Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011484.1 Corchorus olitorius cultivar O-4 contig11517, 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: 2916
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Found at i:421 original size:21 final size:21
Alignment explanation
Indices: 397--530 Score: 191
Period size: 21 Copynumber: 6.4 Consensus size: 21
387 CTTAGGCAAT
*
397 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
**
418 TCCAATGATTTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
439 TCCAATGAACTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
460 TCCAATGAACTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
481 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
502 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
523 TCCAATGA
1 TCCAATGA
531 ACTTCTAGCT
Statistics
Matches: 106, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
20 3 0.03
21 103 0.97
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:542 original size:21 final size:21
Alignment explanation
Indices: 497--560 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
487 GAGCTTGGAA
* ** *
497 CTTGCTCCAATGAGCTTGGAA
1 CTTGCTCCAATGAACTTCTAG
518 CTTGCTCCAATGAACTTCTAG
1 CTTGCTCCAATGAACTTCTAG
539 CTTGCTCCAATGAACTTCTAG
1 CTTGCTCCAATGAACTTCTAG
560 C
1 C
561 ATCTTCAAGC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.23, C:0.28, G:0.17, T:0.31
Consensus pattern (21 bp):
CTTGCTCCAATGAACTTCTAG
Found at i:543 original size:42 final size:42
Alignment explanation
Indices: 397--555 Score: 180
Period size: 42 Copynumber: 3.8 Consensus size: 42
387 CTTAGGCAAT
* **
397 TCCAATGAGCTTGAAACCTT-CTCCAATGATTTTGGAACCTTC
1 TCCAATGAACTTGAAA-CTTGCTCCAATGAACTTGGAACCTTC
*
439 TCCAATGAACTTGGAACCTT-CTCCAATGAACTTGGAACCTTC
1 TCCAATGAACTT-GAAACTTGCTCCAATGAACTTGGAACCTTC
* * *
481 TCCAATGAGCTTGGAACTTGCTCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAACTTGAAACTTGCTCCAATGAACTTGGAACCTT-C
** *
523 TCCAATGAACTTCTAGCTTGCTCCAATGAACTT
1 TCCAATGAACTTGAAACTTGCTCCAATGAACTT
556 CTAGCATCTT
Statistics
Matches: 101, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
41 8 0.08
42 90 0.89
43 3 0.03
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.31
Consensus pattern (42 bp):
TCCAATGAACTTGAAACTTGCTCCAATGAACTTGGAACCTTC
Found at i:547 original size:63 final size:63
Alignment explanation
Indices: 397--551 Score: 190
Period size: 63 Copynumber: 2.5 Consensus size: 63
387 CTTAGGCAAT
* * **
397 TCCAATGAGCTTGAAACCTTCTCCAATGATTTTGGAACCTTCTCCAATGAACTTGGAACCTTC
1 TCCAATGAACTTGCAACCTTCTCCAATGAGCTTGGAACCTTCTCCAATGAACTTGGAACCTTC
* *
460 TCCAATGAACTTGGAACCTTCTCCAATGAGCTTGGAA-CTTGCTCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAACTTGCAACCTTCTCCAATGAGCTTGGAACCTT-CTCCAATGAACTTGGAACCTT-C
* *
523 TCCAATGAACTT-CTAGCTTGCTCCAATGA
1 TCCAATGAACTTGCAACCTT-CTCCAATGA
552 ACTTCTAGCA
Statistics
Matches: 81, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
62 10 0.12
63 71 0.88
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.30
Consensus pattern (63 bp):
TCCAATGAACTTGCAACCTTCTCCAATGAGCTTGGAACCTTCTCCAATGAACTTGGAACCTTC
Found at i:1030 original size:154 final size:155
Alignment explanation
Indices: 658--2085 Score: 2297
Period size: 154 Copynumber: 9.2 Consensus size: 155
648 TGGCGCATCA
658 CTAACTATAATCATTTTGGTGAGATTTGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
1 CTAACTATAATCATTTTGGTGAGATTTGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
* * * * * * *
723 TATTTTGTGCCTATCGAGGCCCATTAGT-TCTGTTTTGAATTGTTTTCGATTTGGCAAACC-TCA
66 TATTTTGGGCCTATCGGGGACCATTAGTGAC-GTTTTGAATCGTCTTCGATTTGGCAAACCTTCG
* *
786 AGGCTTTTCTTTTTCCATTGTTTATGGC
130 ATGCCTTTC--TTTCCATTGTTTATGGC
*
814 CTAACTATAATCATTTTGGTGAGATTTGTCCACTGTGAAGTTTTTAGCTCATTTGGATCACTTGT
1 CTAACTATAATCATTTTGGTGAGATTTGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
* * *
879 TATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCATCTTCGGTTTGG-AAGCCTTCGA
66 TATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTTCGA
943 TGCCTTTCTTTCCATTGTTTATGGC
131 TGCCTTTCTTTCCATTGTTTATGGC
968 CTAACTATAATCATTTTGGTGAGATTTGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
1 CTAACTATAATCATTTTGGTGAGATTTGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
* *
1033 GATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACC-TCAA
66 TATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTTCGA
* *
1097 TGCTTTTCTTTCCTTTGTTTATGGC
131 TGCCTTTCTTTCCATTGTTTATGGC
* *
1122 CTAACTATAATCATTTTGGTGCGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
1 CTAACTATAATCATTTTGGTGAGATTTGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
* * * ** * * * *
1187 TATTTTGTGCCTATCGAGGCCCATTAGTTCCGTTTTGAATTGTTTTCGAGTTGGCAAACC-TCAA
66 TATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTTCGA
* * *
1251 TGCTTTTTTTTCCATTGTTTATGCC
131 TGCCTTTCTTTCCATTGTTTATGGC
1276 CTAACTATAATCATTTTGGTGAGATTTGTCCACTGTGAAGGTTTTTTAGCTCATTTGGAACACTT
1 CTAACTATAATCATTTTGGTGAGATTTGTCCACTGTGAA-G-TTTTTAGCTCATTTGGAACACTT
1341 GCTTATTTTGGGCCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGG-AAACCT
64 G-TTATTTTGGG-CCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCT
*
1405 TCGATGCCTTTCTTTCAATTGTTTATGGC
127 TCGATGCCTTTCTTTCCATTGTTTATGGC
1434 CTAACTATAATCATTTTGGTGAGATTTGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
1 CTAACTATAATCATTTTGGTGAGATTTGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
1499 TATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGG-AAACCTTCGA
66 TATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTTCGA
1563 TGCCTTTCTTTCC-TTCGTTTATGGC
131 TGCCTTTCTTTCCATT-GTTTATGGC
** *
1588 CTAACTATAATCATTTTGGTGAGATAAGTCCAGTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
1 CTAACTATAATCATTTTGGTGAGATTTGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
1653 TATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGC-AACCTTCGA
66 TATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTTCGA
1717 TGCCTTTCTTTCCATTGTTTATGGC
131 TGCCTTTCTTTCCATTGTTTATGGC
*
1742 CTAACTATTATCATTTTGGTGATG-TTTGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG
1 CTAACTATAATCATTTTGGTGA-GATTTGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG
1806 TTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGG-AAACCTTCG
65 TTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTTCG
1870 ATGCCTTTCTTTCC-TTCGTTTATGGC
130 ATGCCTTTCTTTCCATT-GTTTATGGC
* * **
1896 CTATCTATAATCATTTTAGTGAGATAAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
1 CTAACTATAATCATTTTGGTGAGATTTGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
1961 TATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGC-AACCTTCGA
66 TATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTTCGA
*
2025 TGCCTTTCTTTCCATTCTTTATGGC
131 TGCCTTTCTTTCCATTGTTTATGGC
*
2050 CTAACTATAATCATTTTGGTGAGATTAGTCCACTGT
1 CTAACTATAATCATTTTGGTGAGATTTGTCCACTGT
2086 CAATGCTTTT
Statistics
Matches: 1188, Mismatches: 67, Indels: 36
0.92 0.05 0.03
Matches are distributed among these distances:
153 5 0.00
154 877 0.74
155 24 0.02
156 165 0.14
157 16 0.01
158 101 0.09
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.41
Consensus pattern (155 bp):
CTAACTATAATCATTTTGGTGAGATTTGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
TATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTTCGA
TGCCTTTCTTTCCATTGTTTATGGC
Found at i:1893 original size:620 final size:616
Alignment explanation
Indices: 658--2085 Score: 2303
Period size: 620 Copynumber: 2.3 Consensus size: 616
648 TGGCGCATCA
658 CTAACTATAATCATTTTGGTGAGATTTGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
1 CTAACTATAATCATTTTGGTGAGATTTGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
* * * * * * *
723 TATTTTGTGCCTATCGAGGCCCATTAGT-TCTGTTTTGAATTGTTTTCGATTTGGCAAACC-TCA
66 TATTTTGGGCCTATCGGGGACCATTAGTGAC-GTTTTGAATCGTCTTCGATTTGG-AAACCTTCG
* *
786 AGGCTTTTCTTTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTTGTCCACTGTG
129 ATGCCTTTC--TTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTTGTCCACTGTG
*
851 AAGTTTTTAGCTCATTTGGATCACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTG
192 AAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTG
* *
916 AATCATCTTCGGTTTGGAAGCCTTCGATGCCTTTCTTTCCATTGTTTATGGCCTAACTATAATCA
257 AATCATCTTCGATTTGGAAACCTTCGATGCCTTTCTTTCCATTGTTTATGGCCTAACTATAATCA
**
981 TTTTGGTGAGATTTGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTGATTTTGGGCCTA
322 TTTTGGTGAGATAAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTGATTTTGGGCCTA
* *
1046 TCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCT
387 TCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCCTTTCTTTCCA
1111 TTGTTTATGGCCTAACTATAATCATTTTGGTGCGATTAGTCCACTGTGAAGTTTTTAGCTCATTT
452 TTGTTTATGGCCTAACTATAATCATTTTGGTGCGATTAGTCCACTGTGAAGTTTTTAGCTCATTT
* * ** * *
1176 GGAACACTTGTTATTTTGTGCCTATCGAGGCCCATTAGTTCCGTTTTGAATTGTTTTCGAGTTGG
517 GGAACACTTGTTATTTTGGGCCTATCGAGGACCATTAGTGACGTTTTGAATCGTCTTCGAGTTGG
* *
1241 CAAACCTCAATGCTTTTTTTTCCATTGTTTATGCC
582 CAAACCTCAATGCCTTTCTTTCCATTGTTTATGCC
1276 CTAACTATAATCATTTTGGTGAGATTTGTCCACTGTGAAGGTTTTTTAGCTCATTTGGAACACTT
1 CTAACTATAATCATTTTGGTGAGATTTGTCCACTGTGAA-G-TTTTTAGCTCATTTGGAACACTT
1341 GCTTATTTTGGGCCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGAAACCTT
64 G-TTATTTTGGG-CCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGAAACCTT
*
1406 CGATGCCTTTCTTTCAATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTTGTCCACTGTG
127 CGATGCCTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTTGTCCACTGTG
1471 AAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTG
192 AAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTG
*
1536 AATCGTCTTCGATTTGGAAACCTTCGATGCCTTTCTTTCC-TTCGTTTATGGCCTAACTATAATC
257 AATCATCTTCGATTTGGAAACCTTCGATGCCTTTCTTTCCATT-GTTTATGGCCTAACTATAATC
* *
1600 ATTTTGGTGAGATAAGTCCAGTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
321 ATTTTGGTGAGATAAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTGATTTTGGGCCT
*
1665 ATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGC-AACCTTCGATGCCTTTCTTTC
386 ATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACC-TCAATGCCTTTCTTTC
* * *
1729 CATTGTTTATGGCCTAACTATTATCATTTTGGTGATG-TTTGTCCACTGTGAAGTTTTTAGCTCA
450 CATTGTTTATGGCCTAACTATAATCATTTTGGTG-CGATTAGTCCACTGTGAAGTTTTTAGCTCA
* *
1793 TTTGGAACACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATT
514 TTTGGAACACTTGTTATTTTGGGCCTATCGAGGACCATTAGTGACGTTTTGAATCGTCTTCGAGT
* *
1858 TGG-AAACCTTCGATGCCTTTCTTTCC-TTCGTTTATGGC
579 TGGCAAACC-TCAATGCCTTTCTTTCCATT-GTTTATGCC
* * **
1896 CTATCTATAATCATTTTAGTGAGATAAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
1 CTAACTATAATCATTTTGGTGAGATTTGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
*
1961 TATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAACCTTCGAT
66 TATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGAAACCTTCGAT
* *
2026 GCCTTTCTTTCCATTCTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGT
131 GCCTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTTGTCCACTGT
2086 CAATGCTTTT
Statistics
Matches: 755, Mismatches: 44, Indels: 24
0.92 0.05 0.03
Matches are distributed among these distances:
616 112 0.15
617 10 0.01
618 63 0.08
619 15 0.02
620 492 0.65
621 15 0.02
622 47 0.06
623 1 0.00
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.41
Consensus pattern (616 bp):
CTAACTATAATCATTTTGGTGAGATTTGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
TATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGAAACCTTCGAT
GCCTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTTGTCCACTGTGAAGT
TTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATC
ATCTTCGATTTGGAAACCTTCGATGCCTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTT
GGTGAGATAAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTGATTTTGGGCCTATCGG
GGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCCTTTCTTTCCATTGT
TTATGGCCTAACTATAATCATTTTGGTGCGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
CACTTGTTATTTTGGGCCTATCGAGGACCATTAGTGACGTTTTGAATCGTCTTCGAGTTGGCAAA
CCTCAATGCCTTTCTTTCCATTGTTTATGCC
Found at i:2131 original size:64 final size:64
Alignment explanation
Indices: 2024--2149 Score: 218
Period size: 64 Copynumber: 2.0 Consensus size: 64
2014 GCAACCTTCG
2024 ATGCCTTTCTTTCCATTCTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTCA
1 ATGCCTTTCTTTCCATTCTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTCA
* *
2088 ATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATGC-TTTTGGTGAGATTAGTCCACTGT
1 ATGCCTTTCTTTCCATTCTTTATGGCCTAACTATAAT-CATTTTGGTGAGATTAGTCCACTGT
2150 GAAGTTTTTG
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
64 58 0.98
65 1 0.02
ACGTcount: A:0.21, C:0.20, G:0.16, T:0.44
Consensus pattern (64 bp):
ATGCCTTTCTTTCCATTCTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTCA
Found at i:2406 original size:371 final size:372
Alignment explanation
Indices: 1716--2456 Score: 1197
Period size: 371 Copynumber: 2.0 Consensus size: 372
1706 GCAACCTTCG
* *
1716 ATGCCTTTCTTTCCATTGTTTATGGCCTAACTATTATCATTTTGGTGATGTTTGTCCACTGTGAA
1 ATGCCTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGATGTTAGTCCACTGTGAA
*
1781 GTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAA
66 GTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGACCATTAGTGACGTTTTGAA
* * *
1846 TCGTCTTCGATTTGGAAACCTTCGATGCCTTTCTTTCCTTCGTTTATGGCCTATCTATAATCATT
131 TCGTCTTCGATTTGGAAACCTTCGAAGCCTTTCTTTCCTTCGTTTATGGACTAACTATAATCATT
*
1911 TTAGTGAGATAAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATC
196 TTAGTGAGATAAGTCCACTGTGAAGTTTTTAGCTCATTTAGAACACTTGTTATTTTGGGCCTATC
*
1976 GGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAACCTTCGATGCCTTTCTTTCCATT
261 GGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAACCTTCAATGCCTTTCTTTCCATT
*
2041 CTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTCA
326 CTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTCA
*
2088 ATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATGC-TTTTGGTGA-GATTAGTCCACTGTG
1 ATGCCTTTCTTTCCATTGTTTATGGCCTAACTATAAT-CATTTTGGTGATG-TTAGTCCACTGTG
* * * **
2151 AAGTTTTTGGCTCATTTGGAACACTTGTTATTTTGTGCCTATCGAGGCCCATTAGTTCCGTTTTG
64 AAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGACCATTAGTGACGTTTTG
* *
2216 AATCGTCTTCGATTTGGCAAACC-TC-AAGGCTTTTTTTCCATT-GTTTATGGACTAACTATAAT
129 AATCGTCTTCGATTTGG-AAACCTTCGAAGCCTTTCTTTCC-TTCGTTTATGGACTAACTATAAT
* *
2278 CATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTAGAACACTTGTTATTTTGGGCC
192 CATTTTAGTGAGATAAGTCCACTGTGAAGTTTTTAGCTCATTTAGAACACTTGTTATTTTGGGCC
* *
2343 TATCGGGGACCATTAGTGACGTTTTGTATCGTCTTCGATTTGGCAAACC-TCAATGCTTTTCTTT
257 TATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGC-AACCTTCAATGCCTTTCTTT
*
2407 CCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGT
321 CCATTCTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGT
2457 GAACTTTTTA
Statistics
Matches: 342, Mismatches: 22, Indels: 11
0.91 0.06 0.03
Matches are distributed among these distances:
371 196 0.57
372 140 0.41
373 6 0.02
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.42
Consensus pattern (372 bp):
ATGCCTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGATGTTAGTCCACTGTGAA
GTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGACCATTAGTGACGTTTTGAA
TCGTCTTCGATTTGGAAACCTTCGAAGCCTTTCTTTCCTTCGTTTATGGACTAACTATAATCATT
TTAGTGAGATAAGTCCACTGTGAAGTTTTTAGCTCATTTAGAACACTTGTTATTTTGGGCCTATC
GGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAACCTTCAATGCCTTTCTTTCCATT
CTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTCA
Found at i:2482 original size:154 final size:154
Alignment explanation
Indices: 2085--2616 Score: 845
Period size: 154 Copynumber: 3.5 Consensus size: 154
2075 TAGTCCACTG
*
2085 TCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATGC-TTTTGGTGAGATTAGTCCACTG
1 TCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAAT-CATTTTGGTGAGATTAGTCCACTG
* * *
2149 TGAAGTTTTTGGCTCATTTGGAACACTTGTTATTTTGTGCCTATCGAGGCCCATTAGTTCCGTTT
65 TGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTT
2214 TGAATCGTCTTCGATTTGGCAAACC
130 TGAATCGTCTTCGATTTGGCAAACC
*
2239 TCAAGGCTTTT-TTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGT
1 TCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGT
* * **
2303 GAAGTTTTTAGCTCATTTAGAACACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTT
66 GAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTT
*
2368 GTATCGTCTTCGATTTGGCAAACC
131 GAATCGTCTTCGATTTGGCAAACC
2392 TCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGT
1 TCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGT
* * * *
2457 GAACTTTTTAGCTTATTTGGAACACTTGTTATTTTGGACCTGTCGGGGCCCATTAGTTCCGTTTT
66 GAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTT
2522 GAATCGTCTTCGATTTGGCAAACC
131 GAATCGTCTTCGATTTGGCAAACC
* * * * * *
2546 TCAAAGCTTTTCCTT-AAGTTGTTTATGGCCTAACTATAATCATTTTGATGAGATTAGTCCACTA
1 TCAATGCTTTTCTTTCCA-TTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTG
2610 TGAAGTT
65 TGAAGTT
2617 CTTATGGACT
Statistics
Matches: 348, Mismatches: 27, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
152 1 0.00
153 142 0.41
154 205 0.59
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.41
Consensus pattern (154 bp):
TCAATGCTTTTCTTTCCATTGTTTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGT
GAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTT
GAATCGTCTTCGATTTGGCAAACC
Found at i:2573 original size:525 final size:520
Alignment explanation
Indices: 1566--2914 Score: 1899
Period size: 525 Copynumber: 2.6 Consensus size: 520
1556 CCTTCGATGC
* *
1566 CTTTCTTTCCTTCGTTTATGGCCTAACTATAATCATTTTGGTGAGATAAGTCCAGTGTGAAGTTT
1 CTTTCTTTCCTT-GTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTT
*
1631 TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGT
65 TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATC-GGGCCCATTAGTGACGTTTTGAATCGT
* * * *
1696 CTTCGATTTGGC-AACCTTCGATGCCTTTCTTTCCATTGTTTATGGCCTAACTATTATCATTTTG
129 CTTCGATTTGGCAAACC-TC-AAGGCTTTTTTTCCATTGTTTATGG-CTAACTATAATCATTTTG
*
1760 GTGATG-TTTGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGG
191 GTGA-GATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGG
* * *
1824 GGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGAAACCTTCGATGCCTTTCTTTCCTTCGT
255 GGACCATTAGTGACGTTTTGTATCGTCTTCGATTTGGAAACC-TCAATGCTTTTCTTTCCTTCGT
* * *
1889 TTATGGCCTATCTATAATCATTTTAGTGAGATAAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
319 TTATGGACTAACTATAATCATTTTAGTGAGATAAGTCCACTGTGAACTTTTTAGCTCATTTGGAA
*
1954 CACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAC
384 CACTTGTTATTTTGGACCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAC
* * * * *
2019 CTTCGATGCCTTTCTTTCCATTCTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACT
449 CTTCAAAGCCTTTCCTTCAATTCTTTATGGCCTAACTATAATCATTTTGATGAGATTAGTCCACT
*
2084 GTCAATG
514 ATCAATG
2091 CTTTTCTTTCCATTGTTTATGGCCTAACTATAATGC-TTTTGGTGAGATTAGTCCACTGTGAAGT
1 C-TTTCTTTCC-TTGTTTATGGCCTAACTATAAT-CATTTTGGTGAGATTAGTCCACTGTGAAGT
* * **
2155 TTTTGGCTCATTTGGAACACTTGTTATTTTGTGCCTATCGAGGCCCATTAGTTCCGTTTTGAATC
63 TTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCG-GGCCCATTAGTGACGTTTTGAATC
2220 GTCTTCGATTTGGCAAACCTCAAGGCTTTTTTTCCATTGTTTATGGACTAACTATAATCATTTTG
127 GTCTTCGATTTGGCAAACCTCAAGGCTTTTTTTCCATTGTTTATGG-CTAACTATAATCATTTTG
*
2285 GTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTAGAACACTTGTTATTTTGGGCCTATCGGG
191 GTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGG
2350 GACCATTAGTGACGTTTTGTATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATT-GT
256 GACCATTAGTGACGTTTTGTATCGTCTTCGATTTGG-AAACCTCAATGCTTTTCTTTCC-TTCGT
* * *
2414 TTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCTTATTTGGAA
319 TTATGGACTAACTATAATCATTTTAGTGAGATAAGTCCACTGTGAACTTTTTAGCTCATTTGGAA
* * **
2479 CACTTGTTATTTTGGACCTGTCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAA
384 CACTTGTTATTTTGGACCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGC-AA
* *
2544 CC-TCAAAGCTTTTCCTT-AAGTTGTTTATGGCCTAACTATAATCATTTTGATGAGATTAGTCCA
448 CCTTCAAAGCCTTTCCTTCAA-TTCTTTATGGCCTAACTATAATCATTTTGATGAGATTAGTCCA
*
2607 CTATGAA-G
512 CTATCAATG
* * * *
2615 ------TT-C----TTATGGACTAATTGTAATCATTTTGGTGAGATTAGTCCACTGTGATGTTTT
1 CTTTCTTTCCTTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTT
* *
2669 TAGCTCATTTGGAACACTTGTTATTTTGGGCCTATATGGGCCCATTAGTGACGTTTTGAATCGTT
66 TAGCTCATTTGGAACACTTGTTATTTTGGGCCTAT-CGGGCCCATTAGTGACGTTTTGAATCGTC
* * *
2734 TTCGATTTGGCAAACCTCAATGCTTTTCTTTTCATTGTTTATGGCGTAACTATAATCAATTTGGT
130 TTCGATTTGGCAAACCTCAAGGCTTTT-TTTCCATTGTTTATGGC-TAACTATAATCATTTTGGT
* * *
2799 GAGATTAGTCCAGTGTGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGC
193 GAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGA
* ** *
2864 CCATTTATTTCCGTTTT-TAATCGTCTTCAATTTGGAAAACCTCAATGCTTT
258 CCA-TTAGTGACGTTTTGT-ATCGTCTTCGATTTGG-AAACCTCAATGCTTT
2915 CT
Statistics
Matches: 749, Mismatches: 59, Indels: 44
0.88 0.07 0.05
Matches are distributed among these distances:
510 1 0.00
511 129 0.17
512 99 0.13
513 40 0.05
516 1 0.00
517 2 0.00
524 3 0.00
525 327 0.44
526 140 0.19
527 7 0.01
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.41
Consensus pattern (520 bp):
CTTTCTTTCCTTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTT
TAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGCCCATTAGTGACGTTTTGAATCGTCT
TCGATTTGGCAAACCTCAAGGCTTTTTTTCCATTGTTTATGGCTAACTATAATCATTTTGGTGAG
ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGACCA
TTAGTGACGTTTTGTATCGTCTTCGATTTGGAAACCTCAATGCTTTTCTTTCCTTCGTTTATGGA
CTAACTATAATCATTTTAGTGAGATAAGTCCACTGTGAACTTTTTAGCTCATTTGGAACACTTGT
TATTTTGGACCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAACCTTCAAA
GCCTTTCCTTCAATTCTTTATGGCCTAACTATAATCATTTTGATGAGATTAGTCCACTATCAATG
Found at i:2740 original size:358 final size:359
Alignment explanation
Indices: 2260--2914 Score: 1089
Period size: 358 Copynumber: 1.8 Consensus size: 359
2250 TTTCCATTGT
2260 TTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTAGAA
1 TTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTAGAA
* *
2325 CACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGTATCGTCTTCGATTTGGCAAA
66 CACTTGTTATTTTGGGCCTATAGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAA
*
2390 CCTCAATGCTTTTCTTTCCATTGTTTATGGAC-TAACTATAATCATTTTGGTGAGATTAGTCCAC
131 CCTCAATGCTTTTCTTTCCATTGTTTATGG-CGTAACTATAATCAATTTGGTGAGATTAGTCCAC
* * *
2454 TGTGAACTTTTTAGCTTATTTGGAACACTTGTTATTTTGGACCTGTCGGGGCCCA-TTAGTTCCG
195 TGTGAACTTTTTAACTCATTTGGAACACTTGTTATTTTGGACCTATCGGGGCCCATTTAGTTCCG
* *
2518 TTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCCTTAAGTTGTTTATGGCCTAACTAT
260 TTTTGAATCGTCTTCAATTTGGAAAACCTCAAAGCTTTTCCTTAAGTTGTTTATGGCCTAACTAT
2583 AATCATTTTGATGAGATTAGTCCACTATGAAGTTC
325 AATCATTTTGATGAGATTAGTCCACTATGAAGTTC
* * * *
2618 TTATGGACTAATTGTAATCATTTTGGTGAGATTAGTCCACTGTGATGTTTTTAGCTCATTTGGAA
1 TTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTAGAA
* * *
2683 CACTTGTTATTTTGGGCCTATATGGGCCCATTAGTGACGTTTTGAATCGTTTTCGATTTGGCAAA
66 CACTTGTTATTTTGGGCCTATAGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAA
* *
2748 CCTCAATGCTTTTCTTTTCATTGTTTATGGCGTAACTATAATCAATTTGGTGAGATTAGTCCAGT
131 CCTCAATGCTTTTCTTTCCATTGTTTATGGCGTAACTATAATCAATTTGGTGAGATTAGTCCACT
* * *
2813 GTGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTTATTTCCGT
196 GTGAACTTTTTAACTCATTTGGAACACTTGTTATTTTGGACCTATCGGGGCCCATTTAGTTCCGT
* *
2878 TTTTAATCGTCTTCAATTTGGAAAACCTCAATGCTTT
261 TTTGAATCGTCTTCAATTTGGAAAACCTCAAAGCTTT
2915 CT
Statistics
Matches: 273, Mismatches: 22, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
357 1 0.00
358 230 0.84
359 42 0.15
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (359 bp):
TTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTAGAA
CACTTGTTATTTTGGGCCTATAGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAA
CCTCAATGCTTTTCTTTCCATTGTTTATGGCGTAACTATAATCAATTTGGTGAGATTAGTCCACT
GTGAACTTTTTAACTCATTTGGAACACTTGTTATTTTGGACCTATCGGGGCCCATTTAGTTCCGT
TTTGAATCGTCTTCAATTTGGAAAACCTCAAAGCTTTTCCTTAAGTTGTTTATGGCCTAACTATA
ATCATTTTGATGAGATTAGTCCACTATGAAGTTC
Found at i:2774 original size:204 final size:204
Alignment explanation
Indices: 2414--2820 Score: 618
Period size: 204 Copynumber: 2.0 Consensus size: 204
2404 TTTCCATTGT
*
2414 TTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCTTATTTGGAA
1 TTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCTCATTTGGAA
* * **
2479 CACTTGTTATTTTGGACCTGTCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAA
66 CACTTGTTATTTTGGACCTATAGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAA
*
2544 CCTCAAAGCTTTTCCTTAAGTTGTTTATGGCCTAACTATAATCATTTTGATGAGATTAGTCCACT
131 CCTCAAAGCTTTTCCTTAAGTTGTTTATGGCCTAACTATAATCAATTTGATGAGATTAGTCCACT
2609 ATGAAGTTC
196 ATGAAGTTC
* * **
2618 TTATGGACTAATTGTAATCATTTTGGTGAGATTAGTCCACTGTGATGTTTTTAGCTCATTTGGAA
1 TTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCTCATTTGGAA
* * *
2683 CACTTGTTATTTTGGGCCTATATGGGCCCATTAGTGACGTTTTGAATCGTTTTCGATTTGGCAAA
66 CACTTGTTATTTTGGACCTATAGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAA
* * * * * *
2748 CCTCAATGCTTTTCTTTTCA-TTGTTTATGGCGTAACTATAATCAATTTGGTGAGATTAGTCCAG
131 CCTCAAAGCTTTTC-CTTAAGTTGTTTATGGCCTAACTATAATCAATTTGATGAGATTAGTCCAC
*
2812 TGTGAAGTT
195 TATGAAGTT
2821 TTTAACTCAT
Statistics
Matches: 182, Mismatches: 20, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
204 179 0.98
205 3 0.02
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.41
Consensus pattern (204 bp):
TTATGGACTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCTCATTTGGAA
CACTTGTTATTTTGGACCTATAGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAA
CCTCAAAGCTTTTCCTTAAGTTGTTTATGGCCTAACTATAATCAATTTGATGAGATTAGTCCACT
ATGAAGTTC
Found at i:2916 original size:154 final size:154
Alignment explanation
Indices: 2632--2914 Score: 440
Period size: 154 Copynumber: 1.8 Consensus size: 154
2622 GGACTAATTG
* * *
2632 TAATCATTTTGGTGAGATTAGTCCACTGTGATGTTTTTAGCTCATTTGGAACACTTGTTATTTTG
1 TAATCAATTTGGTGAGATTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTG
* * * *
2697 GGCCTATATGGGCCCATTAGTGACGTTTTGAATCGTTTTCGATTTGGCAAACCTCAATGCTTTTC
66 GGCCTATAGGGGCCCATTAGTGACGTTTTGAATCGTCTTCAATTTGGAAAACCTCAATGCTTTTC
2762 TTTTCATTGTTTATGGCGTAACTA
131 TTTTCATTGTTTATGGCGTAACTA
*
2786 TAATCAATTTGGTGAGATTAGTCCAGTGTGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTG
1 TAATCAATTTGGTGAGATTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTG
* * ** *
2851 GGCCTATCGGGGCCCATTTATTTCCGTTTTTAATCGTCTTCAATTTGGAAAACCTCAATGCTTT
66 GGCCTATAGGGGCCCA-TTAGTGACGTTTTGAATCGTCTTCAATTTGGAAAACCTCAATGCTTT
2915 CT
Statistics
Matches: 115, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
154 75 0.65
155 40 0.35
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (154 bp):
TAATCAATTTGGTGAGATTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTG
GGCCTATAGGGGCCCATTAGTGACGTTTTGAATCGTCTTCAATTTGGAAAACCTCAATGCTTTTC
TTTTCATTGTTTATGGCGTAACTA
Done.