Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019686.1 Corchorus olitorius cultivar O-4 contig19719, 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: 19646
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:746 original size:3 final size:3
Alignment explanation
Indices: 738--825 Score: 176
Period size: 3 Copynumber: 29.3 Consensus size: 3
728 GTGGACAATA
738 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
786 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
826 GTGTATGAAC
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 85 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2029 original size:5 final size:5
Alignment explanation
Indices: 2006--2047 Score: 59
Period size: 5 Copynumber: 8.4 Consensus size: 5
1996 TAATATGTAG
*
2006 TATAA TATA- TATAT ATATAT TATAT TATAT TATAT TATAT TA
1 TATAT TATAT TATAT -TATAT TATAT TATAT TATAT TATAT TA
2048 AATATCTCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
4 4 0.11
5 26 0.74
6 5 0.14
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (5 bp):
TATAT
Found at i:2046 original size:15 final size:16
Alignment explanation
Indices: 2006--2052 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 16
1996 TAATATGTAG
*
2006 TATAATATA-TATATA
1 TATATTATATTATATA
2021 TATATTATATTATAT-
1 TATATTATATTATATA
*
2036 TATATTATATTAAATA
1 TATATTATATTATATA
2052 T
1 T
2053 CTCAACCTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 22 0.79
16 6 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TATATTATATTATATA
Found at i:2480 original size:22 final size:22
Alignment explanation
Indices: 2434--2578 Score: 75
Period size: 22 Copynumber: 6.5 Consensus size: 22
2424 GGAATGTTTT
**
2434 TATGAAATTTTGATAATTATCC
1 TATGAAATTTTGATAAACATCC
*
2456 TATTAAATTTTGATAAACA-CGC
1 TATGAAATTTTGATAAACATC-C
* *
2478 TATGAAATATTGAT-AA-TTGCC
1 TATGAAATTTTGATAAACAT-CC
** *
2499 TATGAAATCGTGATAATAAACTCC
1 TATGAAATTTTGATAA-ACA-TCC
* * **
2523 ATATG-AACTTTGAT-AACCTAAA
1 -TATGAAATTTTGATAAACAT-CC
*
2545 TATGAAATTTTAATAAACCATCC
1 TATGAAATTTTGATAAA-CATCC
2568 TATGAAATTTT
1 TATGAAATTTT
2579 CTAACCTTCT
Statistics
Matches: 90, Mismatches: 21, Indels: 23
0.67 0.16 0.17
Matches are distributed among these distances:
21 21 0.23
22 39 0.43
23 15 0.17
24 10 0.11
25 5 0.06
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.37
Consensus pattern (22 bp):
TATGAAATTTTGATAAACATCC
Found at i:2503 original size:21 final size:21
Alignment explanation
Indices: 2434--2515 Score: 83
Period size: 22 Copynumber: 3.8 Consensus size: 21
2424 GGAATGTTTT
2434 TATGAAATTTTGATAATTATCC
1 TATGAAATTTTGATAATTA-CC
* **
2456 TATTAAATTTTGATAAACACGC
1 TATGAAATTTTGATAATTAC-C
* *
2478 TATGAAATATTGATAATTGCC
1 TATGAAATTTTGATAATTACC
**
2499 TATGAAATCGTGATAAT
1 TATGAAATTTTGATAAT
2516 AAACTCCATA
Statistics
Matches: 49, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
21 17 0.35
22 32 0.65
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TATGAAATTTTGATAATTACC
Found at i:2642 original size:22 final size:22
Alignment explanation
Indices: 2594--2646 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
2584 CTTCTTATGA
**
2594 TTTTTGATAATCTCCCTATGAG
1 TTTTTGATAATCTCCCTACAAG
* * *
2616 ATTTTGTTAATCTCCCTACAAT
1 TTTTTGATAATCTCCCTACAAG
2638 TTTTTGATA
1 TTTTTGATA
2647 TTATAGTATG
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.25, C:0.17, G:0.09, T:0.49
Consensus pattern (22 bp):
TTTTTGATAATCTCCCTACAAG
Found at i:3953 original size:30 final size:30
Alignment explanation
Indices: 3894--3954 Score: 72
Period size: 30 Copynumber: 2.0 Consensus size: 30
3884 TCTAAATTTC
*
3894 TATTATTTTAATAATTGAATAATTAAAATAT
1 TATTATTTTAATAATGGAAT-ATTAAAATAT
3925 TATTA-TTTAATAATGGCAAT-TTAGAAATAT
1 TATTATTTTAATAATGG-AATATTA-AAATAT
3955 ATTTGAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
29 3 0.11
30 16 0.59
31 8 0.30
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.46
Consensus pattern (30 bp):
TATTATTTTAATAATGGAATATTAAAATAT
Found at i:17065 original size:332 final size:331
Alignment explanation
Indices: 16139--17915 Score: 1675
Period size: 332 Copynumber: 5.4 Consensus size: 331
16129 ATACTTTACA
* * * ** * * *
16139 TCATCTAACCAAAGCTCAGCAACATTGGATTTAAAAATTTGTTTTTATGAGTATTTGAATCTTGT
1 TCATCTAATCAAATCTCAGCTACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * * *
16204 TTCGATTTAATTAGAAATTAATTTTGAAAAAATAAGTAATACGATATTAAAAGCGTGAAAAGCCC
66 TTCGATTTAATTAGAAATTAATTTCGAAAAAATAGGAAAAACGATATTAAAAGCGTGAAAAGCCC
* * * * *
16269 -TC-GTCTCTTCGGCGTTAAATTATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGAGAAAT
131 TTCAATCTTTTTGGCGTTAAATTATATATTTTTATGAGTATTTTAGCAAAAAATTGAGGAAAAAT
* * * ***
16332 CTTTCGTGTCAATTTTTGCAAAATTTTAGCCGAAATCCTGTACTATAACAACCATCACGGGTTTT
196 CTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAC--T---AATCATCACAATTTTT
* * ** * * * *
16397 CGCTAAAAACGCG-TTCTGGGG-ACTTGTCTCAATTTTGCATGATTTTTGACTCCGAGACTGCTT
256 GGCTAAAAACGCGTTTC-GGGGCCCCAG-CTCAGTTTTGCATGATTTTTGACGCCAAGACTCCTT
16460 GAAATATCTATAT
319 GAAATATCTATAT
* * *
16473 TCATCTAAACAAATCTCAG-TCACAGTGGATTTAAGGATTTGTTTTTACGAGCATCCGAATCTTG
1 TCATCTAATCAAATCTCAGCT-ACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTG
* * *
16537 TTTCGATTTAATTAGAAACTAA-TTCGAAAAAATAGGAAAAACAATATTAGAAA-CGTCAAAAGC
65 TTTCGATTTAATTAGAAATTAATTTCGAAAAAATAGGAAAAACGATATTA-AAAGCGTGAAAAGC
16600 CCTTCAATCTTTTTGGCGTTGAAA-TATATATTTTCTATGAGTATTTTAGCAAAAAATTGAGGAA
129 CCTTCAATCTTTTTGGCGTT-AAATTATATATTTT-TATGAGTATTTTAGCAAAAAATTGAGGAA
* * * * * * *
16664 ATATCTTTCAGGTCAATTTTTACAAAATTTTAACCGAAATCATGTAATAACCATCACAATTTTTG
192 AAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAATCATCACAATTTTTG
* * * *
16729 GCTAAAAAAGCGTTTCGGGGCCCCAGCTCAGTTTTGCATGATTTTTGACGCTAAGATTCCTTGAG
257 GCTAAAAACGCGTTTCGGGGCCCCAGCTCAGTTTTGCATGATTTTTGACGCCAAGACTCCTTGAA
*
16794 ATATCCATAT
322 ATATCTATAT
* * * *
16804 TCATATACTCAAATCTCAGCTACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATTTTGT
1 TCATCTAATCAAATCTCAGCTACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * * * * *
16869 TTCGATTTAATGAGAAATTAATTTTGAAAAAATATGAAAAACAATATTAAAAGTGTGAAAAGTCC
66 TTCGATTTAATTAGAAATTAATTTCGAAAAAATAGGAAAAACGATATTAAAAGCGTGAAAAGCCC
* * * * *
16934 TCCAATATTTTTGGTGTTAAATTATTTATATTTTATGAGTATTTTATCAAAAAATTGAGGAAAAA
131 TTCAATCTTTTTGGCGTTAAATTATATAT-TTTTATGAGTATTTTAGCAAAAAATTGAGGAAAAA
* * * *
16999 TTTTTCGGGTCATTTTTTGCAAAATTTTAGACAAAATCGTGTACTAATCATCACAATTTTTGGCT
195 TCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAATCATCACAATTTTTGGCT
* * * * * * * * * *
17064 AAAAATGTGTGTCGGGGTCTCGGCTCAGTTTTGCATGATTTTGGGCGCCGAGGCTCCTTGAAATA
260 AAAAACGCGTTTCGGGGCCCCAGCTCAGTTTTGCATGATTTTTGACGCCAAGACTCCTTGAAATA
17129 TCTATAT
325 TCTATAT
* * * * * * *
17136 TCATCTAATAAAAACTTAGCCACATTGCATTTAAGGATTTGCTTTTACGAGCATCTGAATATTGT
1 TCATCTAATCAAATCTCAGCTACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * * * *
17201 TTCGATTTAATTAGAAATTCA-TTCAAAAAAGATATGAAAAACGATATTAAAAGCAT-CAAAGCC
66 TTCGATTTAATTAGAAATTAATTTCGAAAAA-ATAGGAAAAACGATATTAAAAGCGTGAAAAGCC
** ** * *** *
17264 CTTTTATCTTTTTGGTTTTGAATTATATATTTTTTTATGAGTATTGCGGCTAAAAATTG-GGAAA
130 CTTCAATCTTTTTGGCGTTAAATTATATA--TTTTTATGAGTATTTTAGCAAAAAATTGAGGAAA
* * * *
17328 ATATCTTTCGGGTCAATTTTCG-AAAATTTTAGCCGAAATCGTGTAAATAATAATCACGATTTTT
193 A-ATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGT-ACTAATCATCACAATTTTT
* * * * * * * * *
17392 GGCGAAAAACGCGTTCCGGGGCCCGA-TTCAGTTTTACATGATTTTTTACACCAACAGTCCTTGA
256 GGCTAAAAACGCGTTTCGGGGCCCCAGCTCAGTTTTGCATGATTTTTGACGCCAAGACTCCTTGA
17456 AATATCTATAT
321 AATATCTATAT
* * * * *
17467 TCATCTTA-CTGAATCTCAGC--C-------------A-TTGTTTTTACAAGCATCTGAATCATA
1 TCATCTAATC-AAATCTCAGCTACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTG
* * *
17515 TTTTGATTTAATTAGAAATTAA-TTCAGAAAAAAATAGGAAAAACGATATTAGAAGAGTGAAAAG
65 TTTCGATTTAATTAGAAATTAATTTC-G-AAAAAATAGGAAAAACGATATTAAAAGCGTGAAAAG
* * * * *
17579 CCCTTCAATCTTTTTTGCGTTGAATTATATATTTTTTATGAGTATTGTGGCTAAAAATTGAGGAA
128 CCCTTCAATCTTTTTGGCGTTAAATTATATA-TTTTTATGAGTATTTTAGCAAAAAATTGAGGAA
* * * * ***
17644 AAATATTTCGGATCAATTTTTGCAAAATATTAGCCGAAATCGTGTAC-CATCA--AGGTGTTTTT
192 AAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAATCATCA-CAATTTTT
* * * * * ** * * * ** *
17706 GGCTATAAATGCG-TTCCGAGCTCTGGGTCAGTTTTGCATGATATTTGGCGTTAAAACTCCTTGA
256 GGCTAAAAACGCGTTTCGGGGCCCCAGCTCAGTTTTGCATGATTTTTGACGCCAAGACTCCTTGA
17770 AATATCTATAT
321 AATATCTATAT
* * * * *
17781 TTATCTGATAAAATCTTAG-TCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTG
1 TCATCTAATCAAATCTCAGCT-ACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTG
* * * * * *
17845 TTTCGATTTAATTAGAAATTAA-TTCGGAAAAAGTAGGATAAACGATATTAGAATCGTAAAAACC
65 TTTCGATTTAATTAGAAATTAATTTC-GAAAAAATAGGAAAAACGATATTAAAAGCGTGAAAAGC
17909 CCTTCAA
129 CCTTCAA
17916 AGACCCTGAC
Statistics
Matches: 1182, Mismatches: 217, Indels: 93
0.79 0.15 0.06
Matches are distributed among these distances:
313 7 0.01
314 67 0.06
315 47 0.04
316 69 0.06
317 62 0.05
329 40 0.03
330 47 0.04
331 263 0.22
332 372 0.31
333 37 0.03
334 80 0.07
335 21 0.02
336 70 0.06
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (331 bp):
TCATCTAATCAAATCTCAGCTACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
TTCGATTTAATTAGAAATTAATTTCGAAAAAATAGGAAAAACGATATTAAAAGCGTGAAAAGCCC
TTCAATCTTTTTGGCGTTAAATTATATATTTTTATGAGTATTTTAGCAAAAAATTGAGGAAAAAT
CTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAATCATCACAATTTTTGGCTA
AAAACGCGTTTCGGGGCCCCAGCTCAGTTTTGCATGATTTTTGACGCCAAGACTCCTTGAAATAT
CTATAT
Found at i:17434 original size:663 final size:658
Alignment explanation
Indices: 16148--17915 Score: 1965
Period size: 663 Copynumber: 2.7 Consensus size: 658
16138 ATCATCTAAC
* * * *
16148 CAAAGCTCAGCAACATTGGATTTAAAAATTTGTTTTTATGAGTATTTGAATCTTGTTTCGATTTA
1 CAAATCTCAGC-ACATTGGATTT-AAAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTA
* * * * *
16213 ATTAGAAATTAATTTTGAAAAAATAAGTAATACGATATTAAAAGCGTGAAAAGCCCTC-GTCTCT
64 ATTAGAAATTAATTTTGAAAAAATAAGAAAAACGATATTAAAAGAGTGAAAAGCCCTCAATCTTT
* * * * *
16277 TCGGCGTTAAATTATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGAGAAATCTTTCGTGTC
129 TTGGCGTTAAATTATATATTTTTATGAGTATTTTAGCAAAAAATTGAGGAAAAATATTTCGGGTC
* * * * * *
16342 AATTTTTGCAAAATTTTAGCCGAAATCCTGTACTATAACAACCATCACGGGTTTTCGCTAAAAAC
194 AATTTTTGCAAAATTTTAGCCGAAATCGTGTAC--T---AATCATCACAGTTTTTGGCTAAAAAT
* * * * * *
16407 GCGTTCTGGGGACTTGTCTCAATTTTGCATGATTTTTGACTCCGAGACTGCTTGAAATATCTATA
254 GCGTTC-GGGG-CTCGGCTCAGTTTTGCATGA-TTTTGGCGCCGAGACTCCTTGAAATATCTATA
* * *
16472 TTCATCTAA-ACAAATCTCAGTCACAGTGGATTTAAGGATTTGTTTTTACGAGCATCCGAATCTT
316 TTCATCTAATA-AAATCTTAGTCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTT
* * *
16536 GTTTCGATTTAATTAGAAACTAATTCGAAAAA-ATAGGAAAAACAATATTAGAAACGTCAAAAGC
380 GTTTCGATTTAATTAGAAATTAATTCGAAAAAGATAGGAAAAACGATATTAGAAACATCAAAAGC
**
16600 CCTTCAATCTTTTTGGCGTTGAAATATATATTTTCTATGAGTATTTTAGCAAAAAATTGAGGAAA
445 CCTTCAATCTTTTTGGCGTTGAAATATATATTTTCTATGAGTATTGCAGCAAAAAATTGAGGAAA
*
16665 TATCTTTCAGGTCAATTTTTACAAAATTTTAACCGAAATCATGTAATAACCATCACAATTTTTGG
510 TATCTTTCAGGTCAATTTTTACAAAATTTTAACCGAAATCATGTAATAACAATCACAATTTTTGG
* * * * * * * *
16730 CTAAAAAAGCGTTTCGGGGCCCCAGCTCAGTTTTGCATGATTTTTGACGCTAAGATTCCTTGAGA
575 CGAAAAAAGCGTTCCGGGGCCCCAGCTCAGTTTTACATGATTTTTGACACCAACAGTCCTTGAAA
16795 TATCCATATTCAT-ATACT
640 TATCCATATTCATCATACT
*
16813 CAAATCTCAGCTACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATTTTGTTTCGATTTA
1 CAAATCTCAGC-ACATTGGATTTAA-AATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTA
* * * * * *
16878 ATGAGAAATTAATTTTGAAAAAATATGAAAAACAATATTAAAAGTGTGAAAAGTCCTCCAATATT
64 ATTAGAAATTAATTTTGAAAAAATAAGAAAAACGATATTAAAAGAGTGAAAAGCCCT-CAATCTT
* * * *
16943 TTTGGTGTTAAATTATTTATATTTTATGAGTATTTTATCAAAAAATTGAGGAAAAATTTTTCGGG
128 TTTGGCGTTAAATTATATAT-TTTTATGAGTATTTTAGCAAAAAATTGAGGAAAAATATTTCGGG
* * * * *
17008 TCATTTTTTGCAAAATTTTAGACAAAATCGTGTACTAATCATCACAATTTTTGGCTAAAAATGTG
192 TCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAATCATCACAGTTTTTGGCTAAAAATGCG
*
17073 TGTCGGGGTCTCGGCTCAGTTTTGCATGATTTTGGGCGCCGAGGCTCCTTGAAATATCTATATTC
257 T-TCGGGG-CTCGGCTCAGTTTTGCATGATTTT-GGCGCCGAGACTCCTTGAAATATCTATATTC
* * * * *
17138 ATCTAATAAAAACTTAGCCACATTGCATTTAAGGATTTGCTTTTACGAGCATCTGAATATTGTTT
319 ATCTAATAAAATCTTAGTCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTT
* * *
17203 CGATTTAATTAGAAATTCATTCAAAAAAGATATGAAAAACGATATTA-AAAGCATC-AAAGCCCT
384 CGATTTAATTAGAAATTAATTCGAAAAAGATAGGAAAAACGATATTAGAAA-CATCAAAAGCCCT
** ** * * * *
17266 TTTATCTTTTTGGTTTTGAATTATATATTTTTTTATGAGTATTGCGGCTAAAAATTG-GGAAAAT
448 TCAATCTTTTTGGCGTTGAAATATATA-TTTTCTATGAGTATTGCAGCAAAAAATTGAGG-AAAT
* * * * *
17330 ATCTTTCGGGTCAA-TTTT-CGAAAATTTTAGCCGAAATCGTGTAAATAATAATCACGATTTTTG
511 ATCTTTCAGGTCAATTTTTAC-AAAATTTTAACCGAAATCATGT-AATAACAATCACAATTTTTG
* * * *
17393 GCGAAAAACGCGTTCCGGGGCCCGA-TTCAGTTTTACATGATTTTTTACACCAACAGTCCTTGAA
574 GCGAAAAAAGCGTTCCGGGGCCCCAGCTCAGTTTTACATGATTTTTGACACCAACAGTCCTTGAA
* *
17457 ATATCTATATTCATCTTACT
639 ATATCCATATTCATCATACT
* * * * *
17477 -GAATCTCAGC-C------------A-TTGTTTTTACAAGCATCTGAATCATATTTTGATTTAAT
1 CAAATCTCAGCACATTGGATTTAAAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAAT
** * *
17527 TAGAAATTAATTCAGAAAAAAATAGGAAAAACGATATTAGAAGAGTGAAAAGCCCTTCAATCTTT
66 TAGAAATTAATTTTG-AAAAAATAAGAAAAACGATATTAAAAGAGTGAAAAGCCC-TCAATCTTT
* * * * * *
17592 TTTGCGTTGAATTATATATTTTTTATGAGTATTGTGGCTAAAAATTGAGGAAAAATATTTCGGAT
129 TTGGCGTTAAATTATATA-TTTTTATGAGTATTTTAGCAAAAAATTGAGGAAAAATATTTCGGGT
* * ** *
17657 CAATTTTTGCAAAATATTAGCCGAAATCGTGTAC-CATCA--AGGTGTTTTTGGCTATAAATGCG
193 CAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAATCATCA-CAGTTTTTGGCTAAAAATGCG
* * * *** * *
17719 TTCCGAGCTCTGGGTCAGTTTTGCATGATATTTGGCGTTAAAACTCCTTGAAATATCTATATTTA
257 TTCGGGGCTC-GGCTCAGTTTTGCATGAT-TTTGGCGCCGAGACTCCTTGAAATATCTATATTCA
* *
17784 TCTGATAAAATCTTAGTCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTC
320 TCTAATAAAATCTTAGTCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTC
* * * * *
17849 GATTTAATTAGAAATTAATTCGGAAAAAG-TAGGATAAACGATATTAGAATCGTAAAAACCCCTT
385 GATTTAATTAGAAATTAATTC-GAAAAAGATAGGAAAAACGATATTAGAAACATCAAAAGCCCTT
17913 CAA
449 CAA
17916 AGACCCTGAC
Statistics
Matches: 932, Mismatches: 148, Indels: 65
0.81 0.13 0.06
Matches are distributed among these distances:
644 3 0.00
645 143 0.15
646 37 0.04
647 49 0.05
648 125 0.13
649 2 0.00
661 1 0.00
662 5 0.01
663 263 0.28
664 107 0.11
665 106 0.11
666 2 0.00
667 19 0.02
668 70 0.08
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (658 bp):
CAAATCTCAGCACATTGGATTTAAAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAAT
TAGAAATTAATTTTGAAAAAATAAGAAAAACGATATTAAAAGAGTGAAAAGCCCTCAATCTTTTT
GGCGTTAAATTATATATTTTTATGAGTATTTTAGCAAAAAATTGAGGAAAAATATTTCGGGTCAA
TTTTTGCAAAATTTTAGCCGAAATCGTGTACTAATCATCACAGTTTTTGGCTAAAAATGCGTTCG
GGGCTCGGCTCAGTTTTGCATGATTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAAT
AAAATCTTAGTCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTA
ATTAGAAATTAATTCGAAAAAGATAGGAAAAACGATATTAGAAACATCAAAAGCCCTTCAATCTT
TTTGGCGTTGAAATATATATTTTCTATGAGTATTGCAGCAAAAAATTGAGGAAATATCTTTCAGG
TCAATTTTTACAAAATTTTAACCGAAATCATGTAATAACAATCACAATTTTTGGCGAAAAAAGCG
TTCCGGGGCCCCAGCTCAGTTTTACATGATTTTTGACACCAACAGTCCTTGAAATATCCATATTC
ATCATACT
Found at i:18675 original size:335 final size:331
Alignment explanation
Indices: 17928--19512 Score: 1268
Period size: 335 Copynumber: 4.8 Consensus size: 331
17918 ACCCTGACTT
* * ** * ** * *
17928 AGTTTTGCATGATTTTTGGTGCAAAGACTCCTTGAGGTATCCATATTCATCTAATCAAATCTCAG
1 AGTTTTGCATAATTTTTGGCGCGGAGAATCCTTGAAATATCTATATTCATCTAACCAAATCTCAG
* * * * ** * * *
17993 CCACATTGCATTGAAGGATTTGTTTTTATGAGCATCTGAATTTTGTTTGGATTTGA-TAAAA-AA
66 CCACATTGGATTTAAGGATTTGATTTTACGAGCATCTGAATCATGTTTCGATTTAATTAAAATTA
* * * *
18056 ATT-----AATTCA-GAAAAACGATATGAAAAGCGTGAAAAGTCCTCCAA-CTTTTTTGG-TGTC
131 ATTCAGAAAAAT-ATGAAAAACAATATTAAAAGCATGAAAAGTCCTCCAATC-TTTTTGGAT-T-
* * * *
18113 AAATTATATATATTTCATGAGTATT-TTAGCCAAAAATTGAGG-AAATATATTTCGGGTCATTTT
192 GAATTATATATATTTTATGAGTATTGTGA-CTAAAAATTGAGGTAAA-ATATTTCGGGTCA----
* * * * * * *
18176 TTTTTTGCAAAATTTTAGCCGAACTCGTGTAC-TAA-CCATCACGGTTATTTG-GTAAAAATGCG
251 ATTTTTGCAAAATTTTAGCCGAAATCGTGTACGTAATACATCACAGTT-TTTGACTAAAAACGCA
** *
18238 TT-TCG-GGACCCCGACTC
315 TTCT-GAGG-CCAAGAATC
* ** * * *
18255 AATTTTGCACGATTTTTGGCACCGG-GACTCCTTGAAATATCTATATTCATCTAATCAAATCTCA
1 AGTTTTGCATAATTTTTGGC-GCGGAGAATCCTTGAAATATCTATATTCATCTAACCAAATCTCA
* * * * *
18319 GCCAGATTGCATTTAAGGATTTGATTTCACGAGCATATGAATCTTGTTTCGATTTAATTAAAAAT
65 GCCACATTGGATTTAAGGATTTGATTTTACGAGCATCTGAATCATGTTTCGATTTAATT-AAAAT
* * **
18384 TAATTCAGAAAAATATGAAAAACAATATTAAAAGCATG-AAAGACCTCCAATCTTTTCGGAGAAG
129 TAATTCAGAAAAATATGAAAAACAATATTAAAAGCATGAAAAGTCCTCCAATCTTTTTGGA-TTG
* * * *
18448 AATTATATATATTTTACGAGTATTTTAGAC-AAAAATTGAGGAAAAATATTTCTGGTCAATTTTT
193 AATTATATATATTTTATGAGTATTGT-GACTAAAAATTGAGGTAAAATATTTCGGGTCAATTTTT
** * *
18512 GCAAAATAATAGCCGAAATCGTGTACGTTAATTAAAATCACGGTTTTTGACTAAAAACGCATTCT
257 GCAAAATTTTAGCCGAAATCGTGTACG-TAA-T-ACATCACAGTTTTTGACTAAAAACGCATTCT
*
18577 GAGGCCAAG-TTC
319 GAGGCCAAGAATC
* *
18589 AGTGTTT-TATTAATTTTTGGCGCGGAGAATCCTTGAAATATCTACATTCATCTAACCAAATCTC
1 AGT-TTTGCA-TAATTTTTGGCGCGGAGAATCCTTGAAATATCTATATTCATCTAACCAAATCTC
* * * *
18653 AGCCACATTGGATTTAAGGATTTGTAATATA--AGAATCCGAATCATGTTTCGATTTAATTAAAA
64 AGCCACATTGGATTTAAGGATTTG-ATTTTACGAGCATCTGAATCATGTTTCGATTTAATTAAAA
* * * * * * * *
18716 TTAATTCGGAAAATAACAGGAAAAACATTATTAGAAGCTTGAAAAGTCCTTCAATCTTTTTGGCT
128 TTAATTCAG-AAA-AATATGAAAAACAATATTAAAAGCATGAAAAGTCCTCCAATCTTTTTGG-A
*
18781 TTGAATTATATA-ATTTTCATGAGTATTGTGACTAAAAATTGA--TAAAATAACTTTCGGGTAAA
190 TTGAATTATATATATTTT-ATGAGTATTGTGACTAAAAATTGAGGTAAAAT-A-TTTCGGGTCAA
* * * * * *
18843 TTTTTGCAAAATTTTAGCTGAAATCGTGTA-ATAAT-CATCACAGTTTTAGATTAAAAACGCGTC
252 TTTTTGCAAAATTTTAGCCGAAATCGTGTACGTAATACATCACAGTTTTTGACTAAAAACGCATT
* ** * *
18906 CCGAGGCCCTGACTA
317 CTGAGGCCAAGAATC
* * ** * ** * * *
18921 AGTTTTGCATGATTTTTGGCACCAAGACTTTTTTGAGATATCCATATTCATCTAATCAAATCTCA
1 AGTTTTGCATAATTTTTGGCGCGGAGA-ATCCTTGAAATATCTATATTCATCTAACCAAATCTCA
* * * * * * *
18986 ACTACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTATCGATTTAATTAGAATT
65 GCCACATTGGATTTAAGGATTTGATTTTACGAGCATCTGAATCATGTTTCGATTTAATTAAAATT
* * *
19051 AATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATTTTTTTGGCATTGA
130 AATTCAGAAAAATATGAAAAACAATATTAAAAGCATGAAAAGTCCTCCAATCTTTTTGG-ATTGA
*
19116 ATTATATATATTTTATGAGTATTGTGGCTAAAAATTGAGGTAAAATATTTCGGGTCAATTTTTGC
194 ATTATATATATTTTATGAGTATTGTGACTAAAAATTGAGGTAAAATATTTCGGGTCAATTTTTGC
* * * *
19181 AAAATTTTAGCCGAAATCATGAAC-CAGTACGATCACACGATTTTTTTTG-CTAAAAACGCATT-
259 AAAATTTTAGCCGAAATCGTGTACGTAATAC-ATCACA-G----TTTTTGACTAAAAACGCATTC
* **
19243 TCAGGGCCTCGAATC
318 TGA-GGCCAAGAATC
* * *
19258 AGTTTTGCATATTTTTTGTG-GC--AAAACTCCTTGAAATATCTATATTCATCTAACCAAATCTT
1 AGTTTTGCATAATTTTTG-GCGCGGAGAA-TCCTTGAAATATCTATATTCATCTAACCAAATCTC
* * *
19320 AGCCACATTGGATTTAAGGATTTGTTTTTACGATCATTTGAATCATGTTTCGATTTAATTAGAAA
64 AGCCACATTGGATTTAAGGATTTGATTTTACGAGCATCTGAATCATGTTTCGATTTAATTA-AAA
* * * * * *
19385 TTAATTTGATAAAAAAATTGTAAAAACAATATTAGAAGCATGAGAAG-CTCTTCAATCTTTTTGG
128 TTAA-TTCAGAAAAATA-TG-AAAAACAATATTAAAAGCATGAAAAGTC-CTCCAATCTTTTTGG
* * * * * * * *
19449 CGTTGAACTATATACT-TTCTAAGGGTATTTTGGCTAAACATTGA-G-AAAATATTTCGGGTCAA
189 -ATTGAATTATATA-TATTTTATGAGTATTGTGACTAAAAATTGAGGTAAAATATTTCGGGTCAA
19511 TT
252 TT
19513 CCATAATATT
Statistics
Matches: 1019, Mismatches: 178, Indels: 112
0.78 0.14 0.09
Matches are distributed among these distances:
327 101 0.10
328 2 0.00
329 4 0.00
330 32 0.03
331 166 0.16
332 68 0.07
333 60 0.06
334 111 0.11
335 236 0.23
336 96 0.09
337 62 0.06
338 10 0.01
339 70 0.07
340 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (331 bp):
AGTTTTGCATAATTTTTGGCGCGGAGAATCCTTGAAATATCTATATTCATCTAACCAAATCTCAG
CCACATTGGATTTAAGGATTTGATTTTACGAGCATCTGAATCATGTTTCGATTTAATTAAAATTA
ATTCAGAAAAATATGAAAAACAATATTAAAAGCATGAAAAGTCCTCCAATCTTTTTGGATTGAAT
TATATATATTTTATGAGTATTGTGACTAAAAATTGAGGTAAAATATTTCGGGTCAATTTTTGCAA
AATTTTAGCCGAAATCGTGTACGTAATACATCACAGTTTTTGACTAAAAACGCATTCTGAGGCCA
AGAATC
Found at i:19174 original size:667 final size:667
Alignment explanation
Indices: 18177--19462 Score: 1584
Period size: 667 Copynumber: 1.9 Consensus size: 667
18167 GGTCATTTTT
* * * * * **
18177 TTTTTGCAAAATTTTAGCCGAACTCGTGTACTAACCATCACGGTTATTTGGTAAAAATGCGTTTC
1 TTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACAGTTATTAGGTAAAAACGCGTCCC
** *
18242 GGGACCCCGACTCAATTTTGCACGATTTTTGGCACCGGGACTCCTTGAAATATCTATATTCATCT
66 GGGACCCCGACTCAATTTTGCACGATTTTTGGCACCAAGACTCCTTGAAATATCCATATTCATCT
* * * *
18307 AATCAAATCTCAGCCAGATTGCATTTAAGGATTTGATTTCACGAGCATATGAATCTTGTTTCGAT
131 AATCAAATCTCAACCACATTGCATTTAAGAATTTGATTTCACGAGCATATGAATCTTGTATCGAT
18372 TTAATTAAAAATTAATTCAGAAAAATATGAAAAACAATATTAAAAGCATGAAAGACCTCCAATCT
196 TTAATTAAAAATTAATTCAGAAAAATATGAAAAACAATATTAAAAGCATGAAAGACCTCCAATCT
* *
18437 TTTCGGAGAAGAATTATATATATTTTACGAGTATTTTAGACAAAAATTGAGGAAAAATATTTCTG
261 TTTCGGAGAAGAATTATATATATTTTACGAGTATTGTAGACAAAAATTGAGGAAAAATATTTCGG
* *
18502 GTCAATTTTTGCAAAATAATAGCCGAAATCGTGTA-C-GTTA-ATTAAAATC-ACGGTTTTTGAC
326 GTCAATTTTTGCAAAATAATAGCCGAAATCATGAACCAG-TACA-TAAAA-CGACGGTTTTTG-C
* * * *
18563 TAAAAACGCA-TTCTGAGGCCAAG-TTCAGTGTTT-TATTAATTTTTG-GCGCGGAGAA-TCCTT
387 TAAAAACGCATTTCAG-GGCCAAGAATCAGT-TTTGCA-TAATTTTTGTG-GC--AAAACTCCTT
18623 GAAATATCTACATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTAATATAAGA-
446 GAAATATCTACATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGT-ATATAAGAC
* *
18687 ATCCGAATCATGTTTCGATTTAATTA-AAATTAATTCG-GAAAATAACAGGAAAAACATTATTAG
510 ATCCGAATCATGTTTCGATTTAATTAGAAATTAATTCGAGAAAAAAACAGGAAAAACAATATTAG
* * *
18750 AAGCTTGAAAAG-TCCTTCAATCTTTTTGGCTTTGAATTATATAATTTTCATGAGTATTGTGACT
575 AAGCATGAAAAGCT-CTTCAATCTTTTTGGCGTTGAACTATATAATTTTCATGAGTATTGTGACT
18814 AAAAATTGATAAAATAACTTTCGGGTAAA
639 AAAAATTGATAAAATAACTTTCGGGTAAA
* * *
18843 TTTTTGCAAAATTTTAGCTGAAATCGTGTAATAATCATCACAGTT-TTAGATTAAAAACGCGTCC
1 TTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACAGTTATTAG-GTAAAAACGCGTCC
* * ** *
18907 CGAGG-CCCTGACT-AAGTTTTGCATGATTTTTGGCACCAAGACTTTTTTGAGATATCCATATTC
65 CG-GGACCCCGACTCAA-TTTTGCACGATTTTTGGCACCAAGAC-TCCTTGAAATATCCATATTC
* * * * *
18970 ATCTAATCAAATCTCAACTACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTAT
127 ATCTAATCAAATCTCAACCACATTGCATTTAAGAATTTGATTTCACGAGCATATGAATCTTGTAT
* * * *
19035 CGATTTAATT-AGAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCC
192 CGATTTAATTAAAAATTAATTCAGAAAAATATGAAAAACAATATTAAAAGCATG-AAAGACCTCC
* * ** * * *
19099 AATTTTTTTGGCA-TTGAATTATATATATTTTATGAGTATTGT-GGCTAAAAATTGAGGTAAAAT
256 AATCTTTTCGG-AGAAGAATTATATATATTTTACGAGTATTGTAGAC-AAAAATTGAGGAAAAAT
** * * ***
19162 ATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCATGAACCAGTACGATCACACGATTTTTT
319 ATTTCGGGTCAATTTTTGCAAAATAATAGCCGAAATCATGAACCAGTAC-ATAAAACGACGGTTT
** *
19227 TTGCTAAAAACGCATTTCAGGGCCTCGAATCAGTTTTGCATATTTTTTGTGGCAAAACTCCTTGA
383 TTGCTAAAAACGCATTTCAGGGCCAAGAATCAGTTTTGCATAATTTTTGTGGCAAAACTCCTTGA
* * * * *
19292 AATATCTATATTCATCTAACCAAATCTTAGCCACATTGGATTTAAGGATTTGTTTTTACGATCAT
448 AATATCTACATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTATATAAGA-CAT
** * * ** *
19357 TTGAATCATGTTTCGATTTAATTAGAAATTAATTTGATAAAAAAATTGTAAAAACAATATTAGAA
512 CCGAATCATGTTTCGATTTAATTAGAAATTAATTCGAGAAAAAAACAGGAAAAACAATATTAGAA
*
19422 GCATGAGAAGCTCTTCAATCTTTTTGGCGTTGAACTATATA
577 GCATGAAAAGCTCTTCAATCTTTTTGGCGTTGAACTATATA
19463 CTTTCTAAGG
Statistics
Matches: 524, Mismatches: 74, Indels: 40
0.82 0.12 0.06
Matches are distributed among these distances:
665 5 0.01
666 132 0.25
667 238 0.45
668 58 0.11
669 32 0.06
670 58 0.11
671 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (667 bp):
TTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACAGTTATTAGGTAAAAACGCGTCCC
GGGACCCCGACTCAATTTTGCACGATTTTTGGCACCAAGACTCCTTGAAATATCCATATTCATCT
AATCAAATCTCAACCACATTGCATTTAAGAATTTGATTTCACGAGCATATGAATCTTGTATCGAT
TTAATTAAAAATTAATTCAGAAAAATATGAAAAACAATATTAAAAGCATGAAAGACCTCCAATCT
TTTCGGAGAAGAATTATATATATTTTACGAGTATTGTAGACAAAAATTGAGGAAAAATATTTCGG
GTCAATTTTTGCAAAATAATAGCCGAAATCATGAACCAGTACATAAAACGACGGTTTTTGCTAAA
AACGCATTTCAGGGCCAAGAATCAGTTTTGCATAATTTTTGTGGCAAAACTCCTTGAAATATCTA
CATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTATATAAGACATCCGAATCAT
GTTTCGATTTAATTAGAAATTAATTCGAGAAAAAAACAGGAAAAACAATATTAGAAGCATGAAAA
GCTCTTCAATCTTTTTGGCGTTGAACTATATAATTTTCATGAGTATTGTGACTAAAAATTGATAA
AATAACTTTCGGGTAAA
Done.