Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008812.1 Corchorus capsularis cultivar CVL-1 contig08833, 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: 21019
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:642 original size:202 final size:202
Alignment explanation
Indices: 290--840 Score: 829
Period size: 205 Copynumber: 2.7 Consensus size: 202
280 ATACACTAAT
* * * * * ** *
290 GGTGTAAATTCTGGACTCTACAAGTGGGTTGTGAAGTTGATATATGTCTTTTTTTTTAATTATTT
1 GGTGTAAATTTTGGACTCCACAAGCGGGTTGTGGAGTTGATACATGTC-CATTTTTTAATTAATT
*
355 AAGTTTTAAATATTTCAATCTAG-TCCTAAGAGACACATGTCACCCTTCAGGACCCGCTTGTGTA
65 AAGTTTTAAATATTTCAATCTAGTTCCTAAG-GACACATGTCACCCTTCAGGACCCGCTTGTGCA
419 GTCTGCTAAACTCCACTGACGGTGTATTGTATAATTTGCCTTAT-AAAAAT-GGTAATTATTTGA
129 GTCTGCTAAACTCCACTGACGGTGTATTGTATAATTTGCCTTATAAAAAATAGGTAATTATTTGA
**
482 TATTCCGGC
194 TACACCGGC
* * *
491 GGTGTAAATTTTGGACTCCACAAACGCGTTGTGGAGTTGACACATGTCCAATTTTTTAATTAATT
1 GGTGTAAATTTTGGACTCCACAAGCGGGTTGTGGAGTTGATACATGTCC-ATTTTTTAATTAATT
556 AAGTTTTAAATATTTCAATCTAGTTCCTAGAGGACACATGTCACCCTTCAGGACCCGCTTGTGCA
65 AAGTTTTAAATATTTCAATCTAGTTCCTA-AGGACACATGTCACCCTTCAGGACCCGCTTGTGCA
621 GTCTGCTAAACTCCACTGACGGTGTATTGTATAATTTGCCTTATAAAAAATAGGGTAATTATTTG
129 GTCTGCTAAACTCCACTGACGGTGTATTGTATAATTTGCCTTATAAAAAATA-GGTAATTATTTG
686 ATACACCGGC
193 ATACACCGGC
*
696 GGTGTAAATTTTGGATTCCACAAGCGGGTTGTGGAGTTGATACATGTCCATTTTCTTAATTAATT
1 GGTGTAAATTTTGGACTCCACAAGCGGGTTGTGGAGTTGATACATGTCCATTTT-TTAATTAATT
* * * * *
761 AAATTTTATATATTTCAATCTAGTCCCTAAGGGACACATGTCACCCTTCAAGACCCACTTGTGCA
65 AAGTTTTAAATATTTCAATCTAGTTCCTAA-GGACACATGTCACCCTTCAGGACCCGCTTGTGCA
*
826 GTCTGTTAAACTCCA
129 GTCTGCTAAACTCCA
841 ACACCGTCAC
Statistics
Matches: 318, Mismatches: 24, Indels: 12
0.90 0.07 0.03
Matches are distributed among these distances:
201 76 0.24
202 81 0.25
203 8 0.03
204 6 0.02
205 147 0.46
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (202 bp):
GGTGTAAATTTTGGACTCCACAAGCGGGTTGTGGAGTTGATACATGTCCATTTTTTAATTAATTA
AGTTTTAAATATTTCAATCTAGTTCCTAAGGACACATGTCACCCTTCAGGACCCGCTTGTGCAGT
CTGCTAAACTCCACTGACGGTGTATTGTATAATTTGCCTTATAAAAAATAGGTAATTATTTGATA
CACCGGC
Found at i:2609 original size:156 final size:156
Alignment explanation
Indices: 2343--2699 Score: 366
Period size: 156 Copynumber: 2.3 Consensus size: 156
2333 TCATCTCAAA
* * * * ** * * **
2343 CAGACTTTGTATGAAAAACTTATGCAAGTTTTTCAGTTAAGGACAGTTTGGGGTGTTAAACCAAC
1 CAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAACTTAGGGAGAGAAACCAAC
* * * * *
2408 TTCTCTATGCTAGAGAGTTCGGGTTTACTTAGAATTTTTCCCATAGCCTCATG-G-GGATAATCT
66 TTCACCATGCAAGAGAGCTCGGGTTTACTTAGAATTTTTCCCATAG--TCATGCGCAGATAATCT
* *
2471 AAGTCTAC-TGGTGGAAA-ATCAGCCTCGTT
129 AAGTC-ACTTGG-CGAAATATCAG-CTCATT
* * * *
2500 -GGACTTAGCATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAACTTAGGGAGAGAAACCTAG
1 CAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAACTTAGGGAGAGAAACCAAC
* ** *
2564 TTCACCAT-CAAGGAGAGCTCGGTTTTACTTAGAATTTTTTTCATAGTCTTGCGCAGATAATCTA
66 TTCACCATGCAA-GAGAGCTCGGGTTTACTTAGAATTTTTCCCATAGTCATGCGCAGATAATCTA
* *
2628 AGTCCCTTGGCGAAATTTCAGCTCATT
130 AGTCACTTGGCGAAATATCAGCTCATT
*
2655 CAGACTTAGAATGAAAAACTTATGCTTGTTTTTCATTTAAGGACA
1 CAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACA
2700 GTTTGAGGTG
Statistics
Matches: 165, Mismatches: 29, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
154 4 0.02
155 13 0.08
156 148 0.90
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (156 bp):
CAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAACTTAGGGAGAGAAACCAAC
TTCACCATGCAAGAGAGCTCGGGTTTACTTAGAATTTTTCCCATAGTCATGCGCAGATAATCTAA
GTCACTTGGCGAAATATCAGCTCATT
Found at i:3081 original size:17 final size:18
Alignment explanation
Indices: 3059--3096 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
3049 GTTATCCAGC
3059 ACCTCATGCTACCTA-GT
1 ACCTCATGCTACCTAGGT
*
3076 ACCTCATGTTACCTAGGT
1 ACCTCATGCTACCTAGGT
3094 ACC
1 ACC
3097 ATGAGGAGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.24, C:0.34, G:0.13, T:0.29
Consensus pattern (18 bp):
ACCTCATGCTACCTAGGT
Found at i:6241 original size:29 final size:29
Alignment explanation
Indices: 6204--6278 Score: 109
Period size: 29 Copynumber: 2.6 Consensus size: 29
6194 GAGTCATCCA
6204 GGGGCATTTTGGTCATTTTT-CATATCTA-G
1 GGGGCATTTTGGTCATTTTTGCAT-T-TAGG
6233 GGGGCATTTTGGTCATTTTTGCATTTAGG
1 GGGGCATTTTGGTCATTTTTGCATTTAGG
*
6262 GGGGTATTTTGGTCATT
1 GGGGCATTTTGGTCATT
6279 CTTAATCTAC
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
28 2 0.05
29 38 0.88
30 3 0.07
ACGTcount: A:0.15, C:0.11, G:0.29, T:0.45
Consensus pattern (29 bp):
GGGGCATTTTGGTCATTTTTGCATTTAGG
Found at i:9109 original size:26 final size:28
Alignment explanation
Indices: 9062--9114 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 28
9052 ATTTAATTCA
*
9062 GTTTAGGGTGTAATTGACTTGACTTTTT
1 GTTTAGGGTGTAATTGAATTGACTTTTT
* *
9090 GTTTA-GGT-TAATTTAATTGAGTTTT
1 GTTTAGGGTGTAATTGAATTGACTTTT
9115 AAGTAATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 14 0.64
27 3 0.14
28 5 0.23
ACGTcount: A:0.21, C:0.04, G:0.23, T:0.53
Consensus pattern (28 bp):
GTTTAGGGTGTAATTGAATTGACTTTTT
Found at i:9834 original size:54 final size:54
Alignment explanation
Indices: 9772--9964 Score: 257
Period size: 54 Copynumber: 3.6 Consensus size: 54
9762 TCAGTAAAGA
9772 GTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAAAAATTAATTAGAGTCAAG
1 GTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAAAAATTAATTAGAGTCAAG
* * * *
9826 GTAATAGAAATCAGTAAATCAATAATTAAGTGAAAAGAAATTAA-T-CAGTAAAG
1 GTAATAGAAATCAGTAAATCAGTAATTAAGT-AAAAAAAATTAATTAGAGTCAAG
* * *
9879 AGTAATAGAAATCAGTAAATCAGTAATTAGGTAAAAAGAGATTAATTAGAGTCAAA
1 -GTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAA-AAATTAATTAGAGTCAAG
*
9935 GTAATAGTAATCAGTAAATC-GATAATTAAG
1 GTAATAGAAATCAGTAAATCAG-TAATTAAG
9965 AGTTAAAATG
Statistics
Matches: 120, Mismatches: 13, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
53 10 0.08
54 67 0.56
55 38 0.32
56 5 0.04
ACGTcount: A:0.52, C:0.06, G:0.16, T:0.26
Consensus pattern (54 bp):
GTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAAAAATTAATTAGAGTCAAG
Found at i:9880 original size:108 final size:109
Alignment explanation
Indices: 9759--9964 Score: 360
Period size: 108 Copynumber: 1.9 Consensus size: 109
9749 AGTAAAGTGA
9759 TAATCAGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAA-AAATTAATTAGAGTC
1 TAATCAGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAAGAAATTAATTAGAGTC
*
9823 AAGGTAATAGAAATCAGTAAATCAATAATTAAGTGAAAAGAAAT
66 AAAGTAATAGAAATCAGTAAATCAATAATTAAGTGAAAAGAAAT
* *
9867 TAATCAGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAGGTAAAAAGAGATTAATTAGAGTC
1 TAATCAGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAAGAAATTAATTAGAGTC
* *
9932 AAAGTAATAGTAATCAGTAAATCGATAATTAAG
66 AAAGTAATAGAAATCAGTAAATCAATAATTAAG
9965 AGTTAAAATG
Statistics
Matches: 92, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
108 48 0.52
109 44 0.48
ACGTcount: A:0.52, C:0.06, G:0.16, T:0.26
Consensus pattern (109 bp):
TAATCAGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAAGAAATTAATTAGAGTC
AAAGTAATAGAAATCAGTAAATCAATAATTAAGTGAAAAGAAAT
Found at i:9990 original size:109 final size:106
Alignment explanation
Indices: 9766--9964 Score: 317
Period size: 109 Copynumber: 1.8 Consensus size: 106
9756 TGATAATCAG
*
9766 TAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAAAAATTAATTAGAGTCAAGGTAAT
1 TAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAAAAATTAATTAGAGTCAAAGTAAT
*
9831 AGAAATCAGTAAATCAATAATTAAGTGAAAAGAAATTAATCA
66 AGAAATCAGTAAATCAATAATTAAGTGAAAAGAAAGTAAT-A
* *
9873 GTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAGGTAAAAAGAGATTAATTAGAGTCAAAGTA
1 -TAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAA-AAATTAATTAGAGTCAAAGTA
* *
9938 ATAGTAATCAGTAAATCGATAATTAAG
64 ATAGAAATCAGTAAATCAATAATTAAG
9965 AGTTAAAATG
Statistics
Matches: 85, Mismatches: 5, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
108 41 0.48
109 44 0.52
ACGTcount: A:0.53, C:0.06, G:0.16, T:0.26
Consensus pattern (106 bp):
TAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAAAAATTAATTAGAGTCAAAGTAAT
AGAAATCAGTAAATCAATAATTAAGTGAAAAGAAAGTAATA
Found at i:10251 original size:43 final size:42
Alignment explanation
Indices: 10201--10538 Score: 274
Period size: 43 Copynumber: 7.7 Consensus size: 42
10191 TAATCAGTAA
10201 AAGAGTAAAATAGTAATCAGTAAAAAGTAAGAAGGTAATCAAC
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAA-AAGGTAATCAAC
* **
10244 AAGAGTAAAATAGTAGTCAGTAAAAAGTAAATA-GTAATCAGT
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAAA-AGGTAATCAAC
* * * **
10286 AAGAGTAAAA-AGTAATAAGTAAGAAGTAAAAGGAAATCAGT
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAAAAGGTAATCAAC
* * * *
10327 AAGAGTAAAA-AGGTGATCAGTAAAGAGTAAAAAGCTAATCAGC
1 AAGAGTAAAATA-GTAATCAGTAAAAAGT-AAAAGGTAATCAAC
* * *
10370 AAGAAGTAAAA-AGATAATCAGTAAAACGCAAAAGGTAATTAGTA-
1 AAG-AGTAAAATAG-TAATCAGTAAAAAGTAAAAGGTAATCA--AC
* * * *
10414 AAAACTAAAAGAGTAATCAGTAAAAAAG-AAGAAGAAAATAGTAATCAGTAA
1 AAGAGTAAAATAGTAATCAGT-AAAAAGTAA-AAG------GTAATCA--AC
*
10465 AAGAGTAAAATGGTAATCAGTAAAAAGTAAGAAGGTAATCAAC
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAA-AAGGTAATCAAC
*
10508 AAGAGTAAAATAGTAATCAGTACAAAGTAAA
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAAA
10539 GAATAATCAG
Statistics
Matches: 244, Mismatches: 32, Indels: 39
0.77 0.10 0.12
Matches are distributed among these distances:
40 1 0.00
41 36 0.15
42 31 0.13
43 100 0.41
44 31 0.13
45 7 0.03
50 15 0.06
51 23 0.09
ACGTcount: A:0.56, C:0.06, G:0.19, T:0.18
Consensus pattern (42 bp):
AAGAGTAAAATAGTAATCAGTAAAAAGTAAAAGGTAATCAAC
Found at i:10272 original size:7 final size:7
Alignment explanation
Indices: 10262--10494 Score: 53
Period size: 7 Copynumber: 32.7 Consensus size: 7
10252 AATAGTAGTC
10262 AGTAAAA
1 AGTAAAA
*
10269 AGTAAAT
1 AGTAAAA
**
10276 AGTAATC
1 AGTAAAA
*
10283 AGT-AAG
1 AGTAAAA
10289 AGTAAAA
1 AGTAAAA
*
10296 AGTAATA
1 AGTAAAA
*
10303 AGTAAGA
1 AGTAAAA
10310 AGT-AAA
1 AGTAAAA
* *
10316 AGGAAATC
1 AGTAAA-A
*
10324 AGT-AAG
1 AGTAAAA
10330 AGTAAAA
1 AGTAAAA
* **
10337 AGGTGATC
1 A-GTAAAA
*
10345 AGTAAAG
1 AGTAAAA
10352 AGTAAAA
1 AGTAAAA
**
10359 AGCTAATC
1 AG-TAAAA
* *
10367 AGCAAGA
1 AGTAAAA
10374 AGTAAAA
1 AGTAAAA
**
10381 AGATAATC
1 AG-TAAAA
10389 AGTAAAA
1 AGTAAAA
* *
10396 CGCAAAA
1 AGTAAAA
* **
10403 GGTAATT
1 AGTAAAA
10410 AGTAAAA
1 AGTAAAA
*
10417 ACTAAAA
1 AGTAAAA
**
10424 GAGTAATC
1 -AGTAAAA
10432 AGTAAAAA
1 AGT-AAAA
*
10440 AG-AAGA
1 AGTAAAA
10446 AG-AAAA
1 AGTAAAA
**
10452 TAGTAATC
1 -AGTAAAA
10460 AGTAAAA
1 AGTAAAA
10467 GAGTAAAA
1 -AGTAAAA
* **
10475 TGGTAATC
1 -AGTAAAA
10483 AGTAAAA
1 AGTAAAA
10490 AGTAA
1 AGTAA
10495 GAAGGTAATC
Statistics
Matches: 154, Mismatches: 60, Indels: 24
0.65 0.25 0.10
Matches are distributed among these distances:
6 19 0.12
7 98 0.64
8 37 0.24
ACGTcount: A:0.57, C:0.06, G:0.19, T:0.18
Consensus pattern (7 bp):
AGTAAAA
Found at i:10277 original size:21 final size:21
Alignment explanation
Indices: 10189--10572 Score: 205
Period size: 21 Copynumber: 17.6 Consensus size: 21
10179 GGGTAAAAAG
10189 AGTAATCAGTAAAAGAGTAAAAT
1 AGTAATCAGTAAAA-AGT-AAAT
10212 AGTAATCAGTAAAAAGTAAGA-
1 AGTAATCAGTAAAAAGTAA-AT
*
10233 AGGTAATCA--ACAAGAGTAAAAT
1 A-GTAATCAGTA-AAAAGT-AAAT
*
10255 AGTAGTCAGTAAAAAGTAAAT
1 AGTAATCAGTAAAAAGTAAAT
* *
10276 AGTAATCAGT-AAGAGTAAAA
1 AGTAATCAGTAAAAAGTAAAT
* *
10296 AGTAATAAGTAAGAAGTAAA-
1 AGTAATCAGTAAAAAGTAAAT
* * *
10316 AGGAAATCAGT-AAGAGTAAAA
1 A-GTAATCAGTAAAAAGTAAAT
* * *
10337 AGGTGATCAGTAAAGAGTAAAA
1 A-GTAATCAGTAAAAAGTAAAT
* * *
10359 AGCTAATCAGCAAGAAGTAAAA
1 AG-TAATCAGTAAAAAGTAAAT
* *
10381 AGATAATCAGTAAAACGCAAA-
1 AG-TAATCAGTAAAAAGTAAAT
* * *
10402 AGGTAATTAGTAAAAACTAAAAG
1 A-GTAATCAGTAAAAAGT-AAAT
*
10425 AGTAATCAGTAAAAAAGAAGAAGAAAAT
1 AGTAATCAGT-----A-AA-AAGTAAAT
10453 AGTAATCAGTAAAAGAGTAAAAT
1 AGTAATCAGTAAAA-AGT-AAAT
*
10476 GGTAATCAGTAAAAAGTAAGA-
1 AGTAATCAGTAAAAAGTAA-AT
*
10497 AGGTAATCA--ACAAGAGTAAAAT
1 A-GTAATCAGTA-AAAAGT-AAAT
* *
10519 AGTAATCAGTACAAAGTAAAG
1 AGTAATCAGTAAAAAGTAAAT
* *
10540 AATAATCAGTGAAATAGT-AAT
1 AGTAATCAGT-AAAAAGTAAAT
*
10561 GGTAATCAGTAA
1 AGTAATCAGTAA
10573 TTCAGTAAAA
Statistics
Matches: 284, Mismatches: 45, Indels: 67
0.72 0.11 0.17
Matches are distributed among these distances:
20 29 0.10
21 102 0.36
22 100 0.35
23 35 0.12
27 1 0.00
28 15 0.05
29 2 0.01
ACGTcount: A:0.55, C:0.06, G:0.19, T:0.19
Consensus pattern (21 bp):
AGTAATCAGTAAAAAGTAAAT
Found at i:10313 original size:27 final size:27
Alignment explanation
Indices: 10262--10314 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
10252 AATAGTAGTC
**
10262 AGTAAAAAGTAAATAGTAATCAGTAAG
1 AGTAAAAAGTAAATAGTAAGAAGTAAG
10289 AGTAAAAAGT-AATAAGTAAGAAGTAA
1 AGTAAAAAGTAAAT-AGTAAGAAGTAA
10315 AAGGAAATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 3 0.13
27 20 0.87
ACGTcount: A:0.58, C:0.02, G:0.19, T:0.21
Consensus pattern (27 bp):
AGTAAAAAGTAAATAGTAAGAAGTAAG
Found at i:12174 original size:27 final size:27
Alignment explanation
Indices: 12136--12189 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
12126 TAAGCTGGAA
12136 CCTTCTTACTAATATATACTAAACCTT
1 CCTTCTTACTAATATATACTAAACCTT
12163 CCTTCTTACTAATATATACTAAACCTT
1 CCTTCTTACTAATATATACTAAACCTT
12190 ATTTGAGACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.26, G:0.00, T:0.41
Consensus pattern (27 bp):
CCTTCTTACTAATATATACTAAACCTT
Found at i:15852 original size:49 final size:49
Alignment explanation
Indices: 15785--15930 Score: 211
Period size: 49 Copynumber: 3.0 Consensus size: 49
15775 AACTGAGAAC
* * * * * *
15785 AAGACGAAACTAATCAACACCTTCCGATCGTGAAAGGCAAACTGGGAAT
1 AAGACAAAACTAAACAACACCTTCCGACCGGGAAGGGCAAACTAGGAAT
* * *
15834 AAGACAAAATTGAACAACACCTTCCGGCCGGGAAGGGCAAACTAGGAAT
1 AAGACAAAACTAAACAACACCTTCCGACCGGGAAGGGCAAACTAGGAAT
15883 AAGACAAAACTAAACAACACCTTCCGACCGGGAAGGGCAAACTAGGAA
1 AAGACAAAACTAAACAACACCTTCCGACCGGGAAGGGCAAACTAGGAA
15931 AAGTAAACAA
Statistics
Matches: 85, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 85 1.00
ACGTcount: A:0.42, C:0.23, G:0.22, T:0.12
Consensus pattern (49 bp):
AAGACAAAACTAAACAACACCTTCCGACCGGGAAGGGCAAACTAGGAAT
Found at i:15960 original size:41 final size:39
Alignment explanation
Indices: 15888--16463 Score: 335
Period size: 41 Copynumber: 13.9 Consensus size: 39
15878 GGAATAAGAC
* *
15888 AAAACTAAACAACACCTTCCGACCGGGAAGGGCAAACTAGG
1 AAAAGTAAACAACACCTTCCG--TGGGAAGGGCAAACTAGG
* **
15929 AAAAGTAAACAACACCTTCTAGTGGGAAAGGGCAAACGGGG
1 AAAAGTAAACAACACCTTC-CGTGGG-AAGGGCAAACTAGG
** * *
15970 AAACTTAAACAGCACCTTCCGGTGAGGAAGGGCAAACTGGG
1 AAAAGTAAACAACACCTTCC-GTG-GGAAGGGCAAACTAGG
* * *
16011 AACAGTAAACAACACCTTCCGATGGGGAATGGCAAACTGGG
1 AAAAGTAAACAACACCTTCCG-T-GGGAAGGGCAAACTAGG
* * *
16052 AAATGTAGACTTAGACAACACCTTCCGGTGGGGAAGGGCAAAATGGG
1 AAA---AG---TAAACAACACCTTCC-GT-GGGAAGGGCAAACTAGG
* * * *
16099 AAATGTGAACAACACCTTCCGATGGGGAAGAGCAGACT-GG
1 AAAAGTAAACAACACCTTCCG-T-GGGAAGGGCAAACTAGG
* *
16139 TTAAAGTAAACAACACCTTCCGATGGGGAAGGGCAAACTGGG
1 -AAAAGTAAACAACACCTTCCG-T-GGGAAGGGCAAACTAGG
* * *
16181 AAAACTAAACAACACCTTTCGTCAGGGAAGGGCAAACCA-G
1 AAAAGTAAACAACACCTTCCGT--GGGAAGGGCAAACTAGG
* * ** *
16221 -AATGTGAACAACACCTTCCGACTACGAAGGGCAAACTGAGA
1 AAAAGTAAACAACACCTTCCG--TGGGAAGGGCAAACT-AGG
*
16262 AATATAGACTTAAACAACAACTTCCGATGAGGAA-GGCAAAAC-AGG
1 AA-A-AG---TAAACAACACCTTCCG-TG-GGAAGGGC-AAACTAGG
* *
16307 AAAACTAAACAACACCTTCCGACTGGGAATGGCAAACT-GG
1 AAAAGTAAACAACACCTTCCG--TGGGAAGGGCAAACTAGG
* * * *
16347 -AATGTAATCAACACCTTCTGGTGGGGAAGGGAAAACT-GG
1 AAAAGTAAACAACACCTTC-CGT-GGGAAGGGCAAACTAGG
* *
16386 AAAAACTAAACAACACCTTCCGGTGAGGAAGGGTAAAC-AGG
1 -AAAAGTAAACAACACCTTCC-GTG-GGAAGGGCAAACTAGG
* *
16427 AATA-TAAACGACACCTTCCTGTGGGGAAGGGCAAACT
1 AAAAGTAAACAACACCTTCC-GT-GGGAAGGGCAAACT
16464 GGGGATGAGC
Statistics
Matches: 425, Mismatches: 69, Indels: 83
0.74 0.12 0.14
Matches are distributed among these distances:
38 1 0.00
39 83 0.20
40 41 0.10
41 222 0.52
42 7 0.02
43 2 0.00
44 5 0.01
45 4 0.01
46 4 0.01
47 55 0.13
48 1 0.00
ACGTcount: A:0.39, C:0.21, G:0.26, T:0.15
Consensus pattern (39 bp):
AAAAGTAAACAACACCTTCCGTGGGAAGGGCAAACTAGG
Found at i:16045 original size:82 final size:82
Alignment explanation
Indices: 15889--16468 Score: 399
Period size: 82 Copynumber: 7.0 Consensus size: 82
15879 GAATAAGACA
** * *
15889 AAAC-TAAACAACACCTTCCGACCG-GGAAGGGCAAACTAGGAAAAGTAAACAACACCTT-CTAG
1 AAACTTAAACAACACCTTCCG-GTGAGGAAGGGCAAACT-GGGAAAGTAAACAACACCTTCCGA-
*
15951 TGGGAAAGGGCAAAC-GGGG
63 TGGGGAAGGGCAAACTGGGG
*
15970 AAACTTAAACAGCACCTTCCGGTGAGGAAGGGCAAACTGGGAACAGTAAACAACACCTTCCGATG
1 AAACTTAAACAACACCTTCCGGTGAGGAAGGGCAAACTGGGAA-AGTAAACAACACCTTCCGATG
*
16035 GGGAATGGCAAACTGGGAAATG
65 GGGAAGGGCAAACTGGG----G
* * * * *
16057 TAGACTTAGACAACACCTTCCGGTGGGGAAGGGCAAAATGGGAAATGTGAACAACACCTTCCGAT
1 -AAACTTAAACAACACCTTCCGGTGAGGAAGGGCAAACTGGGAAA-GTAAACAACACCTTCCGAT
* * **
16122 GGGGAAGAGCAGACTGGTT
64 GGGGAAGGGCAAACTGGGG
* * * * *
16141 AAA-GTAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAAACTAAACAACACCTTTCG-TC
1 AAACTTAAACAACACCTTCCGGTGAGGAAGGGCAAACTGGG-AAAGTAAACAACACCTTCCGAT-
* **
16204 AGGGAAGGGCAAAC--CAG
64 GGGGAAGGGCAAACTGGGG
* * * * *
16221 -AA-TGTGAACAACACCTTCCGACT-ACGAAGGGCAAACTGAGAAATATAGACTTAAACAACAAC
1 AAACT-TAAACAACACCTTCCG-GTGAGGAAGGGCAAACTG-G-GA-A-AG---TAAACAACACC
* * *
16283 TTCCGATGAGGAA-GGCAAAAC-AGGA
57 TTCCGATGGGGAAGGGC-AAACTGGGG
* * * * * *
16308 AAAC-TAAACAACACCTTCCGACTG-GGAATGGCAAACT-GGAATGTAATCAACACCTTCTGGTG
1 AAACTTAAACAACACCTTCCG-GTGAGGAAGGGCAAACTGGGAAAGTAAACAACACCTTCCGATG
* **
16370 GGGAAGGGAAAACTGGAA
65 GGGAAGGGCAAACTGGGG
* * *
16388 AAAC-TAAACAACACCTTCCGGTGAGGAAGGGTAAAC-AGGAATA-TAAACGACACCTTCCTG-T
1 AAACTTAAACAACACCTTCCGGTGAGGAAGGGCAAACTGGGAA-AGTAAACAACACCTTCC-GAT
16449 GGGGAAGGGCAAACTGGGG
64 GGGGAAGGGCAAACTGGGG
16468 A
1 A
16469 TGAGCAAATA
Statistics
Matches: 396, Mismatches: 69, Indels: 69
0.74 0.13 0.13
Matches are distributed among these distances:
79 27 0.07
80 96 0.24
81 14 0.04
82 116 0.29
83 12 0.03
84 1 0.00
85 4 0.01
86 22 0.06
87 32 0.08
88 72 0.18
ACGTcount: A:0.38, C:0.21, G:0.26, T:0.15
Consensus pattern (82 bp):
AAACTTAAACAACACCTTCCGGTGAGGAAGGGCAAACTGGGAAAGTAAACAACACCTTCCGATGG
GGAAGGGCAAACTGGGG
Found at i:16115 original size:129 final size:123
Alignment explanation
Indices: 15893--16461 Score: 369
Period size: 129 Copynumber: 4.6 Consensus size: 123
15883 AAGACAAAAC
** * *
15893 TAAACAACACCTTCCGACCGGGAAGGGCAAACTAGGAAAAGTAAACAACACCTTCTAGTGGGAAA
1 TAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAAAGTAAACAACACCTTCCAGTGGGAAA
* * * *
15958 GGGCAAACGGGGAAACTTAAACAGCACCTTCCGGTGAGGAAGGGCAAACTGG-GAACAG
66 GGGCAAAAGGGGAAACTTAAACAACACCTTCCGATGAGGAAGAGCAAACTGGTGAA-AG
* * *
16016 TAAACAACACCTTCCGATGGGGAATGGCAAACTGGGAAATGTAGACTTAGACAACACCTTCCGGT
1 TAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAA---AG---TAAACAACACCTTCCAGT
* * * * * *
16081 GGGGAAGGGCAAAATGGGAAA-TGTGAACAACACCTTCCGATGGGGAAGAGCAGACTGGTTAAAG
60 GGGAAAGGGCAAAAGGGGAAACT-TAAACAACACCTTCCGATGAGGAAGAGCAAACTGGTGAAAG
* *
16145 TAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAAACTAAACAACACCTTTC-GTCAGGG-
1 TAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAAAGTAAACAACACCTTCCAGT--GGGA
*** * * * **
16208 AAGGGC-AAACCAG-AA-TGTGAACAACACCTTCCGACT-ACGAAGGGCAAACTGAGAAATATAG
64 AAGGGCAAAAGGGGAAACT-TAAACAACACCTTCCGA-TGAGGAAGAGCAAACTG-GTGA-A-AG
* * * * *
16269 ACTTAAACAACAACTTCCGATGAGGAA-GGCAAAAC-AGGAAAACTAAACAACACCTTCCGACTG
1 ---TAAACAACACCTTCCGATGGGGAAGGGC-AAACTGGGAAAAGTAAACAACACCTTCC-AGTG
* ** * * * * * * ** *
16332 GG-AATGGC-AAACTGG-AA-TGTAATCAACACCTTCTGGTGGGGAAGGGAAAACTGGAAAAAC
61 GGAAAGGGCAAAAGGGGAAACT-TAAACAACACCTTCCGATGAGGAAGAGCAAACTGGTGAAAG
* * * * * * * *
16392 TAAACAACACCTTCCGGTGAGGAAGGGTAAAC-AGGAATA-TAAACGACACCTTCCTGTGGGGAA
1 TAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAAAGTAAACAACACCTTCCAGTGGGAAA
16455 GGGCAAA
66 GGGCAAA
16462 CTGGGGATGA
Statistics
Matches: 368, Mismatches: 54, Indels: 51
0.78 0.11 0.11
Matches are distributed among these distances:
118 4 0.01
119 19 0.05
120 34 0.09
121 34 0.09
122 9 0.02
123 56 0.15
124 6 0.02
125 5 0.01
126 69 0.19
127 26 0.07
128 2 0.01
129 102 0.28
130 2 0.01
ACGTcount: A:0.38, C:0.21, G:0.26, T:0.15
Consensus pattern (123 bp):
TAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAAAGTAAACAACACCTTCCAGTGGGAAA
GGGCAAAAGGGGAAACTTAAACAACACCTTCCGATGAGGAAGAGCAAACTGGTGAAAG
Found at i:16217 original size:170 final size:170
Alignment explanation
Indices: 15896--16217 Score: 398
Period size: 170 Copynumber: 1.9 Consensus size: 170
15886 ACAAAACTAA
* * *
15896 ACAACACCTTCCGACCGGGAAGGGCAAACTAGGAAAAGTAAACAACACCTTCTAGTGGGAAAGGG
1 ACAACACCTTCCGACCGGGAAGGGCAAAATAGGAAAAGTAAACAACACCTTCGAGTGGGAAAGAG
* * * * *
15961 CAAACGGGGAAACTTAAACAGCACCTTCCGGTGAGGAAGGGCAAACTGGGAACAGTAAACAACAC
66 CAAACGGGGAAACGTAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAAACTAAACAACAC
* *
16026 CTTCCGATGGGGAATGGCAAACTGGGAAATGTAGACTTAG
131 CTTCCGATAGGGAAGGGCAAACTGGGAAATGTAGACTTAG
*** * * * *
16066 ACAACACCTTCCGGTGGGGAAGGGCAAAATGGGAAATGTGAACAACACCTTCCGA-TGGGGAAGA
1 ACAACACCTTCCGACCGGGAAGGGCAAAATAGGAAAAGTAAACAACACCTT-CGAGTGGGAAAGA
* ** *
16130 GCAGACTGGTTAAA-GTAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAAACTAAACAAC
65 GCAAAC-GGGGAAACGTAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAAACTAAACAAC
*
16194 ACCTTTCG-TCAGGGAAGGGCAAAC
129 ACCTTCCGAT-AGGGAAGGGCAAAC
16218 CAGAATGTGA
Statistics
Matches: 127, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
169 1 0.01
170 119 0.94
171 7 0.06
ACGTcount: A:0.37, C:0.21, G:0.28, T:0.14
Consensus pattern (170 bp):
ACAACACCTTCCGACCGGGAAGGGCAAAATAGGAAAAGTAAACAACACCTTCGAGTGGGAAAGAG
CAAACGGGGAAACGTAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAAACTAAACAACAC
CTTCCGATAGGGAAGGGCAAACTGGGAAATGTAGACTTAG
Found at i:16374 original size:39 final size:39
Alignment explanation
Indices: 16272--16465 Score: 151
Period size: 39 Copynumber: 4.9 Consensus size: 39
16262 AATATAGACT
* * * * * *
16272 TAAACAACAACTTCCGATGAGGAA-GGCAAAACAGGAAAA
1 TAAACAACACCTTCTGGTGGGGAAGGGC-AAACTGGAATA
* * * *
16311 CTAAACAACACCTTCCGACT-GGGAATGGCAAACTGGAATG
1 -TAAACAACACCTTCTG-GTGGGGAAGGGCAAACTGGAATA
* * *
16351 TAATCAACACCTTCTGGTGGGGAAGGGAAAACTGGAAAAA
1 TAAACAACACCTTCTGGTGGGGAAGGGCAAACTGG-AATA
* * * *
16391 CTAAACAACACCTTCCGGTGAGGAAGGGTAAACAGGAATA
1 -TAAACAACACCTTCTGGTGGGGAAGGGCAAACTGGAATA
*
16431 TAAACGACACCTTCCT-GTGGGGAAGGGCAAACTGG
1 TAAACAACACCTT-CTGGTGGGGAAGGGCAAACTGG
16466 GGATGAGCAA
Statistics
Matches: 124, Mismatches: 24, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
38 1 0.01
39 56 0.45
40 33 0.27
41 34 0.27
ACGTcount: A:0.39, C:0.20, G:0.25, T:0.15
Consensus pattern (39 bp):
TAAACAACACCTTCTGGTGGGGAAGGGCAAACTGGAATA
Found at i:16429 original size:80 final size:79
Alignment explanation
Indices: 16272--16465 Score: 223
Period size: 80 Copynumber: 2.4 Consensus size: 79
16262 AATATAGACT
* * * *
16272 TAAACAACAACTTCC-GATGAGGAAGGCAAAACAGGAAAACTAAACAACACCTTCCGACTGGGAA
1 TAAACAACACCTTCCTG-TGGGGAAGGGAAAACTGGAAAACTAAACAACACCTTCCGACTGGGAA
* * *
16336 TGGCAAACTGGAATG
65 GGGCAAACAGGAATA
* *
16351 TAATCAACACCTT-CTGGTGGGGAAGGGAAAACTGGAAAAACTAAACAACACCTTCCG-GTGAGG
1 TAAACAACACCTTCCT-GTGGGGAAGGGAAAACTGG-AAAACTAAACAACACCTTCCGACTG-GG
*
16414 AAGGGTAAACAGGAATA
63 AAGGGCAAACAGGAATA
* *
16431 TAAACGACACCTTCCTGTGGGGAAGGGCAAACTGG
1 TAAACAACACCTTCCTGTGGGGAAGGGAAAACTGG
16466 GGATGAGCAA
Statistics
Matches: 97, Mismatches: 13, Indels: 9
0.82 0.11 0.08
Matches are distributed among these distances:
78 1 0.01
79 28 0.29
80 66 0.68
81 2 0.02
ACGTcount: A:0.39, C:0.20, G:0.25, T:0.15
Consensus pattern (79 bp):
TAAACAACACCTTCCTGTGGGGAAGGGAAAACTGGAAAACTAAACAACACCTTCCGACTGGGAAG
GGCAAACAGGAATA
Found at i:16676 original size:47 final size:45
Alignment explanation
Indices: 16389--16676 Score: 184
Period size: 46 Copynumber: 6.3 Consensus size: 45
16379 AAACTGGAAA
* * *
16389 AACTAAACAACACCTTCCGGTGAGGAAGGGTAAACAGGAATAT---
1 AACT-AACAACACCTTCCGGTGGGGAAGGGCAAATAGGAATATGAC
* * **
16432 -A--AACGACACCTTCCTGTGGGGAAGGGCAAACT-GG-GGATGAGC
1 AACTAACAACACCTTCCGGTGGGGAAGGGCAAA-TAGGAATATGA-C
* * * *
16474 AAATAGACAACACCTTCCGATGGGGAAGGGCAAA-ACGAGAATAAGGC
1 AACTA-ACAACACCTTCCGGTGGGGAAGGGCAAATA-G-GAATATGAC
* * *
16521 AACTTAAGCAACAGCTTCCGGTGGGGAATGGCAAACTA-GAATAAGAC
1 AAC-TAA-CAACACCTTCCGGTGGGGAAGGGCAAA-TAGGAATATGAC
* * * ** *
16568 AACTAAGCAGCACCTTCTGGTGGGGAAGGGCGAACCGGAA-ATTGGC
1 AACTAA-CAACACCTTCCGGTGGGGAAGGGCAAATAGGAATA-TGAC
*
16614 AACTATACAACACCTTCCGGTGGGGAAGGGCAAATTAGGAATTTGAC
1 AACTA-ACAACACCTTCCGGTGGGGAAGGGCAAA-TAGGAATATGAC
16661 AACTAGACAACACCTT
1 AACTA-ACAACACCTT
16677 GCAACTGGGA
Statistics
Matches: 187, Mismatches: 36, Indels: 40
0.71 0.14 0.15
Matches are distributed among these distances:
38 2 0.01
39 27 0.14
42 1 0.01
43 1 0.01
45 2 0.01
46 86 0.46
47 39 0.21
48 28 0.15
50 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.27, T:0.16
Consensus pattern (45 bp):
AACTAACAACACCTTCCGGTGGGGAAGGGCAAATAGGAATATGAC
Found at i:17622 original size:51 final size:51
Alignment explanation
Indices: 17392--17967 Score: 611
Period size: 51 Copynumber: 11.3 Consensus size: 51
17382 CATTTTCATC
* * **
17392 AAAA-ATTCAATCTTTTAATTCAAAGGTCT-CATTTTTATTTACAAATCGCTT
1 AAAAGATTCAATCTTTT-ACTCAAAGGT-TACATCTTTATTTACAAATTACTT
* ** * * * *
17443 AAAAG-TTCAAT-TTTTACTCAAAGATGGCATTTTTTTTTACCAATCACTT
1 AAAAGATTCAATCTTTTACTCAAAGGTTACATCTTTATTTACAAATTACTT
17492 AAAAG-TTCAATCTTTTACTCAAAGGTTACATCTTTATTTACAAATTACTT
1 AAAAGATTCAATCTTTTACTCAAAGGTTACATCTTTATTTACAAATTACTT
*
17542 AAAA-ATTCAATCTTTTACTCAAAGGTTGCATCTTTATTTACAAATTACTT
1 AAAAGATTCAATCTTTTACTCAAAGGTTACATCTTTATTTACAAATTACTT
*
17592 AAAAGATTCAATCTTTTACTCAAAGGTTGCATCTTTATTTACAAATTACTT
1 AAAAGATTCAATCTTTTACTCAAAGGTTACATCTTTATTTACAAATTACTT
* *
17643 AAAAGATTCAATCTTTTACTCAAAGGTTACATCTTTATTTACAAATTGCCT
1 AAAAGATTCAATCTTTTACTCAAAGGTTACATCTTTATTTACAAATTACTT
* * * *
17694 AGAAGATTCAAT-TTTTCACTTAAAGGTTACATCTTTATTTACAAATTGCCT
1 AAAAGATTCAATCTTTT-ACTCAAAGGTTACATCTTTATTTACAAATTACTT
* * * *
17745 AAAAGATTCAAT-TTTTCACTTAAAAGGTTAAATCTTTATTCACAAATTACCT
1 AAAAGATTCAATCTTTT-AC-TCAAAGGTTACATCTTTATTTACAAATTACTT
* * * *
17797 AAAAGATTCAAAT-TTTCACTTAAAAGGTTACATCTTTATTCACTAATTACTT
1 AAAAGATTC-AATCTTTTAC-TCAAAGGTTACATCTTTATTTACAAATTACTT
* ** * *
17849 AAAAGATTCAAAT-TTTCACTCAAAAAAATT-CAGTCTTTATTCACAAATTACCT
1 AAAAGATTC-AATCTTTTACTC--AAAGGTTACA-TCTTTATTTACAAATTACTT
* * ** *
17902 AAAAGATTCAATCTTTCACTTAAACATTTA-ATCTTTATTTACAAATTACTG
1 AAAAGATTCAATCTTTTACTCAAA-GGTTACATCTTTATTTACAAATTACTT
*
17953 AAAA-ATCCAATCTTT
1 AAAAGATTCAATCTTT
17968 GTTTACAAAT
Statistics
Matches: 472, Mismatches: 39, Indels: 29
0.87 0.07 0.05
Matches are distributed among these distances:
49 38 0.08
50 101 0.21
51 191 0.40
52 97 0.21
53 45 0.10
ACGTcount: A:0.37, C:0.16, G:0.06, T:0.40
Consensus pattern (51 bp):
AAAAGATTCAATCTTTTACTCAAAGGTTACATCTTTATTTACAAATTACTT
Found at i:17996 original size:30 final size:28
Alignment explanation
Indices: 17919--17997 Score: 68
Period size: 30 Copynumber: 2.6 Consensus size: 28
17909 TCAATCTTTC
17919 ACTTAAACATTTAATCTTTATTTACAAATT
1 ACTTAAA-ATTT-ATCTTTATTTACAAATT
* ** *
17949 ACTGAAAAATCCAATCTTTGTTTACAAATT
1 ACT-TAAAAT-TTATCTTTATTTACAAATT
17979 ACTTAAAGACTTTATCTTT
1 ACTTAAA-A-TTTATCTTT
17998 CAACACAATG
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
29 3 0.08
30 31 0.82
31 4 0.11
ACGTcount: A:0.38, C:0.15, G:0.04, T:0.43
Consensus pattern (28 bp):
ACTTAAAATTTATCTTTATTTACAAATT
Found at i:20758 original size:24 final size:24
Alignment explanation
Indices: 20678--20759 Score: 85
Period size: 24 Copynumber: 3.4 Consensus size: 24
20668 TTGGGAGAGT
* *
20678 GAGAGAT-GATTAACTTGCGAGAGA
1 GAGAGATCGATTAACTAGAG-GAGA
* * * * *
20702 GAGAGGTCAATTGATTGGAGGAGA
1 GAGAGATCGATTAACTAGAGGAGA
20726 GAGAGATCGATTAACTAGAGGAGA
1 GAGAGATCGATTAACTAGAGGAGA
20750 GAGAGATCGA
1 GAGAGATCGA
20760 AGGGAGGGAC
Statistics
Matches: 46, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
24 39 0.85
25 7 0.15
ACGTcount: A:0.38, C:0.07, G:0.37, T:0.18
Consensus pattern (24 bp):
GAGAGATCGATTAACTAGAGGAGA
Done.