Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022978.1 Corchorus olitorius cultivar O-4 contig23011, 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: 60353
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:4697 original size:44 final size:43
Alignment explanation
Indices: 4647--4801 Score: 194
Period size: 44 Copynumber: 3.7 Consensus size: 43
4637 AACGTTTTTA
4647 AAGTAATTCCAAAAGAAGATTTTGGAAAATAAAAGTTTTTATTC
1 AAGTAATTCCAAAAGAAGATTTTGGAAAAT-AAAGTTTTTATTC
*
4691 AAGTAATTCCAAAAGAAGATTTTGGAAAATAAAGTTTTCAATTC
1 AAGTAATTCCAAAAGAAGATTTTGGAAAATAAAGTTTT-TATTC
** * *
4735 AAGTACCTCCAAAAGAAGATTTTGGAAAGTTAAAG--TCT-TT-
1 AAGTAATTCCAAAAGAAGATTTTGGAAA-ATAAAGTTTTTATTC
*
4775 AAG-AAATCCAAAAGAAGATTTTGGAAA
1 AAGTAATTCCAAAAGAAGATTTTGGAAA
4802 TTGATAAAAT
Statistics
Matches: 101, Mismatches: 8, Indels: 9
0.86 0.07 0.08
Matches are distributed among these distances:
39 22 0.22
40 3 0.03
41 2 0.02
43 9 0.09
44 60 0.59
45 5 0.05
ACGTcount: A:0.46, C:0.09, G:0.15, T:0.30
Consensus pattern (43 bp):
AAGTAATTCCAAAAGAAGATTTTGGAAAATAAAGTTTTTATTC
Found at i:16956 original size:32 final size:31
Alignment explanation
Indices: 16914--17007 Score: 107
Period size: 31 Copynumber: 3.0 Consensus size: 31
16904 CTTTGTTATG
* ** *
16914 AATAGCGGCGTCTCTCATGACAGACGCCGCTA
1 AATAGTGGCGTCTCT-AAAACAAACGCCGCTA
* *
16946 AATAGTGGCGTTTCTAAAATAAACGCCGCTA
1 AATAGTGGCGTCTCTAAAACAAACGCCGCTA
* *
16977 AATAGTGGCGTTTCTAAAATAAACGCCGCTA
1 AATAGTGGCGTCTCTAAAACAAACGCCGCTA
17008 TATATAATGT
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
31 43 0.77
32 13 0.23
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.23
Consensus pattern (31 bp):
AATAGTGGCGTCTCTAAAACAAACGCCGCTA
Found at i:16975 original size:31 final size:31
Alignment explanation
Indices: 16937--17007 Score: 142
Period size: 31 Copynumber: 2.3 Consensus size: 31
16927 CTCATGACAG
16937 ACGCCGCTAAATAGTGGCGTTTCTAAAATAA
1 ACGCCGCTAAATAGTGGCGTTTCTAAAATAA
16968 ACGCCGCTAAATAGTGGCGTTTCTAAAATAA
1 ACGCCGCTAAATAGTGGCGTTTCTAAAATAA
16999 ACGCCGCTA
1 ACGCCGCTA
17008 TATATAATGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.24
Consensus pattern (31 bp):
ACGCCGCTAAATAGTGGCGTTTCTAAAATAA
Found at i:17095 original size:156 final size:156
Alignment explanation
Indices: 16811--17136 Score: 537
Period size: 156 Copynumber: 2.1 Consensus size: 156
16801 TCTGATGCAT
* *
16811 AACGCCGCTAAATAGTGGCTTTTCTAAAGTAAACGACGCTATATATAATGTTTTCCAAAGAATAG
1 AACGCCGCTAAATAGTGGCGTTTCTAAAATAAACGACGCTATATATAATGTTTTCCAAAGAATAG
* *
16876 AAATTTGGTGAAATTAAAAACACAATTTCTTTGTTATGAATAGCGGCGTCTCTCATGACAGACGC
66 AAATTTGGTGAAACTAAAAACACAATTTCTTTGTTATGAATAGCGACGTCTCTCATGACAGACGC
*
16941 CGCTAAATAGTGGCGTTTCTA-AAATA
131 CACTAAATAGTGGCGTTTCTATAAA-A
* * *
16967 AACGCCGCTAAATAGTGGCGTTTCTAAAATAAACGCCGCTATATATAATGTTTTCCGAATAATAG
1 AACGCCGCTAAATAGTGGCGTTTCTAAAATAAACGACGCTATATATAATGTTTTCCAAAGAATAG
*
17032 AAATTTGGTGAAACTAAAAACACAATTTCTTTGTTATGAATAGCGACGTTTCTCATGACAGACGC
66 AAATTTGGTGAAACTAAAAACACAATTTCTTTGTTATGAATAGCGACGTCTCTCATGACAGACGC
* *
17097 CACTAAATAGTGGCGTTTTTATGAAA
131 CACTAAATAGTGGCGTTTCTATAAAA
17123 AACGCCGCTAAATA
1 AACGCCGCTAAATA
17137 TAATCTTCTA
Statistics
Matches: 158, Mismatches: 11, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
156 156 0.99
157 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (156 bp):
AACGCCGCTAAATAGTGGCGTTTCTAAAATAAACGACGCTATATATAATGTTTTCCAAAGAATAG
AAATTTGGTGAAACTAAAAACACAATTTCTTTGTTATGAATAGCGACGTCTCTCATGACAGACGC
CACTAAATAGTGGCGTTTCTATAAAA
Found at i:17190 original size:125 final size:125
Alignment explanation
Indices: 16968--17230 Score: 402
Period size: 125 Copynumber: 2.1 Consensus size: 125
16958 TCTAAAATAA
* * * * * * *
16968 ACGCCGCTAAATAGTGGCGTTTCTAAAATAAACGCCGCTATATATAATGTTTTCCGAATAATAGA
1 ACGCCACTAAATAGTGGCGTTTCTAAAATAAACGCCGCTAAATATAATCTTCTACAAAGAATAGA
17033 AATTTGGTGAAACTAAAAACACAATTTCTTTGTTATGAATAGCGACGTTTCTCATGACAG
66 AATTTGGTGAAACTAAAAACACAATTTCTTTGTTATGAATAGCGACGTTTCTCATGACAG
* *
17093 ACGCCACTAAATAGTGGCGTTTTTATGAA-AAACGCCGCTAAATATAATCTTCTACAAAGAATAG
1 ACGCCACTAAATAGTGGCGTTTCTA-AAATAAACGCCGCTAAATATAATCTTCTACAAAGAATAG
* * *
17157 AAATTTGGTGAAACTAAAAACACCATTTCTTTGTTATGAATCGCGGCGTTTCTCATGACAG
65 AAATTTGGTGAAACTAAAAACACAATTTCTTTGTTATGAATAGCGACGTTTCTCATGACAG
17218 ACGCCACTAAATA
1 ACGCCACTAAATA
17231 TAATCTTCTA
Statistics
Matches: 125, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
125 123 0.98
126 2 0.02
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (125 bp):
ACGCCACTAAATAGTGGCGTTTCTAAAATAAACGCCGCTAAATATAATCTTCTACAAAGAATAGA
AATTTGGTGAAACTAAAAACACAATTTCTTTGTTATGAATAGCGACGTTTCTCATGACAG
Found at i:17285 original size:94 final size:94
Alignment explanation
Indices: 17124--17324 Score: 366
Period size: 94 Copynumber: 2.1 Consensus size: 94
17114 TTTATGAAAA
17124 ACGCCGCTAAATATAATCTTCTACAAAGAATAGAAATTTGGTGAAACTAAAAACACCATTTCTTT
1 ACGCCGCTAAATATAATCTTCTACAAAGAATAGAAATTTGGTGAAACTAAAAACACCATTTCTTT
* *
17189 GTTATGAATCGCGGCGTTTCTCATGACAG
66 GTTATGAATAGCAGCGTTTCTCATGACAG
*
17218 ACGCCACTAAATATAATCTTCTACAAAGAATAGAAATTTGGTGAAACTAAAAACACCATTTCTTT
1 ACGCCGCTAAATATAATCTTCTACAAAGAATAGAAATTTGGTGAAACTAAAAACACCATTTCTTT
*
17283 GTTATGAATAGCAGCGTTTCTCATGTCAG
66 GTTATGAATAGCAGCGTTTCTCATGACAG
17312 ACGCCGCTAAATA
1 ACGCCGCTAAATA
17325 GTGGCGTTTT
Statistics
Matches: 102, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
94 102 1.00
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.29
Consensus pattern (94 bp):
ACGCCGCTAAATATAATCTTCTACAAAGAATAGAAATTTGGTGAAACTAAAAACACCATTTCTTT
GTTATGAATAGCAGCGTTTCTCATGACAG
Found at i:17625 original size:28 final size:26
Alignment explanation
Indices: 17583--17639 Score: 78
Period size: 28 Copynumber: 2.1 Consensus size: 26
17573 CGGCTTAATT
*
17583 AAATTTGCTTCTTCATTTTCTACCCA
1 AAATTTGCTTCTTCATTTTCGACCCA
*
17609 AAATTTGTTCTTCTTCATTTTCGACTCA
1 AAATTTG--CTTCTTCATTTTCGACCCA
17637 AAA
1 AAA
17640 GCAAGAAGCC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 7 0.26
28 20 0.74
ACGTcount: A:0.26, C:0.23, G:0.05, T:0.46
Consensus pattern (26 bp):
AAATTTGCTTCTTCATTTTCGACCCA
Found at i:19895 original size:85 final size:85
Alignment explanation
Indices: 19752--19912 Score: 295
Period size: 85 Copynumber: 1.9 Consensus size: 85
19742 AATGAATTTA
**
19752 TCCTCTTATGAATGAATTGTATTTGGGATGTTATTATGCTGTAAATTTGAAGTCTTTATTAAGTA
1 TCCTCTTATGAATGAATTAAATTTGGGATGTTATTATGCTGTAAATTTGAAGTCTTTATTAAGTA
19817 AATGCCTATAATAGATTGGT
66 AATGCCTATAATAGATTGGT
*
19837 TCCTCTTATGAATGAATTAAATTTGGGATGTTATTATGCTGTAAATTTTAAGTCTTTATTAAGTA
1 TCCTCTTATGAATGAATTAAATTTGGGATGTTATTATGCTGTAAATTTGAAGTCTTTATTAAGTA
19902 AATGCCTATAA
66 AATGCCTATAA
19913 AAATTTGGTT
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
85 73 1.00
ACGTcount: A:0.31, C:0.09, G:0.17, T:0.43
Consensus pattern (85 bp):
TCCTCTTATGAATGAATTAAATTTGGGATGTTATTATGCTGTAAATTTGAAGTCTTTATTAAGTA
AATGCCTATAATAGATTGGT
Found at i:20712 original size:27 final size:27
Alignment explanation
Indices: 20666--20739 Score: 139
Period size: 27 Copynumber: 2.7 Consensus size: 27
20656 TTCTCTCTAT
20666 GTGGGGCTTTTTTTTTTCATATGGTAAA
1 GTGGGGC-TTTTTTTTTCATATGGTAAA
20694 GTGGGGCTTTTTTTTTCATATGGTAAA
1 GTGGGGCTTTTTTTTTCATATGGTAAA
20721 GTGGGGCTTTTTTTTTCAT
1 GTGGGGCTTTTTTTTTCAT
20740 CGCCAAAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
27 39 0.85
28 7 0.15
ACGTcount: A:0.15, C:0.08, G:0.26, T:0.51
Consensus pattern (27 bp):
GTGGGGCTTTTTTTTTCATATGGTAAA
Found at i:21494 original size:32 final size:32
Alignment explanation
Indices: 21400--21529 Score: 134
Period size: 32 Copynumber: 4.0 Consensus size: 32
21390 AAAACCAAAA
* * * **
21400 TAGCGGCGTTTAAGTTCAGAAACGCCACTAAA
1 TAGCGGCGTTTATGTACGGAAACGCCACTATT
*
21432 TAGCGGCGTTTCTGTACGGAAACGCCACTATT
1 TAGCGGCGTTTATGTACGGAAACGCCACTATT
* *
21464 TAGTGGCTTTTATGTACGGAAACGCCACTATT
1 TAGCGGCGTTTATGTACGGAAACGCCACTATT
* ** * *
21496 TAGCGGTGTTTCGGTACAGAAAACGCCGCTATT
1 TAGCGGCGTTTATGTAC-GGAAACGCCACTATT
21529 T
1 T
21530 GCAATTTTTT
Statistics
Matches: 81, Mismatches: 16, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
32 67 0.83
33 14 0.17
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (32 bp):
TAGCGGCGTTTATGTACGGAAACGCCACTATT
Found at i:34359 original size:29 final size:29
Alignment explanation
Indices: 34282--34507 Score: 178
Period size: 29 Copynumber: 7.8 Consensus size: 29
34272 ACCCAGAGTA
* * *
34282 TGCACAAATGACCAAAACGTCCCT-GGATG
1 TGCAAAAATGACCAAAATG-CCTTCGGATG
*
34311 TGC-AAAATGACCAAAGTGCCTTCGGATG
1 TGCAAAAATGACCAAAATGCCTTCGGATG
* * * *
34339 TGCAAAAACGATCAAAATGCC-CCTGAATTG
1 TGCAAAAATGACCAAAATGCCTTC-GGA-TG
* *
34369 TGCAAAAATGACCAAAATGCCCTTC-AATA
1 TGCAAAAATGACCAAAATG-CCTTCGGATG
* **
34398 TGCGAAAATGAAAAAAATGCCCTT-GGATG
1 TGCAAAAATGACCAAAATG-CCTTCGGATG
* *
34427 TGC-AAAATGACCAAAATGCC-CCTAGATG
1 TGCAAAAATGACCAAAATGCCTTC-GGATG
* *
34455 TGCAAAAATGACCAAAATGCCTTTGGATA
1 TGCAAAAATGACCAAAATGCCTTCGGATG
*
34484 TGCGAAAATGACCAAAATGGCCTT
1 TGCAAAAATGACCAAAAT-GCCTT
34508 AGATATGCGA
Statistics
Matches: 158, Mismatches: 27, Indels: 23
0.76 0.13 0.11
Matches are distributed among these distances:
27 5 0.03
28 41 0.26
29 83 0.53
30 26 0.16
31 2 0.01
32 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.20
Consensus pattern (29 bp):
TGCAAAAATGACCAAAATGCCTTCGGATG
Found at i:34363 original size:57 final size:57
Alignment explanation
Indices: 34282--34562 Score: 219
Period size: 57 Copynumber: 4.8 Consensus size: 57
34272 ACCCAGAGTA
* * * * *
34282 TGCACAAATGACCAAAACGTCCCTGGATGTGC-AAAATGACCAAAGTGCCTTCGGATG
1 TGCAAAAATGAACAAAATGCCCCTGGATGTGCAAAAATGACCAAAATGCCTTC-GATG
* * * * *
34339 TGCAAAAACGATCAAAATGCCCCTGAATTGTGCAAAAATGACCAAAATGCCCTTCAATA
1 TGCAAAAATGAACAAAATGCCCCTGGA-TGTGCAAAAATGACCAAAATG-CCTTCGATG
* * * * *
34398 TGCGAAAATGAAAAAAATGCCCTTGGATGTGC-AAAATGACCAAAATGCCCCTAGATG
1 TGCAAAAATGAACAAAATGCCCCTGGATGTGCAAAAATGACCAAAATG-CCTTCGATG
* ** * * * *
34455 TGCAAAAATGACCAAAATGCCTTTGGATATGCGAAAATGACCAAAATGGCCTTAGATA
1 TGCAAAAATGAACAAAATGCCCCTGGATGTGCAAAAATGACCAAAAT-GCCTTCGATG
* * **
34513 TGCGAAAAAATG-ACAAAAAT-ACCCTAGATGTAAAAAAAATGACCAAAATG
1 TGC--AAAAATGAAC-AAAATGCCCCTGGATGT-GCAAAAATGACCAAAATG
34563 ACATTGGATG
Statistics
Matches: 180, Mismatches: 35, Indels: 16
0.78 0.15 0.07
Matches are distributed among these distances:
57 69 0.38
58 34 0.19
59 46 0.26
60 31 0.17
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (57 bp):
TGCAAAAATGAACAAAATGCCCCTGGATGTGCAAAAATGACCAAAATGCCTTCGATG
Found at i:34472 original size:86 final size:87
Alignment explanation
Indices: 34329--34562 Score: 267
Period size: 86 Copynumber: 2.7 Consensus size: 87
34319 GACCAAAGTG
* *
34329 CCTTCGGATGTGCAAAAACGATCAAAATGCCCCT-GAATTGTGCAAAAATGACCAAAATGCCCTT
1 CCTT-GGATGTGCAAAAATGACCAAAATGCCCCTAG-A-TGTGCAAAAATGACCAAAATGCCCTT
34393 CAATATGCGAAAATGAAAAAAATGC
63 CAATATGCGAAAATGAAAAAAATGC
* **
34418 CCTTGGATGTGC-AAAATGACCAAAATGCCCCTAGATGTGCAAAAATGACCAAAATGCCTTTGGA
1 CCTTGGATGTGCAAAAATGACCAAAATGCCCCTAGATGTGCAAAAATGACCAAAATGCCCTTCAA
** *
34482 TATGCGAAAATGACCAAAATGG
66 TATGCGAAAATGAAAAAAATGC
* * * * **
34504 CCTTAGATATGCGAAAAAATGACAAAAAT-ACCCTAGATGTAAAAAAAATGACCAAAATG
1 CCTTGGATGTGC--AAAAATGACCAAAATGCCCCTAGATGT-GCAAAAATGACCAAAATG
34563 ACATTGGATG
Statistics
Matches: 126, Mismatches: 14, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
86 55 0.44
87 19 0.15
88 19 0.15
89 33 0.26
ACGTcount: A:0.43, C:0.19, G:0.18, T:0.20
Consensus pattern (87 bp):
CCTTGGATGTGCAAAAATGACCAAAATGCCCCTAGATGTGCAAAAATGACCAAAATGCCCTTCAA
TATGCGAAAATGAAAAAAATGC
Found at i:34541 original size:30 final size:30
Alignment explanation
Indices: 34372--34562 Score: 132
Period size: 29 Copynumber: 6.5 Consensus size: 30
34362 TGAATTGTGC
34372 AAAAATGACCAAAAT-GCCCTTCA-ATATGCG
1 AAAAATGACCAAAATGGCCC-T-AGATATGCG
** * *
34402 -AAAATGAAAAAAAT-GCCCTTGGATGTGC-
1 AAAAATGACCAAAATGGCCC-TAGATATGCG
* *
34430 -AAAATGACCAAAATGCCCCTAGATGTGC-
1 AAAAATGACCAAAATGGCCCTAGATATGCG
* *
34458 AAAAATGACCAAAAT-GCCTTTGGATATGCG
1 AAAAATGACCAAAATGGCC-CTAGATATGCG
*
34488 -AAAATGACCAAAATGGCCTTAGATATGCG
1 AAAAATGACCAAAATGGCCCTAGATATGCG
* * * ***
34517 AAAAAATGACAAAAAT-ACCCTAGATGTAAA
1 -AAAAATGACCAAAATGGCCCTAGATATGCG
34547 AAAAATGACCAAAATG
1 AAAAATGACCAAAATG
34563 ACATTGGATG
Statistics
Matches: 131, Mismatches: 21, Indels: 18
0.77 0.12 0.11
Matches are distributed among these distances:
28 22 0.17
29 85 0.65
30 11 0.08
31 13 0.10
ACGTcount: A:0.46, C:0.18, G:0.17, T:0.19
Consensus pattern (30 bp):
AAAAATGACCAAAATGGCCCTAGATATGCG
Found at i:34543 original size:116 final size:115
Alignment explanation
Indices: 34302--34562 Score: 294
Period size: 116 Copynumber: 2.2 Consensus size: 115
34292 ACCAAAACGT
* * * *
34302 CCCTGGATGTGCAAAATGACCAAAGTGCCTTCGGATGTGCAAAAACGATCAAAATGCCCCTGAAT
1 CCCTGGATGTGCAAAATGACCAAAATGCCCTCAGATGTGCAAAAACGACCAAAATGCCCCTGAAT
* *
34367 TGTGCAAAAATGACCAAAATGCCCTTCAATATGCGAAAATGAAAAAAATG
66 TATGCAAAAATGACCAAAATGCCCTTCAATATGCGAAAATGAAAAAAATA
* ** *
34417 CCCTTGGATGTGCAAAATGACCAAAATGCCC-CTAGATGTGCAAAAATGACCAAAATGCCTTTGG
1 CCC-TGGATGTGCAAAATGACCAAAATGCCCTC-AGATGTGCAAAAACGACCAAAATGCCCCTGA
* * *
34481 A-TATGCGAAAATGACCAAAATGGCCTT-AGATATGCGAAAAAATGACAAAAATA
64 ATTATGCAAAAATGACCAAAATGCCCTTCA-ATATGCG--AAAATGAAAAAAATA
* **
34534 CCCTAGATGTAAAAAAAATGACCAAAATG
1 CCCTGGATGT--GCAAAATGACCAAAATG
34563 ACATTGGATG
Statistics
Matches: 123, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
114 1 0.01
115 34 0.28
116 57 0.46
117 16 0.13
118 15 0.12
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (115 bp):
CCCTGGATGTGCAAAATGACCAAAATGCCCTCAGATGTGCAAAAACGACCAAAATGCCCCTGAAT
TATGCAAAAATGACCAAAATGCCCTTCAATATGCGAAAATGAAAAAAATA
Found at i:37909 original size:22 final size:22
Alignment explanation
Indices: 37879--37921 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
37869 AAAATTCAGA
* *
37879 ACAAGTCCTACCCAGGACTTGG
1 ACAACTCCTACACAGGACTTGG
*
37901 ACAACTCCTGCACAGGACTTG
1 ACAACTCCTACACAGGACTTG
37922 TTGCGGGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.28, C:0.33, G:0.21, T:0.19
Consensus pattern (22 bp):
ACAACTCCTACACAGGACTTGG
Found at i:42396 original size:43 final size:43
Alignment explanation
Indices: 42260--42588 Score: 385
Period size: 41 Copynumber: 7.8 Consensus size: 43
42250 ATAAGGAGAA
* *
42260 ATGCCTCTGTG-T-TATATGTTTTTGAGGACTTTTGTAATAGAG
1 ATGCCCCTGTGTTATATATGTGTTTGAGGAC-TTTGTAATAGAG
* *
42302 ATGCCCTTGTGTTATATATGTGTTTGGGGACTTTG-ATATA-A-
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTA-ATAGAG
* *
42343 ATGCCTCTGTGCTATATATGTGTTTGAGGACTTTGTAATAGAG
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
*
42386 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTTG-ATATA-A-
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTA-ATAGAG
*
42427 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
* * *
42470 TTGCCCCTGTGTTATATATGTGTTTGGGGAC-TTGGATATAG-G
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTA-ATAGAG
* * *
42512 -TGCCTCTGTGTTATATATGTGTTTAAGGACTTTTGGAATAGA-
1 ATGCCCCTGTGTTATATATGTGTTTGAGGAC-TTTGTAATAGAG
*
42554 ATTGCCCCTGTGTTATATATGTGTTTGGGGACTTT
1 A-TGCCCCTGTGTTATATATGTGTTTGAGGACTTT
42589 TTGGTTATTG
Statistics
Matches: 248, Mismatches: 23, Indels: 31
0.82 0.08 0.10
Matches are distributed among these distances:
41 97 0.39
42 26 0.10
43 83 0.33
44 42 0.17
ACGTcount: A:0.21, C:0.11, G:0.26, T:0.43
Consensus pattern (43 bp):
ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
Found at i:42398 original size:84 final size:85
Alignment explanation
Indices: 42258--42588 Score: 537
Period size: 84 Copynumber: 3.9 Consensus size: 85
42248 CCATAAGGAG
* *
42258 AAATGCCTCTGTG-T-TATATGTTTTTGAGGACTTTTGTAATAGAGATGCCCTTGTGTTATATAT
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGTAATAGAGATGCCCCTGTGTTATATAT
42321 GTGTTTGGGGACTTTGATAT
66 GTGTTTGGGGACTTTGATAT
*
42341 AAATGCCTCTGTGCTATATATGTGTTTGAGGAC-TTTGTAATAGAGATGCCCCTGTGTTATATAT
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGTAATAGAGATGCCCCTGTGTTATATAT
42405 GTGTTTGGGGACTTTGATAT
66 GTGTTTGGGGACTTTGATAT
*
42425 AAATGCCTCTGTGTTATATATGTGTTTGAGGAC-TTTGTAATAGAGTTGCCCCTGTGTTATATAT
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGTAATAGAGATGCCCCTGTGTTATATAT
*
42489 GTGTTTGGGGACTTGGATAT
66 GTGTTTGGGGACTTTGATAT
** * *
42509 AGGTGCCTCTGTGTTATATATGTGTTTAAGGACTTTTGGAATAGA-ATTGCCCCTGTGTTATATA
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGTAATAGAGA-TGCCCCTGTGTTATATA
42573 TGTGTTTGGGGACTTT
65 TGTGTTTGGGGACTTT
42589 TTGGTTATTG
Statistics
Matches: 233, Mismatches: 11, Indels: 6
0.93 0.04 0.02
Matches are distributed among these distances:
83 13 0.06
84 162 0.70
85 58 0.25
ACGTcount: A:0.21, C:0.11, G:0.25, T:0.42
Consensus pattern (85 bp):
AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGTAATAGAGATGCCCCTGTGTTATATAT
GTGTTTGGGGACTTTGATAT
Found at i:44357 original size:28 final size:28
Alignment explanation
Indices: 44317--44388 Score: 126
Period size: 28 Copynumber: 2.6 Consensus size: 28
44307 ATTTACTTCT
*
44317 CATTTTGGTCATTTTTCATGTCCAGGGG
1 CATTTTGGTCATTTTGCATGTCCAGGGG
44345 CATTTTGGTCATTTTGCATGTCCAGGGG
1 CATTTTGGTCATTTTGCATGTCCAGGGG
*
44373 TATTTTGGTCATTTTG
1 CATTTTGGTCATTTTG
44389 AGTGCACTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.14, C:0.15, G:0.25, T:0.46
Consensus pattern (28 bp):
CATTTTGGTCATTTTGCATGTCCAGGGG
Found at i:53430 original size:24 final size:24
Alignment explanation
Indices: 53398--53450 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
53388 AGCTAAACGG
* *
53398 AAACAGAGACTGAACTTGCGGCAA
1 AAACAGAGACTAAACTTGCAGCAA
*
53422 AAACAGAGACTAAATTTGCAGCAA
1 AAACAGAGACTAAACTTGCAGCAA
53446 AAACA
1 AAACA
53451 ACACAAAGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.49, C:0.19, G:0.19, T:0.13
Consensus pattern (24 bp):
AAACAGAGACTAAACTTGCAGCAA
Found at i:54462 original size:31 final size:31
Alignment explanation
Indices: 54424--54510 Score: 165
Period size: 31 Copynumber: 2.8 Consensus size: 31
54414 GTTTAACTTG
54424 AAACGTTTGGCCCCAAATCGAGCATCGCGAC
1 AAACGTTTGGCCCCAAATCGAGCATCGCGAC
54455 AAACGTTTGGCCCCAAATCGAGCATCGCGAC
1 AAACGTTTGGCCCCAAATCGAGCATCGCGAC
*
54486 AAACGTTTGGCCCCAAATTGAGCAT
1 AAACGTTTGGCCCCAAATCGAGCAT
54511 TTTGCCGATG
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 55 1.00
ACGTcount: A:0.30, C:0.30, G:0.22, T:0.18
Consensus pattern (31 bp):
AAACGTTTGGCCCCAAATCGAGCATCGCGAC
Found at i:56470 original size:21 final size:21
Alignment explanation
Indices: 56431--56479 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
56421 TCAATGCTTT
**
56431 AGGAATGCAAGAGGGATTTCAA
1 AGGAA-GCAAGAGCCATTTCAA
*
56453 AGGAAGCAAGAGCCATTTCCA
1 AGGAAGCAAGAGCCATTTCAA
56474 A-GAAGC
1 AGGAAGC
56480 TACTATTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.21
21 14 0.58
22 5 0.21
ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14
Consensus pattern (21 bp):
AGGAAGCAAGAGCCATTTCAA
Done.