Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014894.1 Corchorus olitorius cultivar O-4 contig14927, 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: 48165
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:2775 original size:221 final size:222
Alignment explanation
Indices: 2264--3017 Score: 1146
Period size: 221 Copynumber: 3.5 Consensus size: 222
2254 ATCAGAAAAA
* *
2264 AATGTCAAACTCTAAAAAATTTGGGGATGGTGCATATGATTATTTGGGGATGATGAGAAATGATT
1 AATGTCAATCTCTAAAGAATTTGGGGATGGTGCATATGATTATTTGGGGATGATGAGAAATGATT
* * * * **
2329 TGGGTATAAGGTATATTACTTTGGGGATAATGAATTTTACATATTGTTTAATTATTAGATGTTAC
66 TGGGTATAAAGTATATTACTTTGGGGATACTGAATTTGACATTTTGTTTAATTATTAGATGGCAC
* * *
2394 TAAAATCATATAGACGGGGTTTA-T---TTAATCAGAATGAAAAATATGGATTAAAACACTTTTT
131 TAAAATCATATAGACGAGGTTTATTCAATTAATTAGAATGAAAAATATGGATTAAAGCACTTTTT
*
2455 AAAGCCAATTTTGGATATTTGAGAAAAA
196 AAAGCCAATTTTGGATATTTGAG-AAAT
*
2483 AATGTCAATTTCTAAAGAATTTGGGGATGGTGCATATGATTATTTGGGGATGATGAGAAATGATT
1 AATGTCAATCTCTAAAGAATTTGGGGATGGTGCATATGATTATTTGGGGATGATGAGAAATGATT
2548 TGGGTATAAAGTATATTACTTTGGGGATACTGAATTTGACATTTTGTTTAATTATTAGATGGCAC
66 TGGGTATAAAGTATATTACTTTGGGGATACTGAATTTGACATTTTGTTTAATTATTAGATGGCAC
*
2613 TAAAATCATATAGACGAGGTTTATTCAATTAATTAGAATGAAAAATATTGATTAAAGCAC-TTTT
131 TAAAATCATATAGACGAGGTTTATTCAATTAATTAGAATGAAAAATATGGATTAAAGCACTTTTT
2677 AAAGCCAATTTTGGATATTTGAGAAAT
196 AAAGCCAATTTTGGATATTTGAGAAAT
*
2704 AATGTCAATCTCTAAAGAATTTGGGGATGGTGCATATGATTATTTGGGGATGATGAGAAACGATT
1 AATGTCAATCTCTAAAGAATTTGGGGATGGTGCATATGATTATTTGGGGATGATGAGAAATGATT
* *
2769 TGGGTATAAAGTATATTACTTTGGGGATACAGTATTCTG-CATTTTGTTTAATTATTAGATGGCA
66 TGGGTATAAAGTATATTACTTTGGGGATACTGAATT-TGACATTTTGTTTAATTATTAGATGGCA
*
2833 CTAAAATCATATAGAC-ATCGTTTATTCAATTAATTAGAATGAAAAATATGGATTAAAGCACTTT
130 CTAAAATCATATAGACGA-GGTTTATTCAATTAATTAGAATGAAAAATATGGATTAAAGCACTTT
2897 TTAAAGCCAATTTTGG--A--T------T
194 TTAAAGCCAATTTTGGATATTTGAGAAAT
* *
2916 AATGTCAATCTCTAAAGAATTTGGGGATGGTGCATATGATTATTTAGGAATGATGAGAAATGATT
1 AATGTCAATCTCTAAAGAATTTGGGGATGGTGCATATGATTATTTGGGGATGATGAGAAATGATT
* * * *
2981 TGAGTATAGAGTATATCACTTTGGGGATGCTGAATTT
66 TGGGTATAAAGTATATTACTTTGGGGATACTGAATTT
3018 TGTGCATACC
Statistics
Matches: 499, Mismatches: 29, Indels: 22
0.91 0.05 0.04
Matches are distributed among these distances:
211 1 0.00
212 93 0.19
218 1 0.00
219 143 0.29
220 3 0.01
221 182 0.36
222 47 0.09
223 29 0.06
ACGTcount: A:0.35, C:0.07, G:0.21, T:0.36
Consensus pattern (222 bp):
AATGTCAATCTCTAAAGAATTTGGGGATGGTGCATATGATTATTTGGGGATGATGAGAAATGATT
TGGGTATAAAGTATATTACTTTGGGGATACTGAATTTGACATTTTGTTTAATTATTAGATGGCAC
TAAAATCATATAGACGAGGTTTATTCAATTAATTAGAATGAAAAATATGGATTAAAGCACTTTTT
AAAGCCAATTTTGGATATTTGAGAAAT
Found at i:3900 original size:222 final size:222
Alignment explanation
Indices: 3513--4333 Score: 1256
Period size: 222 Copynumber: 3.7 Consensus size: 222
3503 CTTGATATTA
* * * * * *
3513 CTCATCATCCCCAAATAATTATAAGCACCATCCCCAAATTCATTAGACATTGACATTTTTTCTTA
1 CTCATCATCCCCAAATAATCATATGCACCATCCCCAAATTCTTTAGAGATTGACATTTTTCCTCA
* * *
3578 TATAACCAAAATTGGCTTT-AAACGTGCTTTAATCCATA-TTTTCATCCTAATTAACTGAATAAA
66 TATACCCAAAATTGGCTTTAAAAAGTGCTTTAATCCATATTTTTCATCCTAATTAATTGAATAAA
* * * * *
3641 TCCAGTCTAAATGAATTTAGTGCCATCTAATAATTAAACAACATGCAAAATTCAGTATCCCCAAA
131 CCCAGTCTATATGATTTTAATGCCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAA
* *
3706 GTGATATATTTTATACCCAAATCATTT
196 GTAATATACTTTATACCCAAATCATTT
* * *
3733 CTCATCATCCCCACATAATCATATGTACCATCTCCAAATTCTTTAGAGATTGACATTTTTCCTCA
1 CTCATCATCCCCAAATAATCATATGCACCATCCCCAAATTCTTTAGAGATTGACATTTTTCCTCA
*
3798 TATACCCAAAATTGGCTTTAAAAAGTGTTTTAATCCATATTTTTCATCCTAATTAATTGAATAAA
66 TATACCCAAAATTGGCTTTAAAAAGTGCTTTAATCCATATTTTTCATCCTAATTAATTGAATAAA
3863 CCCAGTCTATATGATTTTAATGCCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAA
131 CCCAGTCTATATGATTTTAATGCCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAA
3928 GTAATATACTTTATACCCAAATCATTT
196 GTAATATACTTTATACCCAAATCATTT
3955 CTCATCATCCCCAAATAATCATATGCACCATCCCCAAATTCTTTAGAGATTGACATTTTT-CTCA
1 CTCATCATCCCCAAATAATCATATGCACCATCCCCAAATTCTTTAGAGATTGACATTTTTCCTCA
* * * * * * * *
4019 AATATCCAAAACTGGCTTTAAAAATTGCTTTGATCCACATTTTTTATTCTAATT-ATATGAATAA
66 TATACCCAAAATTGGCTTTAAAAAGTGCTTTAATCCATATTTTTCATCCTAATTAAT-TGAATAA
* * * * *
4083 ACCCCGTCTATATGATTTTAGTGCCATATAATAATTTAACAAAATGTC-AAATTCAGTATTCCCA
130 ACCCAGTCTATATGATTTTAATGCCATCTAATAATTAAACAAAATG-CAAAATTCAGTATCCCCA
*
4147 AAGTAATATACTTTATACTCAAATCATTT
194 AAGTAATATACTTTATACCCAAATCATTT
4176 CTCATCATCCCCAAATAATCATATGCACCATCCCCAAATTCTTTAGAGATTGACATTTTTCCTCA
1 CTCATCATCCCCAAATAATCATATGCACCATCCCCAAATTCTTTAGAGATTGACATTTTTCCTCA
*
4241 TATACCCAAAATTGGCTTTAAAAAGTGTTTTAATCCATATTTTTCATCCTAATTAATTGAATAAA
66 TATACCCAAAATTGGCTTTAAAAAGTGCTTTAATCCATATTTTTCATCCTAATTAATTGAATAAA
* *
4306 CCCAGTTTATATGATTTTAATGTCATCT
131 CCCAGTCTATATGATTTTAATGCCATCT
4334 TTTTTTTTGA
Statistics
Matches: 543, Mismatches: 52, Indels: 10
0.90 0.09 0.02
Matches are distributed among these distances:
220 76 0.14
221 218 0.40
222 247 0.45
223 2 0.00
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (222 bp):
CTCATCATCCCCAAATAATCATATGCACCATCCCCAAATTCTTTAGAGATTGACATTTTTCCTCA
TATACCCAAAATTGGCTTTAAAAAGTGCTTTAATCCATATTTTTCATCCTAATTAATTGAATAAA
CCCAGTCTATATGATTTTAATGCCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAA
GTAATATACTTTATACCCAAATCATTT
Found at i:4752 original size:223 final size:222
Alignment explanation
Indices: 4350--5542 Score: 1768
Period size: 223 Copynumber: 5.4 Consensus size: 222
4340 TTGAATAATT
* *
4350 ATTTTAATGTCATCTAATAATTAAACAAAATGCAAAATTTAGTATCCCCAAAGTAATATACTTTA
1 ATTTTAGTGTCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAAGTAATATACTTTA
*
4415 TACCCAAATCATTTCTCATCATCCCCAAATAATAATATGCACCATCCCCAAATTCTTTAGAGATT
66 TACCCAAATCATTTCTCATCATCCCCAAATAATCATATGCACCATCCCCAAATTCTTTAGAGATT
* * * * *
4480 GACATTTTTTTCTCAAATATCCAAAACTGGCATTAAAAATTGCTTTAATCCACATTGTTCATTCT
131 GACA-TTTTTTCTCAAATATCCAAAATTGGCTTTAAAAAGTGCTTTAATCCATATTTTTCATTCT
*
4545 AATTAAATGAATAAACCCCGTCTATATG
195 AATTAACTGAATAAACCCCGTCTATATG
* *
4573 ATTTTAGTGTCATATAATAATTTAACAAAATGTC-AAATTCAGTATCCCCAAAGTAATATACTTT
1 ATTTTAGTGTCATCTAATAATTAAACAAAATG-CAAAATTCAGTATCCCCAAAGTAATATACTTT
* *
4637 ATACCCAAATCATTTCTCGTCATCCCCAAATAATCATATGCACCATCCTCAAATTCTTTAGAGAT
65 ATACCCAAATCATTTCTCATCATCCCCAAATAATCATATGCACCATCCCCAAATTCTTTAGAGAT
*
4702 TGACATTTTTTTCTCAAATATCTAAAATTGGCTTTAAAAAGTGCTTTAATCCATATTTTTCATTC
130 TGACA-TTTTTTCTCAAATATCCAAAATTGGCTTTAAAAAGTGCTTTAATCCATATTTTTCATTC
* **
4767 TAATTAACTGAATAAATCTTGTCTATATG
194 TAATTAACTGAATAAACCCCGTCTATATG
* *
4796 ATTTTTAGTGTCATATAATAATTAAACAAAATTCAAAATTCAGTATCCCCAAAGTAATATACTTT
1 A-TTTTAGTGTCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAAGTAATATACTTT
* *
4861 ATACCCAAATCGTTTCTCATCAT-CCCAAATAATCATATGCACCATCTCCAAATTCTTTAGAGAT
65 ATACCCAAATCATTTCTCATCATCCCCAAATAATCATATGCACCATCCCCAAATTCTTTAGAGAT
*
4925 TGAGATTTTTTCTCAAATATCCAAAATTGGCTTTAAAAAGTGCTTTAATCCATATTTTTCATTCT
130 TGACATTTTTTCTCAAATATCCAAAATTGGCTTTAAAAAGTGCTTTAATCCATATTTTTCATTCT
4990 AATTAACTGAATAAACCCCGTCTATATG
195 AATTAACTGAATAAACCCCGTCTATATG
* ** *
5018 ATTTTAGTGTCATCTAACAATTAAACAGTATGTAAAATTCAGTATCCCCAAAGTAATATACTTTA
1 ATTTTAGTGTCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAAGTAATATACTTTA
*
5083 TTCCCAAATCA--T-T--TC-T--CCAAATAATCATATGCACCATCCCCAAATTCTTTAGAGATT
66 TACCCAAATCATTTCTCATCATCCCCAAATAATCATATGCACCATCCCCAAATTCTTTAGAGATT
* * * * * *
5140 GACATTTTTCCTCATATACCCAAAATTGGCTTTAAAAAGTGCTTTAATACGTATTTTTCATCCTA
131 GACATTTTTTCTCAAATATCCAAAATTGGCTTTAAAAAGTGCTTTAATCCATATTTTTCATTCTA
* **
5205 ATTAATTGAATAAACCATGTCTATATG
196 ATTAACTGAATAAACCCCGTCTATATG
* *
5232 ATTTTAGTGTCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAACTGATATACTTTA
1 ATTTTAGTGTCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAAGTAATATACTTTA
* * *
5297 TACTCAAATCATTTCTCATCATCCCCAAATAATCATATGCACCATCCCCAAATTTTTTAGACATT
66 TACCCAAATCATTTCTCATCATCCCCAAATAATCATATGCACCATCCCCAAATTCTTTAGAGATT
* * * * * * *
5362 GACA-ATTTT-T-ATATACCCAAAATTGG-TTTTAAACGTGTTTTAATCCATA-TTTTCTTTCTA
131 GACATTTTTTCTCAAATATCCAAAATTGGCTTTAAAAAGTGCTTTAATCCATATTTTTCATTCTA
* *
5422 ATTAATTGAATAAACCTCGTCTATATG
196 ATTAACTGAATAAACCCCGTCTATATG
* *
5449 AATTTAGTGTCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAACTAATATACTTTA
1 ATTTTAGTGTCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAAGTAATATACTTTA
*
5514 TATCCAAATCATTTCTCATCATCCCCAAA
66 TACCCAAATCATTTCTCATCATCCCCAAA
5543 ATTTTTAGAG
Statistics
Matches: 887, Mismatches: 72, Indels: 28
0.90 0.07 0.03
Matches are distributed among these distances:
214 190 0.21
215 1 0.00
216 3 0.00
217 125 0.14
218 19 0.02
219 19 0.02
220 2 0.00
221 70 0.08
222 128 0.14
223 249 0.28
224 81 0.09
ACGTcount: A:0.37, C:0.20, G:0.07, T:0.36
Consensus pattern (222 bp):
ATTTTAGTGTCATCTAATAATTAAACAAAATGCAAAATTCAGTATCCCCAAAGTAATATACTTTA
TACCCAAATCATTTCTCATCATCCCCAAATAATCATATGCACCATCCCCAAATTCTTTAGAGATT
GACATTTTTTCTCAAATATCCAAAATTGGCTTTAAAAAGTGCTTTAATCCATATTTTTCATTCTA
ATTAACTGAATAAACCCCGTCTATATG
Found at i:5674 original size:194 final size:194
Alignment explanation
Indices: 5339--5929 Score: 673
Period size: 194 Copynumber: 2.9 Consensus size: 194
5329 TCATATGCAC
* * * *
5339 CATCCCCAAATTTTTTAGACATTGACAATTTTTATATACCCAAAATTGGTTTTAAACGTGTTTTA
1 CATCCCCAAAATTTTTAGACATTGACAATTTTTATATACCCAAAAGTGGCTTTAAACGTGCTTTA
* * * *
5404 ATCCATATTTTCTTTCTAATTAATTGAATAAACCTCGTCTATATGAATTTAGTGTCATCTAATAA
66 ATCCATATTTTCATCCTAATTAATTGAATAAACCCCGTCTATATGAATTTACTGTCATCTAATAA
* * *
5469 TTAAACAAAATGCAAAATTCAGTATCCCCAAACTAATATACTTTATATCCAAATCATTTCTCAT
131 TTAAACAAAATGCAAAATTCAGTATCACCAAACTAATATACCTTATACCCAAATCATTTCTCAT
** *
5533 CATCCCCAAAATTTTTAGAGGTTGACATTTTTTATATACCCAAAAGTGGCTTTAAACGTGCTTTA
1 CATCCCCAAAATTTTTAGACATTGACAATTTTTATATACCCAAAAGTGGCTTTAAACGTGCTTTA
5598 ATCCATATTTTCATCCTAATTAATTGAATAAACCCCGTCTATATGAATTTACTGTCATCTAATAA
66 ATCCATATTTTCATCCTAATTAATTGAATAAACCCCGTCTATATGAATTTACTGTCATCTAATAA
* *
5663 TTAATCAAAATGCAAAATTCAGTATCACCAAACTGATATACCTTATACCCAAATCATTTCTCAT
131 TTAAACAAAATGCAAAATTCAGTATCACCAAACTAATATACCTTATACCCAAATCATTTCTCAT
* * * *
5727 CATCCCCAAATAATCATATGCACCATCCCCAAATTCTTTAGAGATTGTCATTTTTTATATACCCA
1 CATCCCC-AA-AAT--T-T------T---TAGA--C-------ATTGACAATTTTTATATACCCA
* * * * *
5792 AAATTGGCTTT-AACATGTTTTAATCCATATTTTTCATCCTAATTAGTTGAATAAACCCCCTCTA
43 AAAGTGGCTTTAAACGTGCTTTAATCCATA-TTTTCATCCTAATTAATTGAATAAACCCCGTCTA
* * * *
5856 TATGAATTTACTGCCATCTAATAATTAATCAAAATGCAAAATTCAGTATC-CTCAAATTGATATA
107 TATGAATTTACTGTCATCTAATAATTAAACAAAATGCAAAATTCAGTATCAC-CAAACTAATATA
*
5920 CTTTATACCC
171 CCTTATACCC
5930 TAGTCATTGA
Statistics
Matches: 343, Mismatches: 29, Indels: 27
0.86 0.07 0.07
Matches are distributed among these distances:
194 185 0.54
195 2 0.01
196 3 0.01
198 1 0.00
199 1 0.00
205 1 0.00
208 2 0.01
216 17 0.05
217 131 0.38
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.37
Consensus pattern (194 bp):
CATCCCCAAAATTTTTAGACATTGACAATTTTTATATACCCAAAAGTGGCTTTAAACGTGCTTTA
ATCCATATTTTCATCCTAATTAATTGAATAAACCCCGTCTATATGAATTTACTGTCATCTAATAA
TTAAACAAAATGCAAAATTCAGTATCACCAAACTAATATACCTTATACCCAAATCATTTCTCAT
Found at i:5919 original size:217 final size:217
Alignment explanation
Indices: 5533--5929 Score: 656
Period size: 217 Copynumber: 1.8 Consensus size: 217
5523 CATTTCTCAT
* *
5533 CATCCCCAAAATTTTTAGAGGTTGACATTTTTTATATACCCAAAAGTGGCTTTAAACGTGCTTTA
1 CATCCCCAAAATTTTTAGAGATTGACATTTTTTATATACCCAAAAGTGGCTTTAAACATGCTTTA
* *
5598 ATCCATATTTTCATCCTAATTAATTGAATAAACCCCGTCTATATGAATTTACTGTCATCTAATAA
66 ATCCATATTTTCATCCTAATTAATTGAATAAACCCCCTCTATATGAATTTACTGCCATCTAATAA
5663 TTAATCAAAATGCAAAATTCAGTATCACCAAACTGATATACCTTATACCCAAATCATTTCTCATC
131 TTAATCAAAATGCAAAATTCAGTATCACCAAACTGATATACCTTATACCCAAATCATTTCTCATC
5728 ATCCCCAAATAATCATATGCAC
196 ATCCCCAAATAATCATATGCAC
* * *
5750 CATCCCC-AAATTCTTTAGAGATTGTCATTTTTTATATACCCAAAATTGGCTTT-AACATGTTTT
1 CATCCCCAAAATT-TTTAGAGATTGACATTTTTTATATACCCAAAAGTGGCTTTAAACATGCTTT
*
5813 AATCCATATTTTTCATCCTAATTAGTTGAATAAACCCCCTCTATATGAATTTACTGCCATCTAAT
65 AATCCATA-TTTTCATCCTAATTAATTGAATAAACCCCCTCTATATGAATTTACTGCCATCTAAT
* *
5878 AATTAATCAAAATGCAAAATTCAGTATC-CTCAAATTGATATACTTTATACCC
129 AATTAATCAAAATGCAAAATTCAGTATCAC-CAAACTGATATACCTTATACCC
5930 TAGTCATTGA
Statistics
Matches: 167, Mismatches: 10, Indels: 6
0.91 0.05 0.03
Matches are distributed among these distances:
216 22 0.13
217 145 0.87
ACGTcount: A:0.35, C:0.21, G:0.08, T:0.36
Consensus pattern (217 bp):
CATCCCCAAAATTTTTAGAGATTGACATTTTTTATATACCCAAAAGTGGCTTTAAACATGCTTTA
ATCCATATTTTCATCCTAATTAATTGAATAAACCCCCTCTATATGAATTTACTGCCATCTAATAA
TTAATCAAAATGCAAAATTCAGTATCACCAAACTGATATACCTTATACCCAAATCATTTCTCATC
ATCCCCAAATAATCATATGCAC
Found at i:8092 original size:19 final size:19
Alignment explanation
Indices: 8064--8105 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
8054 TTATATGGAA
*
8064 ATAAACATGGATGCAAATG
1 ATAAACATGGATCCAAATG
*
8083 ATAAATATGGATCCAAATG
1 ATAAACATGGATCCAAATG
8102 ATAA
1 ATAA
8106 TTTCTTTTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.50, C:0.10, G:0.17, T:0.24
Consensus pattern (19 bp):
ATAAACATGGATCCAAATG
Found at i:11080 original size:13 final size:13
Alignment explanation
Indices: 11064--11088 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11054 TTTTGTGTTT
11064 TTTTTTCTTTTTC
1 TTTTTTCTTTTTC
11077 TTTTTTCTTTTT
1 TTTTTTCTTTTT
11089 TTCTACAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTCTTTTTC
Found at i:12357 original size:6 final size:6
Alignment explanation
Indices: 12346--12404 Score: 102
Period size: 6 Copynumber: 10.0 Consensus size: 6
12336 ATTATTATAT
*
12346 ATACTA ATACTA ATACCA ATACTA ATACTA ATACT- ATACTA ATACTA
1 ATACTA ATACTA ATACTA ATACTA ATACTA ATACTA ATACTA ATACTA
12393 ATACTA ATACTA
1 ATACTA ATACTA
12405 TCTCAATGGC
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
5 5 0.10
6 45 0.90
ACGTcount: A:0.49, C:0.19, G:0.00, T:0.32
Consensus pattern (6 bp):
ATACTA
Found at i:18677 original size:21 final size:21
Alignment explanation
Indices: 18638--18677 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
18628 AACAAGTAGT
*
18638 AACCTGCTGCACTGTTGGCAG
1 AACCTGCTGCACTGCTGGCAG
18659 AACCT-CTGCATCTGCTGGC
1 AACCTGCTGCA-CTGCTGGC
18678 CAACAGGAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.17, C:0.33, G:0.25, T:0.25
Consensus pattern (21 bp):
AACCTGCTGCACTGCTGGCAG
Found at i:21670 original size:7 final size:7
Alignment explanation
Indices: 21658--21683 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
21648 CATGGACATG
21658 AAAAGGA
1 AAAAGGA
21665 AAAAGGA
1 AAAAGGA
21672 AAAAGGA
1 AAAAGGA
21679 AAAAG
1 AAAAG
21684 CATAAGATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (7 bp):
AAAAGGA
Found at i:22676 original size:7 final size:7
Alignment explanation
Indices: 22666--22696 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
22656 AACACACTGA
22666 TTTTTCT
1 TTTTTCT
22673 TTTTTCT
1 TTTTTCT
22680 TTTTTCT
1 TTTTTCT
22687 TTTTT-T
1 TTTTTCT
22693 TTTT
1 TTTT
22697 GAGGGAACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.21
7 19 0.79
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (7 bp):
TTTTTCT
Found at i:24156 original size:28 final size:28
Alignment explanation
Indices: 24116--24171 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
24106 CGATGAGGAT
24116 CCAACCCACAACAAAGAAATTACCATAA
1 CCAACCCACAACAAAGAAATTACCATAA
24144 CCAACCCACAACAAAGAAATTACCATAA
1 CCAACCCACAACAAAGAAATTACCATAA
24172 ATAAGCTGCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.54, C:0.32, G:0.04, T:0.11
Consensus pattern (28 bp):
CCAACCCACAACAAAGAAATTACCATAA
Found at i:24993 original size:18 final size:17
Alignment explanation
Indices: 24946--24993 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
24936 ATTCAACTTC
*
24946 ATTATTTATAAAT-TTA
1 ATTATTTATATATATTA
24962 ATTATTTA-ATTATATTA
1 ATTATTTATA-TATATTA
24979 TATTATTTATATATA
1 -ATTATTTATATATA
24994 AAAAGGGGCC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 1 0.04
16 10 0.37
17 3 0.11
18 12 0.44
19 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTATTTATATATATTA
Found at i:25419 original size:11 final size:11
Alignment explanation
Indices: 25403--25441 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
25393 ATAGTAACAT
25403 ATAACATAATA
1 ATAACATAATA
25414 ATAACAT--TA
1 ATAACATAATA
25423 CATAACATAATA
1 -ATAACATAATA
25435 ATAACAT
1 ATAACAT
25442 TGTATAAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
9 2 0.08
10 7 0.28
11 14 0.56
12 2 0.08
ACGTcount: A:0.59, C:0.13, G:0.00, T:0.28
Consensus pattern (11 bp):
ATAACATAATA
Found at i:25429 original size:21 final size:21
Alignment explanation
Indices: 25403--25442 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
25393 ATAGTAACAT
25403 ATAACATAATAATAACATTAC
1 ATAACATAATAATAACATTAC
25424 ATAACATAATAATAACATT
1 ATAACATAATAATAACATT
25443 GTATAAGAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.30
Consensus pattern (21 bp):
ATAACATAATAATAACATTAC
Found at i:25448 original size:21 final size:21
Alignment explanation
Indices: 25401--25448 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
25391 ATATAGTAAC
25401 ATATAACATAATAATAACATT
1 ATATAACATAATAATAACATT
*
25422 ACATAACATAATAATAACATT
1 ATATAACATAATAATAACATT
*
25443 GTATAA
1 ATATAA
25449 GAGTAGTGCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.31
Consensus pattern (21 bp):
ATATAACATAATAATAACATT
Found at i:26719 original size:125 final size:124
Alignment explanation
Indices: 26587--26853 Score: 457
Period size: 125 Copynumber: 2.2 Consensus size: 124
26577 TTTAAATTAT
*
26587 TAAAATGGTATAAATAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAATAGAGTTTTTA
1 TAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAATAGAGTTTTTA
** *
26652 ATAGAATCAAACTATATATTAAAATTTTTTAATATATCCAAGTTTTTTAATGAAAAATAG
66 ATAGAATCAAACTATATATTAAAAAATTTTAATATATCCAAG-TTTTAAATGAAAAATAG
*
26712 TAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATGAAATTAGAGTTTTTA
1 TAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAATAGAGTTTTTA
*
26777 GTAGAATCAAACTATATATTAAAAAATTTTAATATATCCAAGTTTTAAATGAAAAATAG
66 ATAGAATCAAACTATATATTAAAAAATTTTAATATATCCAAGTTTTAAATGAAAAATAG
26836 T--AATGGTAAAAATAAAAT
1 TAAAATGGTAAAAATAAAAT
26854 TTTAAACTAA
Statistics
Matches: 136, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
122 17 0.12
124 17 0.12
125 102 0.75
ACGTcount: A:0.52, C:0.03, G:0.09, T:0.36
Consensus pattern (124 bp):
TAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAATAGAGTTTTTA
ATAGAATCAAACTATATATTAAAAAATTTTAATATATCCAAGTTTTAAATGAAAAATAG
Found at i:26883 original size:149 final size:149
Alignment explanation
Indices: 26712--27118 Score: 690
Period size: 149 Copynumber: 2.7 Consensus size: 149
26702 TGAAAAATAG
26712 TAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATG-AAATTAGAGTTTTT
1 TAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAATT-GAGTTTTT
*
26776 AGTAGAATCAAACTATATATTAAAAAATTTTAATATATCCAAGTTTTAAATGAAAAATAGTAATG
65 AGTAGAATCAAACTATATATTAAAAAATTTTAATATATCCAAGTTTTAAATGAAAAATAGAAATG
26841 GTAAAAATAAAATTTTAAAC
130 GTAAAAATAAAATTTTAAAC
*
26861 TAAAATGGTAAAAAGAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAATTGAGTTTTTA
1 TAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAATTGAGTTTTTA
** * *
26926 GTAGAATCAAACTATATATTAAAATTTTTTGATATATCCAAGTTTTTAATGAAAAATAGAAATGG
66 GTAGAATCAAACTATATATTAAAAAATTTTAATATATCCAAGTTTTAAATGAAAAATAGAAATGG
* * * *
26991 TAAGAATAAACTTTTATAT
131 TAAAAATAAAATTTTAAAC
*
27010 TAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAGTTAAATGAAAATTGAGTTTTTA
1 TAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAATTGAGTTTTTA
*
27075 GTAGAATCAAACTATATATTAAAAAACTTTAATATATCCAAGTT
66 GTAGAATCAAACTATATATTAAAAAATTTTAATATATCCAAGTT
27119 AAAATGGTAA
Statistics
Matches: 241, Mismatches: 16, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
149 236 0.98
150 5 0.02
ACGTcount: A:0.51, C:0.04, G:0.10, T:0.36
Consensus pattern (149 bp):
TAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAATTGAGTTTTTA
GTAGAATCAAACTATATATTAAAAAATTTTAATATATCCAAGTTTTAAATGAAAAATAGAAATGG
TAAAAATAAAATTTTAAAC
Found at i:28390 original size:39 final size:38
Alignment explanation
Indices: 28349--28725 Score: 370
Period size: 39 Copynumber: 9.7 Consensus size: 38
28339 TTATCTGCGT
*** *
28349 AAACCTGCTTAGGTCCCCATTTA-AAGTTGTCGTTTAAGT
1 AAACCTGCTTAGGTCCTTGTTTAGAA-TT-TCGTTTAAGC
* * * * *
28388 AAACCTGTTTAGGT-CTACGTTTAGAATCTCATTTAAGG
1 AAACCTGCTTAGGTCCT-TGTTTAGAATTTCGTTTAAGC
*
28426 AAACCTGCCTAGGTCCTTGTTTAGAATTTTCGTTTAAGC
1 AAACCTGCTTAGGTCCTTGTTTAGAA-TTTCGTTTAAGC
28465 AAACCTGCTTAGGTCCTTGTTTAGAATCTTCGTTTAAGC
1 AAACCTGCTTAGGTCCTTGTTTAGAAT-TTCGTTTAAGC
28504 AAACCTGCTTAGGTCCTTGTTTAGAATCTTCGTTTAAGC
1 AAACCTGCTTAGGTCCTTGTTTAGAAT-TTCGTTTAAGC
*
28543 AAACCTGCTTAGTTCCTTGTTTAGAATTTTCGTTTAAGC
1 AAACCTGCTTAGGTCCTTGTTTAGAA-TTTCGTTTAAGC
* *
28582 AAACCTGCTTAGGTCCTTGTTTAGAATGTCCGTTTAAGT
1 AAACCTGCTTAGGTCCTTGTTTAGAAT-TTCGTTTAAGC
* * * * *
28621 GAACCTGCTTAGGATCCCTGCTTT-G-AGTTCATTCGAA-C
1 AAACCTGCTTAGG-TCCTTG-TTTAGAATTTCGTT-TAAGC
* * ** *
28659 AACCCTGCTTAGGT-CTATGTCTAGGGGTTTCGTTTAATC
1 AAACCTGCTTAGGTCCT-TGTTTA-GAATTTCGTTTAAGC
* *
28698 AAACATGATTAGGTCCTTGTTTAGAATT
1 AAACCTGCTTAGGTCCTTGTTTAGAATT
28726 CCTGTTTGAG
Statistics
Matches: 284, Mismatches: 38, Indels: 33
0.80 0.11 0.09
Matches are distributed among these distances:
36 3 0.01
37 3 0.01
38 52 0.18
39 212 0.75
40 11 0.04
41 3 0.01
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (38 bp):
AAACCTGCTTAGGTCCTTGTTTAGAATTTCGTTTAAGC
Found at i:28782 original size:116 final size:113
Alignment explanation
Indices: 28380--28789 Score: 328
Period size: 116 Copynumber: 3.5 Consensus size: 113
28370 TAAAGTTGTC
* * * * * * *
28380 GTTTAAGTAAACCTGTTTAGGTCTACGTTTAGAATCTC-ATTTAAGGAAACCTGCCTAGGTCCTT
1 GTTTAAGTGAACCTGCTTAGGT-TTCGCTTAGAGTTTCGA-TTAA-GAAACCTGCTTAGGT-CTT
* * *
28444 GTTTAGAATTTTCGTTTAAGCAAACCTGCTTAGGTCCTTGTTTAGAA-TCTT
62 GTCTAGAAGTTTCGTTTAAGCAAACCTGCTTAGGTCCTTGTTTAGAATTCCT
** * * * *
28495 CGTTTAAGCAAACCTGCTTAGGTCCTT-GTTTAGAATCTTCGTTTAAGCAAACCTGCTTAGTTCC
1 -GTTTAAGTGAACCTGCTTAGGT--TTCGCTTAGAGT-TTCGATTAAG-AAACCTGCTTAGGT-C
* *
28559 TTGTTTAGAATTTTCGTTTAAGCAAACCTGCTTAGGTCCTTGTTTAGAATGTCC-
60 TTGTCTAGAAGTTTCGTTTAAGCAAACCTGCTTAGGTCCTTGTTTAGAAT-TCCT
** * * *
28613 GTTTAAGTGAACCTGCTTAGGATCCCTGCTTTGAG-TTC-ATTCGAACAACCCTGCTTAGGTCTA
1 GTTTAAGTGAACCTGCTTAGG-TTTC-GCTTAGAGTTTCGATT--AAGAAACCTGCTTAGGTCT-
** * * *
28676 TGTCTAGGGGTTTCGTTTAATCAAACATGATTAGGTCCTTGTTTAGAATTCCT
61 TGTCTAGAAGTTTCGTTTAAGCAAACCTGCTTAGGTCCTTGTTTAGAATTCCT
* * * *
28729 GTTTGAGTGAACTTGCTTAGGTTTACGCTTAGAGTTTCGCTTAATGAAACCTGCTCAGGTC
1 GTTTAAGTGAACCTGCTTAGGTTT-CGCTTAGAGTTTCGATTAA-GAAACCTGCTTAGGTC
28790 CATCTTTCAA
Statistics
Matches: 242, Mismatches: 35, Indels: 34
0.78 0.11 0.11
Matches are distributed among these distances:
115 17 0.07
116 123 0.51
117 94 0.39
118 6 0.02
119 2 0.01
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.38
Consensus pattern (113 bp):
GTTTAAGTGAACCTGCTTAGGTTTCGCTTAGAGTTTCGATTAAGAAACCTGCTTAGGTCTTGTCT
AGAAGTTTCGTTTAAGCAAACCTGCTTAGGTCCTTGTTTAGAATTCCT
Found at i:30998 original size:21 final size:22
Alignment explanation
Indices: 30968--31009 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
30958 CACGTGAGAT
30968 CAAAAATTG-AGAGACAAAATG
1 CAAAAATTGAAGAGACAAAATG
*
30989 CAAAACTTGAAAGAGACAAAA
1 CAAAAATTG-AAGAGACAAAA
31010 ATAACTGCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
23 10 0.56
ACGTcount: A:0.60, C:0.12, G:0.17, T:0.12
Consensus pattern (22 bp):
CAAAAATTGAAGAGACAAAATG
Found at i:45793 original size:39 final size:39
Alignment explanation
Indices: 45752--46075 Score: 404
Period size: 39 Copynumber: 8.3 Consensus size: 39
45742 TTATCTGCGT
*** * *
45752 AAACCTGCTTAGGTCCCCATTTA-AAGTTGTCGTTTAAGT
1 AAACCTGCTTAGGTCCTTGTTTAGAA-TTTTCGTTTAAGC
* * *
45791 AAACCTGCTTAGGT--TTACGTTTAGAA-TCTCATTTAAGG
1 AAACCTGCTTAGGTCCTT--GTTTAGAATTTTCGTTTAAGC
*
45829 AAACCTGCCTAGGTCCTTGTTTAGAATTTTCGTTTAAGC
1 AAACCTGCTTAGGTCCTTGTTTAGAATTTTCGTTTAAGC
* *
45868 AAACCTCCTTAGGTCTTTGTTTAGAATTTTCGTTTAAGC
1 AAACCTGCTTAGGTCCTTGTTTAGAATTTTCGTTTAAGC
* *
45907 AAACCTACTTAGGTCCTTGTTTAGAATCTTCGTTTAAGC
1 AAACCTGCTTAGGTCCTTGTTTAGAATTTTCGTTTAAGC
45946 AAACCTGCTTAGGTCCTTGTTTAGAATTTTCGTTTAAGC
1 AAACCTGCTTAGGTCCTTGTTTAGAATTTTCGTTTAAGC
* *
45985 AAACCTGCTTAGGTCCTTGTTTACAATTTCCGTTTAAGC
1 AAACCTGCTTAGGTCCTTGTTTAGAATTTTCGTTTAAGC
* * * * *
46024 AAACCTGTTTAGGTCCTGGTTTAGAATGTCCGTTTAAGT
1 AAACCTGCTTAGGTCCTTGTTTAGAATTTTCGTTTAAGC
*
46063 GAACCTGCTTAGG
1 AAACCTGCTTAGG
46076 ATCCCTGCTT
Statistics
Matches: 252, Mismatches: 27, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
38 30 0.12
39 218 0.87
40 4 0.02
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.38
Consensus pattern (39 bp):
AAACCTGCTTAGGTCCTTGTTTAGAATTTTCGTTTAAGC
Done.