Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006754.1 Corchorus capsularis cultivar CVL-1 contig06775, 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: 40370
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:418 original size:15 final size:15
Alignment explanation
Indices: 395--435 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
385 TTTCTTAATA
395 TATTCTTTTATAATTT
1 TATT-TTTTATAATTT
411 T-TCTTTTTATAATTT
1 TAT-TTTTTATAATTT
426 TATTTTTTAT
1 TATTTTTTAT
436 TAATAATCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 20 0.87
16 3 0.13
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (15 bp):
TATTTTTTATAATTT
Found at i:8106 original size:22 final size:22
Alignment explanation
Indices: 8078--8173 Score: 91
Period size: 22 Copynumber: 4.7 Consensus size: 22
8068 ATTGATATGT
8078 TAAGTGGGTTTTTAATATGTTA
1 TAAGTGGGTTTTTAATATGTTA
* *
8100 TAAGTGGGTTTTTAAT-TCCTTT
1 TAAGTGGGTTTTTAATAT-GTTA
* *
8122 TAA-----TTATTGATATG-T-
1 TAAGTGGGTTTTTAATATGTTA
8137 TAAGTGGGTTTTTAATATGTTA
1 TAAGTGGGTTTTTAATATGTTA
8159 TAAGTGGGTTTTTAA
1 TAAGTGGGTTTTTAA
8174 GACATCTCAT
Statistics
Matches: 58, Mismatches: 7, Indels: 18
0.70 0.08 0.22
Matches are distributed among these distances:
15 3 0.05
16 1 0.02
17 6 0.10
18 1 0.02
20 9 0.16
21 2 0.03
22 36 0.62
ACGTcount: A:0.26, C:0.02, G:0.21, T:0.51
Consensus pattern (22 bp):
TAAGTGGGTTTTTAATATGTTA
Found at i:8129 original size:59 final size:59
Alignment explanation
Indices: 8056--8173 Score: 227
Period size: 59 Copynumber: 2.0 Consensus size: 59
8046 TAATTTGAGG
8056 TTCCCTTTAATTATTGATATGTTAAGTGGGTTTTTAATATGTTATAAGTGGGTTTTTAA
1 TTCCCTTTAATTATTGATATGTTAAGTGGGTTTTTAATATGTTATAAGTGGGTTTTTAA
*
8115 TTCCTTTTAATTATTGATATGTTAAGTGGGTTTTTAATATGTTATAAGTGGGTTTTTAA
1 TTCCCTTTAATTATTGATATGTTAAGTGGGTTTTTAATATGTTATAAGTGGGTTTTTAA
8174 GACATCTCAT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.25, C:0.04, G:0.19, T:0.52
Consensus pattern (59 bp):
TTCCCTTTAATTATTGATATGTTAAGTGGGTTTTTAATATGTTATAAGTGGGTTTTTAA
Found at i:8545 original size:27 final size:27
Alignment explanation
Indices: 8490--8548 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
8480 TTTATTACTC
* *
8490 AACTTTTCCTACTTCTTTACATTACCA
1 AACTGTTCCTACTTCTTTACACTACCA
8517 AACTGTTCCTAC-TCTTTA-ACTACATCA
1 AACTGTTCCTACTTCTTTACACTAC--CA
8544 AACTG
1 AACTG
8549 AAGGCAATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 4 0.14
26 6 0.21
27 18 0.64
ACGTcount: A:0.29, C:0.29, G:0.03, T:0.39
Consensus pattern (27 bp):
AACTGTTCCTACTTCTTTACACTACCA
Found at i:8830 original size:22 final size:22
Alignment explanation
Indices: 8805--8873 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 22
8795 ATTACACTAT
* * *
8805 TTTTAATGACCTTCTTATTAAA
1 TTTTAATAACCTTCCTATGAAA
*
8827 TTTTGATAACCTTCCTATGAAA
1 TTTTAATAACCTTCCTATGAAA
** *
8849 TTTTAATAACAATACTATGAAA
1 TTTTAATAACCTTCCTATGAAA
8871 TTT
1 TTT
8874 CGAGAACCTT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.36, C:0.13, G:0.06, T:0.45
Consensus pattern (22 bp):
TTTTAATAACCTTCCTATGAAA
Found at i:8935 original size:21 final size:22
Alignment explanation
Indices: 8887--8935 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
8877 GAACCTTTTT
*
8887 ATTTTTTTAACCTTCTTATGAA
1 ATTTTTTTAACCTTCTTAAGAA
*
8909 ATTTTTTTAACC-TCTCTAAGGA
1 ATTTTTTTAACCTTCT-TAAGAA
8931 ATTTT
1 ATTTT
8936 GAAGAACTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 3 0.12
22 21 0.88
ACGTcount: A:0.27, C:0.14, G:0.06, T:0.53
Consensus pattern (22 bp):
ATTTTTTTAACCTTCTTAAGAA
Found at i:10804 original size:22 final size:22
Alignment explanation
Indices: 10759--10804 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
10749 GAATTGTTAG
* **
10759 TAATCACACTCTGAAATTTTGA
1 TAATCACACTATGAAATTGCGA
*
10781 TAATCACTCTATGAAATTGCGA
1 TAATCACACTATGAAATTGCGA
10803 TA
1 TA
10805 GCCTCGTTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (22 bp):
TAATCACACTATGAAATTGCGA
Found at i:10850 original size:23 final size:23
Alignment explanation
Indices: 10824--10895 Score: 94
Period size: 23 Copynumber: 3.2 Consensus size: 23
10814 TGAAATTTTA
10824 ATAAACCTTCCTATAAAATCTTG
1 ATAAACCTTCCTATAAAATCTTG
* *
10847 ATAAACCTCCCTATAAAATTTTG
1 ATAAACCTTCCTATAAAATCTTG
*
10870 ATAAA-C-TCCTTATGAAATCTTG
1 ATAAACCTTCC-TATAAAATCTTG
10892 ATAA
1 ATAA
10896 CTACAAATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
21 2 0.05
22 15 0.35
23 26 0.60
ACGTcount: A:0.40, C:0.19, G:0.06, T:0.35
Consensus pattern (23 bp):
ATAAACCTTCCTATAAAATCTTG
Found at i:10887 original size:22 final size:22
Alignment explanation
Indices: 10770--11001 Score: 94
Period size: 22 Copynumber: 10.8 Consensus size: 22
10760 AATCACACTC
10770 TGAAATTTTGAT-AA-TCACTCTA
1 TGAAATTTTGATAAACTC-CT-TA
** ** *
10792 TGAAATTGCGATAGCCTCGTTA
1 TGAAATTTTGATAAACTCCTTA
*
10814 TGAAATTTTAATAAACCTTCC-TA
1 TGAAATTTTGATAAA-C-TCCTTA
* * *
10837 TAAAATCTTGATAAACCTCCCTA
1 TGAAATTTTGATAAA-CTCCTTA
*
10860 TAAAATTTTGATAAACTCCTTA
1 TGAAATTTTGATAAACTCCTTA
*
10882 TGAAATCTTGAT-AA---C-TA
1 TGAAATTTTGATAAACTCCTTA
* *
10899 -CAAATTTTGAT-AACTTCCCTA
1 TGAAATTTTGATAAAC-TCCTTA
** * * **
10920 TGATTTTTTGATTACCTTATTA
1 TGAAATTTTGATAAACTCCTTA
* *
10942 TGAAATTTTGTTAATCT-CTCTA
1 TGAAATTTTGATAAACTCCT-TA
* *
10964 TGAAATTTTGGT-AACCCTCTTA
1 TGAAATTTTGATAAACTC-CTTA
10986 TGAAATTTTGA-AAACT
1 TGAAATTTTGATAAACT
11002 AAACTATGAA
Statistics
Matches: 156, Mismatches: 38, Indels: 32
0.69 0.17 0.14
Matches are distributed among these distances:
16 11 0.07
17 2 0.01
18 1 0.01
20 1 0.01
21 7 0.04
22 92 0.59
23 38 0.24
24 4 0.03
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (22 bp):
TGAAATTTTGATAAACTCCTTA
Found at i:10965 original size:44 final size:44
Alignment explanation
Indices: 10900--11001 Score: 107
Period size: 44 Copynumber: 2.3 Consensus size: 44
10890 TGATAACTAC
** * *
10900 AAATTTTGATAACTTCCCTATGATTTTTTGATTACCTTATTATG
1 AAATTTTGATAACTTCCCTATGAAATTTTGATAACCCTATTATG
* * * *
10944 AAATTTTGTTAA-TCTCTCTATGAAATTTTGGTAACCCTCTTATG
1 AAATTTTGATAACT-TCCCTATGAAATTTTGATAACCCTATTATG
*
10988 AAATTTTGAAAACT
1 AAATTTTGATAACT
11002 AAACTATGAA
Statistics
Matches: 46, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
43 1 0.02
44 44 0.96
45 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.10, T:0.46
Consensus pattern (44 bp):
AAATTTTGATAACTTCCCTATGAAATTTTGATAACCCTATTATG
Found at i:11267 original size:29 final size:29
Alignment explanation
Indices: 11228--11304 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 29
11218 ATTTGCTAAC
* *
11228 GTTTAGGCTCAATTTGGTCATGTTT-AAAG
1 GTTTAGACTCAATTTGG-CAAGTTTGAAAG
*
11257 GTTTAGACTCAAATTGAGCAAGTTTGGAAAG
1 GTTTAGACTCAATTTG-GCAAGTTT-GAAAG
*
11288 GTTTAGACCCAATTTGG
1 GTTTAGACTCAATTTGG
11305 ACATTAGGCC
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
29 20 0.50
30 2 0.05
31 18 0.45
ACGTcount: A:0.29, C:0.12, G:0.25, T:0.35
Consensus pattern (29 bp):
GTTTAGACTCAATTTGGCAAGTTTGAAAG
Found at i:11462 original size:22 final size:22
Alignment explanation
Indices: 11429--11580 Score: 103
Period size: 22 Copynumber: 6.8 Consensus size: 22
11419 GAAATACCAC
* * *
11429 TATGAAAATTTGGTAATCACATT
1 TATGAAATTTTGATAACCAC-TT
*
11452 T-TGAAATTTTGATAACCTCTT
1 TATGAAATTTTGATAACCACTT
* *
11473 TATGAAATTTTGATAACCTCTC
1 TATGAAATTTTGATAACCACTT
* * * *
11495 TATAAAATTTTGTTGACCCACCCTC
1 TATGAAATTTTGAT-AACCA--CTT
* *
11520 TATGAAATTTTGATAATCACAT
1 TATGAAATTTTGATAACCACTT
*
11542 TATGTAATTTTGATAA-C-CTT
1 TATGAAATTTTGATAACCACTT
*
11562 GCTTTGAAATTTTGATAAC
1 --TATGAAATTTTGATAAC
11581 AACACTGAAA
Statistics
Matches: 103, Mismatches: 19, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
20 2 0.02
21 4 0.04
22 75 0.73
23 4 0.04
24 3 0.03
25 15 0.15
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACTT
Found at i:11637 original size:25 final size:22
Alignment explanation
Indices: 11453--11683 Score: 93
Period size: 22 Copynumber: 10.5 Consensus size: 22
11443 AATCACATTT
*
11453 TGAAATTTTGATAACCTCTT-TA
1 TGAAATTTTGATAATCT-TTCTA
* *
11475 TGAAATTTTGATAACCTCTCTA
1 TGAAATTTTGATAATCTTTCTA
* * **
11497 TAAAATTTTGTTGACCCA-CCCTCTA
1 TGAAATTTTGAT-A---ATCTTTCTA
**
11522 TGAAATTTTGATAATCACAT-TA
1 TGAAATTTTGATAATC-TTTCTA
* * * *
11544 TGTAATTTTGATAACCTTGCTT
1 TGAAATTTTGATAATCTTTCTA
**
11566 TGAAATTTTGATAA-C-AAC-A
1 TGAAATTTTGATAATCTTTCTA
*
11585 CTGAAATTTCGATAATCTTTCTA
1 -TGAAATTTTGATAATCTTTCTA
*
11608 T-AAATTTTGATAATCTGATCTCTG
1 TGAAATTTTGATAATCT--T-TCTA
* **
11632 TGAAATTCTGATAATCACTCTA
1 TGAAATTTTGATAATCTTTCTA
* * *
11654 TCAGA-TTTGATTATC-TTCTA
1 TGAAATTTTGATAATCTTTCTA
*
11674 TCAAATTTTG
1 TGAAATTTTG
11684 GTACTCCTTA
Statistics
Matches: 160, Mismatches: 32, Indels: 35
0.70 0.14 0.15
Matches are distributed among these distances:
20 22 0.14
21 30 0.19
22 68 0.43
23 5 0.03
24 5 0.03
25 29 0.18
26 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.42
Consensus pattern (22 bp):
TGAAATTTTGATAATCTTTCTA
Found at i:11664 original size:21 final size:20
Alignment explanation
Indices: 11634--11681 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
11624 GATCTCTGTG
11634 AAATTCTGATAATCACTCTATC
1 AAATT-TGATAATC-CTCTATC
* * *
11656 AGATTTGATTATCTTCTATC
1 AAATTTGATAATCCTCTATC
11676 AAATTT
1 AAATTT
11682 TGGTACTCCT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 11 0.50
21 7 0.32
22 4 0.18
ACGTcount: A:0.33, C:0.17, G:0.06, T:0.44
Consensus pattern (20 bp):
AAATTTGATAATCCTCTATC
Found at i:11753 original size:22 final size:21
Alignment explanation
Indices: 11724--11764 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
11714 CCTTCATATG
11724 AAAATTTGATAACCACACTAA
1 AAAATTTGATAACCACACTAA
11745 AAAATTTTGATAACCACACT
1 AAAA-TTTGATAACCACACT
11765 GAAATTTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.49, C:0.20, G:0.05, T:0.27
Consensus pattern (21 bp):
AAAATTTGATAACCACACTAA
Found at i:11771 original size:20 final size:20
Alignment explanation
Indices: 11722--11771 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 20
11712 AACCTTCATA
*
11722 TGAAAATTTGATAACCACAC
1 TGAAATTTTGATAACCACAC
*
11742 TAAAAAATTTTGATAACCACAC
1 T--GAAATTTTGATAACCACAC
11764 TGAAATTT
1 TGAAATTT
11772 CAATAACCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
20 7 0.28
22 18 0.72
ACGTcount: A:0.46, C:0.16, G:0.08, T:0.30
Consensus pattern (20 bp):
TGAAATTTTGATAACCACAC
Found at i:11825 original size:88 final size:87
Alignment explanation
Indices: 11710--11911 Score: 230
Period size: 88 Copynumber: 2.3 Consensus size: 87
11700 TGAGACTTTT
* * *
11710 ATAACCTTCATATGAAAATTTGATAACCACACTAAAAAATTTTGATAA-C-CACACTGAAATTTC
1 ATAACCATCCTATGAAATTTTGATAACCACACTAAAAAATTTTGATAAGCTCACA-TGAAATTTC
* *
11773 AATAACCTTCCTGA-GAAATTTTA
65 AATAA-CTTCCTCATGAAATTATA
* ** * *
11796 ATAACCTGATCCTATGAAATTTTGGTAACCACACTATGATATTTTGATAAGCTTCTCATGAAATT
1 ATAACC--ATCCTATGAAATTTTGATAACCACACTAAAAAATTTTGATAAGC-TCACATGAAATT
*
11861 TTAATAACTTCCTCATGAAATTATA
63 TCAATAACTTCCTCATGAAATTATA
*
11886 ATAACCATCTTATGAAATTTTGATAA
1 ATAACCATCCTATGAAATTTTGATAA
11912 TCACGAAGAG
Statistics
Matches: 97, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
86 6 0.06
88 53 0.55
89 8 0.08
90 27 0.28
91 3 0.03
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.35
Consensus pattern (87 bp):
ATAACCATCCTATGAAATTTTGATAACCACACTAAAAAATTTTGATAAGCTCACATGAAATTTCA
ATAACTTCCTCATGAAATTATA
Found at i:11856 original size:22 final size:21
Alignment explanation
Indices: 11831--11911 Score: 81
Period size: 22 Copynumber: 3.7 Consensus size: 21
11821 TAACCACACT
* *
11831 ATGATATTTTGATAAGCTTCTC
1 ATGAAATTTTAATAA-CTTCTC
11853 ATGAAATTTTAATAACTTCCTC
1 ATGAAATTTTAATAACTT-CTC
* * *
11875 ATGAAATTATAATAACCATCTT
1 ATGAAATTTTAATAA-CTTCTC
*
11897 ATGAAATTTTGATAA
1 ATGAAATTTTAATAA
11912 TCACGAAGAG
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
21 3 0.06
22 45 0.90
23 2 0.04
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (21 bp):
ATGAAATTTTAATAACTTCTC
Found at i:11901 original size:44 final size:43
Alignment explanation
Indices: 11764--11911 Score: 118
Period size: 44 Copynumber: 3.3 Consensus size: 43
11754 ATAACCACAC
* *
11764 TGAAATTTCAATAACCTTCCTGA-GAAATTTTAATAACCTGATCCTA
1 TGAAATTTTAATAA-CTTCCT-ATGAAATTTTAATAACC--ATCTTA
** ** * * * * *
11810 TGAAATTTTGGTAACCACACTATGATATTTTGATAAGCTTCTCA
1 TGAAATTTTAATAACTTC-CTATGAAATTTTAATAACCATCTTA
*
11854 TGAAATTTTAATAACTTCCTCATGAAATTATAATAACCATCTTA
1 TGAAATTTTAATAACTTCCT-ATGAAATTTTAATAACCATCTTA
*
11898 TGAAATTTTGATAA
1 TGAAATTTTAATAA
11912 TCACGAAGAG
Statistics
Matches: 77, Mismatches: 22, Indels: 8
0.72 0.21 0.07
Matches are distributed among these distances:
43 2 0.03
44 47 0.61
45 3 0.04
46 25 0.32
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.38
Consensus pattern (43 bp):
TGAAATTTTAATAACTTCCTATGAAATTTTAATAACCATCTTA
Found at i:13059 original size:374 final size:365
Alignment explanation
Indices: 12376--13119 Score: 1215
Period size: 374 Copynumber: 2.0 Consensus size: 365
12366 ATAATAAATT
**
12376 TTAATATTATAAATTTAGAAATATATTTGAAAAAAGGTACAAAAACATAAAGTTTTCCATTATTC
1 TTAATATTATAAATTTAGAAATATATTTGAAAAAAGGTACAAAAACATAAAACTTTCCATTATTC
*
12441 GTACTTTTGTATATGGTATAGATTAATTATTAAAAAAACACTATTATAATCCCTTGTATGGTTTT
66 GTACTTTTGTATATAGTATAGATTAATTATTAAAAAAACACTATTATAATCCCTTGTATGGTTTT
12506 GAAGCCAAAAAAAATCCCTTGTATGGTTTTGGATTTGAAGCATATTTCATCAATTCAAACGTAAG
131 GAAGCCAAAAAAAATCCCTTGTA--G-TTTGGATTTGAAGCATATTTCATCAATTCAAACGTAAG
*
12571 CAGAGTGGATATTGAATTGTAAATGACTTAACTTTTTCATTGCGACAAATAAGAGTAAGATGGCT
193 CAGAATGGATATTGAATTGTAAATGACTTAACTTTTTCATTGCGACAAATAAGAGTAAGATGGCT
* *
12636 TATAGTTTTTAGCTTCAAAACAAATTCAAAGGAATTGATTTAGCTCTTGAACTAAAGACAATCAA
258 TACAGTTTTTAGCTTCAAAACAAATTCAAAGGAATTGATTTAACTCTTGAACTAAAGACAATCAA
12701 GGCTTGTACACAATTTCTCAGATAATATAGAAGTACAAATTAG
323 GGCTTGTACACAATTTCTCAGATAATATAGAAGTACAAATTAG
*
12744 TTAATATTATCAATTTAGAAATATATTTGAAAAAA-GTAC-AAAACATAAAACTTTCCATTATTC
1 TTAATATTATAAATTTAGAAATATATTTGAAAAAAGGTACAAAAACATAAAACTTTCCATTATTC
12807 GTACTTTTGTATATATAGTATAGATTAATTATTAAAAAAACACTATTATAATCCCTTGTATGGTT
66 GTACTTTTG--TATATAGTATAGATTAATTATTAAAAAAACACTATTATAATCCCTTGTATGGTT
*
12872 TTGATGCCAAAAAAAAATCCCTTGTA-TTTGGATTTGAAGCATATTTCATCAATTCAAACGTAAG
129 TTGAAGCC-AAAAAAAATCCCTTGTAGTTTGGATTTGAAGCATATTTCATCAATTCAAACGTAAG
*
12936 TATACAACTTATAATGGATATTGAATTGTAAATGACTTAACTTTTTCATTGCGACAAATAAGAGT
193 -------C--AGAATGGATATTGAATTGTAAATGACTTAACTTTTTCATTGCGACAAATAAGAGT
* *
13001 AAGATGGCTTACAGTTTTTAGTTTCAAAACAAATTCGAAGGAATTGATTTAACTCTTGAACTAAA
249 AAGATGGCTTACAGTTTTTAGCTTCAAAACAAATTCAAAGGAATTGATTTAACTCTTGAACTAAA
* *
13066 GATAATCAAGGCTTGTACACAATTTCTCAGATAATATAGAAGTATAAATTAG
314 GACAATCAAGGCTTGTACACAATTTCTCAGATAATATAGAAGTACAAATTAG
13118 TT
1 TT
13120 TGAAATTTGT
Statistics
Matches: 351, Mismatches: 13, Indels: 18
0.92 0.03 0.05
Matches are distributed among these distances:
365 38 0.11
366 31 0.09
367 4 0.01
368 94 0.27
369 17 0.05
372 1 0.00
374 166 0.47
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (365 bp):
TTAATATTATAAATTTAGAAATATATTTGAAAAAAGGTACAAAAACATAAAACTTTCCATTATTC
GTACTTTTGTATATAGTATAGATTAATTATTAAAAAAACACTATTATAATCCCTTGTATGGTTTT
GAAGCCAAAAAAAATCCCTTGTAGTTTGGATTTGAAGCATATTTCATCAATTCAAACGTAAGCAG
AATGGATATTGAATTGTAAATGACTTAACTTTTTCATTGCGACAAATAAGAGTAAGATGGCTTAC
AGTTTTTAGCTTCAAAACAAATTCAAAGGAATTGATTTAACTCTTGAACTAAAGACAATCAAGGC
TTGTACACAATTTCTCAGATAATATAGAAGTACAAATTAG
Found at i:15741 original size:20 final size:20
Alignment explanation
Indices: 15716--15754 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
15706 CTAATGTGAA
15716 TTACTAAATACCGCCCCCTT
1 TTACTAAATACCGCCCCCTT
**
15736 TTACTAGCTACCGCCCCCT
1 TTACTAAATACCGCCCCCT
15755 CTTGGACTAT
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:0.21, C:0.44, G:0.08, T:0.28
Consensus pattern (20 bp):
TTACTAAATACCGCCCCCTT
Found at i:16230 original size:33 final size:33
Alignment explanation
Indices: 16121--16222 Score: 159
Period size: 33 Copynumber: 3.1 Consensus size: 33
16111 AAGAAGAACA
*
16121 GCGGGTCGCGACCCGCCACGGTCCGGGTCGTGC
1 GCGGGTCGCGACCCGCCACGGTCCGGGTCGCGC
* * *
16154 GCGGGTCGTGACCTGCCACGGTCCCGGTCGCGC
1 GCGGGTCGCGACCCGCCACGGTCCGGGTCGCGC
*
16187 GCGGGTCGCGACCCGCCACGGTTCGGGTCGCGC
1 GCGGGTCGCGACCCGCCACGGTCCGGGTCGCGC
16220 GCG
1 GCG
16223 ACCCGCGATC
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 61 1.00
ACGTcount: A:0.06, C:0.39, G:0.42, T:0.13
Consensus pattern (33 bp):
GCGGGTCGCGACCCGCCACGGTCCGGGTCGCGC
Found at i:17016 original size:93 final size:93
Alignment explanation
Indices: 16857--17037 Score: 263
Period size: 93 Copynumber: 1.9 Consensus size: 93
16847 AACCTTCAAC
16857 TTTCTTAACATTTTCTATATAATTTTACATGGTGCCCACCCTTACATGGTCCTAGATGCCCACCC
1 TTTCTTAACATTTTCTATATAATTTTACATGGTGCCCACCCTTACATGGTCCTAGATGCCCACCC
16922 TCAATTAATTAACTCGTCAAAATGCTCA
66 TCAATTAATTAACTCGTCAAAATGCTCA
* * * ** ** **
16950 TTTCTTAATATTTTGTATGTAATTTTACATGGTGTTCACCCTTATTTGGTCCTAGATGTTCACCC
1 TTTCTTAACATTTTCTATATAATTTTACATGGTGCCCACCCTTACATGGTCCTAGATGCCCACCC
* *
17015 TCAATTGATTAACTTGTCAAAAT
66 TCAATTAATTAACTCGTCAAAAT
17038 ATCTTTGAAT
Statistics
Matches: 77, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
93 77 1.00
ACGTcount: A:0.27, C:0.22, G:0.11, T:0.40
Consensus pattern (93 bp):
TTTCTTAACATTTTCTATATAATTTTACATGGTGCCCACCCTTACATGGTCCTAGATGCCCACCC
TCAATTAATTAACTCGTCAAAATGCTCA
Found at i:23332 original size:1 final size:1
Alignment explanation
Indices: 23326--23351 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
23316 TCCGTTTAGA
23326 GGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGG
23352 AAAAGAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:23380 original size:2 final size:2
Alignment explanation
Indices: 23375--23399 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
23365 AAAAGAAGAA
23375 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
23400 AGATACCGAA
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:32350 original size:156 final size:155
Alignment explanation
Indices: 32043--32406 Score: 423
Period size: 156 Copynumber: 2.3 Consensus size: 155
32033 GAGCCTCTCA
* * *
32043 CCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGAGCTGAAA
1 CCTCAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTCAACGAGCTG-AA
** * * * *
32108 TTTTGTCAAGAGACTTAGATTATCTCCATGAGACTATGGAAAATATTCTAAGTAAAACCGAGCTC
65 TTTTCACAAGAGACTTAGATTATCTCCATAAGACTATAGAAAAAATTCTAAGTAAAACCGAACTC
* * * *
32173 CCCTTGATGGTGAACTAGGTTTCTCT
130 CCCTAGATAGAGAACTAGGTTTCACT
* *
32199 CC-CTGAGTTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTC-CAACGAAGCTG-
1 CCTC-AAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTCAACG-AGCTGA
*
32261 ATTTTCCACAAGTAGGCTTAGATTATCTCCATAA-AGCTATAGAAAAAATTCTAAGTAAAACCGA
64 ATTTT-CACAAG-AGACTTAGATTATCTCCATAAGA-CTATAGAAAAAATTCTAAGTAAAACCGA
* * * *
32325 ACT-CTCTAGCATAGAGAAGTTGGTTTGACT
126 ACTCCCCTAG-ATAGAGAACTAGGTTTCACT
** *
32355 CCTCAAATTGTCCTTATTTGAAAAACTAGCATAAGTTTTTCATACTAAGTCT
1 CCTCAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCT
32407 GTTCGAGATG
Statistics
Matches: 175, Mismatches: 25, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
154 5 0.03
155 13 0.07
156 156 0.89
157 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (155 bp):
CCTCAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTCAACGAGCTGAAT
TTTCACAAGAGACTTAGATTATCTCCATAAGACTATAGAAAAAATTCTAAGTAAAACCGAACTCC
CCTAGATAGAGAACTAGGTTTCACT
Found at i:33191 original size:7 final size:7
Alignment explanation
Indices: 33179--33207 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
33169 ATTTATTTAG
33179 TATAATA
1 TATAATA
33186 TATAATA
1 TATAATA
33193 TATAATA
1 TATAATA
33200 TATAATA
1 TATAATA
33207 T
1 T
33208 TTGTAGAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (7 bp):
TATAATA
Found at i:34276 original size:17 final size:16
Alignment explanation
Indices: 34236--34286 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 16
34226 CATATAATCT
*
34236 TTGATCACCGGTGATC
1 TTGATCACAGGTGATC
34252 TTGCATCACAGGTGATC
1 TTG-ATCACAGGTGATC
34269 TTAGATCACTA-GTGATC
1 TT-GATCAC-AGGTGATC
34286 T
1 T
34287 GGGGGGTGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
16 3 0.10
17 26 0.84
18 2 0.06
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.33
Consensus pattern (16 bp):
TTGATCACAGGTGATC
Found at i:35501 original size:17 final size:16
Alignment explanation
Indices: 35453--35506 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
35443 CTAATGGGGA
*
35453 TAATTATGTAAAACAT
1 TAATTATGTAAAAAAT
* *
35469 TAATTTATATATAAAAT
1 TAA-TTATGTAAAAAAT
35486 TAATTATGTAACAAAAAT
1 TAATTATGT-A-AAAAAT
35504 TAA
1 TAA
35507 GTGAAAAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
16 8 0.27
17 14 0.47
18 8 0.27
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.39
Consensus pattern (16 bp):
TAATTATGTAAAAAAT
Found at i:35779 original size:30 final size:29
Alignment explanation
Indices: 35707--35782 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
35697 ACTTATAGCG
* *
35707 TTTGGA-AGTTTTGCCCCATGAATTTTAAT
1 TTTGGACAG-TTTGCCCCATGAACTTCAAT
* *
35736 TTTGGACATTTTGCCCCTTGAACTTCAAT
1 TTTGGACAGTTTGCCCCATGAACTTCAAT
35765 TTTGGGACAGTTTGCCCC
1 TTT-GGACAGTTTGCCCC
35783 CTCAGCCTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
29 26 0.65
30 14 0.35
ACGTcount: A:0.20, C:0.21, G:0.18, T:0.41
Consensus pattern (29 bp):
TTTGGACAGTTTGCCCCATGAACTTCAAT
Found at i:39361 original size:24 final size:24
Alignment explanation
Indices: 39323--39620 Score: 416
Period size: 24 Copynumber: 12.0 Consensus size: 24
39313 AGTTCCATAT
**
39323 GCCATGTGTGGACTTGGTTTTCATGA
1 GCCATG-G-GGACTTGGTTGCCATGA
39349 GCCATGGGGACTTGGTTGCCATGA
1 GCCATGGGGACTTGGTTGCCATGA
39373 GCCATGTGGGGACTTGGTTGCCATGA
1 GCCA--TGGGGACTTGGTTGCCATGA
*
39399 GCCGTGGGGACTTGGTTGCCATGA
1 GCCATGGGGACTTGGTTGCCATGA
*
39423 GCCGTGGGGACTTGGTTGCCATGA
1 GCCATGGGGACTTGGTTGCCATGA
*
39447 GTCATGGGGACTTGGTTGCCATGA
1 GCCATGGGGACTTGGTTGCCATGA
*
39471 GCCATGTGGGGACTTGGTTGCAATGA
1 GCCA--TGGGGACTTGGTTGCCATGA
39497 GCCATGGGGACTTGGTTGCCATGA
1 GCCATGGGGACTTGGTTGCCATGA
*
39521 GCCATGTGGGGACTCGGTTGCCATGA
1 GCCA--TGGGGACTTGGTTGCCATGA
*
39547 GCCATGGGGACTCGGTTGCCATGA
1 GCCATGGGGACTTGGTTGCCATGA
* *
39571 GCCATGGGGAATTGGTTGCGATGA
1 GCCATGGGGACTTGGTTGCCATGA
39595 GCCATGTGGGGACTTGGTTGCCATGA
1 GCCA--TGGGGACTTGGTTGCCATGA
39621 TACGGCACAT
Statistics
Matches: 250, Mismatches: 14, Indels: 16
0.89 0.05 0.06
Matches are distributed among these distances:
24 156 0.62
25 1 0.00
26 93 0.37
ACGTcount: A:0.16, C:0.19, G:0.38, T:0.27
Consensus pattern (24 bp):
GCCATGGGGACTTGGTTGCCATGA
Found at i:39386 original size:50 final size:50
Alignment explanation
Indices: 39323--39620 Score: 460
Period size: 50 Copynumber: 6.0 Consensus size: 50
39313 AGTTCCATAT
* **
39323 GCCATGTGTGGACTTGGTTTTCATGAGCCATGGGGACTTGGTTGCCATGA
1 GCCATGTGGGGACTTGGTTGCCATGAGCCATGGGGACTTGGTTGCCATGA
*
39373 GCCATGTGGGGACTTGGTTGCCATGAGCCGTGGGGACTTGGTTGCCATGA
1 GCCATGTGGGGACTTGGTTGCCATGAGCCATGGGGACTTGGTTGCCATGA
*
39423 GCC--GTGGGGACTTGGTTGCCATGAGTCATGGGGACTTGGTTGCCATGA
1 GCCATGTGGGGACTTGGTTGCCATGAGCCATGGGGACTTGGTTGCCATGA
*
39471 GCCATGTGGGGACTTGGTTGCAATGAGCCATGGGGACTTGGTTGCCATGA
1 GCCATGTGGGGACTTGGTTGCCATGAGCCATGGGGACTTGGTTGCCATGA
* *
39521 GCCATGTGGGGACTCGGTTGCCATGAGCCATGGGGACTCGGTTGCCATGA
1 GCCATGTGGGGACTTGGTTGCCATGAGCCATGGGGACTTGGTTGCCATGA
* *
39571 GCCA--TGGGGAATTGGTTGCGATGAGCCATGTGGGGACTTGGTTGCCATGA
1 GCCATGTGGGGACTTGGTTGCCATGAGCCA--TGGGGACTTGGTTGCCATGA
39621 TACGGCACAT
Statistics
Matches: 229, Mismatches: 15, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
48 67 0.29
50 162 0.71
ACGTcount: A:0.16, C:0.19, G:0.38, T:0.27
Consensus pattern (50 bp):
GCCATGTGGGGACTTGGTTGCCATGAGCCATGGGGACTTGGTTGCCATGA
Found at i:39415 original size:74 final size:74
Alignment explanation
Indices: 39332--39620 Score: 456
Period size: 74 Copynumber: 3.9 Consensus size: 74
39322 TGCCATGTGT
**
39332 GGACTTGGTTTTCATGAGCCATGGGGACTTGGTTGCCATGAGCCATGTGGGGACTTGGTTGCCAT
1 GGACTTGGTTGCCATGAGCCATGGGGACTTGGTTGCCATGAGCCATGTGGGGACTTGGTTGCCAT
39397 GAGCCGTGG
66 GAGCCGTGG
* *
39406 GGACTTGGTTGCCATGAGCCGTGGGGACTTGGTTGCCATGAGTCA--TGGGGACTTGGTTGCCAT
1 GGACTTGGTTGCCATGAGCCATGGGGACTTGGTTGCCATGAGCCATGTGGGGACTTGGTTGCCAT
39469 GAGCCATGTGG
66 GAGCC--GTGG
* *
39480 GGACTTGGTTGCAATGAGCCATGGGGACTTGGTTGCCATGAGCCATGTGGGGACTCGGTTGCCAT
1 GGACTTGGTTGCCATGAGCCATGGGGACTTGGTTGCCATGAGCCATGTGGGGACTTGGTTGCCAT
*
39545 GAGCCATGG
66 GAGCCGTGG
* * *
39554 GGACTCGGTTGCCATGAGCCATGGGGAATTGGTTGCGATGAGCCATGTGGGGACTTGGTTGCCAT
1 GGACTTGGTTGCCATGAGCCATGGGGACTTGGTTGCCATGAGCCATGTGGGGACTTGGTTGCCAT
39619 GA
66 GA
39621 TACGGCACAT
Statistics
Matches: 197, Mismatches: 14, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
72 23 0.12
74 152 0.77
76 22 0.11
ACGTcount: A:0.16, C:0.19, G:0.38, T:0.26
Consensus pattern (74 bp):
GGACTTGGTTGCCATGAGCCATGGGGACTTGGTTGCCATGAGCCATGTGGGGACTTGGTTGCCAT
GAGCCGTGG
Done.