Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018680.1 Corchorus olitorius cultivar O-4 contig18713, 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: 43177
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1052 original size:23 final size:23
Alignment explanation
Indices: 1009--1052 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
999 AAGTTTTTTT
*
1009 AATAAAATTAGTAAAATGATAAA
1 AATAAAATTAGTAAAAGGATAAA
*
1032 AATAAAA-TAGGTATAAGGATA
1 AATAAAATTA-GTAAAAGGATA
1053 TTATATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 16 0.89
ACGTcount: A:0.61, C:0.00, G:0.14, T:0.25
Consensus pattern (23 bp):
AATAAAATTAGTAAAAGGATAAA
Found at i:1134 original size:98 final size:102
Alignment explanation
Indices: 994--1202 Score: 266
Period size: 105 Copynumber: 2.0 Consensus size: 102
984 AATTCTAATA
* * * *
994 TATAAAAGTTTTTTTAATAAAATTAGTAAAATGATAAAAAT-AA-AATAGGTATAAGGATATTAT
1 TATAAAAGTTATTTTAATAAAATTAGTAAAATGATAAAAATAAAGAACACGTATAAGGATATTAG
1057 ATTTAAT-TAAAAAAAGAGTTTTTAATTGAGTAAAAC
66 ATTTAATATAAAAAAAGAGTTTTTAATTGAGTAAAAC
* *
1093 TATAAAAG-TATTTTAATTAAAA-TAGTAAAATGGTAAAAATAAAAGAACACTTATAAGGATATT
1 TATAAAAGTTATTTTAA-TAAAATTAGTAAAATGATAAAAAT-AAAGAACACGTATAAGGATATT
* *
1156 AGATTTAATCAAATAAAAATAGAGTTTTTAGTTGAGTAAAAC
64 AGATTTAAT---ATAAAAAAAGAGTTTTTAATTGAGTAAAAC
1198 TATAA
1 TATAA
1203 TAAAAATTTA
Statistics
Matches: 94, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
98 24 0.26
99 13 0.14
100 2 0.02
101 23 0.24
105 32 0.34
ACGTcount: A:0.52, C:0.02, G:0.11, T:0.34
Consensus pattern (102 bp):
TATAAAAGTTATTTTAATAAAATTAGTAAAATGATAAAAATAAAGAACACGTATAAGGATATTAG
ATTTAATATAAAAAAAGAGTTTTTAATTGAGTAAAAC
Found at i:1359 original size:60 final size:60
Alignment explanation
Indices: 1289--1409 Score: 233
Period size: 60 Copynumber: 2.0 Consensus size: 60
1279 GTGAACGTAC
*
1289 TTTTTAATATAGTATAGATAGATAGATAATAATATTTTGGACGAGATTAGGTAGGTGAAA
1 TTTTTAATATAGTATAGATAGATAGATAATAATATTTTGGACGACATTAGGTAGGTGAAA
1349 TTTTTAATATAGTATAGATAGATAGATAATAATATTTTGGACGACATTAGGTAGGTGAAA
1 TTTTTAATATAGTATAGATAGATAGATAATAATATTTTGGACGACATTAGGTAGGTGAAA
1409 T
1 T
1410 ACACGCATAG
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.40, C:0.02, G:0.21, T:0.37
Consensus pattern (60 bp):
TTTTTAATATAGTATAGATAGATAGATAATAATATTTTGGACGACATTAGGTAGGTGAAA
Found at i:3079 original size:22 final size:22
Alignment explanation
Indices: 3051--3264 Score: 109
Period size: 22 Copynumber: 9.7 Consensus size: 22
3041 TGTCTCTGTG
3051 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
3073 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AAGA
* * *
3096 -GGTTATCGAAATTCCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* * *
3117 TGGTTACCAAAATTTTATATGGA
1 TGGTTATCAAAATTTCATA-AGA
* **
3140 -AGTT-TCAAAATTTCATGGGA
1 TGGTTATCAAAATTTCATAAGA
* *
3160 AGGTTATCAAAATTTCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* *
3182 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAAGA
* *
3204 TTAGGTTATTAAAATTTC-TTAGA
1 -T-GGTTATCAAAATTTCATAAGA
* * **
3227 AGATTATTGAAATTTCATAATG-
1 TGGTTATCAAAATTTCATAA-GA
3249 TGGTTATCATAAATTT
1 TGGTTATCA-AAATTT
3265 ATAGAAAGGT
Statistics
Matches: 140, Mismatches: 38, Indels: 27
0.68 0.19 0.13
Matches are distributed among these distances:
20 4 0.03
21 27 0.19
22 80 0.57
23 15 0.11
24 14 0.10
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.39
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:3311 original size:22 final size:22
Alignment explanation
Indices: 3286--3709 Score: 151
Period size: 22 Copynumber: 18.9 Consensus size: 22
3276 ATAAAAGAGA
*
3286 TTATCAAAATGTCATAGTGAGG
1 TTATCAAAATTTCATAGTGAGG
*
3308 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGTGAGG
* *
3330 TTAACAAAATTTCCTTAAG-GAGG
1 TTATCAAAATTT-CAT-AGTGAGG
* * *
3353 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCATAGTGAGG
** * *
3375 TTATCAAAATTTTTTATTGTGG
1 TTATCAAAATTTCATAGTGAGG
3397 TTATCAAAATTTCATA-TGAAGG
1 TTATCAAAATTTCATAGTG-AGG
* **
3419 TTATAAAAGTCTCAATTTCATAACGA-G
1 TTAT-CAA-----AATTTCATAGTGAGG
* * *
3446 TT-CCAAAATTTGATAG-AAGG
1 TTATCAAAATTTCATAGTGAGG
*
3466 TTATC-AAATCTCATAGAATGA--
1 TTATCAAAATTTCATAG--TGAGG
* *
3487 TTATCGAAATTTCATAGAGATCGG
1 TTATCAAAATTTCATAGTGA--GG
* *
3511 ATTATCAAAATTT-ATAGTAAGA
1 -TTATCAAAATTTCATAGTGAGG
*
3533 TTATCAAAATTTTATAGT---G
1 TTATCAAAATTTCATAGTGAGG
* *
3552 TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
*
3574 TT-TCAAAATTACATAATGTGAATGTG
1 TTATCAAAATTTCAT-A-GTG-A-G-G
* *
3600 ATTATCAAAATTTCGTAGAG-GAG
1 -TTATCAAAATTTCATAGTGAG-G
* ** *
3623 TTAACAAAATTTTGTAGAGAGG
1 TTATCAAAATTTCATAGTGAGG
* *
3645 TTATCAAAATTTCACAAAGAGAGG
1 TTATCAAAATTT--CATAGTGAGG
* * * * *
3669 TTATCAAATTTTCAAAATGTGA
1 TTATCAAAATTTCATAGTGAGG
*
3691 TTACCAAAATTTCATAGTG
1 TTATCAAAATTTCATAGTG
3710 GTATTTCTGG
Statistics
Matches: 301, Mismatches: 61, Indels: 80
0.68 0.14 0.18
Matches are distributed among these distances:
19 16 0.05
20 22 0.07
21 33 0.11
22 135 0.45
23 25 0.08
24 26 0.09
25 14 0.05
26 3 0.01
27 6 0.02
28 20 0.07
29 1 0.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:3521 original size:25 final size:21
Alignment explanation
Indices: 3451--3565 Score: 80
Period size: 21 Copynumber: 5.4 Consensus size: 21
3441 ACGAGTTCCA
* *
3451 AAATTTGATAGAA-GGTTATC
1 AAATTTCATAGAATGATTATC
*
3471 AAATCTCATAGAATGATTATC
1 AAATTTCATAGAATGATTATC
3492 GAAATTTCATAGAGATCGGATTATC
1 -AAATTTCATAGA-AT--GATTATC
3517 AAAATTT-ATAGTAA-GATTATC
1 -AAATTTCATAG-AATGATTATC
*
3538 AAAATTTTATAG--TG-TTATC
1 -AAATTTCATAGAATGATTATC
3557 AAAATTTCA
1 -AAATTTCA
3566 AAGCGAGGTT
Statistics
Matches: 81, Mismatches: 6, Indels: 17
0.78 0.06 0.16
Matches are distributed among these distances:
19 13 0.16
20 12 0.15
21 20 0.25
22 15 0.19
23 2 0.02
24 5 0.06
25 14 0.17
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.37
Consensus pattern (21 bp):
AAATTTCATAGAATGATTATC
Found at i:3557 original size:19 final size:21
Alignment explanation
Indices: 3510--3563 Score: 78
Period size: 19 Copynumber: 2.7 Consensus size: 21
3500 ATAGAGATCG
3510 GATTATCAAAA-TTTATAGTAA
1 GATTATCAAAATTTTATAGT-A
3531 GATTATCAAAATTTTATAGT-
1 GATTATCAAAATTTTATAGTA
3551 G-TTATCAAAATTT
1 GATTATCAAAATTT
3564 CAAAGCGAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
19 12 0.38
20 1 0.03
21 11 0.34
22 8 0.25
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.43
Consensus pattern (21 bp):
GATTATCAAAATTTTATAGTA
Found at i:3955 original size:22 final size:22
Alignment explanation
Indices: 3788--3978 Score: 114
Period size: 22 Copynumber: 9.0 Consensus size: 22
3778 TTATGGAATA
*
3788 ATCAAAATTTC--AGGGAGGAT
1 ATCAAAATTTCATAGGGAGGTT
* * *
3808 ATCAAAATTTCATA-GTATGTAG
1 ATCAAAATTTCATAGGGAGGT-T
* *
3830 ATCAAAATTTCATAAGGAGATT
1 ATCAAAATTTCATAGGGAGGTT
* **
3852 AACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
**
3874 ATCAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
**
3896 ATCAAAA-TT--T---GTTGTT
1 ATCAAAATTTCATAGGGAGGTT
* *
3912 ATCAAGATTTCAGAAGGG-GGTT
1 ATCAAAATTTCA-TAGGGAGGTT
*
3934 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATAGGGAGG-TT
* * *
3957 CTCAAAATTTTATAGGAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
3979 TCATAGTGAG
Statistics
Matches: 131, Mismatches: 27, Indels: 24
0.72 0.15 0.13
Matches are distributed among these distances:
16 10 0.08
17 2 0.02
19 1 0.01
20 11 0.08
21 8 0.06
22 75 0.57
23 24 0.18
ACGTcount: A:0.39, C:0.08, G:0.19, T:0.33
Consensus pattern (22 bp):
ATCAAAATTTCATAGGGAGGTT
Found at i:3965 original size:23 final size:23
Alignment explanation
Indices: 3935--3980 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
3925 AAGGGGGTTA
*
3935 TCAAAATTTTATAGGGAGGTTTC
1 TCAAAATTTTATAGGAAGGTTTC
3958 TCAAAATTTTATAGGAAGGTTTC
1 TCAAAATTTTATAGGAAGGTTTC
3981 ATAGTGAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.39
Consensus pattern (23 bp):
TCAAAATTTTATAGGAAGGTTTC
Found at i:4003 original size:22 final size:22
Alignment explanation
Indices: 3977--4204 Score: 87
Period size: 22 Copynumber: 10.3 Consensus size: 22
3967 TATAGGAAGG
*
3977 TTTCATAGTGAGATTATCACAA
1 TTTCATAGTGAGATTATCAAAA
*
3999 TTTCATAGTGTGATTATCAAAA
1 TTTCATAGTGAGATTATCAAAA
* * *
4021 TTTCAGAATGCGATTA-CTAACAA
1 TTTCATAGTGAGATTATC-AA-AA
* * * *
4044 -TTCATA-TGGAGGTTTTTAAAT
1 TTTCATAGT-GAGATTATCAAAA
*
4065 TTTCATAACGTG-G-TTATCAATA
1 TTTCAT-A-GTGAGATTATCAAAA
* * *
4087 TATCATA-TGGAGGTTATCAACA
1 TTTCATAGT-GAGATTATCAAAA
* *
4109 TCTCATAGT-ATTGGTTATCAAAA
1 TTTCATAGTGA--GATTATCAAAA
* *
4132 TTTCATTGGGA-AGTTATCAAAA
1 TTTCATAGTGAGA-TTATCAAAA
* *
4154 TTTCATAATGAGGTCT-TCAAAA
1 TTTCATAGTGAGAT-TATCAAAA
* * * * *
4176 TTCCTTAGGGAGGTTAACAAAA
1 TTTCATAGTGAGATTATCAAAA
4198 TTTCATA
1 TTTCATA
4205 AGGTTAAAAA
Statistics
Matches: 153, Mismatches: 34, Indels: 38
0.68 0.15 0.17
Matches are distributed among these distances:
19 1 0.01
20 1 0.01
21 7 0.05
22 119 0.78
23 22 0.14
24 2 0.01
25 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.37
Consensus pattern (22 bp):
TTTCATAGTGAGATTATCAAAA
Found at i:4148 original size:45 final size:45
Alignment explanation
Indices: 4075--4160 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
4065 TTTCATAACG
* * *
4075 TGGTTATCAATATATCATATGGAGGTTATCAACATCTCATAGTAT
1 TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTAT
* *
4120 TGGTTATCAAAATTTCAT-TGGGAAGTTATCAAAATTTCATA
1 TGGTTATCAAAATATCATAT-GGAAGTTATCAAAATCTCATA
4161 ATGAGGTCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 1 0.03
45 34 0.97
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (45 bp):
TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTAT
Found at i:4305 original size:23 final size:22
Alignment explanation
Indices: 4256--4303 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
4246 TATCGTAATT
* *
4256 AAAATTTCATAGGAAGGTTATC
1 AAAATTTCATAGGAAGGTCATA
4278 AAAATTTCATAAGGAA-GTCATA
1 AAAATTTCAT-AGGAAGGTCATA
4300 AAAA
1 AAAA
4304 ATAGTGTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.50, C:0.08, G:0.15, T:0.27
Consensus pattern (22 bp):
AAAATTTCATAGGAAGGTCATA
Found at i:6849 original size:30 final size:30
Alignment explanation
Indices: 6813--6869 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
6803 AGTTCGTGAT
6813 TGAAGATTAATTGAAGACA-ATTTCAAGTCA
1 TGAAGA-TAATTGAAGACATATTTCAAGTCA
* *
6843 TGAAGATCATTGAAGATATATTTCAAG
1 TGAAGATAATTGAAGACATATTTCAAG
6870 GAGAAAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 10 0.42
30 14 0.58
ACGTcount: A:0.42, C:0.09, G:0.18, T:0.32
Consensus pattern (30 bp):
TGAAGATAATTGAAGACATATTTCAAGTCA
Found at i:12211 original size:30 final size:30
Alignment explanation
Indices: 12175--12231 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
12165 AGTTCGTGAT
12175 TGAAGATTAATTGAAGACA-ATTTCAAGTCA
1 TGAAGA-TAATTGAAGACATATTTCAAGTCA
* *
12205 TGAAGATCATTGAAGATATATTTCAAG
1 TGAAGATAATTGAAGACATATTTCAAG
12232 GAGAAAGAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 10 0.42
30 14 0.58
ACGTcount: A:0.42, C:0.09, G:0.18, T:0.32
Consensus pattern (30 bp):
TGAAGATAATTGAAGACATATTTCAAGTCA
Found at i:14533 original size:2 final size:2
Alignment explanation
Indices: 14526--14562 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
14516 AAATAATTTT
14526 TA TA TA TA TA TA TA TA -A 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
14563 AGTTAGTTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:17693 original size:36 final size:37
Alignment explanation
Indices: 17653--17729 Score: 111
Period size: 37 Copynumber: 2.1 Consensus size: 37
17643 ATTGAAACTC
**
17653 TTTTGTAAACATTTA-TCAGATCAGAAATTCTATTTA
1 TTTTGTAAACACATATTCAGATCAGAAATTCTATTTA
* *
17689 TTTTGTAAACACATATTCATATCAGAAATTGTATTTA
1 TTTTGTAAACACATATTCAGATCAGAAATTCTATTTA
17726 TTTT
1 TTTT
17730 AATTTGGTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 13 0.36
37 23 0.64
ACGTcount: A:0.35, C:0.10, G:0.08, T:0.47
Consensus pattern (37 bp):
TTTTGTAAACACATATTCAGATCAGAAATTCTATTTA
Found at i:18736 original size:19 final size:19
Alignment explanation
Indices: 18712--18748 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
18702 GTATAATACC
18712 TAATCTAATCTGTACAGTG
1 TAATCTAATCTGTACAGTG
*
18731 TAATCTCATCTGTACAGT
1 TAATCTAATCTGTACAGT
18749 TGCTAAACAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (19 bp):
TAATCTAATCTGTACAGTG
Found at i:20355 original size:16 final size:16
Alignment explanation
Indices: 20334--20366 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
20324 CGGGATGTGA
20334 GTTTATTT-TGTAATTT
1 GTTTATTTGTGT-ATTT
20350 GTTTATTTGTGTATTT
1 GTTTATTTGTGTATTT
20366 G
1 G
20367 GTAGGTAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.15, C:0.00, G:0.18, T:0.67
Consensus pattern (16 bp):
GTTTATTTGTGTATTT
Found at i:21224 original size:13 final size:13
Alignment explanation
Indices: 21206--21232 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
21196 AAATATAATA
21206 AATATGATTTATG
1 AATATGATTTATG
21219 AATATGATTTATG
1 AATATGATTTATG
21232 A
1 A
21233 GGTTATAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (13 bp):
AATATGATTTATG
Found at i:23631 original size:82 final size:79
Alignment explanation
Indices: 23386--23621 Score: 391
Period size: 82 Copynumber: 2.9 Consensus size: 79
23376 CGATAGGCAC
** *
23386 AATTTTGTTTATAACTCTTCTAAAAGTTGATTCAAAACATGAAAATCTTACTGAATTTCAATTTC
1 AATTTTGTTTAGGACTCTTCTAAAAGTTGATCCAAAACATGAAAATCTTACTGAATTTCAATTTC
*
23451 TTAAAAGAAAGCAT
66 TTGAAAGAAAGCAT
*
23465 AATTTTGTTTAGGACTCTTCTAAAAGTTGATCCAAAACATGAAAATCTTATTGAATTTCAACTTT
1 AATTTTGTTTAGGACTCTTCTAAAAGTTGATCCAAAACATGAAAATCTTACTGAATTTCAA---T
*
23530 TTTTTGAAAGAAAGCAT
63 TTCTTGAAAGAAAGCAT
23547 AATTTTGTTTAGGACTCTTCTAAAAGTTGATCCAAAACATGAAAATCTTACTGAATTTCAATTTC
1 AATTTTGTTTAGGACTCTTCTAAAAGTTGATCCAAAACATGAAAATCTTACTGAATTTCAATTTC
23612 TTGAAAGAAA
66 TTGAAAGAAA
23622 AGCCGATAAT
Statistics
Matches: 146, Mismatches: 8, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
79 70 0.48
82 76 0.52
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.38
Consensus pattern (79 bp):
AATTTTGTTTAGGACTCTTCTAAAAGTTGATCCAAAACATGAAAATCTTACTGAATTTCAATTTC
TTGAAAGAAAGCAT
Found at i:25622 original size:70 final size:68
Alignment explanation
Indices: 25509--25642 Score: 241
Period size: 70 Copynumber: 1.9 Consensus size: 68
25499 CGAAACATTC
*
25509 AAACCCAAACTATCAACAAGACCATGCAACCACATACCTTCTTTAATATCTCTTCAGTCAATGAC
1 AAACCCAAACTATCAACAAGACCATGCAACCACATACCTTCTTT-A-ATCCCTTCAGTCAATGAC
25574 AATTA
64 AATTA
25579 AAACCCAAACTATCAACAAGACCATGCAACCACATACCTTCTTTAATCCCTTCAGTCAATGACA
1 AAACCCAAACTATCAACAAGACCATGCAACCACATACCTTCTTTAATCCCTTCAGTCAATGACA
25643 TATATTCTGC
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
68 18 0.29
69 1 0.02
70 44 0.70
ACGTcount: A:0.40, C:0.31, G:0.06, T:0.24
Consensus pattern (68 bp):
AAACCCAAACTATCAACAAGACCATGCAACCACATACCTTCTTTAATCCCTTCAGTCAATGACAA
TTA
Found at i:26831 original size:52 final size:53
Alignment explanation
Indices: 26769--26906 Score: 228
Period size: 53 Copynumber: 2.6 Consensus size: 53
26759 GAAAATGACA
26769 GGAACTTTCCCAATTT-AAAAACTG-GCTAAATTGGATACTTTAAAAAC-TGATG
1 GGAACTTTCCCAATTTGAAAAA--GAGCTAAATTGGATACTTTAAAAACTTGATG
*
26821 GGAACTTTCCCAATTTGAAAAAGAGCTAAATTGGATACTTTGAAAACTTGATG
1 GGAACTTTCCCAATTTGAAAAAGAGCTAAATTGGATACTTTAAAAACTTGATG
26874 GGAACTTTCCCAATTTGAAAAAGAGCTAAATTG
1 GGAACTTTCCCAATTTGAAAAAGAGCTAAATTG
26907 ATGAAATTCT
Statistics
Matches: 82, Mismatches: 1, Indels: 5
0.93 0.01 0.06
Matches are distributed among these distances:
51 1 0.01
52 38 0.46
53 43 0.52
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.30
Consensus pattern (53 bp):
GGAACTTTCCCAATTTGAAAAAGAGCTAAATTGGATACTTTAAAAACTTGATG
Found at i:39055 original size:25 final size:25
Alignment explanation
Indices: 39024--39073 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
39014 CAATTTAGGG
39024 AAGACATTTCCAGAACAAGGATGGA
1 AAGACATTTCCAGAACAAGGATGGA
39049 AAGACATTTCCAGAACAAGGATGGA
1 AAGACATTTCCAGAACAAGGATGGA
39074 TATTGAAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.44, C:0.16, G:0.24, T:0.16
Consensus pattern (25 bp):
AAGACATTTCCAGAACAAGGATGGA
Found at i:42963 original size:2 final size:2
Alignment explanation
Indices: 42956--42993 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
42946 AAAAGCTAAT
*
42956 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA GA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
42994 GACTTCATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Done.