Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009412.1 Corchorus capsularis cultivar CVL-1 contig09433, 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: 32540
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1058 original size:38 final size:38
Alignment explanation
Indices: 1006--1195 Score: 271
Period size: 38 Copynumber: 5.1 Consensus size: 38
996 ACCCCAATAA
*
1006 AATTAAG-GACCAAAGTAATAGTAATAAGTAAAATTGAT
1 AATTAAGAG-CCAAAGTAATAGTAATCAGTAAAATTGAT
* * *
1044 AATTAATAGTCAAAGTAATAGTAATCCGTAAAATTGAT
1 AATTAAGAGCCAAAGTAATAGTAATCAGTAAAATTGAT
* **
1082 AATTAAGAGTC-AAGGGAT--TAATCAGTAAAATTGAT
1 AATTAAGAGCCAAAGTAATAGTAATCAGTAAAATTGAT
1117 AATTAAGAGCCAAAGTAATAGTAATCAGTAAAATTGAT
1 AATTAAGAGCCAAAGTAATAGTAATCAGTAAAATTGAT
*
1155 AATTAAGAGCCAAAGTAATAGCAATCAGTAAAATTGAT
1 AATTAAGAGCCAAAGTAATAGTAATCAGTAAAATTGAT
1193 AAT
1 AAT
1196 CAAGGGTCAA
Statistics
Matches: 136, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
35 26 0.19
36 5 0.04
37 5 0.04
38 99 0.73
39 1 0.01
ACGTcount: A:0.49, C:0.07, G:0.16, T:0.27
Consensus pattern (38 bp):
AATTAAGAGCCAAAGTAATAGTAATCAGTAAAATTGAT
Found at i:1117 original size:73 final size:73
Alignment explanation
Indices: 1027--1273 Score: 284
Period size: 73 Copynumber: 3.3 Consensus size: 73
1017 AAAGTAATAG
* * *
1027 TAATAAGTAAAATTGATAATTAATAGTCAAAGTAATAGTAATCCGTAAAATTGATAATTAAGAGT
1 TAATCAGTAAAATTGATAATTAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
1092 CAAGGGAT
66 CAAGGGAT
* *
1100 TAATCAGTAAAATTGATAATTAAGAGCCAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGC
1 TAATCAGTAAAATTGATAATTAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
**
1165 CAAAGTAAT
66 C-AAGGGAT
* * * * * *
1174 AGCAATCAGTAAAATTGATAATCAAGGGTCAAGGTAAAAATAGTAATCAG-CAAA-TCAGTAATT
1 --TAATCAGTAAAATTGATAATTAAGAGTCAAAGT---AATAGTAATCAGTAAAATTGA-TAATT
1237 AAGAGTCAAGGGAT
60 AAGAGTCAAGGGAT
*
1251 TAATCAGT-AAATTGATACTTAAG
1 TAATCAGTAAAATTGATAATTAAG
1274 GGAGAGAGTA
Statistics
Matches: 147, Mismatches: 20, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
73 61 0.41
74 18 0.12
75 7 0.05
76 28 0.19
77 7 0.05
78 14 0.10
79 12 0.08
ACGTcount: A:0.48, C:0.08, G:0.17, T:0.27
Consensus pattern (73 bp):
TAATCAGTAAAATTGATAATTAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
CAAGGGAT
Found at i:1205 original size:111 final size:111
Alignment explanation
Indices: 1006--1207 Score: 325
Period size: 111 Copynumber: 1.8 Consensus size: 111
996 ACCCCAATAA
* * * *
1006 AATTAAGGACCAAAGTAATAGTAATAAGTAAAATTGATAATTAATAGTCAAAGTAATAGTAATCC
1 AATTAAGGACCAAAGTAATAGTAATAAGTAAAATTGATAATTAAGAGCCAAAGTAATAGCAATCA
*
1071 GTAAAATTGATAATTAAGAGTCAAGGGATTAATCAGTAAAATTGAT
66 GTAAAATTGATAATCAAGAGTCAAGGGATTAATCAGTAAAATTGAT
*
1117 AATTAA-GAGCCAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGCCAAAGTAATAGCAATC
1 AATTAAGGA-CCAAAGTAATAGTAATAAGTAAAATTGATAATTAAGAGCCAAAGTAATAGCAATC
*
1181 AGTAAAATTGATAATCAAGGGTCAAGG
65 AGTAAAATTGATAATCAAGAGTCAAGG
1208 TAAAAATAGT
Statistics
Matches: 83, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
110 2 0.02
111 81 0.98
ACGTcount: A:0.49, C:0.08, G:0.17, T:0.26
Consensus pattern (111 bp):
AATTAAGGACCAAAGTAATAGTAATAAGTAAAATTGATAATTAAGAGCCAAAGTAATAGCAATCA
GTAAAATTGATAATCAAGAGTCAAGGGATTAATCAGTAAAATTGAT
Found at i:1326 original size:32 final size:33
Alignment explanation
Indices: 1290--1364 Score: 125
Period size: 32 Copynumber: 2.3 Consensus size: 33
1280 AGTAAGAGAG
1290 TAATCAGTAATTAAGAAAGGAAATAAAAA-AAT
1 TAATCAGTAATTAAGAAAGGAAATAAAAAGAAT
* *
1322 TAATCAGTAATTAAGAAAGGAAGTAAAAAGGAT
1 TAATCAGTAATTAAGAAAGGAAATAAAAAGAAT
1355 TAATCAGTAA
1 TAATCAGTAA
1365 ATTAGTAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 28 0.70
33 12 0.30
ACGTcount: A:0.57, C:0.04, G:0.16, T:0.23
Consensus pattern (33 bp):
TAATCAGTAATTAAGAAAGGAAATAAAAAGAAT
Found at i:1636 original size:14 final size:13
Alignment explanation
Indices: 1614--1699 Score: 59
Period size: 14 Copynumber: 6.3 Consensus size: 13
1604 CAGTAAAAAG
1614 GTAAAAGTAATCA
1 GTAAAAGTAATCA
1627 GTAAAGAGTAATCA
1 GTAAA-AGTAATCA
**
1641 GTAAAAAGTAAAAA
1 GT-AAAAGTAATCA
* *
1655 TGGCAAAGAGTAGT-A
1 --GTAAA-AGTAATCA
*
1670 -AAAAAGTAATCA
1 GTAAAAGTAATCA
1682 GTAAGAAGTAATCA
1 GTAA-AAGTAATCA
1696 GTAA
1 GTAA
1700 GAAGGTCAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
11 5 0.09
12 4 0.07
13 7 0.12
14 29 0.51
15 7 0.12
16 5 0.09
ACGTcount: A:0.55, C:0.06, G:0.20, T:0.20
Consensus pattern (13 bp):
GTAAAAGTAATCA
Found at i:1700 original size:14 final size:14
Alignment explanation
Indices: 1673--1703 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1663 AGTAGTAAAA
1673 AAGTAATCAGTAAG
1 AAGTAATCAGTAAG
1687 AAGTAATCAGTAAG
1 AAGTAATCAGTAAG
1701 AAG
1 AAG
1704 GTCAAAAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.52, C:0.06, G:0.23, T:0.19
Consensus pattern (14 bp):
AAGTAATCAGTAAG
Found at i:1742 original size:42 final size:41
Alignment explanation
Indices: 1695--1851 Score: 165
Period size: 42 Copynumber: 3.7 Consensus size: 41
1685 AGAAGTAATC
* * *
1695 AGTAAGAAGGTCAAAAATGGTATCAAGTGAAATATGGTATTG
1 AGTAA-AAGGTCAAAAATGGTATCAAGTAAAAAATGGTATTA
*
1737 AGTAAGAAGGTCAAAAAATGGTGT-AGAGTAAAAAATGGTATTA
1 AGTAA-AAGGTC-AAAAATGGTATCA-AGTAAAAAATGGTATTA
* * *
1780 AGTAAAAGAGT-AAAGAATGGTATTAATTAAAAAATGGTGTTA
1 AGTAAAAG-GTCAAA-AATGGTATCAAGTAAAAAATGGTATTA
*
1822 AGTAAAAGGGTCAAAAATGGTATCCAGTAA
1 AGTAAAA-GGTCAAAAATGGTATCAAGTAA
1852 GTAAGAGATG
Statistics
Matches: 98, Mismatches: 10, Indels: 14
0.80 0.08 0.11
Matches are distributed among these distances:
41 3 0.03
42 59 0.60
43 36 0.37
ACGTcount: A:0.47, C:0.04, G:0.24, T:0.25
Consensus pattern (41 bp):
AGTAAAAGGTCAAAAATGGTATCAAGTAAAAAATGGTATTA
Found at i:1791 original size:25 final size:25
Alignment explanation
Indices: 1761--1811 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
1751 AAAATGGTGT
1761 AGAGTAAAAAATGGTATTAAGTAAA
1 AGAGTAAAAAATGGTATTAAGTAAA
* *
1786 AGAGTAAAGAATGGTATTAATTAAA
1 AGAGTAAAAAATGGTATTAAGTAAA
1811 A
1 A
1812 AATGGTGTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.55, C:0.00, G:0.20, T:0.25
Consensus pattern (25 bp):
AGAGTAAAAAATGGTATTAAGTAAA
Found at i:1815 original size:17 final size:17
Alignment explanation
Indices: 1788--1828 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1778 TAAGTAAAAG
*
1788 AGTAAAGAATGGTATTA
1 AGTAAAAAATGGTATTA
* *
1805 ATTAAAAAATGGTGTTA
1 AGTAAAAAATGGTATTA
1822 AGTAAAA
1 AGTAAAA
1829 GGGTCAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.20, T:0.29
Consensus pattern (17 bp):
AGTAAAAAATGGTATTA
Found at i:1914 original size:63 final size:61
Alignment explanation
Indices: 1792--1914 Score: 142
Period size: 62 Copynumber: 2.0 Consensus size: 61
1782 TAAAAGAGTA
* * **
1792 AAGAATGGTATTAATTAAAAAATGGTGTTAAGTAAAAGGGTCAAAAATGGTATCCAGTAAGT
1 AAGAATGGTATTAA-TAAAAAATGGTATTAAGTAAAAGAGTCAAAAATGGTATAAAGTAAGT
*
1854 AAGAGATGGTATTAA-ACAAAAATGGTATTAAGTAAAAGAGTAAGAAAAATGGTA-AAAGTAA
1 AAGA-ATGGTATTAATA-AAAAATGGTATTAAGTAAAAGAGT--CAAAAATGGTATAAAGTAA
1915 AAATGATAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
61 1 0.02
62 26 0.50
63 15 0.29
64 10 0.19
ACGTcount: A:0.50, C:0.03, G:0.22, T:0.24
Consensus pattern (61 bp):
AAGAATGGTATTAATAAAAAATGGTATTAAGTAAAAGAGTCAAAAATGGTATAAAGTAAGT
Found at i:1918 original size:15 final size:15
Alignment explanation
Indices: 1898--1928 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1888 AAAGAGTAAG
*
1898 AAAAATGGTAAAAGT
1 AAAAATGATAAAAGT
1913 AAAAATGATAAAAGT
1 AAAAATGATAAAAGT
1928 A
1 A
1929 GCAAAAGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.16, T:0.19
Consensus pattern (15 bp):
AAAAATGATAAAAGT
Found at i:7377 original size:6 final size:6
Alignment explanation
Indices: 7362--7391 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
7352 AAAAAGTTGT
7362 TGCC-C TGCCTC TGCCTC TGCCTC TGCCTC T
1 TGCCTC TGCCTC TGCCTC TGCCTC TGCCTC T
7392 TTGGTTAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.17
6 20 0.83
ACGTcount: A:0.00, C:0.50, G:0.17, T:0.33
Consensus pattern (6 bp):
TGCCTC
Found at i:15470 original size:21 final size:21
Alignment explanation
Indices: 15446--15489 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
15436 CAAAACTGGA
*
15446 TTGCTAAAT-ACCGCCTCATTT
1 TTGCT-AATCACCGCCCCATTT
*
15467 TTGCTATTCACCGCCCCATTT
1 TTGCTAATCACCGCCCCATTT
15488 TT
1 TT
15490 TACGTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.18, C:0.32, G:0.09, T:0.41
Consensus pattern (21 bp):
TTGCTAATCACCGCCCCATTT
Found at i:16094 original size:22 final size:22
Alignment explanation
Indices: 16052--16095 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
16042 TATTCATACG
* *
16052 AAATTGTGATAATCTTCCTATT
1 AAATTATGATAATCTACCTATT
16074 AAATTATGATAAT-TACACTATT
1 AAATTATGATAATCTAC-CTATT
16096 TTTTATGACG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (22 bp):
AAATTATGATAATCTACCTATT
Found at i:16150 original size:60 final size:60
Alignment explanation
Indices: 16051--16192 Score: 221
Period size: 60 Copynumber: 2.3 Consensus size: 60
16041 ATATTCATAC
* * *
16051 GAAATTGTGATAATCTTCCTATTAAATTATGATAATTACACTATTTTTTATGACGTCCTTAT
1 GAAATTTTGATAATCTTCC--TGAAATTATGATAATTACACTATTTTTTATAACGTCCTTAT
*
16113 GAAATTTTAATAATCTTCCTGAAATTATGATAATTACACTATTTTTTATAACGTCCTTAT
1 GAAATTTTGATAATCTTCCTGAAATTATGATAATTACACTATTTTTTATAACGTCCTTAT
*
16173 GAAATTTTGATAACCTTCCT
1 GAAATTTTGATAATCTTCCT
16193 ATGAAATTTC
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
60 57 0.77
62 17 0.23
ACGTcount: A:0.33, C:0.14, G:0.08, T:0.44
Consensus pattern (60 bp):
GAAATTTTGATAATCTTCCTGAAATTATGATAATTACACTATTTTTTATAACGTCCTTAT
Found at i:16185 original size:22 final size:22
Alignment explanation
Indices: 16155--16362 Score: 74
Period size: 22 Copynumber: 9.5 Consensus size: 22
16145 ATTACACTAT
*
16155 TTTTTATAA-CGTCCTTATGAAA
1 TTTTGATAACCGTCC-TATGAAA
*
16177 TTTTGATAACCTTCCTATGAAA
1 TTTTGATAACCGTCCTATGAAA
** * *
16199 TTTCAATAA-CGATACTATGGAA
1 TTTTGATAACCG-TCCTATGAAA
* * **
16221 TTTTGAGAACCTTTTTAT--AA
1 TTTTGATAACCGTCCTATGAAA
** * *
16241 TTTTTTTAACCTTCTTATGAAA
1 TTTTGATAACCGTCCTATGAAA
* * *
16263 TTTTGTTAACC-TCCCTAAGGAA
1 TTTTGATAACCGT-CCTATGAAA
*
16285 TTTTGA-AGATC-TCACTATGAAA
1 TTTTGATA-ACCGTC-CTATGAAA
**
16307 TTTTGATAACCAACACTAT-AAGA
1 TTTTGATAACCGTC-CTATGAA-A
* *
16330 TGTTGATAACC-TCCATATGATA
1 TTTTGATAACCGTCC-TATGAAA
*
16352 TATTGATAACC
1 TTTTGATAACC
16363 ACGTTAAGGA
Statistics
Matches: 142, Mismatches: 31, Indels: 26
0.71 0.16 0.13
Matches are distributed among these distances:
20 16 0.11
21 5 0.04
22 97 0.68
23 24 0.17
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.40
Consensus pattern (22 bp):
TTTTGATAACCGTCCTATGAAA
Found at i:16251 original size:20 final size:21
Alignment explanation
Indices: 16219--16274 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
16209 GATACTATGG
** *
16219 AATTTTGAGAACCTTTTTAT-
1 AATTTTGTTAACCTTCTTATA
*
16239 AATTTTTTTAACCTTCTTATGA
1 AATTTTGTTAACCTTCTTAT-A
16261 AATTTTGTTAACCT
1 AATTTTGTTAACCT
16275 CCCTAAGGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 16 0.55
22 13 0.45
ACGTcount: A:0.29, C:0.12, G:0.07, T:0.52
Consensus pattern (21 bp):
AATTTTGTTAACCTTCTTATA
Found at i:16439 original size:22 final size:22
Alignment explanation
Indices: 16411--16710 Score: 183
Period size: 22 Copynumber: 13.8 Consensus size: 22
16401 GTAATCACTC
* *
16411 TGAAATTTTGATAATCACATTA
1 TGAAATTTTGATAACCTCATTA
* **
16433 TGAAATTGTGATAACCTCGCTA
1 TGAAATTTTGATAACCTCATTA
* *
16455 TGGAATTTTGATAAACCTTC-CTA
1 TGAAATTTTGAT-AACC-TCATTA
* * **
16478 TAAAATTTTGATAAATCTCCCTA
1 TGAAATTTTGAT-AACCTCATTA
* *
16501 TAAAATTTTGATAACCTCCTTA
1 TGAAATTTTGATAACCTCATTA
*
16523 TGAAATCTTGATAA---C--TA
1 TGAAATTTTGATAACCTCATTA
* **
16540 -CAAATTTTGATAACCTCCCTA
1 TGAAATTTTGATAACCTCATTA
**
16561 TGATTTTTTGATAACCTCATTA
1 TGAAATTTTGATAACCTCATTA
* *
16583 TGAAATTTTGTTAATCTC-TCTA
1 TGAAATTTTGATAACCTCAT-TA
* * *
16605 TGAAATTTTGATCTACAT-ACTA
1 TGAAATTTTGAT-AACCTCATTA
16627 TGAAATTTTGATAACCCTC-TTA
1 TGAAATTTTGATAA-CCTCATTA
* * *
16649 TGAAATTTTGA-AAACTAAACTA
1 TGAAATTTTGATAACCT-CATTA
*
16671 TGAAATTTTAATAACCTTCA-TA
1 TGAAATTTTGATAACC-TCATTA
*
16693 TGAAATTTTGATATCCTC
1 TGAAATTTTGATAACCTC
16711 CCTGAAATTT
Statistics
Matches: 219, Mismatches: 41, Indels: 37
0.74 0.14 0.12
Matches are distributed among these distances:
16 11 0.05
17 2 0.01
19 2 0.01
20 2 0.01
21 8 0.04
22 149 0.68
23 42 0.19
24 3 0.01
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCATTA
Found at i:16881 original size:58 final size:58
Alignment explanation
Indices: 16810--16919 Score: 148
Period size: 58 Copynumber: 1.9 Consensus size: 58
16800 TACCACTATG
* * *
16810 AAATTTTGGTAATCACATTTTAAAAATTTGATAACCTCTCTATCAAATTTTGTTGTCC
1 AAATTTTGATAATCACATTATAAAAATTTGATAACCTCACTATCAAATTTTGTTGTCC
** * * *
16868 AAATTTTGATAATCACATTATGTAATTTTGATAACCTCACTTTGAAATTTTG
1 AAATTTTGATAATCACATTATAAAAATTTGATAACCTCACTATCAAATTTTG
16920 AAATTTGACC
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
58 44 1.00
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.44
Consensus pattern (58 bp):
AAATTTTGATAATCACATTATAAAAATTTGATAACCTCACTATCAAATTTTGTTGTCC
Found at i:16916 original size:22 final size:22
Alignment explanation
Indices: 16868--16920 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
16858 TTTGTTGTCC
16868 AAATTTTGATAATCACATTATG
1 AAATTTTGATAATCACATTATG
*
16890 TAATTTTGATAACCTCAC-TT-TG
1 AAATTTTGATAA--TCACATTATG
16912 AAATTTTGA
1 AAATTTTGA
16921 AATTTGACCA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 21 0.78
23 2 0.07
24 4 0.15
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.43
Consensus pattern (22 bp):
AAATTTTGATAATCACATTATG
Found at i:17019 original size:37 final size:37
Alignment explanation
Indices: 16978--17073 Score: 120
Period size: 38 Copynumber: 2.6 Consensus size: 37
16968 ATCTAAGACC
* * * *
16978 AAATAGGACGTTGGAGACGAAGACAAAAAGTAAAATT
1 AAATACGACGTTGGAAACAAAGACAAAAAGCAAAATT
* *
17015 AAATACAACGATTGGAAACAAAGACAAAAGGCAAAATT
1 AAATACGACG-TTGGAAACAAAGACAAAAAGCAAAATT
*
17053 AAATATGACGTTGGAAACAAA
1 AAATACGACGTTGGAAACAAA
17074 AAGTCAAATT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
37 19 0.38
38 31 0.62
ACGTcount: A:0.54, C:0.10, G:0.20, T:0.16
Consensus pattern (37 bp):
AAATACGACGTTGGAAACAAAGACAAAAAGCAAAATT
Found at i:17231 original size:31 final size:31
Alignment explanation
Indices: 17196--17261 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
17186 TGGCAATTTA
* * *
17196 GAAATATGTTTTTTAAAAT-AGGGTACAATTG
1 GAAATATG-TTTTAAAAATAAGGATACAATCG
17227 GAAATATGTTTTAAAAATAAGGATACAATCG
1 GAAATATGTTTTAAAAATAAGGATACAATCG
17258 GAAA
1 GAAA
17262 ACATAAAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 9 0.29
31 22 0.71
ACGTcount: A:0.45, C:0.05, G:0.18, T:0.32
Consensus pattern (31 bp):
GAAATATGTTTTAAAAATAAGGATACAATCG
Found at i:17863 original size:15 final size:15
Alignment explanation
Indices: 17845--17893 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
17835 AAATTAACTG
17845 AAACTGACCTAACCC
1 AAACTGACCTAACCC
**
17860 AAACTTTCCTTAACCC
1 AAACTGACC-TAACCC
* *
17876 GAACTGACCTAACTC
1 AAACTGACCTAACCC
17891 AAA
1 AAA
17894 TCTAATCCGA
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
15 14 0.54
16 12 0.46
ACGTcount: A:0.39, C:0.35, G:0.06, T:0.20
Consensus pattern (15 bp):
AAACTGACCTAACCC
Found at i:25203 original size:350 final size:351
Alignment explanation
Indices: 24558--25252 Score: 1338
Period size: 350 Copynumber: 2.0 Consensus size: 351
24548 AGATCGAGCA
*
24558 GCAACCCTCTCATTCCACAGAGCTATCTCTCGATCAATGGTTTTTCCTTCATACTTATCTGCTCA
1 GCAACCCTCTCATTCCACAGAGCTATCTCTCAATCAATGGTTTTTCCTTCATACTTATCTGCTCA
24623 TGTGCTCTCCGAAAATTATCTGGTACGCTTTGCAGAGTTTAAGCTAGTGTTTTTCCAAACACTCT
66 TGTGCTCTCCGAAAATTATCTGGTACGCTTTGCAGAGTTTAAGCTAGTGTTTTTCCAAACA--C-
24688 CTCAATGTCTGGATCAATCCCTTGTCATGCCTGATTATCCTCAATTGCAAGCACATTTGAAGTGG
128 CTCAATGTCTGGATCAATCCCTTGTCATGCCTGATTATCCTCAATTGCAAGCACATTTGAAGTGG
24753 AAATTTCTTCCATTTAATTATTTGTTTGTCTTGTCTGTGGAGGCATGGCAACAACTCCCTAGTGT
193 AAATTTCTTCCATTTAATTATTTGTTTGTCTTGTCTGTGGAGGCATGGCAACAACTCCCTAGTGT
24818 CCCACCAGGTGTGTCAAAATTGTTTGATGGAAAATAAGTCTCCGAGGGTTCTAACCCTTAATGAT
258 CCCACCAGGTGTGTCAAAATTGTTTGATGGAAAATAAGTCTCCGAGGGTTCTAACCCTTAATGAT
24883 TACTTGCAAGAGTGGAGAGATGTTATAAT
323 TACTTGCAAGAGTGGAGAGATGTTATAAT
24912 GCAACCCTCTCATTCCACAGAGCTATCTCTCAATCAATGGTTTTTCCTTCATACTTATCTGCTCA
1 GCAACCCTCTCATTCCACAGAGCTATCTCTCAATCAATGGTTTTTCCTTCATACTTATCTGCTCA
*
24977 TGTGCTCTCCGAAAATTATCTGGTACGCTTTGTAGAGTTTAAGCTAGTGTTTTTCCAAACA-CTC
66 TGTGCTCTCCGAAAATTATCTGGTACGCTTTGCAGAGTTTAAGCTAGTGTTTTTCCAAACACCTC
25041 AATGTCTGGATCAATCCCTTGTCATGCCTGATTATCCTCAATTGCAAGCACATTTGAAGTGGAAA
131 AATGTCTGGATCAATCCCTTGTCATGCCTGATTATCCTCAATTGCAAGCACATTTGAAGTGGAAA
25106 TTTCTTCCATTTAATTATTTGTTTGTCTTGTCTGTGGAGGCATGGCAACAACTCCCTAGTGTCCC
196 TTTCTTCCATTTAATTATTTGTTTGTCTTGTCTGTGGAGGCATGGCAACAACTCCCTAGTGTCCC
25171 ACCAGGTGTGTCAAAATTGTTTGATGGAAAATAAGTCTCCGAGGGTTCTAACCCTTAATGATTAC
261 ACCAGGTGTGTCAAAATTGTTTGATGGAAAATAAGTCTCCGAGGGTTCTAACCCTTAATGATTAC
25236 TTGCAAGAGTGGAGAGA
326 TTGCAAGAGTGGAGAGA
25253 ATAATGCAAA
Statistics
Matches: 339, Mismatches: 2, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
350 215 0.63
354 124 0.37
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (351 bp):
GCAACCCTCTCATTCCACAGAGCTATCTCTCAATCAATGGTTTTTCCTTCATACTTATCTGCTCA
TGTGCTCTCCGAAAATTATCTGGTACGCTTTGCAGAGTTTAAGCTAGTGTTTTTCCAAACACCTC
AATGTCTGGATCAATCCCTTGTCATGCCTGATTATCCTCAATTGCAAGCACATTTGAAGTGGAAA
TTTCTTCCATTTAATTATTTGTTTGTCTTGTCTGTGGAGGCATGGCAACAACTCCCTAGTGTCCC
ACCAGGTGTGTCAAAATTGTTTGATGGAAAATAAGTCTCCGAGGGTTCTAACCCTTAATGATTAC
TTGCAAGAGTGGAGAGATGTTATAAT
Found at i:31357 original size:29 final size:30
Alignment explanation
Indices: 31322--31392 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
31312 CTTGGCAACA
***
31322 GGGCTTATTTGACTT-TTTTAAGAGTTCAG
1 GGGCTTATTTGACTTGAAATAAGAGTTCAG
* *
31351 GGGCTTATTTG-GTTGAAATAATAGTTCAG
1 GGGCTTATTTGACTTGAAATAAGAGTTCAG
31380 GGGCTTATTTGAC
1 GGGCTTATTTGAC
31393 GGTTCGGTGT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
28 2 0.06
29 32 0.94
ACGTcount: A:0.23, C:0.10, G:0.27, T:0.41
Consensus pattern (30 bp):
GGGCTTATTTGACTTGAAATAAGAGTTCAG
Done.