Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013888.1 Corchorus olitorius cultivar O-4 contig13921, 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: 23364
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Found at i:313 original size:22 final size:22
Alignment explanation
Indices: 283--382 Score: 105
Period size: 22 Copynumber: 4.5 Consensus size: 22
273 TCCAACGTAG
283 AAATATTGATAACCACTCTATAA
1 AAAT-TTGATAACCACTCTATAA
* *
306 AAATTTGATAACCTCAT-TAT-G
1 AAATTTGATAACCAC-TCTATAA
* *
327 AAATTTCGATAACCTCTCTATGA
1 AAATTT-GATAACCACTCTATAA
*
350 AAATTTGATAACCACACTATAA
1 AAATTTGATAACCACTCTATAA
*
372 AATTTTGATAA
1 AAATTTGATAA
383 TCATAATCTT
Statistics
Matches: 66, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
21 7 0.11
22 48 0.73
23 11 0.17
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (22 bp):
AAATTTGATAACCACTCTATAA
Found at i:346 original size:44 final size:43
Alignment explanation
Indices: 282--382 Score: 130
Period size: 44 Copynumber: 2.3 Consensus size: 43
272 CTCCAACGTA
* *
282 GAAATATTGATAACCACTCTATAAAAATTTGATAACCTCATTAT
1 GAAAT-TTGATAACCACTCTATAAAAATTTGATAACCACACTAT
* *
326 GAAATTTCGATAACCTCTCTATGAAAATTTGATAACCACACTAT
1 GAAATTT-GATAACCACTCTATAAAAATTTGATAACCACACTAT
*
370 AAAATTTTGATAA
1 GAAA-TTTGATAA
383 TCATAATCTT
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
43 2 0.04
44 45 0.90
45 3 0.06
ACGTcount: A:0.43, C:0.16, G:0.08, T:0.34
Consensus pattern (43 bp):
GAAATTTGATAACCACTCTATAAAAATTTGATAACCACACTAT
Found at i:507 original size:22 final size:22
Alignment explanation
Indices: 410--612 Score: 121
Period size: 22 Copynumber: 9.2 Consensus size: 22
400 TAAAAAAAAA
* *
410 TTGATAACCTTCCTTTGAAATT
1 TTGATAACCTTCATATGAAATT
* * *
432 TTAATAACCTAAT-AAATGTAATT
1 TTGATAACCT--TCATATGAAATT
*
455 TTGATAATCATTC-TATGAAATT
1 TTGATAA-CCTTCATATGAAATT
477 TTGATAACCTTCATATGAAATT
1 TTGATAACCTTCATATGAAATT
* * * *
499 TTGGTAACCGT-AGTATGGATTT
1 TTGATAACCTTCA-TATGAAATT
* * * *
521 TTTATAACCTCCCTAT-AAAAT
1 TTGATAACCTTCATATGAAATT
* **
542 TTGGTAACC-GGACTATGAAATT
1 TTGATAACCTTCA-TATGAAATT
* *
564 TTGATAACCTCCTTATGAAATT
1 TTGATAACCTTCATATGAAATT
* *
586 TTGATAATC-TCATTATAAAATT
1 TTGATAACCTTCA-TATGAAATT
608 TTGAT
1 TTGAT
613 TACCAAACAA
Statistics
Matches: 134, Mismatches: 36, Indels: 22
0.70 0.19 0.11
Matches are distributed among these distances:
21 18 0.13
22 101 0.75
23 12 0.09
24 3 0.02
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.41
Consensus pattern (22 bp):
TTGATAACCTTCATATGAAATT
Found at i:546 original size:43 final size:43
Alignment explanation
Indices: 467--586 Score: 141
Period size: 43 Copynumber: 2.8 Consensus size: 43
457 GATAATCATT
* * *
467 CTATGAAATTTTGATAACCTTCATATGAAATTTTGGTAACCGTA
1 CTATGAAATTTTGATAACCTCCATAT-AAAATTTGGTAACCGGA
* * * * *
511 GTATGGATTTTTTATAACCTCCCTATAAAATTTGGTAACCGGA
1 CTATGAAATTTTGATAACCTCCATATAAAATTTGGTAACCGGA
* *
554 CTATGAAATTTTGATAACCTCCTTATGAAATTT
1 CTATGAAATTTTGATAACCTCCATATAAAATTT
587 TGATAATCTC
Statistics
Matches: 62, Mismatches: 14, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
43 42 0.68
44 20 0.32
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (43 bp):
CTATGAAATTTTGATAACCTCCATATAAAATTTGGTAACCGGA
Found at i:1415 original size:22 final size:21
Alignment explanation
Indices: 1316--2356 Score: 286
Period size: 22 Copynumber: 47.6 Consensus size: 21
1306 TATACTGTGA
* *
1316 TTATCAAAATTTCACAATGAGG
1 TTATCAAAATTTCA-TAGGAGG
* * * *
1338 TAATCAAAATTTAACAGTGTGG
1 TTATCAAAATTTCATAG-GAGG
* *
1360 TTATCAACATTTCATATGGATTATG
1 TTATCAAAATTTCATA-GG---AGG
* *
1385 TTATTAAAATTTCATAGGAAAG
1 TTATCAAAATTTCATAGG-AGG
*
1407 TTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAG-GAGG
1429 TTATCAAAATTTCATATGGAGG
1 TTATCAAAATTTCATA-GGAGG
* * *
1451 TTATCAAAATTCCATAGCAAGA
1 TTATCAAAATTTCATAG-GAGG
* *
1473 TTATCAGAATTTCATAGTGTGG
1 TTATCAAAATTTCATAG-GAGG
**
1495 TTATCAAAATTTTTTAAGGAGG
1 TTATCAAAATTTCAT-AGGAGG
*
1517 TTATCAAATATCAAAATTCCATAGCAAGG
1 TTATCAAA-AT-----TT-CATAG-GAGG
* *
1546 TTATCAGAATTTCATAGTGTGG
1 TTATCAAAATTTCATAG-GAGG
**
1568 TTATCAAAATTTTTTAAGGAGG
1 TTATCAAAATTTCAT-AGGAGG
*
1590 TTATCAAAAATTTCATAGTGTGG
1 TTATC-AAAATTTCATAG-GAGG
* * *
1613 TTACCAAAATTTCATAGTAATG
1 TTATCAAAATTTCATAG-GAGG
* * *
1635 TTAGAAAAATCTAAATTTCATACGAAGA
1 TT------ATCAAAATTTCATA-GGAGG
*
1663 TTATCAAAATTT--TA-TA-G
1 TTATCAAAATTTCATAGGAGG
* * *
1680 TAATCAAAATTTCATCGGGAAG
1 TTATCAAAATTTCAT-AGGAGG
** * * * *
1702 CAATCAGAATCTCAAAGTA-G
1 TTATCAAAATTTCATAGGAGG
**
1722 TTAT--AAA--TCATAGAGATCAAA
1 TTATCAAAATTTCATAG-G---AGG
* * *
1743 TTACCAAAATTTCATAGAAATG
1 TTATCAAAATTTCATAG-GAGG
* * *
1765 TTAT-AAAAATTCATAATGTGG
1 TTATCAAAATTTCAT-AGGAGG
* *
1786 TTATCGAAATTTCATAGAAAGG
1 TTATCAAAATTTCATAG-GAGG
* *
1808 TTATCAAAATTTTAAAGCGAGG
1 TTATCAAAATTTCATAG-GAGG
* *
1830 TTATCAAAATTTCCCA-ATGAAG
1 TTATCAAAATTT--CATAGGAGG
* * **
1852 TTATGAAAAATTTTCATATTGTTG
1 TTAT-CAAAA-TTTCATA-GGAGG
*
1876 TTATTAAAATTTCATATGGAGG
1 TTATCAAAATTTCATA-GGAGG
* *
1898 TT-TC-AAATTTCATAGTATGA
1 TTATCAAAATTTCATAGGA-GG
* *
1918 TTATCAAAATTTCAAAGAGCGG
1 TTATCAAAATTTCATAG-GAGG
* * *
1940 TTAGCAACATTTCATTGGAAGG
1 TTATCAAAATTTCATAGG-AGG
* ***
1962 TTATCAAAATTTCATAATGTTA
1 TTATCAAAATTTCAT-AGGAGG
1984 TTATCAAAATTT--TA-GAGTG
1 TTATCAAAATTTCATAGGAG-G
** **
2003 TGGT----ATTTCAAAGGGAGG
1 TTATCAAAATTTC-ATAGGAGG
* *
2021 TTATCAAAATTGCATTTGTGTA-G
1 TTATCAAAATTTCA-TAG-G-AGG
* * * *
2044 TTACCAAAATTTCGTATGAAGA
1 TTATCAAAATTTCATA-GGAGG
* *
2066 TTATCAAAATTTCAAAGGGGG
1 TTATCAAAATTTCATAGGAGG
2087 ATTATCAAAATTTCATAGGGAGG
1 -TTATCAAAATTTCATA-GGAGG
* *
2110 ATATCAAAATTTCATAGTTTA-G
1 TTATCAAAATTTCATAG--GAGG
* *
2132 TTTTCAAAATTTTATAGG-GG
1 TTATCAAAATTTCATAGGAGG
* *
2152 TTATCGAAATTTCATAGGGATG
1 TTATCAAAATTTCATA-GGAGG
* ** *
2174 TTAACAAAATTTCATAATAAAG
1 TTATCAAAATTTCAT-AGGAGG
*
2196 TTATCGAAAA-ATCATAGGGAGG
1 TTATC-AAAATTTCATA-GGAGG
*
2218 TTATCAAAATTT-GT--GA--
1 TTATCAAAATTTCATAGGAGG
2234 TTATCAAAATTTCATAAGGAGG
1 TTATCAAAATTTCAT-AGGAGG
* * *
2256 TTATCAAAATTTTATCGGAAGT
1 TTATCAAAATTTCATAGG-AGG
* * *
2278 TTATCAAAATTTTATATGAATGT
1 TTATCAAAATTTCATA-GGA-GG
*
2301 TTATCAAAATTTCATACTGAGG
1 TTATCAAAATTTCATA-GGAGG
* * * **
2323 TCATTATAATTTCATAGTTTGG
1 TTATCAAAATTTCATAG-GAGG
2345 TTATCAAAATTT
1 TTATCAAAATTT
2357 AACAGTGTGA
Statistics
Matches: 739, Mismatches: 189, Indels: 182
0.67 0.17 0.16
Matches are distributed among these distances:
15 4 0.01
16 17 0.02
17 12 0.02
18 9 0.01
19 9 0.01
20 36 0.05
21 42 0.06
22 457 0.62
23 83 0.11
24 14 0.02
25 22 0.03
28 22 0.03
29 12 0.02
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGAGG
Found at i:1444 original size:44 final size:43
Alignment explanation
Indices: 1384--2356 Score: 315
Period size: 44 Copynumber: 22.3 Consensus size: 43
1374 TATGGATTAT
*
1384 GTTATTAAAATTTCATAGGAAAGTTATCAAAATTTCATAGTGTG
1 GTTATCAAAATTTCATAGG-AAGTTATCAAAATTTCATAGTGTG
* * ***
1428 GTTATCAAAATTTCATATGGAGGTTATCAAAATTCCATAGCAAG
1 GTTATCAAAATTTCATA-GGAAGTTATCAAAATTTCATAGTGTG
* * ** ** *
1472 ATTATCAGAATTTCATAGTGTGGTTATCAAAATTTTTTAAG-GAG
1 GTTATCAAAATTTCATAG-GAAGTTATCAAAATTTCAT-AGTGTG
* *
1516 GTTATCAAATATCAAAATTCCATAGCAAGGTTATCAGAATTTCATAGTGTG
1 GTTATCAAA-AT-----TT-CATAGGAA-GTTATCAAAATTTCATAGTGTG
** *
1567 GTTATCAAAATTTTTTAAGGAGGTTATCAAAAATTTCATAGTGTG
1 GTTATCAAAATTTCAT-AGGAAGTTATC-AAAATTTCATAGTGTG
* * * **
1612 GTTACCAAAATTTCATAGTAATGTTAGAAAAATCTAAATTTCATACG-AAG
1 GTTATCAAAATTTCATAGGAA-GTT------ATCAAAATTTCATA-GTGTG
* * * * * **
1662 ATTATCAAAATTT--TA--TAGTAATCAAAATTTCATCGGGAA
1 GTTATCAAAATTTCATAGGAAGTTATCAAAATTTCATAGTGTG
** * * * * * *
1701 GCAATCAGAATCTCA-AAGTAGTTAT--AAA--TCATAGAGATCAA
1 GTTATCAAAATTTCATAGGAAGTTATCAAAATTTCATAGTG-T--G
* * * * *
1742 ATTACCAAAATTTCATAGAAATGTTAT-AAAAATTCATAATGTG
1 GTTATCAAAATTTCATAGGAA-GTTATCAAAATTTCATAGTGTG
* * * * * *
1785 GTTATCGAAATTTCATAGAAAGGTTATCAAAATTTTAAAGCGAG
1 GTTATCAAAATTTCATAGGAA-GTTATCAAAATTTCATAGTGTG
* * * *
1829 GTTATCAAAATTTCCCA-ATGAAGTTATGAAAAATTTTCATATTGTT
1 GTTATCAAAATTT--CATAGGAAGTTAT-CAAAA-TTTCATAGTGTG
* * *
1875 GTTATTAAAATTTCATATGGAGGTT-TC-AAATTTCATAGTATG
1 GTTATCAAAATTTCATA-GGAAGTTATCAAAATTTCATAGTGTG
* * ** * * * *
1917 ATTATCAAAATTTCAAAGAGCGGTTAGCAACATTTCATTG-GAAG
1 GTTATCAAAATTTCATAG-GAAGTTATCAAAATTTCATAGTG-TG
** * *
1961 GTTATCAAAATTTCATAATGTTA-TTATCAAAATTTTAGAGTGTG
1 GTTATCAAAATTTCAT-A-GGAAGTTATCAAAATTTCATAGTGTG
* * * * *
2005 G---T----ATTTCAAAGGGAGGTTATCAAAATTGCATTTGTGTA
1 GTTATCAAAATTTCATA-GGAAGTTATCAAAATTTCA-TAGTGTG
* * * * *
2043 GTTACCAAAATTTCGTATGAAGATTATCAAAATTTCAAAG-GGG
1 GTTATCAAAATTTCATAGGAAG-TTATCAAAATTTCATAGTGTG
* * * *
2086 GATTATCAAAATTTCATAGGGAGGATATCAAAATTTCATAGTTTA
1 G-TTATCAAAATTTCATA-GGAAGTTATCAAAATTTCATAGTGTG
* * * * *
2131 GTTTTCAAAATTTTATAGG-GGTTATCGAAATTTCATAGGGAT-
1 GTTATCAAAATTTCATAGGAAGTTATCAAAATTTCATAGTG-TG
* ** * * *
2173 GTTAACAAAATTTCATAATAAAGTTATCGAAAA-ATCATAGGGAG
1 GTTATCAAAATTTCAT-AGGAAGTTATC-AAAATTTCATAGTGTG
* *
2217 GTTATCAAAATTT-GT--G-A-TTATCAAAATTTCATAAG-GAG
1 GTTATCAAAATTTCATAGGAAGTTATCAAAATTTCAT-AGTGTG
* * *
2255 GTTATCAAAATTTTATCGGAAGTTTATCAAAATTTTATA-TGAATG
1 GTTATCAAAATTTCATAGGAAG-TTATCAAAATTTCATAGTG--TG
* * * * * * *
2300 TTTATCAAAATTTCATACTGAGGTCATTATAATTTCATAGTTTG
1 GTTATCAAAATTTCATA-GGAAGTTATCAAAATTTCATAGTGTG
2344 GTTATCAAAATTT
1 GTTATCAAAATTT
2357 AACAGTGTGA
Statistics
Matches: 676, Mismatches: 173, Indels: 160
0.67 0.17 0.16
Matches are distributed among these distances:
36 2 0.00
37 22 0.03
38 37 0.05
39 25 0.04
40 4 0.01
41 13 0.02
42 67 0.10
43 42 0.06
44 255 0.38
45 109 0.16
46 37 0.05
48 2 0.00
50 28 0.04
51 33 0.05
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (43 bp):
GTTATCAAAATTTCATAGGAAGTTATCAAAATTTCATAGTGTG
Found at i:1571 original size:73 final size:73
Alignment explanation
Indices: 1452--1597 Score: 283
Period size: 73 Copynumber: 2.0 Consensus size: 73
1442 ATATGGAGGT
1452 TATCAAAATTCCATAGCAAGATTATCAGAATTTCATAGTGTGGTTATCAAAATTTTTTAAGGAGG
1 TATCAAAATTCCATAGCAAGATTATCAGAATTTCATAGTGTGGTTATCAAAATTTTTTAAGGAGG
1517 TTATCAAA
66 TTATCAAA
*
1525 TATCAAAATTCCATAGCAAGGTTATCAGAATTTCATAGTGTGGTTATCAAAATTTTTTAAGGAGG
1 TATCAAAATTCCATAGCAAGATTATCAGAATTTCATAGTGTGGTTATCAAAATTTTTTAAGGAGG
1590 TTATCAAA
66 TTATCAAA
1598 AATTTCATAG
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (73 bp):
TATCAAAATTCCATAGCAAGATTATCAGAATTTCATAGTGTGGTTATCAAAATTTTTTAAGGAGG
TTATCAAA
Found at i:2213 original size:64 final size:65
Alignment explanation
Indices: 2048--2229 Score: 181
Period size: 64 Copynumber: 2.8 Consensus size: 65
2038 GTGTAGTTAC
* * * *
2048 CAAAATTTCGT-ATGAAGATTATCAAAATTTCAAAGGGGGATTATCAAAATTTCATAGGGAGGAT
1 CAAAATTTCATAATAAAG-TTATCAAAATATCATAGGGGG-TTATCAAAATTTCATAGGGAGGAT
*
2112 AT
64 AA
* ** * * * * * *
2114 CAAAATTTCATAGTTTAGTTTTCAAAATTTTATA-GGGGTTATCGAAATTTCATAGGGATGTTAA
1 CAAAATTTCATAATAAAGTTATCAAAATATCATAGGGGGTTATCAAAATTTCATAGGGAGGATAA
2178 CAAAATTTCATAATAAAGTTATCGAAAA-ATCATAGGGAGGTTATCAAAATTT
1 CAAAATTTCATAATAAAGTTATC-AAAATATCATAGGG-GGTTATCAAAATTT
2230 GTGATTATCA
Statistics
Matches: 94, Mismatches: 18, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
64 45 0.48
65 10 0.11
66 36 0.38
67 3 0.03
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (65 bp):
CAAAATTTCATAATAAAGTTATCAAAATATCATAGGGGGTTATCAAAATTTCATAGGGAGGATAA
Found at i:2291 original size:11 final size:11
Alignment explanation
Indices: 2256--2312 Score: 53
Period size: 11 Copynumber: 5.1 Consensus size: 11
2246 CATAAGGAGG
2256 TTATCAAAATT
1 TTATCAAAATT
** *
2267 TTATCGGAAGT
1 TTATCAAAATT
2278 TTATCAAAATT
1 TTATCAAAATT
*
2289 TTAT-ATGAATGT
1 TTATCA-AAAT-T
2301 TTATCAAAATT
1 TTATCAAAATT
2312 T
1 T
2313 CATACTGAGG
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
10 1 0.03
11 25 0.71
12 8 0.23
13 1 0.03
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.46
Consensus pattern (11 bp):
TTATCAAAATT
Found at i:2462 original size:22 final size:22
Alignment explanation
Indices: 2437--2518 Score: 69
Period size: 22 Copynumber: 3.8 Consensus size: 22
2427 CATGGAGATG
2437 TCAAAATTTTA-TAGTACGGTTA
1 TCAAAATTTTAGTAGTA-GGTTA
* * *
2459 TCAAAATTTAAGTGGTTGGTTA
1 TCAAAATTTTAGTAGTAGGTTA
* * * * *
2481 TCAAAATTTCATTAGGAAGTCA
1 TCAAAATTTTAGTAGTAGGTTA
2503 TCAAAATTTTA-TAGTA
1 TCAAAATTTTAGTAGTA
2519 ATGTTTTCAA
Statistics
Matches: 47, Mismatches: 12, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
21 4 0.09
22 40 0.85
23 3 0.06
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.39
Consensus pattern (22 bp):
TCAAAATTTTAGTAGTAGGTTA
Found at i:4915 original size:29 final size:29
Alignment explanation
Indices: 4883--4945 Score: 126
Period size: 29 Copynumber: 2.2 Consensus size: 29
4873 TTTAATCAAT
4883 TATTATGATTTTGCTTTCTTAGATAGTAG
1 TATTATGATTTTGCTTTCTTAGATAGTAG
4912 TATTATGATTTTGCTTTCTTAGATAGTAG
1 TATTATGATTTTGCTTTCTTAGATAGTAG
4941 TATTA
1 TATTA
4946 CTCGCACTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.25, C:0.06, G:0.16, T:0.52
Consensus pattern (29 bp):
TATTATGATTTTGCTTTCTTAGATAGTAG
Found at i:5342 original size:18 final size:18
Alignment explanation
Indices: 5319--5356 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
5309 TGAGGTCATG
5319 TTGGGTTGAGTGGACTCC
1 TTGGGTTGAGTGGACTCC
5337 TTGGGTTGAGTGGACTCC
1 TTGGGTTGAGTGGACTCC
5355 TT
1 TT
5357 AAATAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.11, C:0.16, G:0.37, T:0.37
Consensus pattern (18 bp):
TTGGGTTGAGTGGACTCC
Found at i:9377 original size:42 final size:42
Alignment explanation
Indices: 9330--9568 Score: 210
Period size: 42 Copynumber: 5.7 Consensus size: 42
9320 AGGGTCAACA
* ***
9330 CCTGCATTAAGTGCATCCTTAGCAGCCTCTTTAGACCCAATG
1 CCTGCATCAAGTGCATCCTTAGCAGCCTCCCCAGACCCAATG
* * * * ** * *
9372 CCTGCATCAACTACATCCTGAACAGCCTCCTTAGATCCAACAG
1 CCTGCATCAAGTGCATCCTTAGCAGCCTCCCCAGACCCAA-TG
* * *
9415 -CTGCGTCAAGTGCATGCTTAGCAGCCTCCCCAGACCCAACG
1 CCTGCATCAAGTGCATCCTTAGCAGCCTCCCCAGACCCAATG
* *
9456 CCTGCATCAAGTGCATTCTTAGCAGCTTCCCCAGACCCAATG
1 CCTGCATCAAGTGCATCCTTAGCAGCCTCCCCAGACCCAATG
* * * * * * *
9498 CCTGCATTAAGTACATTCTTAACAGCCTCCCCACAGCCAACG
1 CCTGCATCAAGTGCATCCTTAGCAGCCTCCCCAGACCCAATG
* * * *
9540 CCTACATCAAGTACATCCTGAGCACCCTC
1 CCTGCATCAAGTGCATCCTTAGCAGCCTC
9569 TCTAGACTCA
Statistics
Matches: 160, Mismatches: 35, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
41 1 0.01
42 158 0.99
43 1 0.01
ACGTcount: A:0.26, C:0.37, G:0.15, T:0.22
Consensus pattern (42 bp):
CCTGCATCAAGTGCATCCTTAGCAGCCTCCCCAGACCCAATG
Found at i:10633 original size:26 final size:26
Alignment explanation
Indices: 10604--10656 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
10594 TCAGGCCTTA
*
10604 ATTCAGTTTAACAGAATTCATAAGTG
1 ATTCAATTTAACAGAATTCATAAGTG
10630 ATTCAATTTAACAGAATTCATAAGTG
1 ATTCAATTTAACAGAATTCATAAGTG
10656 A
1 A
10657 AAATAGAGGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (26 bp):
ATTCAATTTAACAGAATTCATAAGTG
Found at i:12130 original size:11 final size:11
Alignment explanation
Indices: 12101--12130 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
12091 GGGGGGGAGT
12101 AAAAAAAA-AA
1 AAAAAAAAGAA
12111 AAAAAAAAGAA
1 AAAAAAAAGAA
12122 AAAAAAAAG
1 AAAAAAAAG
12131 GGGGGCAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.42
11 11 0.58
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:12868 original size:42 final size:42
Alignment explanation
Indices: 12816--13323 Score: 246
Period size: 42 Copynumber: 11.8 Consensus size: 42
12806 TCCATAGAGT
* * * * **
12816 CAACACCTGCATTAAGTGCATCCTTAGTAGCCTCCCTAGACC
1 CAACGCCTGCATCAAGTACATCCTGAACAGCCTCCCTAGACC
* * **
12858 CAATGCCTGCATCAACTACATCCTGAACAGCCT-CCTCAGGTC
1 CAACGCCTGCATCAAGTACATCCTGAACAGCCTCCCT-AGACC
* * * * * * *
12900 CAACGGCTGCATCGAGTGCATCCTTAGCAGCCTCCATAAACC
1 CAACGCCTGCATCAAGTACATCCTGAACAGCCTCCCTAGACC
* *
12942 CAACACCTGCATCAAGTACATCCTGAATAGCCTCTCC-AGACC
1 CAACGCCTGCATCAAGTACATCCTGAACAGCCTC-CCTAGACC
* * ** * *
12984 C-A-G-CAGC-TACAGGTGTATCCTTAGCAGCCTCTCC-AGACC
1 CAACGCCTGCAT-CAAGTACATCCTGAACAGCCTC-CCTAGACC
* * *
13023 CAACCTCCT-CAGGTCCAACGGCTACATCAAGTGCATCCTTAGCAGCCTCCATAGACC
1 CAA-CGCCTGCA--T-CAA--G-TACATC--CTG-A-----A-CAGCCTCCCTAGACC
*
13080 CAACGCCTGCATCAAGTACATCCTGAACAGCCT-CTTCAGACC
1 CAACGCCTGCATCAAGTACATCCTGAACAGCCTCCCT-AGACC
* * * * *
13122 CAGCAG-CTACATCAAGTGCATCCTTAGCAGCCT-CCTCAGACC
1 CAAC-GCCTGCATCAAGTACATCCTGAACAGCCTCCCT-AGACC
* * ** * *
13164 CAACACCTGCATCAAGTGCATCCAAAACAGCCTCCCCAAACC
1 CAACGCCTGCATCAAGTACATCCTGAACAGCCTCCCTAGACC
* * * * * *
13206 CAACGCATGCATCAAGTACTTTCTTAGCAGCCTCCCCAGACC
1 CAACGCCTGCATCAAGTACATCCTGAACAGCCTCCCTAGACC
* * * * *
13248 CAACGCCTGCATCAATTACATCCTTAACAGCCTCCCCACAGC
1 CAACGCCTGCATCAAGTACATCCTGAACAGCCTCCCTAGACC
* * *
13290 CAACGCCTGCATCAAGTACGTCCTTAGCAGCCTC
1 CAACGCCTGCATCAAGTACATCCTGAACAGCCTC
13324 TATAGACTCA
Statistics
Matches: 353, Mismatches: 84, Indels: 58
0.71 0.17 0.12
Matches are distributed among these distances:
38 1 0.00
39 28 0.08
40 1 0.00
41 6 0.02
42 263 0.75
43 8 0.02
45 3 0.01
47 1 0.00
48 5 0.01
49 2 0.01
50 1 0.00
51 7 0.02
52 1 0.00
54 3 0.01
55 1 0.00
56 5 0.01
57 17 0.05
ACGTcount: A:0.27, C:0.38, G:0.15, T:0.19
Consensus pattern (42 bp):
CAACGCCTGCATCAAGTACATCCTGAACAGCCTCCCTAGACC
Found at i:13186 original size:84 final size:83
Alignment explanation
Indices: 13037--13323 Score: 342
Period size: 84 Copynumber: 3.4 Consensus size: 83
13027 CTCCTCAGGT
13037 CCAACGGCTACATCAAGTGCATCCTTAGCAGCCTCCAT-AGACCCAACGCCTGCATCAAGTACAT
1 CCAAC-GCTACATCAAGTGCATCCTTAGCAGCCTCC-TCAGACCCAACGCCTGCATCAAGTACAT
* ** *
13101 CCTGAACAGCCTCTTCAGAC
64 CCTAAACAGCCTCCCCAAAC
* * *
13121 CCAGCAGCTACATCAAGTGCATCCTTAGCAGCCTCCTCAGACCCAACACCTGCATCAAGTGCATC
1 CCAAC-GCTACATCAAGTGCATCCTTAGCAGCCTCCTCAGACCCAACGCCTGCATCAAGTACATC
*
13186 CAAAACAGCCTCCCCAAAC
65 CTAAACAGCCTCCCCAAAC
* * * * * *
13205 CCAACGCATGCATCAAGTACTTTCTTAGCAGCCTCCCCAGACCCAACGCCTGCATCAATTACATC
1 CCAACGC-TACATCAAGTGCATCCTTAGCAGCCTCCTCAGACCCAACGCCTGCATCAAGTACATC
* * *
13270 CTTAACAGCCTCCCCACAG
65 CTAAACAGCCTCCCCAAAC
* * *
13289 CCAACGCCTGCATCAAGTACGTCCTTAGCAGCCTC
1 CCAACG-CTACATCAAGTGCATCCTTAGCAGCCTC
13324 TATAGACTCA
Statistics
Matches: 176, Mismatches: 24, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
83 3 0.02
84 172 0.98
85 1 0.01
ACGTcount: A:0.28, C:0.39, G:0.14, T:0.18
Consensus pattern (83 bp):
CCAACGCTACATCAAGTGCATCCTTAGCAGCCTCCTCAGACCCAACGCCTGCATCAAGTACATCC
TAAACAGCCTCCCCAAAC
Found at i:13321 original size:126 final size:126
Alignment explanation
Indices: 12844--13323 Score: 352
Period size: 126 Copynumber: 3.7 Consensus size: 126
12834 CATCCTTAGT
* * * * * * *** *
12844 AGCCTCCCTAGACCCAA-TGCCTGCATCAACTACATCCTGAACAGCCTCCTCAGGTCCAACGGCT
1 AGCCTCCCCAGACCCAACAG-CTACATCAAGTACATCCTTAACAGCCTCCCCACACCCAACGCCT
* * * * *
12908 GCATCGAGTGCATCCTTAGCAGCCTCCATAAACCCAACACCTGCATCAAGTACATCCTGAAT
65 GCATCAAGTGCATCCTTAGCAGCCTCCACAAACCCAACGCATGCATCAAGTACATCCTGAAC
* * * ** * * * *
12970 AGCCTCTCCAGACCCAGCAGCTACAGGTGTATCCTTAGCAGCCTCTCCAGACCCAACCTCCTCAG
1 AGCCTCCCCAGACCCAACAGCTACA--T-CA--AGTA-CATCCT-T--A-A--CAGCCTCCCCAC
** * * * * *
13035 GTCCAACGGCTACATCAAGTGCATCCTTAGCAGCCTCCATAGACCCAACGCCTGCATCAAGTACA
54 ACCCAACGCCTGCATCAAGTGCATCCTTAGCAGCCTCCACAAACCCAACGCATGCATCAAGTACA
13100 TCCTGAAC
119 TCCTGAAC
** * * * * * *
13108 AGCCTCTTCAGACCCAGCAGCTACATCAAGTGCATCCTTAGCAGCCTCCTCAGACCCAACACCTG
1 AGCCTCCCCAGACCCAACAGCTACATCAAGTACATCCTTAACAGCCTCCCCACACCCAACGCCTG
** * * * * * *
13173 CATCAAGTGCATCCAAAACAGCCTCCCCAAACCCAACGCATGCATCAAGTACTTTCTTAGC
66 CATCAAGTGCATCCTTAGCAGCCTCCACAAACCCAACGCATGCATCAAGTACATCCTGAAC
* * *
13234 AGCCTCCCCAGACCCAAC-GCCTGCATCAATTACATCCTTAACAGCCTCCCCACAGCCAACGCCT
1 AGCCTCCCCAGACCCAACAG-CTACATCAAGTACATCCTTAACAGCCTCCCCACACCCAACGCCT
* *
13298 GCATCAAGTACGTCCTTAGCAGCCTC
65 GCATCAAGTGCATCCTTAGCAGCCTC
13324 TATAGACTCA
Statistics
Matches: 284, Mismatches: 56, Indels: 28
0.77 0.15 0.08
Matches are distributed among these distances:
125 1 0.00
126 158 0.56
127 1 0.00
128 1 0.00
129 2 0.01
131 3 0.01
132 10 0.04
133 1 0.00
135 2 0.01
136 2 0.01
138 103 0.36
ACGTcount: A:0.27, C:0.39, G:0.15, T:0.19
Consensus pattern (126 bp):
AGCCTCCCCAGACCCAACAGCTACATCAAGTACATCCTTAACAGCCTCCCCACACCCAACGCCTG
CATCAAGTGCATCCTTAGCAGCCTCCACAAACCCAACGCATGCATCAAGTACATCCTGAAC
Found at i:17608 original size:16 final size:16
Alignment explanation
Indices: 17589--17621 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
17579 AAATTTAGAA
17589 AGTTAGAAATGATTTG
1 AGTTAGAAATGATTTG
*
17605 AGTTATAAATGATTTG
1 AGTTAGAAATGATTTG
17621 A
1 A
17622 AAGAATTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.21, T:0.39
Consensus pattern (16 bp):
AGTTAGAAATGATTTG
Found at i:17946 original size:20 final size:20
Alignment explanation
Indices: 17909--17945 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
17899 TTAATAATAA
*
17909 TAAATTTTTAATATTTTTGT
1 TAAATTTATAATATTTTTGT
17929 TAAATTTAT-ATATTTTT
1 TAAATTTATAATATTTTT
17946 TTCTTTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (20 bp):
TAAATTTATAATATTTTTGT
Found at i:23093 original size:21 final size:21
Alignment explanation
Indices: 23069--23111 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
23059 TTTTTGGGTA
*
23069 TTACTAAATACCGCCCCCCTT
1 TTACTAAACACCGCCCCCCTT
**
23090 TTACTAGCCACCGCCCCCCTT
1 TTACTAAACACCGCCCCCCTT
23111 T
1 T
23112 GGACTATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.47, G:0.07, T:0.28
Consensus pattern (21 bp):
TTACTAAACACCGCCCCCCTT
Done.