Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021504.1 Corchorus olitorius cultivar O-4 contig21537, 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: 25658
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Found at i:1412 original size:52 final size:52
Alignment explanation
Indices: 1334--1437 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
1324 GACTCGGTTA
1334 TCCCCCAGGATTAAACAAGCTCTTCTCCGAATTTCGGAGGATAACAGGAACC
1 TCCCCCAGGATTAAACAAGCTCTTCTCCGAATTTCGGAGGATAACAGGAACC
1386 TCCCCCAGGATTAAACAAGCTCTTCTCCGAATTTCGGAGGATAACAGGAACC
1 TCCCCCAGGATTAAACAAGCTCTTCTCCGAATTTCGGAGGATAACAGGAACC
1438 ACAAGAAATA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21
Consensus pattern (52 bp):
TCCCCCAGGATTAAACAAGCTCTTCTCCGAATTTCGGAGGATAACAGGAACC
Found at i:3009 original size:8 final size:8
Alignment explanation
Indices: 2998--3043 Score: 74
Period size: 8 Copynumber: 5.8 Consensus size: 8
2988 TCTAACATGT
*
2998 GAACAGCA
1 GAACATCA
3006 GAACATCA
1 GAACATCA
*
3014 GAACATGA
1 GAACATCA
3022 GAACATCA
1 GAACATCA
3030 GAACATCA
1 GAACATCA
3038 GAACAT
1 GAACAT
3044 GTCACATGTG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 35 1.00
ACGTcount: A:0.50, C:0.22, G:0.17, T:0.11
Consensus pattern (8 bp):
GAACATCA
Found at i:3025 original size:24 final size:24
Alignment explanation
Indices: 2991--3044 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2981 TGATTCTTCT
*
2991 AACATGTGAACAGCAGAACATCAG
1 AACATGAGAACAGCAGAACATCAG
*
3015 AACATGAGAACATCAGAACATCAG
1 AACATGAGAACAGCAGAACATCAG
3039 AACATG
1 AACATG
3045 TCACATGTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.48, C:0.20, G:0.19, T:0.13
Consensus pattern (24 bp):
AACATGAGAACAGCAGAACATCAG
Found at i:4553 original size:76 final size:77
Alignment explanation
Indices: 4427--4585 Score: 266
Period size: 76 Copynumber: 2.1 Consensus size: 77
4417 GTTTTCTACT
* * * *
4427 TAAAATAGTAAAATGGTAAACTGAAATAGTTGTAAAGATATTAGATTTAATTAAATAAAAAT-AG
1 TAAAATAGTAAAATGGTAAAATAAAATAGTTATAAAAATATTAGATTTAATTAAATAAAAATAAG
4491 TTTTTAGTTGAG
66 TTTTTAGTTGAG
4503 TAAAATAGTAAAATGGTAAAATAAAATAGTTATAAAAATATTAGATTTAATTAAATAAAAATAGA
1 TAAAATAGTAAAATGGTAAAATAAAATAGTTATAAAAATATTAGATTTAATTAAATAAAAATA-A
4568 GTTTTTAGTTGAG
65 GTTTTTAGTTGAG
4581 TAAAA
1 TAAAA
4586 CTATAAATCT
Statistics
Matches: 77, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
76 58 0.75
78 19 0.25
ACGTcount: A:0.51, C:0.01, G:0.14, T:0.35
Consensus pattern (77 bp):
TAAAATAGTAAAATGGTAAAATAAAATAGTTATAAAAATATTAGATTTAATTAAATAAAAATAAG
TTTTTAGTTGAG
Found at i:6417 original size:19 final size:18
Alignment explanation
Indices: 6389--6430 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
6379 AGTTAATTGT
6389 TTTAATATTAAATTTTTA
1 TTTAATATTAAATTTTTA
*
6407 TTTATATATTATATTTTTA
1 TTTA-ATATTAAATTTTTA
*
6426 CTTAA
1 TTTAA
6431 AAATTACTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTAATATTAAATTTTTA
Found at i:7473 original size:2 final size:2
Alignment explanation
Indices: 7466--7510 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
7456 TAAATAATGC
7466 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7508 TA T
1 TA T
7511 CAATAGGATC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:15173 original size:6 final size:6
Alignment explanation
Indices: 15157--15202 Score: 85
Period size: 6 Copynumber: 7.8 Consensus size: 6
15147 TAATTCACAC
15157 ACAAAA A-AAAA ACAAAA ACAAAA ACAAAA ACAAAA ACAAAA ACAAA
1 ACAAAA ACAAAA ACAAAA ACAAAA ACAAAA ACAAAA ACAAAA ACAAA
15203 GGAACAAAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 5 0.13
6 34 0.87
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (6 bp):
ACAAAA
Found at i:21140 original size:22 final size:22
Alignment explanation
Indices: 21088--21148 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
21078 TTGAATATTT
**
21088 TTATGAAATTTTGATAATTATC
1 TTATGAAATTTTGATAACCATC
* *
21110 CTATTAAATTTTGATAACCA-C
1 TTATGAAATTTTGATAACCATC
*
21131 ATTATGAAATATTGATAA
1 -TTATGAAATTTTGATAA
21149 TTGCCTATGA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
21 1 0.03
22 30 0.97
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.43
Consensus pattern (22 bp):
TTATGAAATTTTGATAACCATC
Found at i:21226 original size:23 final size:22
Alignment explanation
Indices: 21167--21234 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 22
21157 GAAATCGTGA
* *
21167 TAATAAACTTCATATGAAACTT
1 TAATAAACCTCATATGAAATTT
* *
21189 TGAT-AACCTAAATATGAAATTT
1 TAATAAACCT-CATATGAAATTT
21211 TAATAAACCATCATATGAAATTT
1 TAATAAACC-TCATATGAAATTT
21234 T
1 T
21235 GTAACGTTCT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
21 4 0.11
22 16 0.43
23 16 0.43
24 1 0.03
ACGTcount: A:0.46, C:0.12, G:0.06, T:0.37
Consensus pattern (22 bp):
TAATAAACCTCATATGAAATTT
Found at i:22943 original size:23 final size:22
Alignment explanation
Indices: 22872--23322 Score: 279
Period size: 22 Copynumber: 20.6 Consensus size: 22
22862 TTTAACTTCT
* *
22872 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTCAC
*
22894 TAAGAAATTTTGA-AGACCTCAC
1 TATGAAATTTTGATA-ACCTCAC
*
22916 TATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACC-TCAC
* *
22939 TATGAGATGTTGATAACCTC-C
1 TATGAAATTTTGATAACCTCAC
* * * *
22960 ATATGATATATTGATAACCACAT
1 -TATGAAATTTTGATAACCTCAC
* * * *
22983 TATGAAAATTTAAAAACCTTTA-
1 TATGAAATTTTGATAACC-TCAC
* *
23005 TATG-AATTGTT-AGTAATCACAC
1 TATGAAATT-TTGA-TAACCTCAC
* * *
23027 TCTGAAATTTTGATAATCACAC
1 TATGAAATTTTGATAACCTCAC
* * *
23049 TCTGAAATTTTGATAATCACAC
1 TATGAAATTTTGATAACCTCAC
* *
23071 TATGAAATTGTGATAACCTCGC
1 TATGAAATTTTGATAACCTCAC
*
23093 TATAAAATTTTGATAAACCTTC-C
1 TATGAAATTTTGAT-AACC-TCAC
* *
23116 TATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTCAC
*
23139 TATAAAATTTTGATAACCTC-C
1 TATGAAATTTTGATAACCTCAC
*
23160 TTATGAAATCTTGATAA-CT-AC
1 -TATGAAATTTTGATAACCTCAC
*
23181 ----AAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTCAC
** * *
23199 TATGATTTTTTGATAACCTTAT
1 TATGAAATTTTGATAACCTCAC
** *
23221 TATGAAATTTTGATTTGCAT-AC
1 TATGAAATTTTGA-TAACCTCAC
*
23243 TATGAAATTTTGATAACC-CTC
1 TATGAAATTTTGATAACCTCAC
* *
23264 TCATGAAATTTTGA-AAACTAAAC
1 T-ATGAAATTTTGATAACCT-CAC
* *
23287 TATAAAATTTTGATAAGCTTCA-
1 TATGAAATTTTGATAA-CCTCAC
23309 TATGAAATTTTGAT
1 TATGAAATTTTGAT
23323 TATCCTGCCT
Statistics
Matches: 341, Mismatches: 59, Indels: 58
0.74 0.13 0.13
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
18 1 0.00
21 18 0.05
22 233 0.68
23 73 0.21
24 3 0.01
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCAC
Found at i:23157 original size:45 final size:44
Alignment explanation
Indices: 23053--23176 Score: 151
Period size: 45 Copynumber: 2.8 Consensus size: 44
23043 TCACACTCTG
* * * *
23053 AAATTTTGATAATCACACTATGAAATTGTGAT-AACCTCGCTATA
1 AAATTTTGATAACCTC-CTATGAAATTTTGATAAACCTCCCTATA
*
23097 AAATTTTGATAAACCTTCCTATAAAATTTTGATAAACCTCCCTATA
1 AAATTTTGAT-AACC-TCCTATGAAATTTTGATAAACCTCCCTATA
*
23143 AAATTTTGATAACCTCCTTATGAAATCTTGATAA
1 AAATTTTGATAACCTCC-TATGAAATTTTGATAA
23177 CTACAAATTT
Statistics
Matches: 69, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
44 13 0.19
45 34 0.49
46 22 0.32
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (44 bp):
AAATTTTGATAACCTCCTATGAAATTTTGATAAACCTCCCTATA
Found at i:23214 original size:60 final size:61
Alignment explanation
Indices: 23120--23234 Score: 169
Period size: 60 Copynumber: 1.9 Consensus size: 61
23110 CCTTCCTATA
*
23120 AAATTTTGATAAACCTCCCTATAAAATTTTGATAACCTCCTTATGAAATCTTGATAACTAC
1 AAATTTTGATAAACCTCCCTATAAAATTTTGATAACCTCATTATGAAATCTTGATAACTAC
* ** * *
23181 AAATTTTGAT-AACCTCCCTATGATTTTTTGATAACCTTATTATGAAATTTTGAT
1 AAATTTTGATAAACCTCCCTATAAAATTTTGATAACCTCATTATGAAATCTTGAT
23235 TTGCATACTA
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
60 38 0.79
61 10 0.21
ACGTcount: A:0.35, C:0.17, G:0.08, T:0.41
Consensus pattern (61 bp):
AAATTTTGATAAACCTCCCTATAAAATTTTGATAACCTCATTATGAAATCTTGATAACTAC
Found at i:23337 original size:21 final size:21
Alignment explanation
Indices: 23311--23366 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
23301 AAGCTTCATA
23311 TGAAATTTTGATTATCCTGCC
1 TGAAATTTTGATTATCCTGCC
*
23332 TGAAATTTTGATTATTCTGCC
1 TGAAATTTTGATTATCCTGCC
23353 TGAAATTTTGATTA
1 TGAAATTTTGATTA
23367 CTCCATAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.27, C:0.12, G:0.14, T:0.46
Consensus pattern (21 bp):
TGAAATTTTGATTATCCTGCC
Found at i:23498 original size:21 final size:22
Alignment explanation
Indices: 23445--23677 Score: 116
Period size: 22 Copynumber: 10.5 Consensus size: 22
23435 GAAATACCAC
* *
23445 TATGAAATTTTGGTAATCACATT
1 TATGAAATTTTGATAATCTC-TT
*
23468 T-TGAAAATTTGATAATCTCTT
1 TATGAAATTTTGATAATCTCTT
* *
23489 TATGAAATTTTGATAACCTCTC
1 TATGAAATTTTGATAATCTCTT
* * * * *
23511 TATAAAATTTTGTTGACCCCTT
1 TATGAAATTTTGATAATCTCTT
* * *
23533 TGTGAAATTTTGATAATCACAT
1 TATGAAATTTTGATAATCTCTT
* * * *
23555 TATGTAATTTTGTTAACCTCGCT
1 TATGAAATTTTGATAATCTC-TT
** **
23578 T-TGAAATTTTGATAATAACAC
1 TATGAAATTTTGATAATCTCTT
* *
23599 TATAAAATTTTGATAATCTGATCTC
1 TATGAAATTTTGATAATC---TCTT
* * * *
23624 TATGAAATTTCGATAACCACTC
1 TATGAAATTTTGATAATCTCTT
*
23646 TATGAGA-TTTGATAA-C-CTT
1 TATGAAATTTTGATAATCTCTT
*
23665 CTATCAAATTTTG
1 -TATGAAATTTTG
23678 GTACTCCTTA
Statistics
Matches: 158, Mismatches: 44, Indels: 18
0.72 0.20 0.08
Matches are distributed among these distances:
19 2 0.01
20 6 0.04
21 15 0.09
22 115 0.73
23 3 0.02
25 17 0.11
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (22 bp):
TATGAAATTTTGATAATCTCTT
Found at i:23521 original size:22 final size:22
Alignment explanation
Indices: 23469--23677 Score: 136
Period size: 22 Copynumber: 9.5 Consensus size: 22
23459 AATCACATTT
* * *
23469 TGAAAATTTGATAATCTCTTTA
1 TGAAATTTTGATAACCTCTCTA
23491 TGAAATTTTGATAACCTCTCTA
1 TGAAATTTTGATAACCTCTCTA
* * * * * *
23513 TAAAATTTTGTTGACCCCTTTG
1 TGAAATTTTGATAACCTCTCTA
* *
23535 TGAAATTTTGATAATCACAT-TA
1 TGAAATTTTGATAACCTC-TCTA
* * * *
23557 TGTAATTTTGTTAACCTCGCTT
1 TGAAATTTTGATAACCTCTCTA
*** *
23579 TGAAATTTTGATAATAACACTA
1 TGAAATTTTGATAACCTCTCTA
* *
23601 TAAAATTTTGATAATCTGATCTCTA
1 TGAAATTTTGATAA-C--CTCTCTA
* *
23626 TGAAATTTCGATAACCACTCTA
1 TGAAATTTTGATAACCTCTCTA
*
23648 TGAGA-TTTGATAACCT-TCTA
1 TGAAATTTTGATAACCTCTCTA
*
23668 TCAAATTTTG
1 TGAAATTTTG
23678 GTACTCCTTA
Statistics
Matches: 140, Mismatches: 41, Indels: 13
0.72 0.21 0.07
Matches are distributed among these distances:
20 7 0.05
21 13 0.09
22 101 0.72
23 1 0.01
24 1 0.01
25 17 0.12
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTCTA
Found at i:23564 original size:44 final size:43
Alignment explanation
Indices: 23447--23610 Score: 143
Period size: 44 Copynumber: 3.7 Consensus size: 43
23437 AATACCACTA
* * * * * *
23447 TGAAATTTTGGTAATCACATTTTGAAAATTTGATAATCTCTTT
1 TGAAATTTTGATAATCACATTATGAAATTTTGTTAACCCCTTT
* * * *
23490 ATGAAATTTTGATAACCTC-TCTATAAAATTTTGTTGACCCCTTT
1 -TGAAATTTTGATAATCACAT-TATGAAATTTTGTTAACCCCTTT
*
23534 GTGAAATTTTGATAATCACATTATGTAATTTTGTTAACCTCGC-TT
1 -TGAAATTTTGATAATCACATTATGAAATTTTGTTAACC-C-CTTT
* * *
23579 TGAAATTTTGATAATAACACTATAAAATTTTG
1 TGAAATTTTGATAATCACATTATGAAATTTTG
23611 ATAATCTGAT
Statistics
Matches: 96, Mismatches: 20, Indels: 8
0.77 0.16 0.06
Matches are distributed among these distances:
43 1 0.01
44 90 0.94
45 4 0.04
46 1 0.01
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (43 bp):
TGAAATTTTGATAATCACATTATGAAATTTTGTTAACCCCTTT
Found at i:23602 original size:88 final size:88
Alignment explanation
Indices: 23447--23610 Score: 213
Period size: 88 Copynumber: 1.9 Consensus size: 88
23437 AATACCACTA
* * * * ** *
23447 TGAAATTTTGGTAATCACATTTTGAAAATTTGATAATCTCTTTATGAAATTTTGATAACCTCTCT
1 TGAAATTTTGATAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAACACT
23512 ATAAAATTTTGTTGACCCCTTTG
66 ATAAAATTTTGTTGACCCCTTTG
* * * *
23535 TGAAATTTTGATAATCACATTATGTAATTTTGTTAACCTCGCTT-TGAAATTTTGATAATAACAC
1 TGAAATTTTGATAATCACATTATGAAAATTTGATAACCTC-CTTATGAAATTTTGATAACAACAC
23599 TATAAAATTTTG
65 TATAAAATTTTG
23611 ATAATCTGAT
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
88 62 0.97
89 2 0.03
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (88 bp):
TGAAATTTTGATAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAACACT
ATAAAATTTTGTTGACCCCTTTG
Found at i:24828 original size:537 final size:539
Alignment explanation
Indices: 24025--25100 Score: 1704
Period size: 537 Copynumber: 2.0 Consensus size: 539
24015 TAGCCTCGTT
* *
24025 TGAGTCCATGAAGTCCAAATTGTCAAGTCAGATGTTCTAAAGTCTAAATTTGATATTCTTAGACC
1 TGAGTCCATGAAGTCCAAATTGTCAAGCCAGATGTTCTAAAGTCTAAATCTGATATTCTTAGACC
* *
24090 CAATTCGTTAATATGGAAGCCCAAAGAATGAATCCAAGTCCAATCAGTAATTATGATGCAATAAT
66 CAATTCGATAATATGGAAGCCCAAAGAAGGAATCCAAGTCCAATCAGTAATTATGATGCAATAAT
24155 GATTCAGCTCTGATGCAACATTGTTAAATCCTATTTAAAGGAGGACTTCACAAGAGCAGTTTTGG
131 GATTCAGCTCTGATGCAACATTGTTAAATCCTATTTAAAGGAGGACTTCACAAGAGCAGTTTTGG
* * * * * *
24220 AAGAAATTTCATAACTTTTGATTCAGAGTTCTGTAAAATGCAAATGAGGTACCGTTGGAAAGAGG
196 AAGAAAATTCATAACTTTTGATTCAGACTTCAGAAAAATACAAATGAGGTACCGTTGGAAAGAGA
* *
24285 ATTCCGAGATCTACAACTTTTATGTTTATCTCGAAATCTAATTCTGCCGTTTCGGTGGATGATTT
261 ATTCCGAGATCTACAACTTTTATGTTTATCTCGAAACCTAATTCTGCCATTTCGGTGGATGATTT
* *
24350 TACCCTTGAAATTTCTGGACAGAAATGATCTTCTCCTAAACCGACTTTGAGAATGTTTT-AGACG
326 TACCCTTAAAATTTCTGGACAGAAATGATCTTCTCCTAAACCGACTTGGAGAATGTTTTGA-ACG
*
24414 AAAATTCAGATGCTAAAAATGATGTGGGGCATCCCTATTGGCCACGTTGGATTCTAATCAATGAG
390 AAAATTCAGATGCTAAAAATGATGTGGGGCATCCCTATTGGCCACATTGGATTCTAATCAATGAG
* *
24479 GATAATCTAAATTGTTGTCATTATTTTAATAGTGGAATAATT-AAA-A-TA-TTAATAATGGCAA
455 GATAATCTAAA-T-TT-CCATTATTTTAATAGTGGAATAATTAAAATATTATTTAATAATGACAA
*
24540 TTTAGGAATATATTT-GAAAAAA
517 TTTAGAAATATATTTGGAAAAAA
* * *
24562 TGAGTCCATGAAGTCCAAATTGTCAAGCCAGAT-TTATTGAAGTCTAAATCTGATATTCTTAGGC
1 TGAGTCCATGAAGTCCAAATTGTCAAGCCAGATGTT-CTAAAGTCTAAATCTGATATTCTTAGAC
* * *
24626 CCGATTCGATAATATGGAAGCCCAAAGAAGGAGTCCAAGTCCAATCAGTAATTATGATGCAGTAA
65 CCAATTCGATAATATGGAAGCCCAAAGAAGGAATCCAAGTCCAATCAGTAATTATGATGCAATAA
* *
24691 TGATTCAG-TCTTGATGCAACATTGTTAAATCTTATTTAAAGGAGGACTTCACAATAGCAGTTTT
130 TGATTCAGCTC-TGATGCAACATTGTTAAATCCTATTTAAAGGAGGACTTCACAAGAGCAGTTTT
*
24755 GGAAGAAAATTCATAACTTTTGA-TCTAGAACTT-AGAAAAATACAAATGGGGTACCGTTGGAAA
194 GGAAGAAAATTCATAACTTTTGATTC-AG-ACTTCAGAAAAATACAAATGAGGTACCGTTGGAAA
*
24818 GAGAATTCCGAGATCTACAACTTTTATGTTTATCTCGAGACCTAATTCTGCCATTTCGGTGGATG
257 GAGAATTCCGAGATCTACAACTTTTATGTTTATCTCGAAACCTAATTCTGCCATTTCGGTGGATG
* *
24883 ATTTTGCCCTTAAAATTTCTGGACAGAATTGATCTTCTCCTAAACCGACTTGGAGAATGTTTTGA
322 ATTTTACCCTTAAAATTTCTGGACAGAAATGATCTTCTCCTAAACCGACTTGGAGAATGTTTTGA
* * *
24948 ATGAAAATTCAGATGCTAAAAATGATGTGGGGCATCCCTATTGGCCATATTGGATTCTAATTAAT
387 ACGAAAATTCAGATGCTAAAAATGATGTGGGGCATCCCTATTGGCCACATTGGATTCTAATCAAT
*
25013 GAGGATAATCTAAATTTCCATTATTTTAATATTGGAATAATTAAAATATTATTTAATAATGACAA
452 GAGGATAATCTAAATTTCCATTATTTTAATAGTGGAATAATTAAAATATTATTTAATAATGACAA
25078 TTTAGAAATATATTTGGAAAAAA
517 TTTAGAAATATATTTGGAAAAAA
25101 AAGGTATAAT
Statistics
Matches: 495, Mismatches: 34, Indels: 18
0.90 0.06 0.03
Matches are distributed among these distances:
534 23 0.05
535 5 0.01
536 8 0.02
537 422 0.85
538 30 0.06
539 7 0.01
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (539 bp):
TGAGTCCATGAAGTCCAAATTGTCAAGCCAGATGTTCTAAAGTCTAAATCTGATATTCTTAGACC
CAATTCGATAATATGGAAGCCCAAAGAAGGAATCCAAGTCCAATCAGTAATTATGATGCAATAAT
GATTCAGCTCTGATGCAACATTGTTAAATCCTATTTAAAGGAGGACTTCACAAGAGCAGTTTTGG
AAGAAAATTCATAACTTTTGATTCAGACTTCAGAAAAATACAAATGAGGTACCGTTGGAAAGAGA
ATTCCGAGATCTACAACTTTTATGTTTATCTCGAAACCTAATTCTGCCATTTCGGTGGATGATTT
TACCCTTAAAATTTCTGGACAGAAATGATCTTCTCCTAAACCGACTTGGAGAATGTTTTGAACGA
AAATTCAGATGCTAAAAATGATGTGGGGCATCCCTATTGGCCACATTGGATTCTAATCAATGAGG
ATAATCTAAATTTCCATTATTTTAATAGTGGAATAATTAAAATATTATTTAATAATGACAATTTA
GAAATATATTTGGAAAAAA
Found at i:25335 original size:22 final size:22
Alignment explanation
Indices: 25310--25358 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
25300 GAATTTCAAG
* *
25310 AACCTTTTTATAAAATTTTTTT
1 AACCTTCTTATAAAATTTTGTT
*
25332 AACCTTCTTATGAAATTTTGTT
1 AACCTTCTTATAAAATTTTGTT
25354 AACCT
1 AACCT
25359 CCCAAAGGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.31, C:0.14, G:0.04, T:0.51
Consensus pattern (22 bp):
AACCTTCTTATAAAATTTTGTT
Found at i:25512 original size:45 final size:42
Alignment explanation
Indices: 25440--25627 Score: 173
Period size: 45 Copynumber: 4.2 Consensus size: 42
25430 GCTAGCAAAT
*
25440 TTTGATAACTTCCTAATGAAATTTTGATAACCAGCACTAT-AAGA
1 TTTGATAACCTCCT-ATGAAATTTTGATAACCA-CACTATGAA-A
* *
25484 TGTTGATAACCTCCATATGATATATTGATAACCACACTATGAAA
1 T-TTGATAACCTCC-TATGAAATTTTGATAACCACACTATGAAA
* *
25528 TTGTGATAACCTCGCTATGAAATTTTGATAAACCTTC-CTATAAAA
1 TT-TGATAACCTC-CTATGAAATTTTGAT-AACC-ACACTATGAAA
* * *
25573 TTTTGATAAACCTCCCTATAAAATTTTGATAACCTCATTATGAAA
1 -TTTGAT-AACCT-CCTATGAAATTTTGATAACCACACTATGAAA
25618 TCTTGATAAC
1 T-TTGATAAC
25628 TACAAATTTT
Statistics
Matches: 122, Mismatches: 10, Indels: 24
0.78 0.06 0.15
Matches are distributed among these distances:
43 1 0.01
44 37 0.30
45 60 0.49
46 23 0.19
47 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (42 bp):
TTTGATAACCTCCTATGAAATTTTGATAACCACACTATGAAA
Found at i:25568 original size:23 final size:22
Alignment explanation
Indices: 25436--25653 Score: 177
Period size: 22 Copynumber: 10.0 Consensus size: 22
25426 GCTAGCTAGC
*
25436 AAATTTTGATAACTTC-CTAATG
1 AAATTTTGATAACCTCACT-ATG
*
25458 AAATTTTGATAACCAGCACTAT-
1 AAATTTTGATAACC-TCACTATG
*
25480 AAGATGTTGATAACCTC-CATATG
1 AA-ATTTTGATAACCTCAC-TATG
* * *
25503 ATATATTGATAACCACACTATG
1 AAATTTTGATAACCTCACTATG
* *
25525 AAATTGTGATAACCTCGCTATG
1 AAATTTTGATAACCTCACTATG
*
25547 AAATTTTGATAAACCTTC-CTATA
1 AAATTTTGAT-AACC-TCACTATG
* *
25570 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGAT-AACCTCACTATG
*
25593 AAATTTTGATAACCTCATTATG
1 AAATTTTGATAACCTCACTATG
*
25615 AAATCTTGATAA-CT-AC----
1 AAATTTTGATAACCTCACTATG
*
25631 AAATTTTGATAACCTCCCTATG
1 AAATTTTGATAACCTCACTATG
25653 A
1 A
25654 TTTTT
Statistics
Matches: 160, Mismatches: 21, Indels: 30
0.76 0.10 0.14
Matches are distributed among these distances:
16 11 0.07
17 2 0.01
18 1 0.01
20 1 0.01
21 3 0.02
22 84 0.52
23 54 0.34
24 4 0.03
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.35
Consensus pattern (22 bp):
AAATTTTGATAACCTCACTATG
Done.