Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014793.1 Corchorus olitorius cultivar O-4 contig14826, 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: 153198
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:474 original size:121 final size:127
Alignment explanation
Indices: 227--480 Score: 376
Period size: 121 Copynumber: 2.0 Consensus size: 127
217 TTCATTTAAG
*
227 AAATAAATTTAAAAAATTCTTATATATATAAGTTTTTTAATTAAAATATTAAAATGGTAAAAATA
1 AAATAAATTTAAAAAATTCTTATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT-
* *
292 AAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAATAAAACTGTA
65 --ATA-GTATAAGGATATCAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAATAAAACTATA
357 A
127 A
*
358 AAATATATTTAAAAAATTC-TA-ATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT-
1 AAATAAATTTAAAAAATTCTTATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATA
* *
420 TA-TA-AA-GATATCAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTGAAACTATAA
66 TAGTATAAGGATATCAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAATAAAACTATAA
479 AA
1 AA
481 GTTTAAACAA
Statistics
Matches: 117, Mismatches: 6, Indels: 10
0.88 0.05 0.08
Matches are distributed among these distances:
121 51 0.44
122 2 0.02
123 2 0.02
125 2 0.02
129 40 0.34
130 2 0.02
131 18 0.15
ACGTcount: A:0.51, C:0.02, G:0.10, T:0.37
Consensus pattern (127 bp):
AAATAAATTTAAAAAATTCTTATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATA
TAGTATAAGGATATCAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAATAAAACTATAA
Found at i:622 original size:35 final size:35
Alignment explanation
Indices: 583--669 Score: 149
Period size: 34 Copynumber: 2.5 Consensus size: 35
573 GTATAGATAT
583 ATATGGTAAGTTCAGATTTTTTTTTTTTTAGGTAA
1 ATATGGTAAGTTCAGATTTTTTTTTTTTTAGGTAA
**
618 ATATGGTGGGTTCAGA-TTTTTTTTTTTTAGGTAA
1 ATATGGTAAGTTCAGATTTTTTTTTTTTTAGGTAA
652 ATATGGTAAGTTCAGATT
1 ATATGGTAAGTTCAGATT
670 AACAAAAAGC
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
34 32 0.68
35 15 0.32
ACGTcount: A:0.25, C:0.03, G:0.21, T:0.51
Consensus pattern (35 bp):
ATATGGTAAGTTCAGATTTTTTTTTTTTTAGGTAA
Found at i:10437 original size:6 final size:7
Alignment explanation
Indices: 10420--10450 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
10410 CAAAGTTGGA
10420 TTTTTTC
1 TTTTTTC
10427 TTTTTTC
1 TTTTTTC
10434 TTTTTTC
1 TTTTTTC
*
10441 TTTTTCC
1 TTTTTTC
10448 TTT
1 TTT
10451 CTTGTAACTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTTTC
Found at i:20921 original size:2 final size:2
Alignment explanation
Indices: 20909--20938 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
20899 ACATACATAC
20909 AT AT A- 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 AT AT A
20939 GGTAATACTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:22281 original size:12 final size:12
Alignment explanation
Indices: 22264--22291 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
22254 GGATGGATAG
22264 AAAAAATAAAAT
1 AAAAAATAAAAT
22276 AAAAAATAAAAT
1 AAAAAATAAAAT
22288 AAAA
1 AAAA
22292 TAACCCTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (12 bp):
AAAAAATAAAAT
Found at i:22353 original size:10 final size:10
Alignment explanation
Indices: 22327--22356 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
22317 TGCATGCATG
*
22327 TGAAGGCATA
1 TGAAGGTATA
22337 TGAAGGTATA
1 TGAAGGTATA
22347 TGAAGGTATA
1 TGAAGGTATA
22357 AAAATACACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.40, C:0.03, G:0.30, T:0.27
Consensus pattern (10 bp):
TGAAGGTATA
Found at i:23302 original size:16 final size:16
Alignment explanation
Indices: 23253--23304 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
23243 TTTTTTTCTT
23253 CTTTTCAATCAGTCTG
1 CTTTTCAATCAGTCTG
* **
23269 CTGTTC-ATC-G-AAG
1 CTTTTCAATCAGTCTG
23282 CTTTTCAATCAGTCTG
1 CTTTTCAATCAGTCTG
23298 CTTTTCA
1 CTTTTCA
23305 TCTTTATTTG
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
13 6 0.22
14 4 0.15
15 4 0.15
16 13 0.48
ACGTcount: A:0.19, C:0.25, G:0.13, T:0.42
Consensus pattern (16 bp):
CTTTTCAATCAGTCTG
Found at i:28957 original size:2 final size:2
Alignment explanation
Indices: 28950--28988 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
28940 AAAAGAATGG
28950 AT AT AT AT AT AT 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 AT AT AT AT AT AT A
28989 CCCTTGTCTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:29961 original size:44 final size:42
Alignment explanation
Indices: 29584--30030 Score: 178
Period size: 44 Copynumber: 10.3 Consensus size: 42
29574 AATCAATATA
* *
29584 AAATTTTGATAATCTCCATATAAAATTTTGATAA-CTACACTAT-
1 AAATTTTGATAACCT-CTTATAAAATTTTGATAACCT-C-CTATG
* * * * * * *
29627 AAAGTTTTTATGACAATAC-TATACAATTTCGAGAACCTCCATATA
1 AAA-TTTTGATAAC-CT-CTTATAAAATTTTGATAACCTCC-TATG
* * * * * *
29672 AAATTATGTTAACTTCCCTATAAAATTTTG-TTACACTGCCTATA
1 AAATTTTGATAACCT-CTTATAAAATTTTGATAAC-CT-CCTATG
* * * * *
29716 AAATTTTAATAACCACCTAATAAAATTTTGATAACCACCCTACG
1 AAATTTTGATAACC-TCTTATAAAATTTTGATAACC-TCCTATG
** * * * **
29760 AAATTTTGATAACCTCCCAATGAAATGTTGGTAAGCGCATATTATG
1 AAATTTTGATAACCT-CTTATAAAATTTTGATAA-C-C-TCCTATG
* ** * * * * *
29806 AAATTTTGAT-A-TTCCGATAAAATATTGGTAATCACATAATG
1 AAATTTTGATAACCTCTTATAAAATTTTGATAACCTCCT-ATG
* * * *
29847 AAATTTTGATAACCATATCATGAAATTGTGAT-ACCTCACTATG
1 AAATTTTGATAACC-TCTTATAAAATTTTGATAACCTC-CTATG
*
29890 AAAATTTT-ATAAACCTCCCTATAAAATTTTGATAACCTCCTCATG
1 -AAATTTTGAT-AACCT-CTTATAAAATTTTGATAACCTCCT-ATG
* *
29935 AAATTTTGATAACCATCTTATGAAATTTTGATAACATACCTAT-
1 AAATTTTGATAACC-TCTTATAAAATTTTGATAACCT-CCTATG
* * *
29978 AAATTTTCTATAACCTC--ATAAAATTTTGTTAACCTCCTACG
1 AAATTTT-GATAACCTCTTATAAAATTTTGATAACCTCCTATG
30019 AAATTTTGATAA
1 AAATTTTGATAA
30031 GAACACTATT
Statistics
Matches: 303, Mismatches: 72, Indels: 61
0.69 0.17 0.14
Matches are distributed among these distances:
40 9 0.03
41 36 0.12
42 1 0.00
43 41 0.14
44 173 0.57
45 28 0.09
46 15 0.05
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (42 bp):
AAATTTTGATAACCTCTTATAAAATTTTGATAACCTCCTATG
Found at i:29961 original size:66 final size:65
Alignment explanation
Indices: 29847--29996 Score: 164
Period size: 66 Copynumber: 2.3 Consensus size: 65
29837 TCACATAATG
* *
29847 AAATTTTGATAACCAT-ATCATGAAATTGTGATACCTCACTATGAAAATTTT-ATAAACCTCCCT
1 AAATTTTGATAACC-TCATCATGAAATTGTGATACCTCACTATGAAAATTTTGAT-AACATACCT
29910 AT
64 AT
* * *
29912 AAAATTTTGATAACCTCCTCATGAAATTTTGATAACCATC-TTATG-AAATTTTGATAACATACC
1 -AAATTTTGATAACCTCATCATGAAATTGTGAT-ACC-TCACTATGAAAATTTTGATAACATACC
29975 TAT
63 TAT
*
29978 AAATTTTCTATAACCTCAT
1 AAATTTT-GATAACCTCAT
29997 AAAATTTTGT
Statistics
Matches: 72, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
65 8 0.11
66 53 0.74
67 9 0.12
68 2 0.03
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.37
Consensus pattern (65 bp):
AAATTTTGATAACCTCATCATGAAATTGTGATACCTCACTATGAAAATTTTGATAACATACCTAT
Found at i:29983 original size:21 final size:21
Alignment explanation
Indices: 29584--30030 Score: 132
Period size: 22 Copynumber: 20.6 Consensus size: 21
29574 AATCAATATA
*
29584 AAATTTTGATAATC-TCCATATA
1 AAATTTTGATAA-CATCC-TATG
29606 AAATTTTGATAAC-TACACTAT-
1 AAATTTTGATAACAT-C-CTATG
* * *
29627 AAAGTTTTTATGACAATACTAT-
1 AAA-TTTTGATAAC-ATCCTATG
* * * *
29649 ACAATTTCGAGAACCTCCATATA
1 A-AATTTTGATAACATCC-TATG
* * * *
29672 AAATTATGTTAACTTCCCTATA
1 AAATTTTGATAACAT-CCTATG
* *
29694 AAATTTTG-TTACACTGCCTATA
1 AAATTTTGATAACA-T-CCTATG
* *
29716 AAATTTTAATAACCA-CCTAATA
1 AAATTTTGATAA-CATCCT-ATG
* *
29738 AAATTTTGATAACCACCCTACG
1 AAATTTTGATAA-CATCCTATG
* *
29760 AAATTTTGATAACCTCCCAATG
1 AAATTTTGATAACAT-CCTATG
* * **
29782 AAATGTTGGTAAGCGCATATTATG
1 AAATTTTGATAA---CATCCTATG
* * *
29806 AAATTTTGAT-A-TTCCGATA
1 AAATTTTGATAACATCCTATG
* * *
29825 AAATATTGGTAATCA-CATAATG
1 AAATTTTGATAA-CATCCT-ATG
*
29847 AAATTTTGATAACCAT-ATCATG
1 AAATTTTGATAA-CATCCT-ATG
* *
29869 AAATTGTGAT-ACCTCACTATG
1 AAATTTTGATAACATC-CTATG
* *
29890 AAAATTTT-ATAAACCTCCCTATA
1 -AAATTTTGAT-AACAT-CCTATG
*
29913 AAATTTTGATAACCTCCTCATG
1 AAATTTTGATAACATCCT-ATG
*
29935 AAATTTTGATAACCATCTTATG
1 AAATTTTGATAA-CATCCTATG
29957 AAATTTTGATAACATACCTAT-
1 AAATTTTGATAACAT-CCTATG
* * *
29978 AAATTTTCTATAACCT-C-ATA
1 AAATTTT-GATAACATCCTATG
* * *
29998 AAATTTTGTTAACCTCCTACG
1 AAATTTTGATAACATCCTATG
30019 AAATTTTGATAA
1 AAATTTTGATAA
30031 GAACACTATT
Statistics
Matches: 322, Mismatches: 66, Indels: 75
0.70 0.14 0.16
Matches are distributed among these distances:
19 19 0.06
20 12 0.04
21 46 0.14
22 202 0.63
23 26 0.08
24 15 0.05
25 2 0.01
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (21 bp):
AAATTTTGATAACATCCTATG
Found at i:30157 original size:17 final size:17
Alignment explanation
Indices: 30129--30161 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
30119 CCGTTTTTTT
30129 GTTTTATGTTTTTGCTTC
1 GTTTTATG-TTTTGCTTC
30147 GTTTT-TGTTTTGCTT
1 GTTTTATGTTTTGCTT
30162 TTGTTTTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.53
17 2 0.13
18 5 0.33
ACGTcount: A:0.03, C:0.09, G:0.18, T:0.70
Consensus pattern (17 bp):
GTTTTATGTTTTGCTTC
Found at i:31324 original size:22 final size:21
Alignment explanation
Indices: 31299--31350 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
31289 TTTATAGAAT
31299 TTAACCAT-ACTATCAAATTTTG
1 TTAACC-TCACTAT-AAATTTTG
*
31321 TTAATCTCACTATAAATTTTG
1 TTAACCTCACTATAAATTTTG
* *
31342 ATAAACTCA
1 TTAACCTCA
31351 TTATGAAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 16 0.62
22 10 0.38
ACGTcount: A:0.38, C:0.17, G:0.04, T:0.40
Consensus pattern (21 bp):
TTAACCTCACTATAAATTTTG
Found at i:31339 original size:21 final size:22
Alignment explanation
Indices: 31307--31350 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
31297 ATTTAACCAT
* *
31307 ACTATCAAATTTTGTTAATCTC
1 ACTATCAAATTTTGATAAACTC
31329 ACTAT-AAATTTTGATAAACTC
1 ACTATCAAATTTTGATAAACTC
31350 A
1 A
31351 TTATGAAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.39, C:0.16, G:0.05, T:0.41
Consensus pattern (22 bp):
ACTATCAAATTTTGATAAACTC
Found at i:31625 original size:22 final size:22
Alignment explanation
Indices: 31596--31774 Score: 109
Period size: 22 Copynumber: 8.2 Consensus size: 22
31586 ATAAGCGCAT
31596 TATGAAATTTTGATAACCTCCA
1 TATGAAATTTTGATAACCTCCA
* *
31618 TATAAAATTTCGATAATCAC-CCA
1 TATGAAATTTTGATAA-C-CTCCA
* * **
31641 -ATGAAAGTTTGTTAGTCTCCA
1 TATGAAATTTTGATAACCTCCA
**
31662 TATGAAATTTTGATAACC-AGA
1 TATGAAATTTTGATAACCTCCA
* *
31683 GTATGAAATTTTAAAAATCCTCC-
1 -TATGAAATTTTGATAA-CCTCCA
*
31706 TATGAAATTTTGATAACTTCC-
1 TATGAAATTTTGATAACCTCCA
* * * * * *
31727 CATG-AATTTCGATGATCACCT
1 TATGAAATTTTGATAACCTCCA
*
31748 TATGAAAATTTGATAACCTCCCA
1 TATGAAATTTTGATAACCT-CCA
31771 TATG
1 TATG
31775 GAAGCTCAAA
Statistics
Matches: 113, Mismatches: 34, Indels: 19
0.68 0.20 0.11
Matches are distributed among these distances:
20 12 0.11
21 14 0.12
22 74 0.65
23 12 0.11
24 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.35
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCCA
Found at i:36459 original size:32 final size:33
Alignment explanation
Indices: 36423--36487 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
36413 TTAGCAATTT
*
36423 CTCTATAATGACTTCACA-CTAAAATAAAAGGA
1 CTCTAAAATGACTTCACAGCTAAAATAAAAGGA
*
36455 CTCTAAAATGACTTCATATGCTAAAATAAAAGG
1 CTCTAAAATGACTTCACA-GCTAAAATAAAAGG
36488 CTAATGTGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 16 0.55
34 13 0.45
ACGTcount: A:0.46, C:0.17, G:0.11, T:0.26
Consensus pattern (33 bp):
CTCTAAAATGACTTCACAGCTAAAATAAAAGGA
Found at i:42282 original size:15 final size:16
Alignment explanation
Indices: 42249--42288 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
42239 TTACTTTGCT
42249 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
42265 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
*
42280 TTGCTTTCT
1 TTGTTTTCT
42289 TTCAACCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:43341 original size:21 final size:24
Alignment explanation
Indices: 43312--43362 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 24
43302 TTTTGAACTC
43312 ATTATT-TATTATTTAA-AATATAT
1 ATTATTAT-TTATTTAATAATATAT
43335 -TTATTATTTATTTAATAATATAT
1 ATTATTATTTATTTAATAATATAT
43358 ATTAT
1 ATTAT
43363 ATCTAAGATG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 13 0.52
23 8 0.32
24 4 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
ATTATTATTTATTTAATAATATAT
Found at i:43357 original size:25 final size:25
Alignment explanation
Indices: 43312--43360 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
43302 TTTTGAACTC
*
43312 ATTATTTATTATTTAAAATATATTT
1 ATTATTTATTATATAAAATATATTT
*
43337 ATTATTTATT-TAATAATATATATT
1 ATTATTTATTAT-ATAAAATATATT
43361 ATATCTAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTATTTATTATATAAAATATATTT
Found at i:44832 original size:2 final size:2
Alignment explanation
Indices: 44825--44901 Score: 63
Period size: 2 Copynumber: 39.5 Consensus size: 2
44815 TTCGTACTTT
* * * *
44825 TA TA TA TA GTA TA GA TA -A TA CA TA TA TA TA TG TA TA T- TG TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
44866 -A TGA TA TA TA T- TA CA TA TA TA TA TA TA TA TA TA TA T
1 TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
44902 TTAAAAATAA
Statistics
Matches: 60, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
1 4 0.07
2 52 0.87
3 4 0.07
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (2 bp):
TA
Found at i:45168 original size:42 final size:43
Alignment explanation
Indices: 45117--45210 Score: 138
Period size: 45 Copynumber: 2.2 Consensus size: 43
45107 AGTGCATTAC
*
45117 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCTTCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGGTAATTCATCAAAATAAAG
*
45158 CTAATATTCTACTCCTCCATCTCTAGGTAATTCATCAAAGTAAAG
1 CTAATATTCTA--CCTCCATCTCTAGGTAATTCATCAAAATAAAG
45203 CTAATATT
1 CTAATATT
45211 AATTGCTTGA
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 37 0.79
ACGTcount: A:0.35, C:0.22, G:0.07, T:0.35
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGGTAATTCATCAAAATAAAG
Found at i:46830 original size:2 final size:2
Alignment explanation
Indices: 46817--46870 Score: 76
Period size: 2 Copynumber: 27.5 Consensus size: 2
46807 ACTAAAAATA
*
46817 AT AT AT AGT AT AT AT AT GT AT -T AT A- AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
46858 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
46871 CACTAATACA
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
1 2 0.04
2 43 0.91
3 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:50424 original size:14 final size:14
Alignment explanation
Indices: 50405--50432 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
50395 TTTATTGCTA
50405 ATAAAGTATAAACT
1 ATAAAGTATAAACT
50419 ATAAAGTATAAACT
1 ATAAAGTATAAACT
50433 CTCTATGCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (14 bp):
ATAAAGTATAAACT
Found at i:54730 original size:9 final size:9
Alignment explanation
Indices: 54716--54776 Score: 52
Period size: 9 Copynumber: 6.8 Consensus size: 9
54706 ATTATTTGTA
54716 AATATATAT
1 AATATATAT
54725 AATATATAT
1 AATATATAT
* * *
54734 AACAT-CAC
1 AATATATAT
54742 AATATATAT
1 AATATATAT
*
54751 TATACTATAT
1 AATA-TATAT
* *
54761 AAAATATAA
1 AATATATAT
54770 AATATAT
1 AATATAT
54777 TTAGAAAAAA
Statistics
Matches: 39, Mismatches: 11, Indels: 4
0.72 0.20 0.07
Matches are distributed among these distances:
8 5 0.13
9 27 0.69
10 7 0.18
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.38
Consensus pattern (9 bp):
AATATATAT
Found at i:68498 original size:21 final size:21
Alignment explanation
Indices: 68456--68500 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
68446 TTCCGCCGAT
* *
68456 ACACCATCAACCACCACCACC
1 ACACCATCAACAACCACAACC
* *
68477 ACACCATCTACAACTACAACC
1 ACACCATCAACAACCACAACC
68498 ACA
1 ACA
68501 ACTAGCACAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.42, C:0.49, G:0.00, T:0.09
Consensus pattern (21 bp):
ACACCATCAACAACCACAACC
Found at i:70452 original size:29 final size:30
Alignment explanation
Indices: 70420--70478 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
70410 AAGGAAATGA
*
70420 GAATTAATTTTAAAAGT-ACAATGGTTTGG
1 GAATTAATTTTAAAAATCACAATGGTTTGG
* *
70449 GAATTATTTTTAAAAATCACTATGGTTTGG
1 GAATTAATTTTAAAAATCACAATGGTTTGG
70479 TTAAAAACTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.41
Consensus pattern (30 bp):
GAATTAATTTTAAAAATCACAATGGTTTGG
Found at i:73753 original size:140 final size:139
Alignment explanation
Indices: 73496--73774 Score: 441
Period size: 140 Copynumber: 2.0 Consensus size: 139
73486 AATTGTCCAC
* * * *
73496 ATATATTTTTTTTAGTGACTATGGAAATTATTTAAAGGCCAAATTGATAATTAATATGGTGCCTC
1 ATATATTATTTTTAGTGACTATGGAAATTACTTAAAGGCCAAATTGAGAATTAATATGGTGCCAC
*
73561 CTTTTGACTTTTTTTTTGTATTTTCTCACTTTTCGGGTGACTAAAAACGCCCTCGATGAAATTTC
66 CTTTTGACTTTTTTTTGGTATTTTCTCACTTTTCGGGTGACTAAAAACGCCCTCGATG-AATTTC
73626 CGCCCTTACT
130 CGCCCTTACT
* *
73636 ATATATTATTTTTAGTGACTATGGAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGTGCCAC
1 ATATATTATTTTTAGTGACTATGGAAATTACTTAAAGGCCAAATTGAGAATTAATATGGTGCCAC
* * *
73701 CTTTTGGCTTTTTTTTGGTCTTTTCTCACTTTTCGGGTGACTAAAAATGCCCTCGATGAATTTCC
66 CTTTTGACTTTTTTTTGGTATTTTCTCACTTTTCGGGTGACTAAAAACGCCCTCGATGAATTTCC
* *
73766 TCTCTTACT
131 GCCCTTACT
73775 TTTCCTGCTG
Statistics
Matches: 127, Mismatches: 12, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
139 14 0.11
140 113 0.89
ACGTcount: A:0.25, C:0.17, G:0.16, T:0.42
Consensus pattern (139 bp):
ATATATTATTTTTAGTGACTATGGAAATTACTTAAAGGCCAAATTGAGAATTAATATGGTGCCAC
CTTTTGACTTTTTTTTGGTATTTTCTCACTTTTCGGGTGACTAAAAACGCCCTCGATGAATTTCC
GCCCTTACT
Found at i:75902 original size:18 final size:18
Alignment explanation
Indices: 75876--75910 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
75866 CAAAAAAAGA
75876 CTACTAAAATAA-AATTC
1 CTACTAAAATAAGAATTC
75893 CTACTAAAAATAAGAATT
1 CTACT-AAAATAAGAATT
75911 TTTAACAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 7 0.44
19 4 0.25
ACGTcount: A:0.54, C:0.14, G:0.03, T:0.29
Consensus pattern (18 bp):
CTACTAAAATAAGAATTC
Found at i:76144 original size:24 final size:22
Alignment explanation
Indices: 76109--76162 Score: 65
Period size: 24 Copynumber: 2.4 Consensus size: 22
76099 GGGAGCGCCA
*
76109 GTGG-GAGCGGTGGGAGGAGCAG
1 GTGGAGAGCGGTGGGAGAAGC-G
76131 GTGGAGAGCTGGTGGGAGAAGCG
1 GTGGAGAGC-GGTGGGAGAAGCG
76154 GTAGGAGAG
1 GT-GGAGAG
76163 GATGTGGGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 4 0.14
23 7 0.25
24 17 0.61
ACGTcount: A:0.22, C:0.07, G:0.59, T:0.11
Consensus pattern (22 bp):
GTGGAGAGCGGTGGGAGAAGCG
Found at i:76195 original size:21 final size:22
Alignment explanation
Indices: 76160--76205 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
76150 AGCGGTAGGA
*
76160 GAGGATGTGGGGGTTGA-GGTTG
1 GAGGATGTGGCGGTTGACGG-TG
76182 GAGGA-GTGGCGGTTGACGGTG
1 GAGGATGTGGCGGTTGACGGTG
76203 GAG
1 GAG
76206 AGGCGGTTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.15, C:0.04, G:0.59, T:0.22
Consensus pattern (22 bp):
GAGGATGTGGCGGTTGACGGTG
Found at i:76218 original size:12 final size:12
Alignment explanation
Indices: 76201--76241 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
76191 CGGTTGACGG
76201 TGGAGAGGCGGT
1 TGGAGAGGCGGT
76213 TGGAGAGGCGGT
1 TGGAGAGGCGGT
* *
76225 TGGGGAAGCGGT
1 TGGAGAGGCGGT
*
76237 GGGAG
1 TGGAG
76242 TCACAGGAGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.17, C:0.07, G:0.61, T:0.15
Consensus pattern (12 bp):
TGGAGAGGCGGT
Found at i:96038 original size:1 final size:1
Alignment explanation
Indices: 96032--96061 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
96022 GATTACAATT
96032 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
96062 CCATAATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:106219 original size:13 final size:13
Alignment explanation
Indices: 106201--106227 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
106191 TTCTCAAGCT
106201 TATCATCTTCATA
1 TATCATCTTCATA
106214 TATCATCTTCATA
1 TATCATCTTCATA
106227 T
1 T
106228 GTTTTGAAAT
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:0.30, C:0.22, G:0.00, T:0.48
Consensus pattern (13 bp):
TATCATCTTCATA
Found at i:106858 original size:22 final size:23
Alignment explanation
Indices: 106820--106865 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
106810 TTATTATTCT
*
106820 CCCTTGATATTTTTTACAGCTCA
1 CCCTTGATAGTTTTTACAGCTCA
106843 CCCTTGAT-GTTTTTACAGCTCA
1 CCCTTGATAGTTTTTACAGCTCA
106865 C
1 C
106866 AAAAGACCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.20, C:0.28, G:0.11, T:0.41
Consensus pattern (23 bp):
CCCTTGATAGTTTTTACAGCTCA
Found at i:131922 original size:24 final size:24
Alignment explanation
Indices: 131856--131912 Score: 114
Period size: 24 Copynumber: 2.4 Consensus size: 24
131846 CTTTTTTCGT
131856 TGTGTCTCTTGTGGGTCTTTCCTC
1 TGTGTCTCTTGTGGGTCTTTCCTC
131880 TGTGTCTCTTGTGGGTCTTTCCTC
1 TGTGTCTCTTGTGGGTCTTTCCTC
131904 TGTGTCTCT
1 TGTGTCTCT
131913 CTTTGGTCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.00, C:0.25, G:0.25, T:0.51
Consensus pattern (24 bp):
TGTGTCTCTTGTGGGTCTTTCCTC
Found at i:136028 original size:12 final size:12
Alignment explanation
Indices: 136011--136041 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
136001 TACCCTATGT
136011 AAACACGACACG
1 AAACACGACACG
136023 AAACACGACACG
1 AAACACGACACG
136035 AAACACG
1 AAACACG
136042 GATTGCCAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.52, C:0.32, G:0.16, T:0.00
Consensus pattern (12 bp):
AAACACGACACG
Found at i:136118 original size:30 final size:30
Alignment explanation
Indices: 136082--136141 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
136072 AAAGTTCGTG
*
136082 TTTGAAGACCTATTGAAG-ATAATTTGAAGA
1 TTTGAAGACC-ATTGAAGAATAATTTCAAGA
136112 TTTGAAGACCATTGAAGAATAATTTCAAGA
1 TTTGAAGACCATTGAAGAATAATTTCAAGA
136142 AGCAAGAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 7 0.25
30 21 0.75
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32
Consensus pattern (30 bp):
TTTGAAGACCATTGAAGAATAATTTCAAGA
Found at i:137515 original size:22 final size:22
Alignment explanation
Indices: 137465--137517 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
137455 TGCTTTCTGA
*
137465 TTAATTGTTTTCTTTAATTTTC
1 TTAATTGTTTTCTTTAATATTC
*
137487 TTGATTGTTTTC-TTAGATAATT-
1 TTAATTGTTTTCTTTA-AT-ATTC
137509 TTAATTGTT
1 TTAATTGTT
137518 AGATTGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 3 0.12
22 21 0.81
23 2 0.08
ACGTcount: A:0.21, C:0.06, G:0.09, T:0.64
Consensus pattern (22 bp):
TTAATTGTTTTCTTTAATATTC
Found at i:144658 original size:21 final size:20
Alignment explanation
Indices: 144634--144672 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
144624 TATTAAAAGA
144634 TAAAAAGAAATTAAAAAAATC
1 TAAAAAG-AATTAAAAAAATC
*
144655 TAAAAAGATTTAAAAAAA
1 TAAAAAGAATTAAAAAAA
144673 ACGCAGGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.72, C:0.03, G:0.05, T:0.21
Consensus pattern (20 bp):
TAAAAAGAATTAAAAAAATC
Found at i:144836 original size:7 final size:7
Alignment explanation
Indices: 144805--144849 Score: 56
Period size: 7 Copynumber: 6.6 Consensus size: 7
144795 TTCTGGGTTC
144805 TTTTTGT
1 TTTTTGT
* *
144812 TTTCTGC
1 TTTTTGT
*
144819 GTTTT-T
1 TTTTTGT
144825 TTTTTGT
1 TTTTTGT
144832 TTTTTGT
1 TTTTTGT
144839 TTTTTGT
1 TTTTTGT
144846 TTTT
1 TTTT
144850 ATCTTTTTAG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
6 4 0.13
7 27 0.87
ACGTcount: A:0.00, C:0.04, G:0.13, T:0.82
Consensus pattern (7 bp):
TTTTTGT
Found at i:144843 original size:20 final size:20
Alignment explanation
Indices: 144805--144868 Score: 56
Period size: 20 Copynumber: 3.0 Consensus size: 20
144795 TTCTGGGTTC
* **
144805 TTTTTGTTTTCTGCGTTTTT
1 TTTTTGTTTTTTGTTTTTTT
144825 TTTTTGTTTTTTGTTTTTTGT
1 TTTTTGTTTTTTGTTTTTT-T
* *
144846 TTTTATCTTTTTAGATTTTTTT
1 TTTT-TGTTTTTTG-TTTTTTT
144868 T
1 T
144869 AATTTCTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 16 0.44
21 5 0.14
22 9 0.25
23 6 0.17
ACGTcount: A:0.05, C:0.05, G:0.11, T:0.80
Consensus pattern (20 bp):
TTTTTGTTTTTTGTTTTTTT
Found at i:144857 original size:14 final size:14
Alignment explanation
Indices: 144804--144849 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
144794 TTTCTGGGTT
*
144804 CTTTTTGTTTTCTG
1 CTTTTTGTTTTTTG
*
144818 CGTTTT-TTTTTTG
1 CTTTTTGTTTTTTG
*
144831 TTTTTTGTTTTTTG
1 CTTTTTGTTTTTTG
144845 -TTTTT
1 CTTTTT
144850 ATCTTTTTAG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
13 15 0.56
14 12 0.44
ACGTcount: A:0.00, C:0.07, G:0.13, T:0.80
Consensus pattern (14 bp):
CTTTTTGTTTTTTG
Found at i:147071 original size:28 final size:28
Alignment explanation
Indices: 147034--147099 Score: 132
Period size: 28 Copynumber: 2.4 Consensus size: 28
147024 TTGCACCCAC
147034 TAATGCTCTTTTTTTTTTCAAAAATTAA
1 TAATGCTCTTTTTTTTTTCAAAAATTAA
147062 TAATGCTCTTTTTTTTTTCAAAAATTAA
1 TAATGCTCTTTTTTTTTTCAAAAATTAA
147090 TAATGCTCTT
1 TAATGCTCTT
147100 ATTGTTATGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.30, C:0.12, G:0.05, T:0.53
Consensus pattern (28 bp):
TAATGCTCTTTTTTTTTTCAAAAATTAA
Found at i:147357 original size:22 final size:24
Alignment explanation
Indices: 147322--147375 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 24
147312 ATAAATGTTG
* *
147322 CTGATAA-TCTTCT-CTTTTATCT
1 CTGATAATTCTTCTCCATTTATCA
147344 CTGATAATTC-TCTCCATTTATCA
1 CTGATAATTCTTCTCCATTTATCA
147367 CTTGATAAT
1 C-TGATAAT
147376 ATATTGCCAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 10 0.37
23 10 0.37
24 7 0.26
ACGTcount: A:0.24, C:0.22, G:0.06, T:0.48
Consensus pattern (24 bp):
CTGATAATTCTTCTCCATTTATCA
Found at i:152869 original size:67 final size:64
Alignment explanation
Indices: 152743--152889 Score: 223
Period size: 59 Copynumber: 2.3 Consensus size: 64
152733 CAATCTTGGG
152743 ATGACAACTTCTGGTGTCAATAATTTCCTCAGCATGACAACTTCTGGTGTCAAGATAATAATTTG
1 ATGACAACTTCTGGTGTCAATAATTT-CT-A-CATGACAACTTCTGGTGTCAAGATAATAATTTG
152808 AT
63 AT
*
152810 ATGACAACTTCTGGTGTCAATAATTT-T-CATGACAACTTCTGGTGTCAAG---ATAATTTAAT
1 ATGACAACTTCTGGTGTCAATAATTTCTACATGACAACTTCTGGTGTCAAGATAATAATTTGAT
152869 ATGACAACTTCTGGTGTCAAT
1 ATGACAACTTCTGGTGTCAAT
152890 TAAATTTTAA
Statistics
Matches: 79, Mismatches: 1, Indels: 8
0.90 0.01 0.09
Matches are distributed among these distances:
59 30 0.38
62 22 0.28
65 1 0.01
67 26 0.33
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.35
Consensus pattern (64 bp):
ATGACAACTTCTGGTGTCAATAATTTCTACATGACAACTTCTGGTGTCAAGATAATAATTTGAT
Found at i:152876 original size:31 final size:30
Alignment explanation
Indices: 152776--152888 Score: 151
Period size: 31 Copynumber: 3.7 Consensus size: 30
152766 TTTCCTCAGC
152776 ATGACAACTTCTGGTGTCAAGATAATAATTTGAT
1 ATGACAACTTCTGGTGTCAAG---ATAATTT-AT
152810 ATGACAACTTCTGGTGTC-A-ATAATTT-T
1 ATGACAACTTCTGGTGTCAAGATAATTTAT
152837 CATGACAACTTCTGGTGTCAAGATAATTTAAT
1 -ATGACAACTTCTGGTGTCAAGATAATTT-AT
152869 ATGACAACTTCTGGTGTCAA
1 ATGACAACTTCTGGTGTCAA
152889 TTAAATTTTA
Statistics
Matches: 74, Mismatches: 0, Indels: 13
0.85 0.00 0.15
Matches are distributed among these distances:
27 1 0.01
28 18 0.24
29 8 0.11
30 7 0.09
31 20 0.27
32 1 0.01
33 1 0.01
34 18 0.24
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (30 bp):
ATGACAACTTCTGGTGTCAAGATAATTTAT
Done.