Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023187.1 Corchorus olitorius cultivar O-4 contig23220, 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: 16427
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Found at i:820 original size:35 final size:35
Alignment explanation
Indices: 774--1316 Score: 696
Period size: 35 Copynumber: 15.4 Consensus size: 35
764 ATGGTATTAC
774 ATCAGAGTTGATCTCATTTCAAGAAGTTTTCGTTG
1 ATCAGAGTTGATCTCATTTCAAGAAGTTTTCGTTG
*
809 ATCAGAGTTGATCTCATTTCAAGAAGTTTTTTTGTATG
1 ATCAGAGTTGATCTCATTTCAAGAAG--TTTTCGT-TG
* *
847 ATCAGAGTTGATCTCGTTTCAAGAAGTTTT-TTATG
1 ATCAGAGTTGATCTCATTTCAAGAAGTTTTCGT-TG
*
882 ATCAGAGTTGATCTCATTTCAAGAAGTTTTTGTTG
1 ATCAGAGTTGATCTCATTTCAAGAAGTTTTCGTTG
* * * *
917 ATTAGATTTGATTTCATTTCAAGAAGTTTT-TTATG
1 ATCAGAGTTGATCTCATTTCAAGAAGTTTTCGT-TG
* * *
952 ATCAGAGTTGATCTCCTTTCAAGATGTTTTCATTG
1 ATCAGAGTTGATCTCATTTCAAGAAGTTTTCGTTG
* **
987 ATCAGAGTTGATCTCCTTTCAAGAAGTTTTTTTATG
1 ATCAGAGTTGATCTCATTTCAAGAAGTTTTCGT-TG
* *
1023 ATCAGAGTTGATCTCATTCCAAGAAGTTTTCGATG
1 ATCAGAGTTGATCTCATTTCAAGAAGTTTTCGTTG
*
1058 ATCAGAGTTGATCTCATTTCAAGAAGTTTT-TTATG
1 ATCAGAGTTGATCTCATTTCAAGAAGTTTTCGT-TG
* * **
1093 ATCAGAGTTGATCTCGTTTCAAAAAGTTTTCAATG
1 ATCAGAGTTGATCTCATTTCAAGAAGTTTTCGTTG
* * *
1128 ATCAGAGTTGATCTCCTTTCTAGAAGTTTTCGATG
1 ATCAGAGTTGATCTCATTTCAAGAAGTTTTCGTTG
* * *
1163 ATCAGAGTTGATCTCGTTTCAAGAAGTTTTTGATG
1 ATCAGAGTTGATCTCATTTCAAGAAGTTTTCGTTG
* * *
1198 ATCAGAGTTGATCTCCTTTCAAGAAGTTTTTGATG
1 ATCAGAGTTGATCTCATTTCAAGAAGTTTTCGTTG
* **
1233 ATCAGAGTTGATCTCGTTTCAAGAAGTTTTCAATG
1 ATCAGAGTTGATCTCATTTCAAGAAGTTTTCGTTG
*
1268 ATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATG
1 ATCAGAGTTGATCTCATTTCAAGAAGTTTTCGTTG
1303 ATCAGAGTTGATCT
1 ATCAGAGTTGATCT
1317 TCACATTGAT
Statistics
Matches: 456, Mismatches: 43, Indels: 18
0.88 0.08 0.03
Matches are distributed among these distances:
34 1 0.00
35 386 0.85
36 36 0.08
37 6 0.01
38 27 0.06
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.41
Consensus pattern (35 bp):
ATCAGAGTTGATCTCATTTCAAGAAGTTTTCGTTG
Found at i:960 original size:70 final size:70
Alignment explanation
Indices: 774--1316 Score: 775
Period size: 70 Copynumber: 7.7 Consensus size: 70
764 ATGGTATTAC
*
774 ATCAGAGTTGATCTCATTTCAAGAAGTTTTCGT-TGATCAGAGTTGATCTCATTTCAAGAAGTTT
1 ATCAGAGTTGATCTCATTTCAAGAAGTTTT-TTATGATCAGAGTTGATCTCATTTCAAGAAG--T
*
838 TTTTGTATG
63 TTTCG-ATG
*
847 ATCAGAGTTGATCTCGTTTCAAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTT
1 ATCAGAGTTGATCTCATTTCAAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTT
* *
912 TGTTG
66 CGATG
* * * * *
917 ATTAGATTTGATTTCATTTCAAGAAGTTTTTTATGATCAGAGTTGATCTCCTTTCAAGATGTTTT
1 ATCAGAGTTGATCTCATTTCAAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTT
982 C-ATTG
66 CGA-TG
* *
987 ATCAGAGTTGATCTCCTTTCAAGAAGTTTTTTTATGATCAGAGTTGATCTCATTCCAAGAAGTTT
1 ATCAGAGTTGATCTCATTTCAAGAAG-TTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTT
1052 TCGATG
65 TCGATG
* *
1058 ATCAGAGTTGATCTCATTTCAAGAAGTTTTTTATGATCAGAGTTGATCTCGTTTCAAAAAGTTTT
1 ATCAGAGTTGATCTCATTTCAAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTT
*
1123 CAATG
66 CGATG
* * ** *
1128 ATCAGAGTTGATCTCCTTTCTAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCAAGAAGTTTT
1 ATCAGAGTTGATCTCATTTCAAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTT
*
1193 TGATG
66 CGATG
* * *
1198 ATCAGAGTTGATCTCCTTTCAAGAAGTTTTTGATGATCAGAGTTGATCTCGTTTCAAGAAGTTTT
1 ATCAGAGTTGATCTCATTTCAAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTT
*
1263 CAATG
66 CGATG
**
1268 ATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCT
1 ATCAGAGTTGATCTCATTTCAAGAAGTTTTTTATGATCAGAGTTGATCT
1317 TCACATTGAT
Statistics
Matches: 430, Mismatches: 36, Indels: 11
0.90 0.08 0.02
Matches are distributed among these distances:
70 301 0.70
71 70 0.16
72 2 0.00
73 57 0.13
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.41
Consensus pattern (70 bp):
ATCAGAGTTGATCTCATTTCAAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTT
CGATG
Found at i:4906 original size:22 final size:22
Alignment explanation
Indices: 4856--5210 Score: 97
Period size: 22 Copynumber: 16.0 Consensus size: 22
4846 TGTGGTTAAT
**
4856 AAAATTTCATAAAGAGGTTA-C
1 AAAATTTCATAGGGAGGTTATC
*
4877 TAATATTTCAT-GGGAAGGTTATC
1 -AAAATTTCATAGGG-AGGTTATC
* *
4900 AAAATTTCATAGTGTGGTTATC
1 AAAATTTCATAGGGAGGTTATC
* * *
4922 AAAATCTT-TTAGTGTGGTTATC
1 AAAAT-TTCATAGGGAGGTTATC
* * * *
4944 AAAATTACATATGAAGGTTATAA
1 AAAATTTCATAGGGAGGTTAT-C
* *
4967 AAGTCTCAATTTCATAAGGA-G-TACC
1 AA-----AATTTCATAGGGAGGTTATC
* *
4992 AAAA-TACGATA-GAAGGTTATC
1 AAAATTTC-ATAGGGAGGTTATC
* * * *
5013 -AAATCTCATAGAGTGATTATC
1 AAAATTTCATAGGGAGGTTATC
* * *
5034 GAACTTTCATAGAGATCGGATTATC
1 AAAATTTCATAGGGA--GG-TTATC
* * *
5059 -AAATTTTATAGGCAGATTATC
1 AAAATTTCATAGGGAGGTTATC
* * *
5080 AAAA-TTCCTA-GTATTGTTATC
1 AAAATTTCATAGGGA-GGTTATC
*
5101 AAAATTTCAATA-CGAGGTTATC
1 AAAATTTC-ATAGGGAGGTTATC
* ** * *
5123 AAAATTACATAATGTGATTATC
1 AAAATTTCATAGGGAGGTTATC
* **
5145 AAAATTTCATAGAGG-GGTCAAG
1 AAAATTTCATAG-GGAGGTTATC
* *
5167 AAAATTTTATAGAGAGGTTATC
1 AAAATTTCATAGGGAGGTTATC
**
5189 AAAATTTCATAAAGAGGTTATC
1 AAAATTTCATAGGGAGGTTATC
5211 CAATTTTTAA
Statistics
Matches: 242, Mismatches: 64, Indels: 54
0.67 0.18 0.15
Matches are distributed among these distances:
19 4 0.02
20 14 0.06
21 34 0.14
22 148 0.61
23 11 0.05
24 11 0.05
25 7 0.03
26 2 0.01
27 1 0.00
28 10 0.04
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (22 bp):
AAAATTTCATAGGGAGGTTATC
Found at i:5216 original size:21 final size:22
Alignment explanation
Indices: 5095--5210 Score: 108
Period size: 22 Copynumber: 5.3 Consensus size: 22
5085 TCCTAGTATT
*
5095 GTTATCAAAATTTCA-ATACGAG
1 GTTATCAAAATTTCATA-AAGAG
* * *
5117 GTTATCAAAATTACATAATGTG
1 GTTATCAAAATTTCATAAAGAG
* * *
5139 ATTATCAAAATTTCATAGAGGG
1 GTTATCAAAATTTCATAAAGAG
* ** * *
5161 GTCAAGAAAATTTTATAGAGAG
1 GTTATCAAAATTTCATAAAGAG
5183 GTTATCAAAATTTCATAAAGAG
1 GTTATCAAAATTTCATAAAGAG
5205 GTTATC
1 GTTATC
5211 CAATTTTTAA
Statistics
Matches: 74, Mismatches: 19, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
22 73 0.99
23 1 0.01
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.33
Consensus pattern (22 bp):
GTTATCAAAATTTCATAAAGAG
Found at i:5360 original size:115 final size:115
Alignment explanation
Indices: 5232--5475 Score: 470
Period size: 115 Copynumber: 2.1 Consensus size: 115
5222 ATGTGATTAC
5232 CAAAATTTCATAGTGGTATTTCTGGGGAGGTTATCAAAATTTCACAGTATGGTTACCAAATTAGG
1 CAAAATTTCATAGTGGTATTTCTGGGGAGGTTATCAAAATTTCACAGTATGGTTACCAAATTAGG
*
5297 AAGGTTATTAAACTTTTATTATGGAGTAATCAAAATTTTAGGGAGGATAT
66 AAGGTTATTAAACTTTTATTATGGAGTAATCAAAATTTCAGGGAGGATAT
5347 CAAAATTTCATAGTGGTATTTCTGGGGAGGTTATCAAAATTTCACAGTATGGTTACCAAATTAGG
1 CAAAATTTCATAGTGGTATTTCTGGGGAGGTTATCAAAATTTCACAGTATGGTTACCAAATTAGG
*
5412 AAGGTTATTAACCTTTTATTATGGAGTAATCAAAATTTCAGGGAGGATAT
66 AAGGTTATTAAACTTTTATTATGGAGTAATCAAAATTTCAGGGAGGATAT
5462 CAAAATTTCATAGT
1 CAAAATTTCATAGT
5476 TTAGTTTTCA
Statistics
Matches: 127, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
115 127 1.00
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (115 bp):
CAAAATTTCATAGTGGTATTTCTGGGGAGGTTATCAAAATTTCACAGTATGGTTACCAAATTAGG
AAGGTTATTAAACTTTTATTATGGAGTAATCAAAATTTCAGGGAGGATAT
Found at i:5622 original size:38 final size:38
Alignment explanation
Indices: 5580--5677 Score: 151
Period size: 38 Copynumber: 2.6 Consensus size: 38
5570 ATCAAAAAAT
*
5580 CATAGGGAGGTTATAAAAATTTGTAGCTATCAAGATTA
1 CATAGGGAGGTTATCAAAATTTGTAGCTATCAAGATTA
* * *
5618 CATAGGGAGGTCATCAAAATTTGTAGTTATCAAGATTT
1 CATAGGGAGGTTATCAAAATTTGTAGCTATCAAGATTA
*
5656 CATAAGGAGGTTATCAAAATTT
1 CATAGGGAGGTTATCAAAATTT
5678 TATAGGGAGA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 54 1.00
ACGTcount: A:0.38, C:0.09, G:0.20, T:0.33
Consensus pattern (38 bp):
CATAGGGAGGTTATCAAAATTTGTAGCTATCAAGATTA
Found at i:5696 original size:23 final size:22
Alignment explanation
Indices: 5440--5966 Score: 216
Period size: 22 Copynumber: 24.5 Consensus size: 22
5430 TTATGGAGTA
*
5440 ATCAAAATTTC--AGGGAGGAT
1 ATCAAAATTTCATAGGGAGGTT
**
5460 ATCAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATAG-GGAGGTT
* * **
5482 TTCAAAATTTCTTA-AAAGGGTT
1 ATCAAAATTTCATAGGGA-GGTT
* * *
5504 ATCAAAATTTCATA-GTATGTAG
1 ATCAAAATTTCATAGGGAGGT-T
** *
5526 ATCAAAATTTCATAAAGAGATT
1 ATCAAAATTTCATAGGGAGGTT
* * **
5548 AACAAAATTTTATAATGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
**
5570 ATCAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * *
5592 AT-AAAAATT--T--GTA-GCT
1 ATCAAAATTTCATAGGGAGGTT
* * *
5608 ATCAAGATTACATAGGGAGGTC
1 ATCAAAATTTCATAGGGAGGTT
*
5630 ATCAAAA-TT--T--GTA-GTT
1 ATCAAAATTTCATAGGGAGGTT
* *
5646 ATCAAGATTTCATAAGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* *
5668 ATCAAAATTTTATAGGGAGATTT
1 ATCAAAATTTCATAGGGAG-GTT
* * *
5691 ATCAAAATTTTATTGGAAGGTTT
1 ATCAAAATTTCATAGGGAGG-TT
*
5714 ATCAAAATTTCATAGTGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * * *
5736 ATCACAATTTCATAGTGTGATT
1 ATCAAAATTTCATAGGGAGGTT
* * *
5758 ATCAAAATTTCAGAGTGTA-ATT
1 ATCAAAATTTCATAG-GGAGGTT
*
5780 A-CTAACAA-TTCATATGGAGGTT
1 ATC-AA-AATTTCATAGGGAGGTT
* * * ** *
5802 TTTAAATTTTCATAACGTGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * *
5824 ATCAATATATCATATGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * * **
5846 ATCAACATCTCATATTGTTGGTT
1 ATCAAAATTTCATA-GGGAGGTT
5869 ATCAAAATTTCATTAGGGA-GTT
1 ATCAAAATTTCA-TAGGGAGGTT
* *
5891 ATCAAAATTTCATAGTGAGCTCT
1 ATCAAAATTTCATAGGGAGGT-T
* *
5914 -TCAAAATTCCTTAGGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * *
5935 AACAAAATTTCATAAGAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
**
5957 AAAAAAATTT
1 ATCAAAATTT
5967 ATAAAAAGGT
Statistics
Matches: 374, Mismatches: 101, Indels: 62
0.70 0.19 0.12
Matches are distributed among these distances:
16 12 0.03
17 10 0.03
19 4 0.01
20 12 0.03
21 23 0.06
22 251 0.67
23 60 0.16
24 2 0.01
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTCATAGGGAGGTT
Found at i:5892 original size:45 final size:45
Alignment explanation
Indices: 5819--5904 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
5809 TTTCATAACG
* * *
5819 TGGTTATCAATATATCATATGGAGGTTATCAACATCTCATATTGT
1 TGGTTATCAAAATATCATAGGGAGGTTATCAAAATCTCATATTGT
* *
5864 TGGTTATCAAAATTTCATTAGGGA-GTTATCAAAATTTCATA
1 TGGTTATCAAAATATCA-TAGGGAGGTTATCAAAATCTCATA
5905 GTGAGCTCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
45 30 0.86
46 5 0.14
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.40
Consensus pattern (45 bp):
TGGTTATCAAAATATCATAGGGAGGTTATCAAAATCTCATATTGT
Found at i:6042 original size:22 final size:22
Alignment explanation
Indices: 5440--6040 Score: 200
Period size: 22 Copynumber: 27.9 Consensus size: 22
5430 TTATGGAGTA
* *
5440 ATCAAAATTTC--AGGGAGGAT
1 ATCAAAATTTCATAAGGAGGTT
*
5460 ATCAAAATTTCAT-AGTTTA-GTT
1 ATCAAAATTTCATAAG--GAGGTT
* * *
5482 TTCAAAATTTCTTAA-AAGGGTT
1 ATCAAAATTTCATAAGGA-GGTT
* * *
5504 ATCAAAATTTCAT-AGTATGTAG
1 ATCAAAATTTCATAAGGAGGT-T
* *
5526 ATCAAAATTTCATAAAGAGATT
1 ATCAAAATTTCATAAGGAGGTT
* * *
5548 AACAAAATTTTATAATGAGGTT
1 ATCAAAATTTCATAAGGAGGTT
** *
5570 ATCAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCATAAGGAGGTT
* * *
5592 AT-AAAAATT--T--GTA-GCT
1 ATCAAAATTTCATAAGGAGGTT
* * * *
5608 ATCAAGATTACATAGGGAGGTC
1 ATCAAAATTTCATAAGGAGGTT
*
5630 ATCAAAA-TT--T--GTA-GTT
1 ATCAAAATTTCATAAGGAGGTT
*
5646 ATCAAGATTTCATAAGGAGGTT
1 ATCAAAATTTCATAAGGAGGTT
* * *
5668 ATCAAAATTTTATAGGGAGATTT
1 ATCAAAATTTCATAAGGAG-GTT
* *
5691 ATCAAAATTTTAT-TGGAAGGTTT
1 ATCAAAATTTCATAAGG-AGG-TT
5714 ATCAAAATTTCAT-AGTGAGGTT
1 ATCAAAATTTCATAAG-GAGGTT
* * *
5736 ATCACAATTTCAT-AGTGTGATT
1 ATCAAAATTTCATAAG-GAGGTT
* *
5758 ATCAAAATTTCA-GAGTGTA-ATT
1 ATCAAAATTTCATAAG-G-AGGTT
*
5780 A-CTAACAA-TTCATATGGAGGTT
1 ATC-AA-AATTTCATAAGGAGGTT
* * * * *
5802 TTTAAATTTTCATAACGTGGTT
1 ATCAAAATTTCATAAGGAGGTT
* * *
5824 ATCAATATATCATATGGAGGTT
1 ATCAAAATTTCATAAGGAGGTT
* * * **
5846 ATCAACATCTCATATTGTTGGTT
1 ATCAAAATTTCATA-AGGAGGTT
*
5869 ATCAAAATTTCATTAGG-GAGTT
1 ATCAAAATTTCATAAGGAG-GTT
*
5891 ATCAAAATTTCAT-AGTGAGCTCT
1 ATCAAAATTTCATAAG-GAGGT-T
* * *
5914 -TCAAAATTCCTTAGGGAGGTT
1 ATCAAAATTTCATAAGGAGGTT
* *
5935 AACAAAATTTCATAAGAAGGTT
1 ATCAAAATTTCATAAGGAGGTT
** **
5957 AAAAAAATTT-ATAAAAAGGTT
1 ATCAAAATTTCATAAGGAGGTT
* * * * *
5978 CTCGAAATTCCAT-AGTATCGTT
1 ATCAAAATTTCATAAGGA-GGTT
* * * *
6000 TTTAAAATTTCATAAGAAGATT
1 ATCAAAATTTCATAAGGAGGTT
6022 ATCAAAATTTCATAAGGAG
1 ATCAAAATTTCATAAGGAG
6041 ATCATAAAAA
Statistics
Matches: 427, Mismatches: 110, Indels: 86
0.69 0.18 0.14
Matches are distributed among these distances:
16 12 0.03
17 10 0.02
19 4 0.01
20 12 0.03
21 39 0.09
22 283 0.66
23 66 0.15
24 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTCATAAGGAGGTT
Found at i:6050 original size:22 final size:22
Alignment explanation
Indices: 6003--6050 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
5993 TATCGTTTTT
* *
6003 AAAATTTCATAAGAAGATTATC
1 AAAATTTCATAAGAAGATCATA
*
6025 AAAATTTCATAAGGAGATCATA
1 AAAATTTCATAAGAAGATCATA
6047 AAAA
1 AAAA
6051 ATAGTGTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.54, C:0.08, G:0.10, T:0.27
Consensus pattern (22 bp):
AAAATTTCATAAGAAGATCATA
Found at i:7819 original size:439 final size:435
Alignment explanation
Indices: 6989--8026 Score: 1278
Period size: 439 Copynumber: 2.4 Consensus size: 435
6979 TGGGTCCCGC
* * *
6989 TCTCAATAAACAAATCATTTTTTTACTGGATTATTTATCAAATGATCCCTATACTTTTATGCTTT
1 TCTCCATAAACAAAT-ATTTTTTTACTGGATTATTTATTAAATGATCCTTATACTTTTATGCTTT
* * * * * *
7054 ATGTTATTTAATCCCTCACAAATTCTGGGTTGGACGATTGAACGTTTCAGCTTTAATTCTTT-TA
65 ATGCTATTTAATCCTTTA-AAATTATGGGTTGGACGATTTAACG-CTC-GCTTTAATT-TTTGTA
* * * * * *
7118 TTTTTTGTTTTACTTGTCCGATCAAGGTGATTCAAGTGTCTGTTAAAAGGTAATTTCATGATCTA
126 TTTTATGTTCTATTTGTCCGATTAAGGTGATTCAAGTGTCTATTAAAAGGTAATCTCATGATCTA
** * *
7183 CAACTTTCATGAAGGACTGCAAACCAATTTTCATGTTTCAATTCTAAAAAATGCTTCTTGAATTT
191 CAACTTTCATGAAAAACTGCAAACCAATTTTAATGTTTCAATTCTAAAAAATGCTTCTTAAATTT
* * * * *
7248 TGTGGTCTCGATTGTCGGTCTATCTAATATTGTACAACTTTCGATCCACTTGTCCGATTGAGGTT
256 TGTGGTCTCGATTGCCAGTCTATCTAATATCGCACAACTTTCGATCCACTTGTCCGATTGAAGTT
* * * *
7313 GTTCAAGTGTCGGTTAAAAGGTTATTGTGTGATCTATGACTTTCGTCAAGGACCTGAAAGCTGAA
321 GTTCAAGTGTCGGTTAAAAGGTTATTGTGTGATCAACGACTTTCATCAAGGACATGAAAGCTGAA
* * * *
7378 TTTGGTTAATGAGTTTCGTGGTGGGTTCAAGAGGGAATTTTTATG-TTTG
386 TTTGATTAATGAGTTTCGTGGAGGATTCAAGAGAGAATTTTTATGTTTTG
*
7427 ATCTCCATAAACAAATATATTTTTTGCTGGATTATTTATTAAATGATCCTTATACTTTTATGCTT
1 -TCTCCATAAACAAATAT-TTTTTTACTGGATTATTTATTAAATGATCCTTATACTTTTATGCTT
* *
7492 TATGCTATTTAATCCTTTATAATTATGGGTTGGACGATTTAACGCGTCGGCTTTTATTTTTGTAT
64 TATGCTATTTAATCCTTTAAAATTATGGGTTGGACGATTTAACGC-TC-GCTTTAATTTTTGTAT
* *
7557 TTTATGTTCTATTTGTCTGATTAAGGTGATTCACA-TGTCTATTGAAAGGTAATCTCATGATCTA
127 TTTATGTTCTATTTGTCCGATTAAGGTGATTCA-AGTGTCTATTAAAAGGTAATCTCATGATCTA
* * ** * *
7621 CAACTTTCATGAAAAACT-CAGAAGGCAGTTTTAATGTTTTGATTTTAAAAAATGTTTCTTAAAT
191 CAACTTTCATGAAAAACTGCA-AA-CCAATTTTAATGTTTCAATTCTAAAAAATGCTTCTTAAAT
* * *
7685 TTTGTGGT-TCCGATTGCCAGTCTATTTAATATCGCATAATTTTCTG-TCCACTTGTCCGATTGA
254 TTTGTGGTCT-CGATTGCCAGTCTATCTAATATCGCACAACTTTC-GATCCACTTGTCCGATTGA
* * * *
7748 AGTTGTTCAAGTGTCGGTTAAAAGGTTATTGTGTTATCAACGACTTTCATTAAGGGCATGAAAGT
317 AGTTGTTCAAGTGTCGGTTAAAAGGTTATTGTGTGATCAACGACTTTCATCAAGGACATGAAAGC
7813 TGAATTTGATTAATGAGTTTCGTGGAGGATTCAAGAGAGAATTTTTATGTTTTG
382 TGAATTTGATTAATGAGTTTCGTGGAGGATTCAAGAGAGAATTTTTATGTTTTG
* * * * * *
7867 TCTTCATAAAC-TAT-TTTTTTTACTGGATTATTTATCT-AATAACCCTCATACTTTTAT-ATTT
1 TCTCCATAAACAAATATTTTTTTACTGGATTATTTAT-TAAATGATCCTTATACTTTTATGCTTT
* * *
7928 CATGCTATTGAATCCTTTAAAATTATAGGTTGGACGATTTAA--CT--CTTTAACTTTTGT-TTT
65 -ATGCTATTTAATCCTTTAAAATTATGGGTTGGACGATTTAACGCTCGCTTTAATTTTTGTATTT
* *
7988 TATATTCTATTTGTCCCATTAAGGTGATTCAAGTGTCTA
129 TATGTTCTATTTGTCCGATTAAGGTGATTCAAGTGTCTA
8027 CATGAAGAAT
Statistics
Matches: 521, Mismatches: 66, Indels: 34
0.84 0.11 0.05
Matches are distributed among these distances:
428 1 0.00
429 37 0.07
430 11 0.02
433 1 0.00
434 1 0.00
435 3 0.01
436 74 0.14
437 7 0.01
438 112 0.21
439 269 0.52
440 5 0.01
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.43
Consensus pattern (435 bp):
TCTCCATAAACAAATATTTTTTTACTGGATTATTTATTAAATGATCCTTATACTTTTATGCTTTA
TGCTATTTAATCCTTTAAAATTATGGGTTGGACGATTTAACGCTCGCTTTAATTTTTGTATTTTA
TGTTCTATTTGTCCGATTAAGGTGATTCAAGTGTCTATTAAAAGGTAATCTCATGATCTACAACT
TTCATGAAAAACTGCAAACCAATTTTAATGTTTCAATTCTAAAAAATGCTTCTTAAATTTTGTGG
TCTCGATTGCCAGTCTATCTAATATCGCACAACTTTCGATCCACTTGTCCGATTGAAGTTGTTCA
AGTGTCGGTTAAAAGGTTATTGTGTGATCAACGACTTTCATCAAGGACATGAAAGCTGAATTTGA
TTAATGAGTTTCGTGGAGGATTCAAGAGAGAATTTTTATGTTTTG
Found at i:9857 original size:14 final size:15
Alignment explanation
Indices: 9818--9858 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
9808 GAACCGAGAA
9818 GAAGAA-GAAGATCT
1 GAAGAATGAAGATCT
* *
9832 GAAGAGTAAAGAT-T
1 GAAGAATGAAGATCT
9846 GAAGAATGAAGAT
1 GAAGAATGAAGAT
9859 GATGAATACT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 17 0.77
15 5 0.23
ACGTcount: A:0.51, C:0.02, G:0.29, T:0.17
Consensus pattern (15 bp):
GAAGAATGAAGATCT
Found at i:12435 original size:3 final size:3
Alignment explanation
Indices: 12427--12453 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
12417 CGCTATCACT
12427 ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC
12454 TTCTTCTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:13134 original size:2 final size:2
Alignment explanation
Indices: 13127--13153 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
13117 AATAGTGCAA
13127 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
13154 CTAGTTAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13486 original size:10 final size:9
Alignment explanation
Indices: 13466--13490 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
13456 TCTCTGATGC
13466 AAAATAAAA
1 AAAATAAAA
13475 AAAATAAAA
1 AAAATAAAA
13484 AAAATAA
1 AAAATAA
13491 GAATAAGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAATAAAA
Found at i:14743 original size:58 final size:57
Alignment explanation
Indices: 14654--14762 Score: 157
Period size: 58 Copynumber: 1.9 Consensus size: 57
14644 TCAAAAATCA
*
14654 AGTGACATGTTCTTTATTAGATGCATAAAAAAGACGTTTTCGGACCAAGGCTTATCG
1 AGTGACATGTTCTTTATTAGATGCATAAAAAAGACGTTTTAGGACCAAGGCTTATCG
* * *
14711 AGTGACATGTTTTTTTATTAGATGTC-TAAAAAAGATGTTTTAGGACCGAGGC
1 AGTGACATG-TTCTTTATTAGATG-CATAAAAAAGACGTTTTAGGACCAAGGC
14763 ATGATGCTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
57 9 0.20
58 36 0.78
59 1 0.02
ACGTcount: A:0.31, C:0.13, G:0.22, T:0.34
Consensus pattern (57 bp):
AGTGACATGTTCTTTATTAGATGCATAAAAAAGACGTTTTAGGACCAAGGCTTATCG
Done.