGAATG
1 TTATCAAAATTTCATAGGAATG
17154 TTATCAAAA
1 TTATCAAAA
17163 GTTTATAAGG
Statistics
Matches: 140, Mismatches: 28, Indels: 28
0.71 0.14 0.14
Matches are distributed among these distances:
20 15 0.11
21 32 0.23
22 83 0.59
23 7 0.05
24 1 0.01
25 2 0.01
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.38
Consensus pattern (22 bp):
TTATCAAAATTTCATAGGAATG
Found at i:17179 original size:22 final size:22
Alignment explanation
Indices: 17132--17181 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
17122 TAAAGTATCG
*
17132 TTATCAAAATTTCATAGGAATG
1 TTATCAAAATTTCATAGGAATA
17154 TTATCAAAAGTTT-ATAAGGAA-A
1 TTATCAAAA-TTTCAT-AGGAATA
17176 TTATCA
1 TTATCA
17182 TAGAGAGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 17 0.68
23 8 0.32
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAGGAATA
Found at i:18403 original size:16 final size:15
Alignment explanation
Indices: 18369--18407 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
18359 TAATTAATAA
18369 AAAAAATTAATGACT
1 AAAAAATTAATGACT
*
18384 -AAAAATATAATGATT
1 AAAAAAT-TAATGACT
18399 AAAAAATTA
1 AAAAAATTA
18408 TTATACCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 6 0.29
15 9 0.43
16 6 0.29
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (15 bp):
AAAAAATTAATGACT
Found at i:18819 original size:52 final size:52
Alignment explanation
Indices: 18741--18852 Score: 188
Period size: 52 Copynumber: 2.2 Consensus size: 52
18731 TGATCAGGCC
* *
18741 TTTTCTAATATTTATAATGTCATTAGATATAGGCTTAATGGTTTTTGTAACG
1 TTTTCTAATATTCATAATGTCATTAGATATAGACTTAATGGTTTTTGTAACG
*
18793 TTTTCTAATATTCATAATGTCATTAGATATAGACTTAATGGTTTTTGTAATG
1 TTTTCTAATATTCATAATGTCATTAGATATAGACTTAATGGTTTTTGTAACG
*
18845 TTTGCTAA
1 TTTTCTAA
18853 AGACCTATTA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 56 1.00
ACGTcount: A:0.29, C:0.08, G:0.14, T:0.48
Consensus pattern (52 bp):
TTTTCTAATATTCATAATGTCATTAGATATAGACTTAATGGTTTTTGTAACG
Found at i:18994 original size:2 final size:2
Alignment explanation
Indices: 18987--19015 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
18977 TATTTATCAA
18987 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19016 AAATACATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21361 original size:2 final size:2
Alignment explanation
Indices: 21354--21385 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
21344 GTGTAATTTC
*
21354 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21386 CCATGAACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21712 original size:223 final size:221
Alignment explanation
Indices: 21360--21937 Score: 739
Period size: 220 Copynumber: 2.6 Consensus size: 221
21350 TTTCATATAT
*
21360 ATATATATATATATATATGTATATATCCATGAACTAGGACATGTGTAAAACATGCAAAGATTTTA
1 ATATA-AT-TATATATATATATATATCCATGAACTAGGACATGTGTAAAACATGCAAAGATTTTA
* **
21425 TACATGCAACACAACAAGTGTACAATATTACAAATTCCTATCAAAGATTTTCAAAGG-AATCATC
64 AACATGCAACACAACAAGTGTAC-A-A-TAC-AATTCCTATCAAAGCCTTTCAAAGGAAATCATC
*
21489 ATCATTGTATTGTTTGAACTCAACATAAACA-ACATGAAGATG-AACTCGAAAATGGAAGAGAAA
125 ATCATTGCATTGTTTGAACTCAACATAAACATACA-GAAGATGAAAC-CGAAAATGGAAGAGAAA
* **
21552 GA-ATAGAGACTACAATTGTCTCTATGCCC-GTA-
188 GATATA-AGACAACAACCGTCTCTATGCCCTGTAC
* * *
21584 ATTTCATTCATATATATATATATATCCATGAACTAGGACATGTGCAAAACATGCAAAGATTTTAA
1 ATATAATT-ATATATATATATATATCCATGAACTAGGACATGTGTAAAACATGCAAAGATTTTAA
21649 ACATGCAACACAACAAGTGTACAATACACATTCCTATCAAAGCCTTT-AGAAGGAAAT-ATCATC
65 ACATGCAACACAACAAGTGTACAATACA-ATTCCTATCAAAGCCTTTCA-AAGGAAATCATCATC
* * * * *
21712 ATTGCATTGTTTGAACTTAACATAAACATCCAGAAGATGAAACGGAAAATGGAAGATAAAGATTT
128 ATTGCATTGTTTGAACTCAACATAAACATACAGAAGATGAAACCGAAAATGGAAGAGAAAGATAT
21777 AAGACAACAACCGTCTCTATGCCCTGTAC
193 AAGACAACAACCGTCTCTATGCCCTGTAC
* *
21806 GTATAATT-TCAT-T-CATATATATCCATGAATACTAGGACATGTGTAAAACATGCAAAGATTTT
1 ATATAATTAT-ATATATATATATATCCATG-A-ACTAGGACATGTGTAAAACATGCAAAGATTTT
* * *
21868 AAACATGCAACTCAACAAGTGTACAAAAGAATTCCTATCAAAGCCTTTCAAAGGAAA-CATCATC
63 AAACATGCAACACAACAAGTGTACAATACAATTCCTATCAAAGCCTTTCAAAGGAAATCATCATC
*
21932 GTTGCA
128 ATTGCA
21938 ATGCATGAAC
Statistics
Matches: 315, Mismatches: 25, Indels: 32
0.85 0.07 0.09
Matches are distributed among these distances:
219 15 0.05
220 138 0.44
221 75 0.24
222 7 0.02
223 77 0.24
224 3 0.01
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.28
Consensus pattern (221 bp):
ATATAATTATATATATATATATATCCATGAACTAGGACATGTGTAAAACATGCAAAGATTTTAAA
CATGCAACACAACAAGTGTACAATACAATTCCTATCAAAGCCTTTCAAAGGAAATCATCATCATT
GCATTGTTTGAACTCAACATAAACATACAGAAGATGAAACCGAAAATGGAAGAGAAAGATATAAG
ACAACAACCGTCTCTATGCCCTGTAC
Found at i:25228 original size:177 final size:180
Alignment explanation
Indices: 24877--25236 Score: 582
Period size: 177 Copynumber: 2.0 Consensus size: 180
24867 TTCATGAAAG
*
24877 TTGTAGACCATGGAATTACCTTTAAATAGACACTTGAATCACCTAGATCAGTCAAATAGAAAAAA
1 TTGTAGACCATGAAATTACCTTTAAATAGACACTTGAATCACCTAGATCAGTCAAATAG-AAAAA
* * *
24942 AATAAAAGAATTAAAGCCGAAACATTCAATCGTCCAACCCATAATTCTAAGTGATTAAATAGTAT
65 AATAAAACAATTAAAGCCGAAACATTCAATCGTCCAACACATAATTCTAAGTGATTAAATAGCAT
25007 AAATTATAAAAGTATGAGGATCATTTAATAAATAATCAAACAAAAAAATGA
130 AAATTATAAAAGTATGAGGATCATTTAATAAATAATCAAACAAAAAAATGA
* * *
25058 TTGTAGACCATGAAATTACTTTTAAATAGACACTTGAATCACCTTGATCGGTCAAATAG-AAAAA
1 TTGTAGACCATGAAATTACCTTTAAATAGACACTTGAATCACCTAGATCAGTCAAATAGAAAAAA
* * * *
25122 A-GAAACAATTAAAGCCGAAACATTCAATCGTTCAACATATAATTGTAAG-GATTAAATAGCATA
66 ATAAAACAATTAAAGCCGAAACATTCAATCGTCCAACACATAATTCTAAGTGATTAAATAGCATA
*
25185 AATTATAAAAGTATGAGGATCATTTAATAAATAATCCAACAAAAAAATGA
131 AATTATAAAAGTATGAGGATCATTTAATAAATAATCAAACAAAAAAATGA
25235 TT
1 TT
25237 TGTTTATGGA
Statistics
Matches: 167, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
177 64 0.38
178 42 0.25
179 6 0.04
181 55 0.33
ACGTcount: A:0.48, C:0.13, G:0.12, T:0.27
Consensus pattern (180 bp):
TTGTAGACCATGAAATTACCTTTAAATAGACACTTGAATCACCTAGATCAGTCAAATAGAAAAAA
ATAAAACAATTAAAGCCGAAACATTCAATCGTCCAACACATAATTCTAAGTGATTAAATAGCATA
AATTATAAAAGTATGAGGATCATTTAATAAATAATCAAACAAAAAAATGA
Found at i:37070 original size:18 final size:17
Alignment explanation
Indices: 37042--37075 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
37032 ACTCGAACTC
37042 AAACTAACTGACTCAAA
1 AAACTAACTGACTCAAA
37059 AAACTGAACTGACTCAA
1 AAACT-AACTGACTCAA
37076 CTGACTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.50, C:0.24, G:0.09, T:0.18
Consensus pattern (17 bp):
AAACTAACTGACTCAAA
Found at i:37427 original size:48 final size:48
Alignment explanation
Indices: 37375--37470 Score: 174
Period size: 48 Copynumber: 2.0 Consensus size: 48
37365 GGAAAGTTCT
* *
37375 TCTCCATTAAGCAAAGCAAATCTGAAGCAAAGTTCTTCTCCATCAACA
1 TCTCCATCAAGCAAAGCAAATCTGAAGAAAAGTTCTTCTCCATCAACA
37423 TCTCCATCAAGCAAAGCAAATCTGAAGAAAAGTTCTTCTCCATCAACA
1 TCTCCATCAAGCAAAGCAAATCTGAAGAAAAGTTCTTCTCCATCAACA
37471 AAACAACAAC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.39, C:0.27, G:0.10, T:0.24
Consensus pattern (48 bp):
TCTCCATCAAGCAAAGCAAATCTGAAGAAAAGTTCTTCTCCATCAACA
Found at i:38853 original size:45 final size:43
Alignment explanation
Indices: 38783--38868 Score: 136
Period size: 45 Copynumber: 2.0 Consensus size: 43
38773 GAGATTTATA
* *
38783 GGGTAGTTCCTAAATTAGGACATTAATTTTCTAGGGTTTTAAT
1 GGGTAGTCCCTAAATTAAGACATTAATTTTCTAGGGTTTTAAT
38826 GGGTAAGTCCCTAAATTTAAGACATTAATTTTCTAGGGTTTTA
1 GGGT-AGTCCCTAAA-TTAAGACATTAATTTTCTAGGGTTTTA
38869 GAAATTGTAG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
43 4 0.10
44 9 0.23
45 26 0.67
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.41
Consensus pattern (43 bp):
GGGTAGTCCCTAAATTAAGACATTAATTTTCTAGGGTTTTAAT
Found at i:39235 original size:22 final size:21
Alignment explanation
Indices: 39197--39237 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
39187 AGTACTATTC
*
39197 TTTTTAGTCATTTAACTTTAT
1 TTTTTAGTCATTCAACTTTAT
*
39218 TTTTTAGATGATTCAACTTT
1 TTTTTAG-TCATTCAACTTT
39238 TTTATTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.24, C:0.10, G:0.07, T:0.59
Consensus pattern (21 bp):
TTTTTAGTCATTCAACTTTAT
Done.