Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010331.1 Corchorus capsularis cultivar CVL-1 contig10352, 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: 78571
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:1813 original size:322 final size:323
Alignment explanation
Indices: 1--1816 Score: 2177
Period size: 324 Copynumber: 5.6 Consensus size: 323
* * * * **
1 GATTTCAGCTAAAAAATGACATGTAAATTTTTTTCTCAATTTTT-CCCACAATAATCATAAAAAA
1 GATTTCAGCTAAAAACTGACCTGAAAATTTTTTTCTCAATTTTTGGCCACAATGCTCATAAAAAA
* ** * *
65 TATATAATTCAACGTCAAAAAGATTGAAATGTTTTTCAGTCTTCTAAAATCGTTTTTC-A-TTTT
66 TATATAATTCAACGCCAAAAAGATTGAAGGGTTTTTCACTCTTCTAATATCGTTTTTCAATTTTT
* * * * *
128 TTCCCGAATAAATTTCTAATTTAATCGAAACAAGATTCAGAAGCTCGTAAAAACAAAATCCTTTA
131 TTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAC-AAATCCTTAA
* *
193 ATCAAATGTGGCTGAGATTTGATTCGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAAT
195 ATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAAT
* * * * * * *
258 CATGCAAAATTGAGCCGGGGCTCCAAAACGCGTTTTTTAGCTAAAAACTGTGATGGTTTGTACAC
260 CATGCAAAACTGAGTCGGGGCCCCGAAACGCG-TTTTTAGCTAAAAACTATGATAGTTAGTACAC
* * ** *
323 GATTTCAGCTAAAAAACTGACATGTAAA-TTTTTTCTCAATTTTTTCCCACAAT-CATAATAAAA
1 GATTTCAGCT-AAAAACTGACCTGAAAATTTTTTTCTCAATTTTTGGCCACAATGC-TCATAAAA
* * * * * *
386 AATATATTATTGAACGCCAAAGAGATTGAAGGG-TTTTCAATCTTCTAAAATCG-TTTT-AA-AT
64 AATATATAATTCAACGCCAAAAAGATTGAAGGGTTTTTCACTCTTCTAATATCGTTTTTCAATTT
* * * *
447 TTTTTCCGAATTAATTTCTAATTAAAGT-TAAAGAAGATTCAGAAGCTCGTAAAATCAAATCCTT
129 TTTTTCCGAATTAATTTCTAATTAAA-TCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTT
511 AAATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAA
193 AAATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAA
* * ** *
576 ATCATGCAAAACTGTGTCGGTGCCCTAAAACGCGTTTTTTAGCTAAAAAC-AT-A-AGGTAAAGT
258 ATCATGCAAAACTGAGTCGGGGCCCCGAAACGCG-TTTTTAGCTAAAAACTATGATA-GT-TAGT
638 ACAC
320 ACAC
* ***** * *
642 GATTTCAGCTAAAAATTGACCTGAAAA-AAAAAT-TCAATTTTTTTTTGCCACAATACTCATAAA
1 GATTTCAGCTAAAAACTGACCTGAAAATTTTTTTCTCAA---TTTTTGGCCACAATGCTCATAAA
* * * * * *
705 AAATATATAATGCAATGCAAAAAAGATTGAAGGGTTTTTCACGCTTCTAATTTTGTTTTTCAATT
63 AAATATATAATTCAACGCCAAAAAGATTGAAGGGTTTTTCACTCTTCTAATATCGTTTTTCAATT
* * * *
770 TTTTTTCCGAATTAATCTCTAATTAAATCGAAACAAGTTTCAGATACTTGTAAAAACAAATCCTT
128 TTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTT
* * * * *
835 AAATCAAATGTGGCTGAGATTTGGTTTGATAAATATAGATATTTCAAGGAGTCTTCCTACCAAAA
193 AAATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAA
* * * ** * *
900 ACCATGCAAAACTAAGTTGGACCCCCGAAATGCGTTTTTAGCTAAAAACTATAATAGTT-GATAC
258 ATCATGCAAAACTGAGTCGGGGCCCCGAAACGCGTTTTTAGCTAAAAACTATGATAGTTAG-TAC
964 AC
322 AC
* * * * *
966 GGTTTCAGCTAAAAACTGACAC-GAAATTTTTTTTTCTTAATTTTTGGCCACAATGCTCATGAAG
1 GATTTCAGCTAAAAACTGAC-CTGAAA-ATTTTTTTCTCAATTTTTGGCCACAATGCTCATAAAA
** * *
1030 AATATATAATTCAACGTGAAAATGATTGAAGGGATTTTCA-TGCTTCTAATATCGTTTTTCAATT
64 AATATATAATTCAACGCCAAAAAGATTGAAGGGTTTTTCACT-CTTCTAATATCGTTTTTCAATT
* * * * *
1094 TTTTTTCTGAATCAATTTCTAATTAAATCGAAACAAGATTTAGATGCTTGTAAAAAAAAATCCTT
128 TTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTT
* * **
1159 AAATCCAATGTGGCTTAGATTTGATTCGATGAATATAGATATTTCAAGGAGTCTTTCTGCTGAAA
193 AAATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAA
* * * *
1224 TTCATGCAAAACTGAGCCGAGGCCCCGAAACGCGTTTTTAGCTTAAAACCT-TGAT-GATTAGTA
258 ATCATGCAAAACTGAGTCGGGGCCCCGAAACGCGTTTTTAGC-TAAAAACTATGATAG-TTAGTA
* *
1287 TAA
321 CAC
* * *
1290 GATTTTAGCTAAAAACTGACCTGAAATTTTTTTTTCTCAATTTTTGGCCACAATGCTCATAAAGA
1 GATTTCAGCTAAAAACTGACCTGAAA-ATTTTTTTCTCAATTTTTGGCCACAATGCTCATAAAAA
* * * * * *
1355 ATATATAATTCAACGCCAAAAGGATTGAATGGTTTTTCACACTTCCAATATTGTTTTTCAAATTT
65 ATATATAATTCAACGCCAAAAAGATTGAAGGGTTTTTCACTCTTCTAATATCGTTTTTCAATTTT
* * * * *
1420 TTTT-CTAATTAAATTCTAATTAAATCGAAATAAGATTCAAATGCTCGTAAAAACAAATTCTTAA
130 TTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAA
*
1484 ATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGTCAAAAAT
195 ATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAAT
* * *
1549 CATGCAAAACTGAGTCGGGGCCCCGAAACGCGTTTTTAACTAAAAATTGTGATAGTTAGTACAC
260 CATGCAAAACTGAGTCGGGGCCCCGAAACGCGTTTTTAGCTAAAAACTATGATAGTTAGTACAC
* *
1613 CATTTCAGCTAAAAACAGACCTGAAAATTTTTTTCTCAATTTTTGGCCACAATGCTCATAAAAAA
1 GATTTCAGCTAAAAACTGACCTGAAAATTTTTTTCTCAATTTTTGGCCACAATGCTCATAAAAAA
* *
1678 TATATAATTCAACGCCAAAAAGATTGAAGGGTTTTTCACTCTTCTAACATCATTTTTC-ATTTTT
66 TATATAATTCAACGCCAAAAAGATTGAAGGGTTTTTCACTCTTCTAATATCGTTTTTCAATTTTT
**
1742 TTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTTC-GATGCTCAG-AAAAACAAATCCTTA
131 TTTCCGAATTAATTTCTAATTAAATCGAAACAAGA-TTCAGATGCTC-GTAAAAACAAATCCTTA
1805 AATCCAATGTGG
194 AATCCAATGTGG
1817 TAATATAAAT
Statistics
Matches: 1278, Mismatches: 181, Indels: 70
0.84 0.12 0.05
Matches are distributed among these distances:
317 4 0.00
318 18 0.01
319 17 0.01
320 161 0.13
321 78 0.06
322 203 0.16
323 263 0.21
324 517 0.40
325 12 0.01
326 2 0.00
327 3 0.00
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (323 bp):
GATTTCAGCTAAAAACTGACCTGAAAATTTTTTTCTCAATTTTTGGCCACAATGCTCATAAAAAA
TATATAATTCAACGCCAAAAAGATTGAAGGGTTTTTCACTCTTCTAATATCGTTTTTCAATTTTT
TTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAA
TCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATC
ATGCAAAACTGAGTCGGGGCCCCGAAACGCGTTTTTAGCTAAAAACTATGATAGTTAGTACAC
Found at i:2578 original size:72 final size:73
Alignment explanation
Indices: 2494--2639 Score: 231
Period size: 73 Copynumber: 2.0 Consensus size: 73
2484 GACGATTGAC
* *
2494 GAAAATTTTCTGATTCATTATTTTGTATAAGGG-AAAAATCTAAAAAAGACTGCTACCTAACCAT
1 GAAAATTTTCTGATTCATTATTTTGTATAAGGGAAAAAATCAAAAAAAAACTGCTACCTAACCAT
2558 GGAGGATA
66 GGAGGATA
* * * *
2566 GAAAATTTTCTGATTCATTATTTTGTGTAAGGGAAAAAATCAAAAAAAAATTGCTACCTAGCCTT
1 GAAAATTTTCTGATTCATTATTTTGTATAAGGGAAAAAATCAAAAAAAAACTGCTACCTAACCAT
2631 GGAGGATA
66 GGAGGATA
2639 G
1 G
2640 GACATACGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
72 32 0.48
73 35 0.52
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.31
Consensus pattern (73 bp):
GAAAATTTTCTGATTCATTATTTTGTATAAGGGAAAAAATCAAAAAAAAACTGCTACCTAACCAT
GGAGGATA
Found at i:29088 original size:120 final size:120
Alignment explanation
Indices: 28875--29115 Score: 437
Period size: 120 Copynumber: 2.0 Consensus size: 120
28865 AGACAATAAT
28875 AAAGTATATATACATAATAGCTTAGTCAATATTCAACAACATCAAACCGTTCAATGCAGCACAGC
1 AAAGTATATATACATAATAGCTTAGTCAATATTCAACAACATCAAACCGTTCAATGCAGCACAGC
**
28940 AAATAACATGTGAACACTCTAAGCACCGTAACTCTATTTTAACTTTCAATGAAAC
66 AAATAACATGTGAACACTCTAAGCACCGTAACTCTAGATTAACTTTCAATGAAAC
* *
28995 AAAGTATATATACATAATAGCTTAGTCAATATTCAACAACATCAAACCTTTCAATGTAGCACAGC
1 AAAGTATATATACATAATAGCTTAGTCAATATTCAACAACATCAAACCGTTCAATGCAGCACAGC
*
29060 AAATACCATGTGAACACTCTAAGCACCGTAACTCTAGATTAACTTTCAATGAAAC
66 AAATAACATGTGAACACTCTAAGCACCGTAACTCTAGATTAACTTTCAATGAAAC
29115 A
1 A
29116 CTATTCAATA
Statistics
Matches: 116, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
120 116 1.00
ACGTcount: A:0.42, C:0.22, G:0.10, T:0.27
Consensus pattern (120 bp):
AAAGTATATATACATAATAGCTTAGTCAATATTCAACAACATCAAACCGTTCAATGCAGCACAGC
AAATAACATGTGAACACTCTAAGCACCGTAACTCTAGATTAACTTTCAATGAAAC
Found at i:30740 original size:52 final size:52
Alignment explanation
Indices: 30684--30785 Score: 177
Period size: 52 Copynumber: 2.0 Consensus size: 52
30674 TTTATTTGAT
*
30684 ATTGCACTTGGATTCAAAAGCAGCTTTTTTATCTTCAAACGCAATGCCAAGC
1 ATTGCACTTGGATTCAAAAACAGCTTTTTTATCTTCAAACGCAATGCCAAGC
* *
30736 ATTGCATTTGGATTCAAAAACAGCTTTTTTATCTTCAAAGGCAATGCCAA
1 ATTGCACTTGGATTCAAAAACAGCTTTTTTATCTTCAAACGCAATGCCAA
30786 ATCAAGCTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (52 bp):
ATTGCACTTGGATTCAAAAACAGCTTTTTTATCTTCAAACGCAATGCCAAGC
Found at i:30974 original size:43 final size:42
Alignment explanation
Indices: 30913--30997 Score: 143
Period size: 43 Copynumber: 2.0 Consensus size: 42
30903 TCAACCTACC
*
30913 ATGAAAATTAGCATGTTAACCAAATACAATTAGGATTTTCCAA
1 ATGAAAATTAGCATGTTAACC-AATACAATTAGGATTCTCCAA
*
30956 ATGAAAATTAGCATGTTAACCAATAGAATTAGGATTCTCCAA
1 ATGAAAATTAGCATGTTAACCAATACAATTAGGATTCTCCAA
30998 TTCGTTTACA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
42 19 0.47
43 21 0.52
ACGTcount: A:0.44, C:0.14, G:0.13, T:0.29
Consensus pattern (42 bp):
ATGAAAATTAGCATGTTAACCAATACAATTAGGATTCTCCAA
Found at i:30985 original size:21 final size:22
Alignment explanation
Indices: 30916--30987 Score: 78
Period size: 21 Copynumber: 3.4 Consensus size: 22
30906 ACCTACCATG
30916 AAAATTAGCATGTTAACCAAAT
1 AAAATTAGCATGTTAACCAAAT
* * *
30938 ACAATTAGGAT-TT-TCCAAAT
1 AAAATTAGCATGTTAACCAAAT
30958 GAAAATTAGCATGTTAACC-AAT
1 -AAAATTAGCATGTTAACCAAAT
*
30980 AGAATTAG
1 AAAATTAG
30988 GATTCTCCAA
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
20 6 0.15
21 18 0.45
22 14 0.35
23 2 0.05
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.29
Consensus pattern (22 bp):
AAAATTAGCATGTTAACCAAAT
Found at i:44354 original size:44 final size:44
Alignment explanation
Indices: 44305--44447 Score: 182
Period size: 44 Copynumber: 3.2 Consensus size: 44
44295 CATAGTTACC
* * *
44305 TTACCAAAACTTT-ATAGGGAGGTTA-TAAAATTTTCAAATGAAGG
1 TTACCAAAA-TTTCATAGTGAGGTTACTAAAA-TTTCATAGGAAGG
* * *
44349 TTACCAGAATTTCATAGTGAGGTTATTGAAATTTCATAGGAAGG
1 TTACCAAAATTTCATAGTGAGGTTACTAAAATTTCATAGGAAGG
* *
44393 TTACCAAAATTTCATAGTGAAGTTACCAAAATTTCATAGGAAGG
1 TTACCAAAATTTCATAGTGAGGTTACTAAAATTTCATAGGAAGG
44437 TTACCAAAATT
1 TTACCAAAATT
44448 AGAAATCGGT
Statistics
Matches: 87, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
43 3 0.03
44 80 0.92
45 4 0.05
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.32
Consensus pattern (44 bp):
TTACCAAAATTTCATAGTGAGGTTACTAAAATTTCATAGGAAGG
Found at i:44361 original size:22 final size:22
Alignment explanation
Indices: 44331--44447 Score: 103
Period size: 22 Copynumber: 5.3 Consensus size: 22
44321 GGGAGGTTAT
44331 AAAATTTTCAAATGAAGGTTACC
1 AAAA-TTTCAAATGAAGGTTACC
* * **
44354 AGAATTTCATAGTG-AGGTTATT
1 AAAATTTCA-AATGAAGGTTACC
* * *
44376 GAAATTTCATAGGAAGGTTACC
1 AAAATTTCAAATGAAGGTTACC
*
44398 AAAATTTCATAGTGAA-GTTACC
1 AAAATTTCA-AATGAAGGTTACC
* *
44420 AAAATTTCATAGGAAGGTTACC
1 AAAATTTCAAATGAAGGTTACC
44442 AAAATT
1 AAAATT
44448 AGAAATCGGT
Statistics
Matches: 72, Mismatches: 18, Indels: 9
0.73 0.18 0.09
Matches are distributed among these distances:
21 4 0.06
22 59 0.82
23 9 0.12
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (22 bp):
AAAATTTCAAATGAAGGTTACC
Found at i:44447 original size:66 final size:65
Alignment explanation
Indices: 44280--44447 Score: 162
Period size: 66 Copynumber: 2.6 Consensus size: 65
44270 TAGGGAGGTT
* * * ** * *
44280 AGGTTACCACAATTCCATAGTTACCTTACCAAAACTTTATAGGGAGGTTATAAAATTTTCAAATG
1 AGGTTACCAAAATTTCATAGTGAGGTTACCAAAA-TTTATAGGAAGGTTACAAAATTTTCAAATG
44345 A
65 A
* *** *
44346 AGGTTACCAGAATTTCATAGTGAGGTTATTGAAATTTCATAGGAAGGTTACCAAAA-TTTCATAG
1 AGGTTACCAAAATTTCATAGTGAGGTTACCAAAATTT-ATAGGAAGGTTA-CAAAATTTTCA-AA
44410 TGA
63 TGA
44413 A-GTTACCAAAATTTCATAG-GAAGGTTACCAAAATT
1 AGGTTACCAAAATTTCATAGTG-AGGTTACCAAAATT
44448 AGAAATCGGT
Statistics
Matches: 83, Mismatches: 15, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
65 4 0.05
66 70 0.84
67 9 0.11
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.32
Consensus pattern (65 bp):
AGGTTACCAAAATTTCATAGTGAGGTTACCAAAATTTATAGGAAGGTTACAAAATTTTCAAATGA
Found at i:45339 original size:326 final size:325
Alignment explanation
Indices: 44482--45886 Score: 1489
Period size: 326 Copynumber: 4.2 Consensus size: 325
44472 CCGAAATTTC
* *
44482 ATATTTTTTTATGAGTAGTGTGGCCAAAAATTGAGGAAAAATATTTCGTGTCCATTTTTTGAAAA
1 ATATTTTTTTATGAGTA-TTTTGCCAAAAATTGAGGAAAAATATTTCG-GTCCA-TTTTTG-AAA
* * * * * * *
44547 ATTTTAGCCGAAATTGTGTACCATCACGGTTTTTGGCTAAAAACGCGTT-CTGAGCCCCGAT-TC
62 ATTTTCGTCGAAATCGTGTA-CATCACGGTTTTTAGCTAAAAACGCGTTCCGGGGACCCG-TCTC
* * *
44610 AGTTTTACATGATTTTTGGCGTCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAG
125 AGTTTTGCATGATTTTTGGCATCGAGACTCCTTGAAATATCTATATTCATCTAATAAAATCTCAG
* *
44675 CCACGTTGGATTTAAGGATATGTTTTTACGAGCATCTGAAACCGGTTTCGATTTAATTGGAAATT
190 CCACATTGGATTTAAGGATATGTTTTTACGAGCATCTGAAACCGGTTTCGATTTAATTAGAAATT
* * * *
44740 AATTC-AAAAAAATA-GGAATACGATATTAGAAGCGTG-AAAGCCCTCTAATCTTTTTGGAATTA
255 AATTCAAAAAAAATAGGGAAAACGATATTAGAAGCGTGAAAAGCCCTCCAATATTTTTGGCATTA
*
44802 AATTAA
320 AATTAT
* * * * * * *
44808 ATATATTTTTTATGAATATTGTGGCAAAAAACTAAGGAAAAATATTTTAGGTCCTTTTTTGCAAA
1 ATAT-TTTTTTATGAGTATT-TTGCCAAAAATTGAGGAAAAATA-TTTCGGTCCATTTTTG-AAA
* * * *
44873 ATTTTAAC-T-GAAATCGTGTACAAACCATAACGGTTTTTAGCTAAAAATGTGTTCC-GGAACCC
62 ATTTT--CGTCGAAATCGTGT----A-CATCACGGTTTTTAGCTAAAAACGCGTTCCGGGGACCC
* * *
44935 CTGCTAAGTTTTGCATGATTTTTTGTGC--CGAGACTCCTTGAAATATCTATAATCATCTAATAA
120 GT-CTCAGTTTTGCATGA-TTTTTG-GCATCGAGACTCCTTGAAATATCTATATTCATCTAATAA
* * * *
44998 AATCTCAGTCACATTGGATTTAAGGTTATGCTTTTACGAGCATCTGAAACCGGTTTTGATTTAAT
182 AATCTCAGCCACATTGGATTTAAGGATATGTTTTTACGAGCATCTGAAACCGGTTTCGATTTAAT
* * * *
45063 TAGAAATTAATTTAGAAAAAATAGGGAAAACGATATTAGAAGCTTGAAAAGCCCTCCAATCTTTT
247 TAGAAATTAATTCAAAAAAAATAGGGAAAACGATATTAGAAGCGTGAAAAGCCCTCCAATATTTT
* *
45128 TGGCGTTGAATTAT
312 TGGCATTAAATTAT
* * * *
45142 ATATTTTTTTATTAGTATTTTGCCAAAACTTGAGGAAAAATATTTCGGATTCATTTTTGCAAATT
1 ATATTTTTTTATGAGTATTTTGCCAAAAATTGAGGAAAAATATTTCGG-TCCATTTTTGAAAATT
** * * *
45207 TTCGTCGAAATCGTGTATGTCACGGTTTTTCGCTAAAAGCGCGTTCCGGGGGCCCGTCTCAGTTT
65 TTCGTCGAAATCGTGTACATCACGGTTTTTAGCTAAAAACGCGTTCCGGGGACCCGTCTCAGTTT
* * **
45272 TGCATGATTTTTGGCATCGAGACTCCTTGAAATATTTATATTCATCTAATAAAATATCATACACA
130 TGCATGATTTTTGGCATCGAGACTCCTTGAAATATCTATATTCATCTAATAAAATCTCAGCCACA
* * **
45337 TTGGATTTAAGGATAT-TTTTCTACTAGCATATGAAACATGTTTCGATTTAATTAGAAATTAATT
195 TTGGATTTAAGGATATGTTTT-TACGAGCATCTGAAACCGGTTTCGATTTAATTAGAAATTAATT
** * *
45401 CAAAAAAAATAGGGAAAAATATATTAGAATCGTGAAAAGCCCTCCAATATTTTT-GCATTGAATT
259 CAAAAAAAATAGGGAAAACGATATTAGAAGCGTGAAAAGCCCTCCAATATTTTTGGCATTAAATT
45465 AT
324 AT
* *
45467 ATA-TTTTTTATGTGTATTTTGGACAAAAATTGAGGAAAAATATTTCGGGTCCATTTTTTGAATA
1 ATATTTTTTTATGAGTATTTT-GCCAAAAATTGAGGAAAAATATTTC-GGTCCA-TTTTTGAA-A
* * * **
45531 ATTTTAGTCGAAATCTTGTAAGTTACATCACGGTTTTTTATCTAAAAACGCGTTCCGGGGTCTTG
62 ATTTTCGTCGAAATC--GT--G-TACATCACGG-TTTTTAGCTAAAAACGCGTTCCGGGGACCCG
* * * *
45596 ACTCAGTTTTGCATGATTTTTGGCACCAAGACTCC-TGAAATATCTATATTCATCTAATTAAATC
121 TCTCAGTTTTGCATGATTTTTGGCATCGAGACTCCTTGAAATATCTATATTCATCTAATAAAATC
* * * * **
45660 TCAGCCACATTGAATTTAAGAATATTTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAG-
186 TCAGCCACATTGGATTTAAGGATATGTTTTTACGAGCATCTGAAACCGGTTTCGATTTAATTAGA
* * *
45724 -ATTCATTCGGAAAAAAAAAAATAGGTAAAACGATATTAGAAGCGTGAAAAGACCTCCAATATTT
251 AATTAATTC-----AAAAAAAATAGGGAAAACGATATTAGAAGCGTGAAAAGCCCTCCAATATTT
* *
45788 TTAGCTTTAAATTAT
311 TTGGCATTAAATTAT
* *
45803 ATA-TTTCTTATGAGTATTTTGGGCC-AAAATTGAGAAAAAAATATTTCGAGTCCATTTTTGTAA
1 ATATTTTTTTATGAGTATTTT--GCCAAAAATTGAG-GAAAAATATTTCG-GTCCATTTTTG-AA
*
45866 AATTTTAC-CCGAAATCGTGTA
61 AATTTT-CGTCGAAATCGTGTA
45887 TTAACGATTA
Statistics
Matches: 910, Mismatches: 123, Indels: 87
0.81 0.11 0.08
Matches are distributed among these distances:
324 17 0.02
325 49 0.05
326 217 0.24
327 58 0.06
328 4 0.00
329 4 0.00
330 38 0.04
331 142 0.16
332 126 0.14
333 96 0.11
334 33 0.04
335 48 0.05
336 57 0.06
337 21 0.02
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (325 bp):
ATATTTTTTTATGAGTATTTTGCCAAAAATTGAGGAAAAATATTTCGGTCCATTTTTGAAAATTT
TCGTCGAAATCGTGTACATCACGGTTTTTAGCTAAAAACGCGTTCCGGGGACCCGTCTCAGTTTT
GCATGATTTTTGGCATCGAGACTCCTTGAAATATCTATATTCATCTAATAAAATCTCAGCCACAT
TGGATTTAAGGATATGTTTTTACGAGCATCTGAAACCGGTTTCGATTTAATTAGAAATTAATTCA
AAAAAAATAGGGAAAACGATATTAGAAGCGTGAAAAGCCCTCCAATATTTTTGGCATTAAATTAT
Found at i:55109 original size:7 final size:7
Alignment explanation
Indices: 55094--55123 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
55084 AGATGCAGAT
*
55094 GCAACTG
1 GCAAGTG
55101 GCAAGTG
1 GCAAGTG
55108 GCAAGTG
1 GCAAGTG
55115 GCAAGTG
1 GCAAGTG
55122 GC
1 GC
55124 TGAGCTCACG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.27, C:0.20, G:0.40, T:0.13
Consensus pattern (7 bp):
GCAAGTG
Found at i:72494 original size:60 final size:60
Alignment explanation
Indices: 72401--72522 Score: 226
Period size: 60 Copynumber: 2.0 Consensus size: 60
72391 TTGTACGGGA
72401 TCTCCCTAGACCACCATGGGATCGTAAAAAAGAAGATATTACAACCGAAAGAGTTATTCC
1 TCTCCCTAGACCACCATGGGATCGTAAAAAAGAAGATATTACAACCGAAAGAGTTATTCC
* *
72461 TCTCCCTAGACCACCATGGGATCGTAAGAAAGAAGATATTATAACCGAAAGAGTTATTCC
1 TCTCCCTAGACCACCATGGGATCGTAAAAAAGAAGATATTACAACCGAAAGAGTTATTCC
72521 TC
1 TC
72523 CGCCTCCCAT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (60 bp):
TCTCCCTAGACCACCATGGGATCGTAAAAAAGAAGATATTACAACCGAAAGAGTTATTCC
Found at i:73898 original size:1 final size:1
Alignment explanation
Indices: 73892--73920 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
73882 TCACATATAA
73892 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
73921 ATGTTTCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:74771 original size:27 final size:29
Alignment explanation
Indices: 74741--74807 Score: 75
Period size: 33 Copynumber: 2.2 Consensus size: 29
74731 TTGTAAGTAA
74741 GCCTCCT-CC-TATGGTACGTCCTGTTCT
1 GCCTCCTCCCGTATGGTACGTCCTGTTCT
*
74768 GCCTCCTATTCCCGTTGTGGTACGTCCTGTTCT
1 GCCTCC---TCCCG-TATGGTACGTCCTGTTCT
74801 GCCTCCT
1 GCCTCCT
74808 GTAGGTATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
27 6 0.18
30 2 0.06
31 2 0.06
33 23 0.70
ACGTcount: A:0.06, C:0.37, G:0.19, T:0.37
Consensus pattern (29 bp):
GCCTCCTCCCGTATGGTACGTCCTGTTCT
Found at i:74835 original size:33 final size:33
Alignment explanation
Indices: 74798--74865 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
74788 TACGTCCTGT
*
74798 TCTGCCTCCTGTAGGTATGCCTCCTCCTATGCC
1 TCTGCCTCCTGTACGTATGCCTCCTCCTATGCC
74831 TCTGCCTCCTGTACGTATGCCTCCTCCTATGCC
1 TCTGCCTCCTGTACGTATGCCTCCTCCTATGCC
74864 TC
1 TC
74866 CTCCGGTAGG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.09, C:0.41, G:0.16, T:0.34
Consensus pattern (33 bp):
TCTGCCTCCTGTACGTATGCCTCCTCCTATGCC
Found at i:74836 original size:18 final size:18
Alignment explanation
Indices: 74815--74865 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 18
74805 CCTGTAGGTA
74815 TGCCTCCTCCTATGCCTC
1 TGCCTCCTCCTATGCCTC
* * *
74833 TGCCTCCT-GTA--CGTA
1 TGCCTCCTCCTATGCCTC
74848 TGCCTCCTCCTATGCCTC
1 TGCCTCCTCCTATGCCTC
74866 CTCCGGTAGG
Statistics
Matches: 24, Mismatches: 6, Indels: 6
0.67 0.17 0.17
Matches are distributed among these distances:
15 10 0.42
16 2 0.08
17 2 0.08
18 10 0.42
ACGTcount: A:0.08, C:0.45, G:0.14, T:0.33
Consensus pattern (18 bp):
TGCCTCCTCCTATGCCTC
Found at i:74897 original size:12 final size:12
Alignment explanation
Indices: 74880--74907 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
74870 GGTAGGTGAA
74880 TTTGGATTAGTT
1 TTTGGATTAGTT
74892 TTTGGATTAGTT
1 TTTGGATTAGTT
74904 TTTG
1 TTTG
74908 TTTTTGGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.14, C:0.00, G:0.25, T:0.61
Consensus pattern (12 bp):
TTTGGATTAGTT
Done.