Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017350.1 Corchorus olitorius cultivar O-4 contig17383, 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: 17093
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:419 original size:22 final size:22
Alignment explanation
Indices: 394--907 Score: 182
Period size: 22 Copynumber: 23.5 Consensus size: 22
384 ATTACACTAT
* *
394 TTTTGATTACCTCCTTATGAAA
1 TTTTGATAACCTCCATATGAAA
*
416 TTTTGATAACCTTCATATGAAA
1 TTTTGATAACCTCCATATGAAA
* * * *
438 TTTTAATAACGATAC-TATGGAA
1 TTTTGATAAC-CTCCATATGAAA
* * ***
460 TTTCGAGAACCTTTTTAT-AAA
1 TTTTGATAACCTCCATATGAAA
* ***
481 TTTCT-TTAACCTTTTTTATGAAA
1 TTT-TGATAACC-TCCATATGAAA
* * * *
504 TTTTGTTAACCTCCTTAAGGAA
1 TTTTGATAACCTCCATATGAAA
*
526 TTTT-AAAGACCT-CACTATGAAA
1 TTTTGATA-ACCTCCA-TATGAAA
* * *
548 TTTTGATGACTTCC-TAATAAAA
1 TTTTGATAACCTCCAT-ATGAAA
** *
570 TTTTTGATAACCAACACTATGAGA
1 -TTTTGATAACCTCCA-TATGAAA
*
594 TGTTGATAACCTCCATATG-AA
1 TTTTGATAACCTCCATATGAAA
*
615 TTGTT-AGTAA--TCACACTCTGAAA
1 TT-TTGA-TAACCTC-CA-TATGAAA
638 TTTTGATAA--TCACACTATGAAA
1 TTTTGATAACCTC-CA-TATGAAA
* *
660 TGGTT-ATAACCTCGC-TATGAGA
1 T-TTTGATAACCTC-CATATGAAA
*
682 TTTTGATAAACCTTCC-TATAAAA
1 TTTTGAT-AACC-TCCATATGAAA
*
705 TTTT-ATAACCTCCTTATGAAA
1 TTTTGATAACCTCCATATGAAA
* *
726 TCTTGATAA----C-TA-CAAA
1 TTTTGATAACCTCCATATGAAA
* **
742 TTTTGATAACCTCCCTATGATT
1 TTTTGATAACCTCCATATGAAA
764 TTTTGATAACCT-CATTATGAAA
1 TTTTGATAACCTCCA-TATGAAA
* * *
786 TTTTGTTAATCTCCCTATGAAA
1 TTTTGATAACCTCCATATGAAA
* *
808 TTTTGATCTAA-ATAC-TATGAAA
1 TTTTGA--TAACCTCCATATGAAA
*
830 TTTTGATAACC-CTCTTATGAAA
1 TTTTGATAACCTC-CATATGAAA
* *
852 TTTTGATGACCTTCATATGAAA
1 TTTTGATAACCTCCATATGAAA
* *
874 TTTTGATTA-CTCCATAATAAAA
1 TTTTGATAACCTCCAT-ATGAAA
* *
896 GTTTAATAACCT
1 TTTTGATAACCT
908 TCCTAATTTG
Statistics
Matches: 372, Mismatches: 76, Indels: 87
0.70 0.14 0.16
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
18 1 0.00
20 9 0.02
21 42 0.11
22 230 0.62
23 64 0.17
24 12 0.03
25 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (22 bp):
TTTTGATAACCTCCATATGAAA
Found at i:504 original size:23 final size:22
Alignment explanation
Indices: 467--515 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 22
457 GAATTTCGAG
467 AACC-TTTTTATAAATTTCT-TT
1 AACCTTTTTTATAAATTT-TGTT
488 AACCTTTTTTATGAAATTTTGTT
1 AACCTTTTTTAT-AAATTTTGTT
511 AACCT
1 AACCT
516 CCTTAAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.16
22 8 0.32
23 13 0.52
ACGTcount: A:0.29, C:0.14, G:0.04, T:0.53
Consensus pattern (22 bp):
AACCTTTTTTATAAATTTTGTT
Found at i:871 original size:44 final size:43
Alignment explanation
Indices: 409--1562 Score: 242
Period size: 44 Copynumber: 26.9 Consensus size: 43
399 ATTACCTCCT
* **
409 TATGAAATTTTGATAACCTTCATATGAAATTTTAATAACGATAC
1 TATGAAATTTTGATAACCTTCATATGAAATTTTGATAACCCT-C
* * * ** * * *
453 TATGGAATTTCGAGAACCTTTTTAT-AAATTTCT-TTAACCTTTTT
1 TATGAAATTTTGATAACCTTCATATGAAATTT-TGATAACC--CTC
* * * * * * *
497 TATGAAATTTTGTTAACCTCCTTAAGGAATTTT-AAAGACCTCAC
1 TATGAAATTTTGATAACCTTCATATGAAATTTTGATA-ACC-CTC
* * * *
541 TATGAAATTTTGATGA-CTTCCTAATAAAATTTTTGATAACCAACAC
1 TATGAAATTTTGATAACCTTCAT-ATGAAA-TTTTGATAACC--CTC
* * * * *
587 TATGAGATGTTGATAACCTCCATATG-AATTGTT-AGTAATCACAC
1 TATGAAATTTTGATAACCTTCATATGAAATT-TTGA-TAA-CCCTC
* * * * *
631 TCTGAAATTTTGATAATC-ACACTATGAAATGGTT-ATAACCTCGC
1 TATGAAATTTTGATAACCTTCA-TATGAAAT-TTTGATAACC-CTC
* * *
675 TATGAGATTTTGATAAACCTTCCTATAAAATTTT-ATAA-CCTCC
1 TATGAAATTTTGAT-AACCTTCATATGAAATTTTGATAACCCT-C
* * *
718 TTATGAAATCTTGATAA----C-TA-CAAATTTTGATAACCTCCC
1 -TATGAAATTTTGATAACCTTCATATGAAATTTTGATAACC-CTC
** *
757 TATGATTTTTTGATAACC-TCATTATGAAATTTTGTTAATCTCC-C
1 TATGAAATTTTGATAACCTTCA-TATGAAATTTTGATAA-C-CCTC
* *
801 TATGAAATTTTGATCTAA-ATAC-TATGAAATTTTGATAACCCTC
1 TATGAAATTTTGA--TAACCTTCATATGAAATTTTGATAACCCTC
* *
844 TTATGAAATTTTGATGACCTTCATATGAAATTTTGATTACTCCAT-
1 -TATGAAATTTTGATAACCTTCATATGAAATTTTGATAAC-CC-TC
* * * * * * *
889 AATAAAAGTTTAATAACCTTC--CT--AA-TTTGGTAACCATAC
1 TATGAAATTTTGATAACCTTCATATGAAATTTTGATAACCCT-C
* ** *
928 TATGAAATTTTGATAACCTCCCCA-G-AA-----AT-A-CCAC
1 TATGAAATTTTGATAACCTTCATATGAAATTTTGATAACCCTC
* * * * * * * *
962 TATGGAATTTTGGTAATC-ACATTTTGAAAATTTAATAACCTCTT
1 TATGAAATTTTGATAACCTTCA-TATGAAATTTTGATAACC-CTC
* * * *
1006 TACGAAATTTTGATAACCTCTC-TATAAAATTTTGTTGACCCCTC
1 TATGAAATTTTGATAACCT-TCATATGAAATTTTGAT-AACCCTC
* * * *
1050 TATGAAATTTTGATAATC-ACATTATGTAATTTTGATAACCTCGC
1 TATGAAATTTTGATAACCTTCA-TATGAAATTTTGATAACC-CTC
* ** * *
1094 TTTGAAATTTTGATAA-CAACATTATGAAATTTTGATAATCTTCC
1 TATGAAATTTTGATAACCTTCA-TATGAAATTTTGATAACCCT-C
* * * *
1138 TAT-AAATTTTGATAATCCGAACTC-TATGAAATTTCGATAATCACTT
1 TATGAAATTTTGATAA-CC---TTCATATGAAATTTTGATAA-CCCTC
* * *
1184 TATGAGA-TTTGATAACCTTC-TATCAAATTTTG-GAACTCCT-
1 TATGAAATTTTGATAACCTTCATATGAAATTTTGATAAC-CCTC
* * * * ** *
1224 TTTGAAATTTAGATAACATCCCCATGAAATATT-AGTAA-CCTCC
1 TATGAAATTTTGATAACCTTCATATGAAATTTTGA-TAACCCT-C
* * * * *
1267 TTATGAAATTTTGTTAATC-ACACTATGCAATTCTT-ATAACCTCGC
1 -TATGAAATTTTGATAACCTTCA-TATGAAATT-TTGATAACC-CTC
*
1312 TATGAAATTTTGATAACC-TC---------TTTGATAACCTTTC
1 TATGAAATTTTGATAACCTTCATATGAAATTTTGATAACC-CTC
* * ** *
1346 TATAAAATTGTT-ATAACC-ACACTATG-AATTTCAATAACCTTCC
1 TATGAAATT-TTGATAACCTTCA-TATGAAATTTTGATAACCCT-C
* * * *
1389 TAAGAAATTTTAATAACCTGGTCCTATGAAATTTTGATAACCACAC
1 TATGAAATTTTGATAACCT--TCATATGAAATTTTGATAACC-CTC
*** *
1435 TATGAAATTTTGATAACCTTCCCCTGAAATTTTGATAA-CTTGC
1 TATGAAATTTTGATAACCTTCATATGAAATTTTGATAACCCT-C
* *
1478 ATATGAAATTTTGGTAACC-ACACTATGAAATTTTGATAA-CCTCC
1 -TATGAAATTTTGATAACCTTCA-TATGAAATTTTGATAACCCT-C
* * * ** *
1522 TCATGAAATTATAACAACAATCTTATGAAATTTTGATAACC
1 T-ATGAAATTTTGATAACCTTCATATGAAATTTTGATAACC
1563 ACACAGAGAC
Statistics
Matches: 807, Mismatches: 195, Indels: 215
0.66 0.16 0.18
Matches are distributed among these distances:
33 3 0.00
34 40 0.05
35 4 0.00
36 3 0.00
37 9 0.01
38 20 0.02
39 26 0.03
40 9 0.01
41 22 0.03
42 32 0.04
43 73 0.09
44 412 0.51
45 60 0.07
46 86 0.11
47 7 0.01
48 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (43 bp):
TATGAAATTTTGATAACCTTCATATGAAATTTTGATAACCCTC
Found at i:1021 original size:22 final size:22
Alignment explanation
Indices: 986--1334 Score: 171
Period size: 22 Copynumber: 16.0 Consensus size: 22
976 AATCACATTT
* *
986 TGAAAATTTAATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
* *
1008 CGAAATTTTGATAACCTCTCTA
1 TGAAATTTTGATAACCTCTTTA
* * * * *
1030 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTTTA
* * *
1052 TGAAATTTTGATAATCACATTA
1 TGAAATTTTGATAACCTCTTTA
* *
1074 TGTAATTTTGATAACCTCGCTT-
1 TGAAATTTTGATAACCTC-TTTA
** *
1096 TGAAATTTTGATAACAACATTA
1 TGAAATTTTGATAACCTCTTTA
1118 TGAAATTTTGATAA--TCTTCCTA
1 TGAAATTTTGATAACCTCTT--TA
* *
1140 T-AAATTTTGATAATCCGAACTCTA
1 TGAAATTTTGATAA-CC--TCTTTA
* * *
1164 TGAAATTTCGATAATCACTTTA
1 TGAAATTTTGATAACCTCTTTA
* *
1186 TGAGA-TTTGATAACCT-TCTA
1 TGAAATTTTGATAACCTCTTTA
* *
1206 TCAAATTTTG-GAA-CTCCTTT-
1 TGAAATTTTGATAACCT-CTTTA
* * ***
1226 TGAAATTTAGATAACATCCCCA
1 TGAAATTTTGATAACCTCTTTA
* *
1248 TGAAATATT-AGTAACCTCCTTA
1 TGAAATTTTGA-TAACCTCTTTA
* * * **
1270 TGAAATTTTGTTAATCACACTA
1 TGAAATTTTGATAACCTCTTTA
* **
1292 TGCAATTCTT-ATAACCTCGCTA
1 TGAAATT-TTGATAACCTCTTTA
1314 TGAAATTTTGATAACCTCTTT
1 TGAAATTTTGATAACCTCTTT
1335 GATAACCTTT
Statistics
Matches: 241, Mismatches: 66, Indels: 40
0.69 0.19 0.12
Matches are distributed among these distances:
19 2 0.01
20 18 0.07
21 34 0.14
22 166 0.69
23 4 0.02
24 4 0.02
25 11 0.05
26 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTTTA
Found at i:1419 original size:24 final size:22
Alignment explanation
Indices: 1336--1562 Score: 135
Period size: 22 Copynumber: 10.3 Consensus size: 22
1326 AACCTCTTTG
* *
1336 ATAACCTTTCTATAAAATTGTT-
1 ATAACCTTCCTATGAAATT-TTA
* *
1358 ATAACC-ACACTATG-AATTTCA
1 ATAACCTTC-CTATGAAATTTTA
*
1379 ATAACCTTCCTAAGAAATTTTA
1 ATAACCTTCCTATGAAATTTTA
*
1401 ATAACCTGGTCCTATGAAATTTTG
1 ATAACCT--TCCTATGAAATTTTA
* *
1425 ATAACC-ACACTATGAAATTTTG
1 ATAACCTTC-CTATGAAATTTTA
** *
1447 ATAACCTTCCCCTGAAATTTTG
1 ATAACCTTCCTATGAAATTTTA
* *
1469 ATAA-CTTGCATATGAAATTTTG
1 ATAACCTT-CCTATGAAATTTTA
* * *
1491 GTAACC-ACACTATGAAATTTTG
1 ATAACCTTC-CTATGAAATTTTA
*
1513 ATAACC-TCCTCATGAAATTATA
1 ATAACCTTCCT-ATGAAATTTTA
* ** * *
1535 ACAACAATCTTATGAAATTTTG
1 ATAACCTTCCTATGAAATTTTA
1557 ATAACC
1 ATAACC
1563 ACACAGAGAC
Statistics
Matches: 162, Mismatches: 30, Indels: 26
0.74 0.14 0.12
Matches are distributed among these distances:
20 1 0.01
21 21 0.13
22 116 0.72
23 5 0.03
24 19 0.12
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.35
Consensus pattern (22 bp):
ATAACCTTCCTATGAAATTTTA
Found at i:1507 original size:66 final size:68
Alignment explanation
Indices: 1350--1566 Score: 232
Period size: 66 Copynumber: 3.3 Consensus size: 68
1340 CCTTTCTATA
** * *
1350 AAATTGTT-ATAACCACACTATG-AATTTCAATAACCTTCCTAAGAAATTTTAATAACCTGGTCC
1 AAATT-TTGATAACCACACTATGAAATTTTGATAACCTTCCCAAGAAATTTTAATAACCTGGTCA
1413 TATG
65 TATG
** * *
1417 AAATTTTGATAACCACACTATGAAATTTTGATAACCTTCCCCTGAAATTTTGATAA-CTTG-CAT
1 AAATTTTGATAACCACACTATGAAATTTTGATAACCTTCCCAAGAAATTTTAATAACCTGGTCAT
1480 ATG
66 ATG
* * * * ** *
1483 AAATTTTGGTAACCACACTATGAAATTTTGATAACC-TCCTCATGAAATTATAACAA-C-AATCT
1 AAATTTTGATAACCACACTATGAAATTTTGATAACCTTCC-CAAGAAATTTTAATAACCTGGTCA
1545 TATG
65 TATG
1549 AAATTTTGATAACCACAC
1 AAATTTTGATAACCACAC
1567 AGAGACAAGA
Statistics
Matches: 129, Mismatches: 17, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
65 3 0.02
66 77 0.60
67 22 0.17
68 27 0.21
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.34
Consensus pattern (68 bp):
AAATTTTGATAACCACACTATGAAATTTTGATAACCTTCCCAAGAAATTTTAATAACCTGGTCAT
ATG
Found at i:1760 original size:19 final size:20
Alignment explanation
Indices: 1729--1766 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
1719 TATTGACATT
1729 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
1748 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
1767 AATAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:2018 original size:153 final size:148
Alignment explanation
Indices: 1873--2256 Score: 596
Period size: 146 Copynumber: 2.6 Consensus size: 148
1863 AATAATAAAA
* * *
1873 TTATACTAAATTTTCATAATGGCAATTTAGAAATATATTTTAAAAAAAAGGGTACAATCGGAAAA
1 TTATA-TAAATTTTAATAATGTCAATTTAGAAATATA-TTT--AAAAAAGGGTACAATCAGAAAA
*
1938 CATAAAGTTTCCCATTATTCGTAGAAATTTGCATGTTCATCAATGAAAATCAATTTTACAAACTT
62 -ATAAAGTTTTCCATTATTCGTAGAAATTTGCATGTTCATCAATGAAAATCAATTTTACAAACTT
2003 ATAATTCGGTCTAAATTGAAATT
126 ATAATTCGGTCTAAATTGAAATT
2026 TTATAATAAATTTTAATAATGTCAATTTAGAAATATATTTGAAAAAAGGGTACAATCAG-AAAAT
1 TTAT-ATAAATTTTAATAATGTCAATTTAGAAATATATTT-AAAAAAGGGTACAATCAGAAAAAT
*
2090 --A-TTTTCCATTGTTCGTAGAAATTTGCATGTTCATCAATGAAAATCAATTTTACAAACTTATA
64 AAAGTTTTCCATTATTCGTAGAAATTTGCATGTTCATCAATGAAAATCAATTTTACAAACTTATA
2152 ATTCGGTCTAAATTGAAATT
129 ATTCGGTCTAAATTGAAATT
* *
2172 TTATGATAAATTTTAATAATGTCAATTTAGAAATATATTTGAGAAAGGGTACAATCAGAAAAAAT
1 TTAT-ATAAATTTTAATAATGTCAATTTAGAAATATATTTAAAAAAGGGTACAATCAG-AAAAAT
2237 AAAGTTTTCCATTATTCGTA
64 AAAGTTTTCCATTATTCGTA
2257 CTTCTTTTTG
Statistics
Matches: 215, Mismatches: 10, Indels: 15
0.90 0.04 0.06
Matches are distributed among these distances:
145 16 0.07
146 118 0.55
147 6 0.03
149 3 0.01
150 18 0.08
151 17 0.08
152 3 0.01
153 33 0.15
154 1 0.00
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.36
Consensus pattern (148 bp):
TTATATAAATTTTAATAATGTCAATTTAGAAATATATTTAAAAAAGGGTACAATCAGAAAAATAA
AGTTTTCCATTATTCGTAGAAATTTGCATGTTCATCAATGAAAATCAATTTTACAAACTTATAAT
TCGGTCTAAATTGAAATT
Found at i:3667 original size:144 final size:144
Alignment explanation
Indices: 3519--4996 Score: 2091
Period size: 144 Copynumber: 10.3 Consensus size: 144
3509 GTTTGTATTT
** *
3519 CAACAATCTCTCTGGCTCAATCCCCACCTCCATTGGAAACTTAACCAAATTGTCTACTCTTTACC
1 CAACAATCTCTCTGGCTCAATCCCTGCCTCCATTGGAAACCTAACCAAATTGTCTACTCTTTACC
* * * * **
3584 TTCATATAAATCATCTTTCTGGGTCAATACCTGAAGAGATTGGGATGCTTAAATCTCTTATTGAT
66 TTCATACAAATCAGCTTTCCGGGTCAATACCTGAAGAGGTTGGGATGCTTAAATCTCTTACAGAT
* ** *
3649 CTTGAATTGGGTAA
131 CTTGAGTTGAATAC
* * * * *
3663 CAACAATCTCTCTGACCCAATCCCTACATCTATTGGAAACCTAACCAAATTG-CTACTCTTTACC
1 CAACAATCTCTCTGGCTCAATCCCTGCCTCCATTGGAAACCTAACCAAATTGTCTACTCTTTACC
* * * * *
3727 TAT-ATAAAAATCAGCTTTCTGGGTCAATACCTAAAGAGATTGGGATGCTTAAATCTCTTACCGA
66 T-TCATACAAATCAGCTTTCCGGGTCAATACCTGAAGAGGTTGGGATGCTTAAATCTCTTACAGA
**
3791 TCTTGAAATGAATAC
130 TCTTGAGTTGAATAC
* * * *
3806 TAACACTCTCTCTCGCTCAATCCCTGCCTCCATTGGAAACCTAACCAAATTGTCTATTCTTTACC
1 CAACAATCTCTCTGGCTCAATCCCTGCCTCCATTGGAAACCTAACCAAATTGTCTACTCTTTACC
* * * *
3871 TTCATACAAATAAGCTTTACGGGTCAATACCTGAAGAGATTGGGATGCTTAAATCTCTTATAGAT
66 TTCATACAAATCAGCTTTCCGGGTCAATACCTGAAGAGGTTGGGATGCTTAAATCTCTTACAGAT
*
3936 CTTGAGTTGAGTAC
131 CTTGAGTTGAATAC
* * *
3950 CAACATTCTCTCTAGCTCAATCCCTGCCTCCATTGGAAACCTAACCAAATTGCCTACTCTTT-CC
1 CAACAATCTCTCTGGCTCAATCCCTGCCTCCATTGGAAACCTAACCAAATTGTCTACTCTTTACC
*
4014 TTCATACAAATCAGCTTTCCGGGTCAATACATGAAGAGGTTGGGATGCTTAAATCTCTTACAGAT
66 TTCATACAAATCAGCTTTCCGGGTCAATACCTGAAGAGGTTGGGATGCTTAAATCTCTTACAGAT
4079 CTTGAGTT-AAGTAC
131 CTTGAGTTGAA-TAC
* * *
4093 CAACATTCTCTTTGGCTCAATCCCTGCCTCCATTGGAAACCTAACCAAATTGTCTACTTTTTACC
1 CAACAATCTCTCTGGCTCAATCCCTGCCTCCATTGGAAACCTAACCAAATTGTCTACTCTTTACC
* *
4158 TTCATACAAATAAGCTTTCCGGGTCAATACCTGAAGAGGTTGGGATGCTTAAATCTCTTACCGAT
66 TTCATACAAATCAGCTTTCCGGGTCAATACCTGAAGAGGTTGGGATGCTTAAATCTCTTACAGAT
* *
4223 CTTGGGTTAAATAC
131 CTTGAGTTGAATAC
* * * * * *
4237 CAACAATCGCTCTGGCCCAATCCCTGCCTCCAATGGAAACCTCACCAAGTTGTCTACTCTTTTCC
1 CAACAATCTCTCTGGCTCAATCCCTGCCTCCATTGGAAACCTAACCAAATTGTCTACTCTTTACC
** * *
4302 TTCATACAAATCAGCTTTCCAAGTCAATACCTGAAGAGGTTGGGATGCTTAAATTTCTTAAAGAT
66 TTCATACAAATCAGCTTTCCGGGTCAATACCTGAAGAGGTTGGGATGCTTAAATCTCTTACAGAT
*
4367 CTTGAGTTGAGTAC
131 CTTGAGTTGAATAC
*
4381 CAACATTCTCTCTGGCTCAATCCCTGCCTCCATTGGAAACCTAACCAAATTGTCTACTCTTTACC
1 CAACAATCTCTCTGGCTCAATCCCTGCCTCCATTGGAAACCTAACCAAATTGTCTACTCTTTACC
* ** * *
4446 TTCATACAAATAAGCTTTATGGGTCAATACCTGAAGAGGTTGGGATGGTTAAATCTCTTACCGAT
66 TTCATACAAATCAGCTTTCCGGGTCAATACCTGAAGAGGTTGGGATGCTTAAATCTCTTACAGAT
*
4511 CTTGGGTTGAATAC
131 CTTGAGTTGAATAC
* * * * * *
4525 CAACAATCTCTATGGCCCAAGCCCTGCTTCCATTGGAAACCTAACCAAGTTGTCTACTCTTTTCC
1 CAACAATCTCTCTGGCTCAATCCCTGCCTCCATTGGAAACCTAACCAAATTGTCTACTCTTTACC
* *
4590 TTCATACAAATCAGCTTTTCGGGACAATACCTGAAGAGGTTGGGATGCTTAAATCTCTTACAGAT
66 TTCATACAAATCAGCTTTCCGGGTCAATACCTGAAGAGGTTGGGATGCTTAAATCTCTTACAGAT
*
4655 CTTGAGTTGAGTAC
131 CTTGAGTTGAATAC
* * * *
4669 GAACATTCTCTCTGGCTCAATCCCTGCCTCCATTGGAAACCTAACCAAATTGTCTGCTCTTCACC
1 CAACAATCTCTCTGGCTCAATCCCTGCCTCCATTGGAAACCTAACCAAATTGTCTACTCTTTACC
* * * *
4734 TTCATACAAATAAGCTTTCCAGGTCAATACCTGAAGAGGTTGGGATGCTTATATCTCTTACCGAT
66 TTCATACAAATCAGCTTTCCGGGTCAATACCTGAAGAGGTTGGGATGCTTAAATCTCTTACAGAT
**
4799 CTTGAAATGAATAC
131 CTTGAGTTGAATAC
* * * *
4813 CAACACTCTTTCTGGCTCAATCCCTGCCTCCATTGGAAACCTAACCAAATTGTCTACTATCTACC
1 CAACAATCTCTCTGGCTCAATCCCTGCCTCCATTGGAAACCTAACCAAATTGTCTACTCTTTACC
* * *
4878 TTCATACAAATCAGCTTTCCGAGTCAATAACTGAAGAGGTTGGGATGCTTAAATCTCTTACTGAT
66 TTCATACAAATCAGCTTTCCGGGTCAATACCTGAAGAGGTTGGGATGCTTAAATCTCTTACAGAT
*
4943 CTTGGGTTGAATAC
131 CTTGAGTTGAATAC
*
4957 CAACAATCTCTCTGGCTCAATCCCTGCTTCCATTGGAAAC
1 CAACAATCTCTCTGGCTCAATCCCTGCCTCCATTGGAAAC
4997 TTGACGAGTC
Statistics
Matches: 1186, Mismatches: 142, Indels: 12
0.89 0.11 0.01
Matches are distributed among these distances:
142 1 0.00
143 256 0.22
144 927 0.78
145 2 0.00
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.31
Consensus pattern (144 bp):
CAACAATCTCTCTGGCTCAATCCCTGCCTCCATTGGAAACCTAACCAAATTGTCTACTCTTTACC
TTCATACAAATCAGCTTTCCGGGTCAATACCTGAAGAGGTTGGGATGCTTAAATCTCTTACAGAT
CTTGAGTTGAATAC
Found at i:14493 original size:28 final size:29
Alignment explanation
Indices: 14453--14508 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
14443 TGTAGCGTTA
* *
14453 GGACGTTTTGCCCCTGAACT-TCAATTTT
1 GGACATTTTGCCCCTAAACTCTCAATTTT
14481 GGACATTTTGCCCCTAAACTCTCAATTT
1 GGACATTTTGCCCCTAAACTCTCAATTT
14509 GAGCCTCTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 18 0.72
29 7 0.28
ACGTcount: A:0.21, C:0.27, G:0.14, T:0.38
Consensus pattern (29 bp):
GGACATTTTGCCCCTAAACTCTCAATTTT
Found at i:14740 original size:28 final size:30
Alignment explanation
Indices: 14701--14760 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
14691 ACCAACGCTC
* *
14701 AAATTGAGAGTTCA-GGGGTAAAATGTCCA
1 AAATTGAGAGTTCACGGGGCAAAACGTCCA
14730 AAATTGA-AGTTCACGGGGCAAAACGTCCA
1 AAATTGAGAGTTCACGGGGCAAAACGTCCA
14759 AA
1 AA
14761 CACTATAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 6 0.21
29 22 0.79
ACGTcount: A:0.40, C:0.15, G:0.25, T:0.20
Consensus pattern (30 bp):
AAATTGAGAGTTCACGGGGCAAAACGTCCA
Found at i:15520 original size:123 final size:123
Alignment explanation
Indices: 15321--15699 Score: 623
Period size: 123 Copynumber: 3.0 Consensus size: 123
15311 ACTTGTTTAA
* *
15321 ACTTTTATAGTTTTACTCAACTAAAAACTCTACTTTTATTTAATTAAATCTAATATCTTTATAAT
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAAT
*
15386 TTTTACTATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
66 TTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
15444 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAAT
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAAT
15509 TTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
66 TTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
* * *
15567 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTATTTAATTCCAATATCCTTATACT
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATAT-CTT-TA--
15632 TATTTTATTTTTACCATTTTACTATTTTAATTAAAAAAACTTATATATATTAGAATTTTTTAAAT
62 TA----ATTTTTACCATTTTACTATTTTAATT-AAAAAACTTATATATATTAGAATTTTTTAAAT
15697 AT
122 AT
15699 A
1 A
15700 TTTCTTAAAT
Statistics
Matches: 241, Mismatches: 6, Indels: 9
0.94 0.02 0.04
Matches are distributed among these distances:
123 173 0.72
124 3 0.01
125 2 0.01
127 2 0.01
131 26 0.11
132 35 0.15
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50
Consensus pattern (123 bp):
ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAAT
TTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
Found at i:15721 original size:14 final size:13
Alignment explanation
Indices: 15685--15723 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
15675 TATATATTAG
15685 AATTTTTTAAATA
1 AATTTTTTAAATA
* *
15698 TATTTCTTAAATGA
1 AATTTTTTAAAT-A
15712 AATTTTTTAAAT
1 AATTTTTTAAAT
15724 TTTACAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (13 bp):
AATTTTTTAAATA
Found at i:15734 original size:132 final size:122
Alignment explanation
Indices: 15354--15739 Score: 404
Period size: 123 Copynumber: 3.0 Consensus size: 122
15344 AAAACTCTAC
*
15354 TTTTATTTAATTAAATCTAATATCTTTATAATTTTTACTATTTTACTATTTTAATTAAAAAACTT
1 TTTTATTTAATTAAATCTAATATCTTTATAATTTTTACCATTTTACTATTTTAATTAAAAAACTT
* * * * * *
15419 ATATATATTAGAATTTTTTAAATATACTTTTACA-G-TTTTACTCAACTAAAAACTCTAT
66 ATATATATTAGAATTTTTTAAATATACTTTTAAATGATTTT-CTAAAATTACAA-T-TTT
15477 TTTTATTTAATTAAATCTAATATCTTTATAATTTTTACCATTTTACTATTTTAATTAAAAAACTT
1 TTTTATTTAATTAAATCTAATATCTTTATAATTTTTACCATTTTACTATTTTAATTAAAAAACTT
* ** *
15542 ATATATATTAGAATTTTTTAAATATACTTTTACA-G-TTTTACTCAACTAAAAACTCTATTTT
66 ATATATATTAGAATTTTTTAAATATACTTTTAAATGATTTT-CT-AA--AATTA--CAATTTT
* * *
15603 TATTTATTTAATTCCAATATCCTTATA-CTTATTTTATTTTTACCATTTTACTATTTTAATTAAA
1 T-TTTATTTAATT--AA-AT-CTAATATCTT-TATAATTTTTACCATTTTACTATTTTAATT-AA
* * *
15667 AAAACTTATATATATTAGAATTTTTTAAATATATTTCTTAAATGAAATTTTTTAAATTTTACAAT
59 AAAACTTATATATATTAGAATTTTTTAAATATACTT-TTAAATG--ATTTTCTAAA-ATTACAAT
15732 TTT
120 TTT
15735 TTTTA
1 TTTTA
15740 GAAATAAACT
Statistics
Matches: 228, Mismatches: 17, Indels: 28
0.84 0.06 0.10
Matches are distributed among these distances:
123 106 0.46
124 1 0.00
126 6 0.03
127 12 0.05
128 1 0.00
129 2 0.01
130 5 0.02
131 37 0.16
132 44 0.19
133 5 0.02
134 2 0.01
135 2 0.01
136 1 0.00
137 4 0.02
ACGTcount: A:0.37, C:0.09, G:0.02, T:0.52
Consensus pattern (122 bp):
TTTTATTTAATTAAATCTAATATCTTTATAATTTTTACCATTTTACTATTTTAATTAAAAAACTT
ATATATATTAGAATTTTTTAAATATACTTTTAAATGATTTTCTAAAATTACAATTTT
Done.