Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020397.1 Corchorus olitorius cultivar O-4 contig20430, 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: 90960
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:803 original size:29 final size:30
Alignment explanation
Indices: 757--816 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
747 AAAAAATCTT
757 TTATGTTTTTCTTCGGGACAAAATAATCCC
1 TTATGTTTTTCTTCGGGACAAAATAATCCC
* *
787 TTATGTTTTT-TTTGGGACAAATTAATCCC
1 TTATGTTTTTCTTCGGGACAAAATAATCCC
816 T
1 T
817 GTTTAAAGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
29 18 0.64
30 10 0.36
ACGTcount: A:0.25, C:0.17, G:0.13, T:0.45
Consensus pattern (30 bp):
TTATGTTTTTCTTCGGGACAAAATAATCCC
Found at i:1033 original size:29 final size:30
Alignment explanation
Indices: 965--1021 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
955 GTCAGCAAGT
*
965 GATTATTTTGTCAAAAAAAAAATCATAAGC
1 GATTATTTTGTCAAAAAAAAAAGCATAAGC
* *
995 AATTATTTTGTC-CAAAAAAAAGCATAA
1 GATTATTTTGTCAAAAAAAAAAGCATAA
1022 AGGATTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 13 0.54
30 11 0.46
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.30
Consensus pattern (30 bp):
GATTATTTTGTCAAAAAAAAAAGCATAAGC
Found at i:1625 original size:27 final size:28
Alignment explanation
Indices: 1595--1663 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
1585 ACTAAATACC
1595 CAAAA-AATCCCTTATG-TTTTTTTGGGA
1 CAAAATAAT-CCTTATGTTTTTTTTGGGA
*
1622 CAAAATAATCTTTATGTTTTTTTTGGGA
1 CAAAATAATCCTTATGTTTTTTTTGGGA
1650 CAAAATAATTCCTT
1 CAAAATAA-TCCTT
1664 GCTGACGTGG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
27 11 0.30
28 22 0.59
29 4 0.11
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (28 bp):
CAAAATAATCCTTATGTTTTTTTTGGGA
Found at i:4159 original size:15 final size:15
Alignment explanation
Indices: 4139--4167 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4129 TATATAGTAG
4139 TAAGATAAGATAATA
1 TAAGATAAGATAATA
4154 TAAGATAAGATAAT
1 TAAGATAAGATAAT
4168 GTGGTGGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.59, C:0.00, G:0.14, T:0.28
Consensus pattern (15 bp):
TAAGATAAGATAATA
Found at i:14483 original size:22 final size:23
Alignment explanation
Indices: 14444--14489 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
14434 AATTCACTAT
14444 TTTTATATTTATGATTAAGTGTG
1 TTTTATATTTATGATTAAGTGTG
*
14467 TTTTA-ATTATAT-ATTAATTGTG
1 TTTTATATT-TATGATTAAGTGTG
14489 T
1 T
14490 GTGGATATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.28, C:0.00, G:0.13, T:0.59
Consensus pattern (23 bp):
TTTTATATTTATGATTAAGTGTG
Found at i:15836 original size:45 final size:45
Alignment explanation
Indices: 15772--15868 Score: 142
Period size: 45 Copynumber: 2.2 Consensus size: 45
15762 AACAGCAATT
* * *
15772 AATATTAGCTTTACTTTGATGAATTATATAGAGATGTAGGAGTAG
1 AATATTAGCTTTACTTTGATGAATTACATAGAAATGGAGGAGTAG
* *
15817 AATATTAGCTTTATTTTGATGAATTACCTAGAAATGGAGGAGTAG
1 AATATTAGCTTTACTTTGATGAATTACATAGAAATGGAGGAGTAG
15862 AAT-TTAG
1 AATATTAG
15869 GTAATGCACT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 4 0.09
45 43 0.91
ACGTcount: A:0.36, C:0.05, G:0.22, T:0.37
Consensus pattern (45 bp):
AATATTAGCTTTACTTTGATGAATTACATAGAAATGGAGGAGTAG
Found at i:17757 original size:23 final size:23
Alignment explanation
Indices: 17729--17772 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
17719 AACAGCTCTG
17729 TCTCTCTCTCTATATATATATAT
1 TCTCTCTCTCTATATATATATAT
17752 TCTCTCTCTCTATATATATAT
1 TCTCTCTCTCTATATATATAT
17773 CCATCTACTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.25, C:0.23, G:0.00, T:0.52
Consensus pattern (23 bp):
TCTCTCTCTCTATATATATATAT
Found at i:18501 original size:20 final size:20
Alignment explanation
Indices: 18476--18514 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
18466 AATCGCATCA
18476 CTTTTATGACTTTTGAGTTG
1 CTTTTATGACTTTTGAGTTG
18496 CTTTTATGACTTTTGAGTT
1 CTTTTATGACTTTTGAGTT
18515 TTCAGATCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.10, G:0.18, T:0.56
Consensus pattern (20 bp):
CTTTTATGACTTTTGAGTTG
Found at i:19837 original size:16 final size:16
Alignment explanation
Indices: 19816--19847 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
19806 TAACACTAAA
19816 TTAACCCCCAAGGCCC
1 TTAACCCCCAAGGCCC
19832 TTAACCCCCAAGGCCC
1 TTAACCCCCAAGGCCC
19848 ACTAACTCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.50, G:0.12, T:0.12
Consensus pattern (16 bp):
TTAACCCCCAAGGCCC
Found at i:19853 original size:17 final size:16
Alignment explanation
Indices: 19817--19853 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
19807 AACACTAAAT
*
19817 TAACCCCCAAGGCCCT
1 TAACCCCCAAGGCCCC
19833 TAACCCCCAAGGCCCAC
1 TAACCCCCAAGGCCC-C
19850 TAAC
1 TAAC
19854 TCTGTCCACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.30, C:0.49, G:0.11, T:0.11
Consensus pattern (16 bp):
TAACCCCCAAGGCCCC
Found at i:21811 original size:2 final size:2
Alignment explanation
Indices: 21804--21846 Score: 50
Period size: 2 Copynumber: 19.5 Consensus size: 2
21794 TATTGTTATC
21804 TA TA TA TA TA TA TA TGA TA TA TA TGA TA TGA TA TA TGA TA TA T
1 TA TA TA TA TA TA TA T-A TA TA TA T-A TA T-A TA TA T-A TA TA T
21847 GATACTAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
2 29 0.78
3 8 0.22
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (2 bp):
TA
Found at i:21825 original size:7 final size:7
Alignment explanation
Indices: 21807--21850 Score: 65
Period size: 7 Copynumber: 6.4 Consensus size: 7
21797 TGTTATCTAT
21807 ATATAT-
1 ATATATG
21813 ATATATG
1 ATATATG
21820 ATATAT-
1 ATATATG
21826 ATGATATG
1 AT-ATATG
21834 ATATATG
1 ATATATG
21841 ATATATG
1 ATATATG
21848 ATA
1 ATA
21851 CTAATAACTT
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
6 8 0.23
7 25 0.71
8 2 0.06
ACGTcount: A:0.45, C:0.00, G:0.11, T:0.43
Consensus pattern (7 bp):
ATATATG
Found at i:21837 original size:19 final size:17
Alignment explanation
Indices: 21804--21850 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 17
21794 TATTGTTATC
21804 TATATAT-ATATATATGA
1 TATATATGATATATAT-A
21821 TATATATGATATGATATA
1 TATATATGATAT-ATATA
21839 TGATATATGATA
1 T-ATATATGATA
21851 CTAATAACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.26
18 6 0.22
19 14 0.52
ACGTcount: A:0.45, C:0.00, G:0.11, T:0.45
Consensus pattern (17 bp):
TATATATGATATATATA
Found at i:23895 original size:334 final size:327
Alignment explanation
Indices: 23324--24649 Score: 1165
Period size: 334 Copynumber: 4.0 Consensus size: 327
23314 CAATAACTGT
* * * *
23324 GATTTGCTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAACCATGCAAAATTGAA-
1 GATTTGATTAGATGAATATAGATATTTCAAGGAGTC-TGACGCCAAAAATCATGCAAAACT-AAG
* * * * * * *
23388 CCGGACCCCGGAACACGTTTTTAGCTAAAAACCGTGATGATTATTATACGA-TTTCAGGTAAAAT
64 CCGGATCCCGGAACACGTTTTTAGCCAAAAATCGTGATGGTTATTACACGATTTTGA-CTAAAAT
* * *** *
23452 TTTGCAAAAAATGAACCGAAAGA-TATTTCCTTAATTTTTAGCCCCAATACTCATAAAAAATATA
128 TTTGCAAAAAATG-ACCGAAA-ATTATTTCCTCAATTTTTGGCAAAAATAATCATAAAAAATATA
* * *
23516 TAATTTTACACCAAAAATATTGAAAGGTTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCT
191 TAATTTAACACCAAAAAGATTG-AAGGTTTTTCACGTTTTTAATATCGTTTTTCATATTTTTTCT
* * *
23581 GAATTAATTTCTTATTAAATCAAAACAAGATTTAGATGCTCGTAAAAACAAATCCTCAAATGCAA
255 GAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCT-AAATCCAA
*
23646 TGTGGCTAA
319 TGTGGCTGA
23655 GACTTT-ATTAGATGAATATAGATATTTCAAGGAGTCTCGACGCCAAAAATCATGCAAAACTAAG
1 GA-TTTGATTAGATGAATATAGATATTTCAAGGAGTCT-GACGCCAAAAATCATGCAAAACTAAG
* * *
23719 CCAGGATCCCGAAACCCGTTTTTAGCCAAAAAATCGTGATGGTTAGTACACGATTTTGACTAAAA
64 CC-GGATCCCGGAACACGTTTTTAGCC-AAAAATCGTGATGGTTATTACACGATTTTGACTAAAA
* *
23784 TTTTGCAAGAAAATGACCTGAAAATTTTTTCCTCAATTTTTGGAAAAAATAATCATAAAATAA-A
127 TTTTGCAA-AAAATGACC-GAAAATTATTTCCTCAATTTTTGGCAAAAATAATCATAAAA-AATA
* ***
23848 AATAATTTAACACCAAAAAGATTTG-AGGACAATTCACGTTTTTAATATCGTTTTTTCATA-TTT
189 TATAATTTAACACCAAAAAGA-TTGAAGG-TTTTTCACGTTTTTAATATCG-TTTTTCATATTTT
*
23911 TTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAA-AAATTCTTAAAT
251 TTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAA-TCCTAAAT
**
23975 CCAATGTAACTGA
315 CCAATGTGGCTGA
* * * * *
23988 GATTTGATTAGATGAATATGGATATCTCAAGGAGTCTTAGTGCCAAAAATCATGCAAAACTGAGC
1 GATTTGATTAGATGAATATAGATATTTCAAGGAGTCTGA-CGCCAAAAATCATGCAAAACTAAGC
* * * * *
24053 CGG-TGCCTCGGAACGCTTTTTTAGCCAAAAATGGTGATGGTTATTACACGATTTCGGCTAAAAT
65 CGGAT-CC-CGGAACACGTTTTTAGCCAAAAATCGTGATGGTTATTACACGATTTTGACTAAAAT
* ** * *
24117 TTTGTAAAAAAAAAAAACCCAAAAGTTATTTCCTCAATTTTTGGCTAAAATAATCATAAAAAATA
128 TTTG---CAAAAAATGACCGAAAA-TTATTTCCTCAATTTTTGGCAAAAATAATCATAAAAAATA
* ** * *
24182 TATATTTTAATGCCAAAAAGATTGAAGGGTTTTTGACGCATTTTCAATATCGTTTTTC-TATTTT
189 TATAATTTAACACCAAAAAGATTGAA-GGTTTTTCACG--TTTTTAATATCGTTTTTCATATTTT
* **
24246 TT-T-AATTAA--T-TAATTAAATCGAAACAAGATTAAGATGCTAATAAAAACAAATCCATAAAT
251 TTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCC-TAAAT
* * *
24306 TCTATGTGGTTGA
315 CCAATGTGGCTGA
* * * * * *
24319 GATTTGATTAGATGAA-GTAG---TCTC--GGAG--T-----CAAAAGTCATGCAAAATTGAGGC
1 GATTTGATTAGATGAATATAGATATTTCAAGGAGTCTGACGCCAAAAATCATGCAAAACTAAGCC
* * * * * * ** * *
24371 GGGTCCCCGGAACGCATTTTTAGCCAAAAACCGTGATTGTTAGTTAGTAC-ATGAACTCAGCTAG
66 GGAT-CCCGGAACACGTTTTTAGCCAAAAATCGTGATGGTTA-TTA-CACGAT--TTTGA-CTAA
* * * * * * *
24435 ATTTTTGCAAAAATTGACACGAAAGGTT-TCTCCTCAATTTATGGCTAAAA-ACTCAT-AAAAAT
125 AATTTTGCAAAAAATGAC-CGAAA-ATTATTTCCTCAATTTTTGGCAAAAATAATCATAAAAAAT
* * * * * * *
24497 ATATAATTCAACGCCAAAAAGA-TG-GGGGTTTTCACGCTTTTAATATCGTATTTCTTA-TTTTT
188 ATATAATTTAACACCAAAAAGATTGAAGGTTTTTCACGTTTTTAATATCGTTTTTCATATTTTTT
* * * * *
24559 CTAAATTAATTTCTAATTAAATGGAAACAAAATTCAGATGCTCGTAAAAACAAATTCTTAAATCC
253 CTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAA-TCCTAAATCC
*
24624 AATGTTGCTGA
317 AATGTGGCTGA
* *
24635 AATTTGGTTAGATGA
1 GATTTGATTAGATGA
24650 TGTAAAGTAT
Statistics
Matches: 829, Mismatches: 121, Indels: 105
0.79 0.11 0.10
Matches are distributed among these distances:
311 20 0.02
312 3 0.00
313 15 0.02
315 3 0.00
316 88 0.11
317 60 0.07
318 35 0.04
319 8 0.01
321 9 0.01
323 1 0.00
325 4 0.00
327 4 0.00
330 41 0.05
331 87 0.10
332 69 0.08
333 142 0.17
334 200 0.24
335 29 0.03
336 11 0.01
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.33
Consensus pattern (327 bp):
GATTTGATTAGATGAATATAGATATTTCAAGGAGTCTGACGCCAAAAATCATGCAAAACTAAGCC
GGATCCCGGAACACGTTTTTAGCCAAAAATCGTGATGGTTATTACACGATTTTGACTAAAATTTT
GCAAAAAATGACCGAAAATTATTTCCTCAATTTTTGGCAAAAATAATCATAAAAAATATATAATT
TAACACCAAAAAGATTGAAGGTTTTTCACGTTTTTAATATCGTTTTTCATATTTTTTCTGAATTA
ATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTAAATCCAATGTGGCT
GA
Found at i:25039 original size:15 final size:16
Alignment explanation
Indices: 25002--25053 Score: 56
Period size: 15 Copynumber: 3.3 Consensus size: 16
24992 AAGTTTCTTG
*
25002 ATTATAAAT-AATAAT
1 ATTATAATTAAATAAT
25017 ATTATAATTAAAT-AT
1 ATTATAATTAAATAAT
25032 ATTATAATCTAAA-AAT
1 ATTATAAT-TAAATAAT
25048 AATTAT
1 -ATTAT
25054 TAGAAGTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
15 18 0.56
16 9 0.28
17 5 0.16
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTATAATTAAATAAT
Found at i:25310 original size:2 final size:2
Alignment explanation
Indices: 25303--25331 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
25293 ATAAGATAAG
25303 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 A
25332 CTAATTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27423 original size:120 final size:120
Alignment explanation
Indices: 27210--27452 Score: 468
Period size: 120 Copynumber: 2.0 Consensus size: 120
27200 CAGACAAAAA
27210 AAATCTTTCATTACTTTGAGCTCGTCCTCTAATTCTCGAACCCTCTCATCGTAATCACCCCTATC
1 AAATCTTTCATTACTTTGAGCTCGTCCTCTAATTCTCGAACCCTCTCATCGTAATCACCCCTATC
* *
27275 TTTTTTAAAGCATAACCAAAGGTAGCCATACAATATTTCAACCCCTATCTTTTTT
66 TTTTCTAAAGCATAACCAAAGATAGCCATACAATATTTCAACCCCTATCTTTTTT
27330 AAATCTTTCATTACTTTGAGCTCGTCCTCTAATTCTCGAACCCTCTCATCGTAATCACCCCTATC
1 AAATCTTTCATTACTTTGAGCTCGTCCTCTAATTCTCGAACCCTCTCATCGTAATCACCCCTATC
27395 TTTTCTAAAGCATAACCAAAGATAGCCATACAATATTTCAACCCCTATCTTTTTT
66 TTTTCTAAAGCATAACCAAAGATAGCCATACAATATTTCAACCCCTATCTTTTTT
27450 AAA
1 AAA
27453 GCATAACCAA
Statistics
Matches: 121, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 121 1.00
ACGTcount: A:0.29, C:0.28, G:0.07, T:0.36
Consensus pattern (120 bp):
AAATCTTTCATTACTTTGAGCTCGTCCTCTAATTCTCGAACCCTCTCATCGTAATCACCCCTATC
TTTTCTAAAGCATAACCAAAGATAGCCATACAATATTTCAACCCCTATCTTTTTT
Found at i:27458 original size:49 final size:49
Alignment explanation
Indices: 27386--27484 Score: 171
Period size: 49 Copynumber: 2.0 Consensus size: 49
27376 CATCGTAATC
27386 ACCCCTATCTTTTCTAAAGCATAACCAAAGATAGCCATACAATATTTCA
1 ACCCCTATCTTTTCTAAAGCATAACCAAAGATAGCCATACAATATTTCA
* * *
27435 ACCCCTATCTTTTTTAAAGCATAACCAAAGGTAGTCATACAATATTTCA
1 ACCCCTATCTTTTCTAAAGCATAACCAAAGATAGCCATACAATATTTCA
27484 A
1 A
27485 GTGTTGTTCA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.38, C:0.24, G:0.07, T:0.30
Consensus pattern (49 bp):
ACCCCTATCTTTTCTAAAGCATAACCAAAGATAGCCATACAATATTTCA
Found at i:27571 original size:14 final size:14
Alignment explanation
Indices: 27552--27579 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
27542 CAAGTTTTGT
27552 TGTATGTAGCAACC
1 TGTATGTAGCAACC
27566 TGTATGTAGCAACC
1 TGTATGTAGCAACC
27580 CAAGTTTTAA
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:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (14 bp):
TGTATGTAGCAACC
Found at i:29481 original size:6 final size:6
Alignment explanation
Indices: 29470--29516 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
29460 AGATTGACTA
* * *
29470 ATCTAT ATCTAT ATCTAT ATTTAT ATTTAT AT-TAT ATATAT A-CTAT
1 ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT
29516 A
1 A
29517 GTAAAAAGTA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
5 9 0.24
6 29 0.76
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (6 bp):
ATCTAT
Found at i:29799 original size:127 final size:127
Alignment explanation
Indices: 29605--29859 Score: 431
Period size: 127 Copynumber: 2.0 Consensus size: 127
29595 TTGTTTAAAC
* *
29605 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTATTTAATTAAATCTAATATCCTTATAACTAT
1 TTTTATAATTTTACTCAACTAAAAACTCTATTTTATTTAATAAAATCTAATATCCTTATAACTAT
* *
29670 TTTATTTTTACCATTTTACTATTTTAATTAAAAAACTT-ATATATTAGAATTTTTAATATAT
66 TTTATTTTTACCATTTTACTAATTTAATTAAAAAACTTAATATATTAGAATTTTTAAAATAT
* *
29731 TTTTATAATTTTACTCAACTAAAAACTCTATTTCTATTTAATAAAATCTAATATCTTTATACCTA
1 TTTTATAATTTTACTCAACTAAAAACTCTATTT-TATTTAATAAAATCTAATATCCTTATAACTA
29796 TTTTATTTTTACCATTTTACTAATTTAATTAAAAAACTTAGATATATTAGAATTTTTAAAATAT
65 TTTTATTTTTACCATTTTACTAATTTAATTAAAAAACTTA-ATATATTAGAATTTTTAAAATAT
29860 ATTTCTTAAA
Statistics
Matches: 120, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
126 32 0.27
127 66 0.55
129 22 0.18
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (127 bp):
TTTTATAATTTTACTCAACTAAAAACTCTATTTTATTTAATAAAATCTAATATCCTTATAACTAT
TTTATTTTTACCATTTTACTAATTTAATTAAAAAACTTAATATATTAGAATTTTTAAAATAT
Found at i:30971 original size:19 final size:18
Alignment explanation
Indices: 30944--30987 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
30934 GAAGTTTAAC
*
30944 AAATTTAATCATAATATA
1 AAATTTAATAATAATATA
30962 AAATTATAATAATAATATA
1 AAATT-TAATAATAATATA
*
30981 AATTTTA
1 AAATTTA
30988 TTGAATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (18 bp):
AAATTTAATAATAATATA
Found at i:30995 original size:19 final size:19
Alignment explanation
Indices: 30944--30982 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
30934 GAAGTTTAAC
*
30944 AAATT-TAATCATAATATA
1 AAATTATAATAATAATATA
30962 AAATTATAATAATAATATA
1 AAATTATAATAATAATATA
30981 AA
1 AA
30983 TTTTATTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (19 bp):
AAATTATAATAATAATATA
Found at i:32141 original size:12 final size:12
Alignment explanation
Indices: 32126--32152 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
32116 TGAAAATTAT
32126 AATAATAATTGA
1 AATAATAATTGA
32138 AATAATAATTGA
1 AATAATAATTGA
32150 AAT
1 AAT
32153 TTATTATACG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.33
Consensus pattern (12 bp):
AATAATAATTGA
Found at i:35438 original size:22 final size:23
Alignment explanation
Indices: 35412--35465 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
35402 TTATATTATT
35412 ATATATATATTATTTA-GAAATA
1 ATATATATATTATTTATGAAATA
* * *
35434 ATATAGATA-TATTTATTACATA
1 ATATATATATTATTTATGAAATA
35456 ATATATATAT
1 ATATATATAT
35466 ATATATATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 6 0.23
22 20 0.77
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (23 bp):
ATATATATATTATTTATGAAATA
Found at i:35461 original size:24 final size:24
Alignment explanation
Indices: 35434--35479 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
35424 TTTAGAAATA
*
35434 ATATAGATATATTTATTACATAAT
1 ATATAGATATATATATTACATAAT
*
35458 ATATATATATATATATTACATA
1 ATATAGATATATATATTACATA
35480 GTAATTTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (24 bp):
ATATAGATATATATATTACATAAT
Found at i:36280 original size:178 final size:178
Alignment explanation
Indices: 36006--36335 Score: 504
Period size: 178 Copynumber: 1.9 Consensus size: 178
35996 CCAATTAAGG
*
36006 TGATTTAAGTGTCTATTAAAAGATTGTTCCAAGATCTACAACTTTCATGAAGAACTCGAAAACTA
1 TGATTCAAGTGTCTATTAAAAGATTGTTCCAAGATCTACAACTTTCATGAAGAACTCGAAAACTA
** *
36071 AATTTAATGTTTCAAGTATCAAAAATGCTTCCGAAA-AATTTGTTGTTTCGGTTAACGGGAATAG
66 AATTTAATGTTTCAAGTATCAAAAATGCTTCC-AAAGAATTAATTGTTTCGGTTAACGGAAATAG
* *
36135 ACGGTCCACTTGATATTATATAACTTTTGCTCCAGATGTCTGATTGAGA
130 ACGGTCCACTTAATATTACATAACTTTTGCTCCAGATGTCTGATTGAGA
* * * *
36184 TGATTCAAGTGTCTCTTGAAAGGTTGTTCCAAGATCTACAACTTTCATGAAGGACTCGAAAACTA
1 TGATTCAAGTGTCTATTAAAAGATTGTTCCAAGATCTACAACTTTCATGAAGAACTCGAAAACTA
*
36249 AATTTAATG-TTCAAGGTAT-AAAAATTGCTTCCAAAGAATTAATTGTTTTGGTTAACGGAAATA
66 AATTTAATGTTTCAA-GTATCAAAAA-TGCTTCCAAAGAATTAATTGTTTCGGTTAACGGAAATA
*
36312 GACGGTCTACTTAATATTACATAA
129 GACGGTCCACTTAATATTACATAA
36336 TTTGAGCTTA
Statistics
Matches: 137, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
177 13 0.09
178 124 0.91
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (178 bp):
TGATTCAAGTGTCTATTAAAAGATTGTTCCAAGATCTACAACTTTCATGAAGAACTCGAAAACTA
AATTTAATGTTTCAAGTATCAAAAATGCTTCCAAAGAATTAATTGTTTCGGTTAACGGAAATAGA
CGGTCCACTTAATATTACATAACTTTTGCTCCAGATGTCTGATTGAGA
Found at i:41990 original size:23 final size:23
Alignment explanation
Indices: 41945--41991 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
41935 GTAGCATCTG
*
41945 AAAGAGAAAAAAATATTTCAAAA
1 AAAGAGAAAAAAATATCTCAAAA
*
41968 AAAGAAGAAAAAAA-ATCTGAAAA
1 AAAG-AGAAAAAAATATCTCAAAA
41991 A
1 A
41992 GAAAAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.72, C:0.04, G:0.11, T:0.13
Consensus pattern (23 bp):
AAAGAGAAAAAAATATCTCAAAA
Found at i:41995 original size:18 final size:19
Alignment explanation
Indices: 41967--42013 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
41957 ATATTTCAAA
41967 AAAAGAAGAAAAAAA-ATCT
1 AAAA-AAGAAAAAAATATCT
* *
41986 GAAAAAGAAAAAAATATTT
1 AAAAAAGAAAAAAATATCT
42005 AAAAAAGAA
1 AAAAAAGAA
42014 GTCATCTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 10 0.42
19 14 0.58
ACGTcount: A:0.74, C:0.02, G:0.11, T:0.13
Consensus pattern (19 bp):
AAAAAAGAAAAAAATATCT
Found at i:43317 original size:31 final size:28
Alignment explanation
Indices: 43244--43329 Score: 93
Period size: 31 Copynumber: 2.9 Consensus size: 28
43234 AGCAAAACCA
* * *
43244 TAACGTTATATCCTGAAATCACACTTTCG
1 TAACGTTATATCCTGAATTGA-ACATTCG
43273 TAACGTT-TCATCCTGAATTGAACATTCG
1 TAACGTTAT-ATCCTGAATTGAACATTCG
43301 TGCAAACGTTATATCCTGAATTGAACATT
1 T---AACGTTATATCCTGAATTGAACATT
43330 TAGCCTTTCT
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
28 8 0.16
29 17 0.35
31 23 0.47
32 1 0.02
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (28 bp):
TAACGTTATATCCTGAATTGAACATTCG
Found at i:56027 original size:53 final size:52
Alignment explanation
Indices: 55939--56043 Score: 176
Period size: 53 Copynumber: 2.0 Consensus size: 52
55929 ATTTGGTATT
55939 CGATAACCACATTAGATACCATTCACAAGACTCGAAAC-CAAGACCTTGTAAA
1 CGATAACCACATTAGATACCATTCACAAGACTCG-AACTCAAGACCTTGTAAA
*
55991 CGATAACCACATTAGATTATCATTCACAAGACTCGAACTCAAGACCTTGTAAA
1 CGATAACCACATTAGA-TACCATTCACAAGACTCGAACTCAAGACCTTGTAAA
56044 AAGGGTTTAG
Statistics
Matches: 50, Mismatches: 1, Indels: 3
0.93 0.02 0.06
Matches are distributed among these distances:
52 19 0.38
53 31 0.62
ACGTcount: A:0.41, C:0.26, G:0.11, T:0.22
Consensus pattern (52 bp):
CGATAACCACATTAGATACCATTCACAAGACTCGAACTCAAGACCTTGTAAA
Found at i:61197 original size:39 final size:39
Alignment explanation
Indices: 61143--61222 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
61133 GGTTTTTTTC
*
61143 GTCATTTCAATCATAATATAGATAGATTTGGATATAGAT
1 GTCATTTCAATCATAATATAGATAAATTTGGATATAGAT
61182 GTCATTTCAATCATAATATAGATAAATTTGGATATAGAT
1 GTCATTTCAATCATAATATAGATAAATTTGGATATAGAT
61221 GT
1 GT
61223 AGATATAGAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (39 bp):
GTCATTTCAATCATAATATAGATAAATTTGGATATAGAT
Found at i:62458 original size:1 final size:1
Alignment explanation
Indices: 62447--62481 Score: 61
Period size: 1 Copynumber: 35.0 Consensus size: 1
62437 TTGATCTTTC
*
62447 TTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
62482 CTTNTTTTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:62489 original size:8 final size:8
Alignment explanation
Indices: 62441--62500 Score: 68
Period size: 8 Copynumber: 7.4 Consensus size: 8
62431 ATCTAGTTGA
62441 TCTTTCTTT
1 TCTTT-TTT
62450 TCTTTTTT
1 TCTTTTTT
62458 T-TTTTTT
1 TCTTTTTT
*
62465 TTTTTTTT
1 TCTTTTTT
*
62473 TTTTTTTT
1 TCTTTTTT
*
62481 TCTTNTTT
1 TCTTTTTT
62489 TCTTTCTTT
1 TCTTT-TTT
62498 TCT
1 TCT
62501 ATTCATAGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
7 7 0.15
8 28 0.61
9 11 0.24
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.87
Consensus pattern (8 bp):
TCTTTTTT
Found at i:62489 original size:12 final size:11
Alignment explanation
Indices: 62447--62498 Score: 72
Period size: 10 Copynumber: 4.8 Consensus size: 11
62437 TTGATCTTTC
62447 TTTTCTTTTTT
1 TTTTCTTTTTT
62458 TTTT-TTTTTT
1 TTTTCTTTTTT
62468 TTTT-TTTTTT
1 TTTTCTTTTTT
62478 TTTTCTTNTTTT
1 TTTTCTT-TTTT
*
62490 CTTTCTTTT
1 TTTTCTTTT
62499 CTATTCATAG
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
10 20 0.53
11 8 0.21
12 10 0.26
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.90
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:70642 original size:30 final size:30
Alignment explanation
Indices: 70606--70665 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
70596 ATTTATTTTA
70606 GTCTTGCAATTGACACCAGAAGTTGTCATG
1 GTCTTGCAATTGACACCAGAAGTTGTCATG
70636 GTCTTGCAATTGACACCAGAAGTTGTCATG
1 GTCTTGCAATTGACACCAGAAGTTGTCATG
70666 ATAAATTTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (30 bp):
GTCTTGCAATTGACACCAGAAGTTGTCATG
Found at i:83710 original size:29 final size:29
Alignment explanation
Indices: 83649--83738 Score: 121
Period size: 29 Copynumber: 3.2 Consensus size: 29
83639 CAAATTTCCA
*
83649 AGCCTCACCT-AACCCGGAGC-TTCTTTG
1 AGCCTAACCTAAACCCGGAGCTTTCTTTG
*
83676 AACCTAACCTAAACCCGGAGCTTTCTTTG
1 AGCCTAACCTAAACCCGGAGCTTTCTTTG
* **
83705 AGCCTATCCTAAACTTGGAGCTTTCTTTG
1 AGCCTAACCTAAACCCGGAGCTTTCTTTG
83734 AGCCT
1 AGCCT
83739 CATCTAAAAC
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
27 8 0.15
28 10 0.18
29 37 0.67
ACGTcount: A:0.22, C:0.31, G:0.17, T:0.30
Consensus pattern (29 bp):
AGCCTAACCTAAACCCGGAGCTTTCTTTG
Found at i:86842 original size:20 final size:20
Alignment explanation
Indices: 86817--86867 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
86807 AAGGCTAGGG
*
86817 TTCTTCTTCTTCAGATCTGT
1 TTCTTCTTCTTCAGATCTGC
*
86837 TTCTTCTCCTTCAGATCTGC
1 TTCTTCTTCTTCAGATCTGC
86857 TTCTTC-TCTTC
1 TTCTTCTTCTTC
86868 TTCGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 4 0.14
20 24 0.86
ACGTcount: A:0.08, C:0.31, G:0.08, T:0.53
Consensus pattern (20 bp):
TTCTTCTTCTTCAGATCTGC
Done.