Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017681.1 Corchorus olitorius cultivar O-4 contig17714, 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: 44107
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:7453 original size:19 final size:18
Alignment explanation
Indices: 7431--7481 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
7421 GGGCTGAAAT
7431 TAATTGATTATTAATTAAA
1 TAATT-ATTATTAATTAAA
* * *
7450 TAATAATTATTTTATTGAA
1 TAATTATTA-TTAATTAAA
7469 TAATTATTATTAA
1 TAATTATTATTAA
7482 AAATCTTACA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
18 7 0.27
19 19 0.73
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (18 bp):
TAATTATTATTAATTAAA
Found at i:8892 original size:51 final size:50
Alignment explanation
Indices: 8791--8892 Score: 111
Period size: 51 Copynumber: 2.0 Consensus size: 50
8781 GTTCTTCATA
* **
8791 TTTTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCTTTTAGTGT
1 TTTTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGT
*
8841 TTTTCTCTTGTTTCA-ATCTTGTCCTC-GGACATACAAACACT-GTACACGTGT
1 TTTTC-CTTGTTT-AGATCTTGT-CTCAGGACAAACAAACACTCGTACA-GTGT
8892 T
1 T
8893 CTTCATTCAG
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
50 7 0.16
51 33 0.75
52 4 0.09
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.41
Consensus pattern (50 bp):
TTTTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGT
Found at i:9064 original size:24 final size:24
Alignment explanation
Indices: 9017--9065 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
9007 TTCGCTTGCG
* *
9017 GATCCAATGATTTAGATCCACTTT
1 GATCCAATGATTTACAACCACTTT
*
9041 GATCCAATGATTTACAACCTCTTT
1 GATCCAATGATTTACAACCACTTT
9065 G
1 G
9066 TCAATTTCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (24 bp):
GATCCAATGATTTACAACCACTTT
Found at i:9466 original size:22 final size:23
Alignment explanation
Indices: 9427--9469 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
9417 TACAACAACT
9427 TTACAAATTAAATTTGAATGAGA
1 TTACAAATTAAATTTGAATGAGA
*
9450 TTACAAA-TATATTTGAATGA
1 TTACAAATTAAATTTGAATGA
9470 ATATACGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.47, C:0.05, G:0.12, T:0.37
Consensus pattern (23 bp):
TTACAAATTAAATTTGAATGAGA
Found at i:14147 original size:2 final size:2
Alignment explanation
Indices: 14140--14181 Score: 57
Period size: 2 Copynumber: 20.5 Consensus size: 2
14130 AGAGCCCTTG
* *
14140 AT AT AT AT AT AT AT AT AT AT GT AC AGT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT A
14182 ACTATACATT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 34 0.97
3 1 0.03
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (2 bp):
AT
Found at i:22094 original size:328 final size:323
Alignment explanation
Indices: 21464--23804 Score: 1886
Period size: 328 Copynumber: 7.1 Consensus size: 323
21454 AACAAATCGA
* * * * * * * *
21464 AATAAAGATATTTCAAGGAGTCTCGGCGTCAAAAATCATGCAAAACAAAGCTGTGGCCCAGGAAT
1 AATATAGATATTTCAAGGAGT-T--GCGCCAAAAATCATGCAAAACTAAGCCGGGGCCCCGAAAC
21529 GCGTTTTTAGCCAAAAACCGTGATGGTT-GATACACGATTTCGGCTAAACTTTTGCAAAAATTGA
63 GCGTTTTTAGCCAAAAACCGTGATGGTTAG-TACACGATTTCGGCTAAA-TTTTGCAAAAATTGA
* ** ** **
21593 TCCGAAAGATTTTTCCTCAATTTTTGACTAAAATACTCATGAAAAATATATAATTTGAC-ATAAA
126 -CCGAAAGATTTTTCCTCAATTTTT-AGT-AAATACTCAAAAAAAATATATAATTCAACGCCAAA
* * * * * **
21657 AAAAAT-AAGGGCTTTTAACGCTTCTAATATTGTTTTTCCTATTTTTTTCCAAATTAATTTCTAA
188 AAAATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTT-C-ATATTTTTCTGAATTAATTTCTAA
* * *
21721 TTAAATCGAAACAAGGTTCAGATGCTCGTAAAAACAAGTCCTTAAATCTAATATGGCTGAGATTT
251 TTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATC-AATGTGGCTGAGATTT
*
21786 GGTTAGATA
315 GGTTAGATG
* * *
21795 AATATAGATATTTCAAGGA-TTGCCCCAAAAATTATGCAAAACTAAGTC-GGGCCCCGAAACGCG
1 AATATAGATATTTCAAGGAGTTGCGCCAAAAATCATGCAAAACTAAGCCGGGGCCCCGAAACGCG
* * * *
21858 TTTTTAGCCGAACACCGTGATGGTTAGTACATGATTTCAGCTAAAGTTTTGCAAAAATTGATCCG
66 TTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAA-TTTTGCAAAAATTGA-CCG
* * ** * * *
21923 AAAGATTTTTCCTCGATATCCAGTGAAAGTATTCACAAAAAAACATATAATTAAACGCCAAAAAA
129 AAAGATTTTTCCTCAATTTTTAGT-AAA-TACTCA-AAAAAAATATATAATTCAACGCCAAAAAA
* * *
21988 ACTGAAAGCCTTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAA
191 ATTGAAGGGC-TTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAA
* *
22053 ATCGAAACAAGATTCAGATGCTCGTAAAAACAAACCCTTAAATTCAATGTGGCTGAGATTTGATT
255 ATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAA-TCAATGTGGCTGAGATTTGGTT
22118 AGATG
319 AGATG
* * * * *
22123 AATATAGATATTTCAAGGATTCTCGGTGTCAGAAATCATGCAAAACTAAGCCGGGGCCTCGAAAC
1 AATATAGATATTTCAAGGAGT-T--GCGCCAAAAATCATGCAAAACTAAGCCGGGGCCCCGAAAC
* * * *
22188 GCGTTTTTAACCAAAAATCGTGATGG-TAGTACACGATTTCGGCTAAATTTTACAAAAAATGATC
63 GCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAATTTTGCAAAAATTGA-C
* * * *
22252 C-AAAAATTTTTTCCGCCAATTTTTGGCTAAAATACTC--ATAAAATATATAATTCAACGCCAAA
127 CGAAAGA-TTTTTCC-TCAATTTTTAG-T-AAATACTCAAAAAAAATATATAATTCAACGCCAAA
** * *
22314 AAGTTTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATT
188 AAAATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATT
* * * * *
22379 AAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATTCTT-AATCCAATTTAGCTGAGATTTGA
253 AAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAAT-CAATGTGGCTGAGATTTGG
*
22443 TTACATG
317 TTAGATG
* * * * *
22450 AATATGGATATCTCAAAGAGTTTTGACGCCAAAAATCATGCAAAACT-TG-CGGGGCTCC-AGAA
1 AATATAGATATTTCAAGGAG--TTG-CGCCAAAAATCATGCAAAACTAAGCCGGGGCCCCGA-AA
* * *
22512 CGCATTTTTAGCCAAAAACCGTGATGATTA-T-TAC-A--TCGGCT--A----GCAAAAATTGAC
62 CGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAATTTTGCAAAAATTGAC
** * * *
22566 TCGAAAG-TTATTTCCTCAATTTTTAAACACAATAATCATAAAAATTATATAATTCAACGCCAAA
127 -CGAAAGATT-TTTCCTCAATTTTT-AGTA-AATACTCAAAAAAAATATATAATTCAACGCCAAA
** * * * * *
22630 AAAATAAAAAGGCTTTTCATGCTTTTAATATTGTTTTTCCTATTATTTTCCGAATTAATTTCTAA
188 AAAATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATA-T-TTTTCTGAATTAATTTCTAA
* * *** * * *
22695 TTAAATCGAAACATGATTCAGATGCTTGT-TTTACAAATCCTCAAATCCAATTTGGCTGAAATTT
251 TTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAAT-CAATGTGGCTGAGATTT
*
22759 GGTTAGATA
315 GGTTAGATG
* * * * * ** * *
22768 AATGTACATATTTCAAGGAGTCTTGGCGCAAAAAATCATGCAACATTGAA-CC-GGATCTCAAGA
1 AATATAGATATTTCAAGGAG--TT-GCGCCAAAAATCATGCAAAACT-AAGCCGGGGCCCCGA-A
* * * * * * * *
22831 ACGTGCTTTTAGCTAAAAACCGTGATTTCGACTAACGTACACTATTTCAGCTAATATTTTGTAAA
61 ACGCGTTTTTAGCCAAAAACCGTGA--T-G-GTTA-GTACACGATTTCGGCTAA-ATTTTGCAAA
** * * * * * *
22896 AATTGAACATAAATATTTTTTTCTCAATTTTCGT-CTAAAATACTCATAATATATATATATAACT
120 AATTG-ACCGAAAGA-TTTTTCCTCAATTTT--TAGT-AAATACTCA-AA-AAAAATATATAATT
* * * * *
22960 CAACTCCGAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTA
178 CAACGCCAAAAAAATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTA
* *
23025 ATTTCTAATTAAATCAAAACAAGATTCAGATGCTCGTAAAAACAAATCTTTAAATGCAATGT-GC
243 ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAAT-CAATGTGGC
*
23089 TTGAGATTTGATTAGATG
307 -TGAGATTTGGTTAGATG
* * **
23107 AATATAGATATTTCAAGGAGTCTTGACGCCAAAAATCATGCAAAACTGAGCCGGGGTCTTGAAAC
1 AATATAGATATTTCAAGGAG--TTG-CGCCAAAAATCATGCAAAACTAAGCCGGGGCCCCGAAAC
* * * * *
23172 ACATTTTTAGCAAAAAAACCTTGATAGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAAATT-
63 GCGTTTTTAGC-CAAAAACCGTGATGGTTAGTACACGATTTCGGCT-AAATTTTGC-AAAAATTG
* * * *
23236 ACTAGAAA-AATTTTCTTCAATTTTTTAGCTATAATACTCATAAAAAATATATAATTCAACGCCA
125 AC-CGAAAGATTTTTCCTCAA-TTTTTAG-TA-AATACTCAAAAAAAATATATAATTCAACGCCA
* * * * * **
23300 AAAAGATTGAAGGGCTTTTCACGCTTCTAATATGGGTTTTCCTATTTTTTTCCAAATTAATTTCT
186 AAAAAATTGAAGGGCTTTTCACGCTTTTAATAT-CGTTTTTC-ATATTTTTCTGAATTAATTTCT
* * * * * *
23365 AATTAAAGCGAAACATGATTCAAATGTTTGT------AAA-----AAA--GA--TGGCTGAGATT
249 AATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCAATGTGGCTGAGATT
*
23415 TGGTTAGATA
314 TGGTTAGATG
* * * * * *
23425 AAT-TAGATATTTCAAGGAGTCTCAGCGCCAATAATCATTCAAAATTGAA--CTGGGCCCTGGAA
1 AATATAGATATTTCAAGGAGT-T--GCGCCAAAAATCATGCAAAACT-AAGCCGGGGCCCCGAAA
* * * * *
23487 CGCGTTTTTAGCCAAAAACCATAATGATTATTACACGATTTTGGCTAAAATTTTGCAAAAATTGA
62 CGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCT-AAATTTTGCAAAAATTGA
* * * * * *
23552 CTCGAAAGATATTTCCTCGATTTTTAGCCATAATACTCATTAAAAAAAAAATTTAATCCAACG-C
126 C-CGAAAGATTTTTCCTCAATTTTTAG-TA-AATACTC---AAAAAAAATATATAATTCAACGCC
* *
23616 AAAAAATATTGAAGGGATTTTCACGCTTATAATATCGTTTTTCATATTTTTTCTGAATTAATTTC
185 AAAAAA-ATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATA-TTTTTCTGAATTAATTTC
* *
23681 TAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTAAGA
248 TAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAAT-CAATGTGGCTGAGA
*
23746 TTTTGTTAGATG
312 TTTGGTTAGATG
* * * * *
23758 AGTATTGATATTTCAAAGAGTGTTGGCGCCAAAAACCATACAAAACT
1 AATATAGATATTTC-AAG-GAGTT-GCGCCAAAAATCATGCAAAACT
23805 GAGTTTTCCC
Statistics
Matches: 1608, Mismatches: 295, Indels: 211
0.76 0.14 0.10
Matches are distributed among these distances:
313 1 0.00
314 24 0.01
315 77 0.05
316 88 0.05
317 97 0.06
318 171 0.11
319 7 0.00
320 26 0.02
321 6 0.00
322 1 0.00
323 8 0.00
324 5 0.00
325 38 0.02
326 97 0.06
327 98 0.06
328 211 0.13
329 39 0.02
330 33 0.02
331 42 0.03
332 97 0.06
333 74 0.05
334 87 0.05
335 28 0.02
336 14 0.01
337 12 0.01
338 71 0.04
339 88 0.05
340 68 0.04
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (323 bp):
AATATAGATATTTCAAGGAGTTGCGCCAAAAATCATGCAAAACTAAGCCGGGGCCCCGAAACGCG
TTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAATTTTGCAAAAATTGACCGAA
AGATTTTTCCTCAATTTTTAGTAAATACTCAAAAAAAATATATAATTCAACGCCAAAAAAATTGA
AGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAA
ACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCAATGTGGCTGAGATTTGGTTAGATG
Found at i:24710 original size:27 final size:27
Alignment explanation
Indices: 24680--24732 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
24670 CCTTGCTTGT
*
24680 AGATTCTTCTCCAAAATTTGAAGATGC
1 AGATTCTTCTACAAAATTTGAAGATGC
*
24707 AGATTTTTCTACAAAATTTGAAGATG
1 AGATTCTTCTACAAAATTTGAAGATG
24733 TAGGTGATGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (27 bp):
AGATTCTTCTACAAAATTTGAAGATGC
Found at i:26754 original size:15 final size:14
Alignment explanation
Indices: 26737--26865 Score: 132
Period size: 15 Copynumber: 8.6 Consensus size: 14
26727 TGTAAACCTG
*
26737 AATTTGCACCTGCT
1 AATTCGCACCTGCT
* *
26751 GAATTCGAACTTGCT
1 -AATTCGCACCTGCT
26766 GAATTCGCACCTGCT
1 -AATTCGCACCTGCT
26781 ACATTCGCACCTGCT
1 A-ATTCGCACCTGCT
*
26796 ATGTTCGCACCTGCT
1 A-ATTCGCACCTGCT
26811 ATATTCGCACCTGCT
1 A-ATTCGCACCTGCT
* *
26826 ATATTCACACTTGCT
1 A-ATTCGCACCTGCT
26841 GAATTCGCACCTGCT
1 -AATTCGCACCTGCT
26856 AAATTCGCAC
1 -AATTCGCAC
26866 ATTCTAAAGT
Statistics
Matches: 99, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
14 1 0.01
15 97 0.98
16 1 0.01
ACGTcount: A:0.22, C:0.31, G:0.16, T:0.31
Consensus pattern (14 bp):
AATTCGCACCTGCT
Found at i:26793 original size:45 final size:44
Alignment explanation
Indices: 26742--26865 Score: 151
Period size: 45 Copynumber: 2.8 Consensus size: 44
26732 ACCTGAATTT
* *
26742 GCACCTGCTGAATTCGAACTTGCTGAATTCGCACCTGCTACATTC
1 GCACCTGCTGAATTCGCACCTGCT-AATTCGCACCTGCTACATTC
* *
26787 GCACCTGCT-ATGTTCGCACCTGCTATATTCGCACCTGCTATATTC
1 GCACCTGCTGA-ATTCGCACCTGCTA-ATTCGCACCTGCTACATTC
* *
26832 ACACTTGCTGAATTCGCACCTGCTAAATTCGCAC
1 GCACCTGCTGAATTCGCACCTGCT-AATTCGCAC
26866 ATTCTAAAGT
Statistics
Matches: 68, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
44 2 0.03
45 64 0.94
46 2 0.03
ACGTcount: A:0.22, C:0.32, G:0.16, T:0.30
Consensus pattern (44 bp):
GCACCTGCTGAATTCGCACCTGCTAATTCGCACCTGCTACATTC
Found at i:30006 original size:21 final size:21
Alignment explanation
Indices: 29981--30028 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
29971 AATTTTATGA
29981 AGAGAAATT-AGTGGGAGGAGG
1 AGAGAAATTAAGTGGGAGGA-G
* *
30002 AGAGAGATTAAGTGGGGGGAG
1 AGAGAAATTAAGTGGGAGGAG
30023 AGAGAA
1 AGAGAA
30029 GAAGGGCAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.40, C:0.00, G:0.48, T:0.12
Consensus pattern (21 bp):
AGAGAAATTAAGTGGGAGGAG
Found at i:31320 original size:42 final size:43
Alignment explanation
Indices: 31269--31362 Score: 129
Period size: 45 Copynumber: 2.2 Consensus size: 43
31259 AGTGCATTAT
*
31269 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
**
31310 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATTTAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAG
31355 CTAATATT
1 CTAATATT
31363 AATTGTTGTT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 36 0.78
ACGTcount: A:0.36, C:0.22, G:0.05, T:0.36
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:33104 original size:18 final size:19
Alignment explanation
Indices: 33081--33117 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
33071 CACCCTAGCC
33081 CTAAAACTAGAAGA-AAAA
1 CTAAAACTAGAAGAGAAAA
33099 CTAAAACTAGAAGAGAAAA
1 CTAAAACTAGAAGAGAAAA
33118 AGATGAAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.65, C:0.11, G:0.14, T:0.11
Consensus pattern (19 bp):
CTAAAACTAGAAGAGAAAA
Found at i:40960 original size:314 final size:313
Alignment explanation
Indices: 40602--41178 Score: 743
Period size: 314 Copynumber: 1.8 Consensus size: 313
40592 AATGCAAGAT
* * *
40602 TTAGATAAATATAGATATTTCAAGGAGTCTCAACGCAAAAAATCATGCAAAACTGAGTCAGGGCC
1 TTAGATAAATATAGATATTTAAAGGAGTCTCAACACAAAAAATCATGCAAAACTGA-ACAGGGCC
* *** * *
40667 -TGAAACACGTTTTTAGCAACAAACTGTGATGAGTACACGATTTCGGCTAAAATTTTGCAAAAGA
65 ATGAAACACGTTTTTAGCAAAAAAC-CAAATGAGTACACGAATTCGGCTAAAATTTTGCAAAAAA
*
40731 TT-AC-CAGAAA-AAATTTTCCTCAATTTTTAACCGCAATACTCATAAAAAATATATAATTCAAC
129 TTGACTCA-AAAGAAA-TTTCCTCAATTTTTAACCACAATACTCATAAAAAATATATAATTCAAC
*
40793 GTCGAAAAGATTG-AGAGGCCTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTCCGAATTAA
192 GTCAAAAAGATTGAAG-GGCCTTTCACGCTTCTAATATCGTTTTT-C-ATTTTTTTCCGAATTAA
*
40857 TTTCTAATTAAAACGAAACATGATTCAGATTTTTGTAAAAAAAAAATGGCTGGGATTTGG
254 TTTATAATTAAAACGAAACATGATTCAGATTTTTGTAAAAAAAAAATGGCTGGGATTTGG
* ** * * * *
40917 TTAGATGAAT-TAGATATTTAAAGGAGTCTCGGCACGAAAAATCATTCAAAATTGAACCGGGCCA
1 TTAGATAAATATAGATATTTAAAGGAGTCTCAACACAAAAAATCATGCAAAACTGAACAGGGCCA
* * * * *
40981 TGGAACGCGTTTTTAGCAAAAAACCAAATTATTACACTAATTCGGCTAAAATTTTGCAAAAAATT
66 TGAAACACGTTTTTAGCAAAAAACCAAATGAGTACACGAATTCGGCTAAAATTTTGCAAAAAATT
* * * * *
41046 GACTCAAAAGACATTTCCTCGATTTTTAGCCATAATACTCATAGAAAATATATAATTCAACGTCA
131 GACTCAAAAGAAATTTCCTCAATTTTTAACCACAATACTCATAAAAAATATATAATTCAACGTCA
** * * *
41111 AAAAGATTGAAGGGTTTTTCACGCTTTTAATATCGTTTTTCATTTTTTTCTGAATTATTTTATAA
196 AAAAGATTGAAGGGCCTTTCACGCTTCTAATATCGTTTTTCATTTTTTTCCGAATTAATTTATAA
41176 TTA
261 TTA
41179 TATCAAAATT
Statistics
Matches: 223, Mismatches: 34, Indels: 13
0.83 0.13 0.05
Matches are distributed among these distances:
312 24 0.11
313 40 0.18
314 144 0.65
315 15 0.07
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.33
Consensus pattern (313 bp):
TTAGATAAATATAGATATTTAAAGGAGTCTCAACACAAAAAATCATGCAAAACTGAACAGGGCCA
TGAAACACGTTTTTAGCAAAAAACCAAATGAGTACACGAATTCGGCTAAAATTTTGCAAAAAATT
GACTCAAAAGAAATTTCCTCAATTTTTAACCACAATACTCATAAAAAATATATAATTCAACGTCA
AAAAGATTGAAGGGCCTTTCACGCTTCTAATATCGTTTTTCATTTTTTTCCGAATTAATTTATAA
TTAAAACGAAACATGATTCAGATTTTTGTAAAAAAAAAATGGCTGGGATTTGG
Found at i:41581 original size:328 final size:328
Alignment explanation
Indices: 40437--42246 Score: 1265
Period size: 328 Copynumber: 5.6 Consensus size: 328
40427 TTTTTTCTTG
* * * * * *
40437 ATTTTTGTCTAAAATAATCATAAAATATATATATAATAT-AACTCCAAAAAGATTGGATGACTTT
1 ATTTTTGGCTAAAATACTCGT-AAA-A-ATATATAAT-TCAACGCCAAAAAGATTGAAGGACTTT
* * ** * *
40501 TCACGCTTTAAATATC-ATTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCAAAACAAGAT
62 TCACGCTTTTAATATCGAGTTTTCATA-TTTTCCAAATTAATTTATAATTAAATCGAAACAAGAT
* * * *
40565 TTAGATGCTCGTAAGAACAAAT-CTT---T--AA-AT-GC-AAGA--T--TTAGATAAATATAGA
126 TTAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGA
* * * * * *
40617 TATTTCAAGGAGTCTCAACGCAAAAAATCATGCAAAACTGAGTCAGGG--CCTGAAACACGTTTT
191 TATTTCAAGGAGTCTCGACGCCAAAAATCATGCAAAACTGAG-CTGGGACCCCGAAACGCCTTTT
* * * * *
40680 TAGCAACAAA-C-TG-TGATGAGTACACGATTTCGGCTAAAATTTTGCAAAAGATT-ACCAGAAA
255 TAGCAAAAAACCATGATGGTTAGTACTCGATTTCGGCTAAAATTTTGCAAAA-ATTGACC-CAAA
40741 AAATTTTCCTCA
318 AAATTTTCC-CA
** *** * * * *
40753 ATTTTTAACCGCAATACTCATAAAAAATATATAATTCAACGTCGAAAAGATTGAGAGG-CCTTTC
1 ATTTTTGGCTAAAATACTCGT-AAAAATATATAATTCAACGCCAAAAAGATTGA-AGGACTTTTC
* * * * * * *
40817 ACGCTTCTAATATCG-TTTTTCCTATTTTTTTCCGAATTAATTTCTAATTAAAACGAAACATGAT
64 ACGCTTTTAATATCGAGTTTT-C-A-TATTTTCCAAATTAATTTATAATTAAATCGAAACAAGAT
* ** * * *
40881 TCAGATTTTTGT---AA-AAA-----AAA---AA--TGGCTGGGATTTGGTTAGATGAAT-TAGA
126 TTAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGA
* * * * * * * * ** * *
40931 TATTTAAAGGAGTCTCGGCACGAAAAATCATTCAAAATTGAACCGGG-CCATGGAACGCGTTTTT
191 TATTTCAAGGAGTCTCGACGCCAAAAATCATGCAAAACTGAGCTGGGACCCCGAAACGCCTTTTT
* * * * * *
40995 AGCAAAAAACCA--A--ATTATTACACTAATTCGGCTAAAATTTTGCAAAAAATTGACTCAAAAG
256 AGCAAAAAACCATGATGGTTAGTACTCGATTTCGGCTAAAATTTTGC-AAAAATTGACCCAAAA-
*
41056 ACA-TTTCCTCG
319 A-ATTTTCC-CA
* * * * * **
41067 ATTTTTAGCCATAATACTCATAGAAAATATATAATTCAACGTCAAAAAGATTGAAGGGTTTTTCA
1 ATTTTTGGCTAAAATACTCGTA-AAAATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCA
* * ** * * * ** *
41132 CGCTTTTAATATCG-TTTTTCATTTTTTTCTGAATTATTTTATAATTATATCAAAATTAGATTTT
65 CGCTTTTAATATCGAGTTTTCA-TATTTTCCAAATTAATTTATAATTAAATCGAAACAAGATTTA
* * * * * *
41196 GATTCTCGTAAAAACAAATCCTTAAATGCAATGAGGATAAGATTTTATTAGATGAATATAGATAT
129 GATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATAT
* * * * *
41261 TTCAAGGAGTGTCGACGCCAAAAACCATGCAAAACTGAGCTGGGGCCCCGAAACGCGTTTTTAGT
194 TTCAAGGAGTCTCGACGCCAAAAATCATGCAAAACTGAGCTGGGACCCCGAAACGCCTTTTTAGC
* * *
41326 AAAAAACCATGATGGTAAGTACTCGAGTTT-GGCTAAAATTTTGCAAAAAATAACCCAAAAAATT
259 AAAAAACCATGATGGTTAGTACTCGA-TTTCGGCTAAAATTTTGCAAAAATTGACCCAAAAAATT
41390 TTACCCA
323 TT-CCCA
* * * * * *
41397 ATTTTTGGATAAAATTCGCGTAAAATATATATAATTTAACGTCAAAAAGATTGGAGGACTTTTCA
1 ATTTTTGGCTAAAATACTCGTAAAA-ATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCA
* * *
41462 TGTTTTTAATATC-A-TTTTCATATTTTCCGAATTAATTTATAATTAAATCGAAACAAGATTTAG
65 CGCTTTTAATATCGAGTTTTCATATTTTCCAAATTAATTTATAATTAAATCGAAACAAGATTTAG
* * * * *
41525 ATGCTTGTAAAAACAAATTCTTAAATCCAATGTGGCCGAGATTTGATTAGATGAATATGGATATC
130 ATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATT
* * ** * * * * *
41590 TCAAGGAGTCTTGGCGTAAAAAATCATGCAAAACTGAGCCGGGACCCCAAAATGCTTTTTTAGCC
195 TCAAGGAGTCTCGACGCCAAAAATCATGCAAAACTGAGCTGGGACCCCGAAACGCCTTTTTAGCA
** * * * *
41655 AAAAACTGTGATGGTTATTACACGATTTCGGCTAAAATTTTGTAAAAATTGACCCGAAATATATT
260 AAAAACCATGATGGTTAGTACTCGATTTCGGCTAAAATTTTGCAAAAATTGACCC-AAA-AAATT
*
41720 TT-TCA
323 TTCCCA
* * *
41725 ATTTTTGGCTAAAGA-ACTCATAAAAAATATATAATTCAACACCAAAAAAATTGAAGGGA-TTTT
1 ATTTTTGGCTAAA-ATACTCGT-AAAAATATATAATTCAACGCCAAAAAGATTGAA-GGACTTTT
* * * * *
41788 GACG-TTTCTAATATC-ATTTTTCCTATATTTTCCAAATTAATTTCTAACTAAATTGAAACAAGA
63 CACGCTTT-TAATATCGAGTTTT-C-ATATTTTCCAAATTAATTTATAATTAAATCGAAACAAGA
* *
41851 TTGATCAGTTGCTTGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATA
125 TT--T-AGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATA
* * ** * * * *
41916 TAGATTTTTCAAGTAGTCTCGGA-GCCATGAATCATGCAAAATTGAG-TCGGGTCCCCGGAACTC
187 TAGATATTTCAAGGAGTCTC-GACGCCAAAAATCATGCAAAACTGAGCT-GGGACCCCGAAACGC
* * *
41979 CTTTTTAGCCAAAAACCGCGATGGTTTGTTAGTACAT-GATTTCGGCTAAAATTTTGCAAAAATT
250 CTTTTTAG-CAAAAAAC-C-AT-GATGGTTAGTAC-TCGATTTCGGCTAAAATTTTGCAAAAATT
** *
42043 GACATAAAAGATTTCTCCTCA
310 GACCCAAAAAATTT-TCC-CA
* *
42064 ATTTTTGGCTAAAATACTCGTAAAAATATATAATTTAACGCCAAAAAGATTTG-AGGACTTTTTA
1 ATTTTTGGCTAAAATACTCGTAAAAATATATAATTCAACGCCAAAAAGA-TTGAAGGACTTTTCA
* ** *
42128 --CTTTTAATATCGTAGTTCTT-ATTTGTTTTAAAATTAATTTCTAATTAAATCGAAACAAGATT
65 CGCTTTTAATATCG-AGTT-TTCATAT-TTTCCAAATTAATTTATAATTAAATCGAAACAAGATT
* * * * * ** * *
42190 CAGATGCTCGTAAAAATAAATTCTTAAATCTACTGTTACTGAGAATTGGTTAGATGA
127 TAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGA
42247 TGTAAAGTAT
Statistics
Matches: 1191, Mismatches: 222, Indels: 144
0.76 0.14 0.09
Matches are distributed among these distances:
309 1 0.00
310 4 0.00
311 2 0.00
312 43 0.04
313 46 0.04
314 188 0.16
315 17 0.01
316 64 0.05
317 1 0.00
321 3 0.00
324 2 0.00
326 18 0.02
327 47 0.04
328 264 0.22
329 25 0.02
330 74 0.06
331 52 0.04
332 21 0.02
333 3 0.00
334 152 0.13
335 7 0.01
336 15 0.01
337 44 0.04
338 73 0.06
339 25 0.02
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (328 bp):
ATTTTTGGCTAAAATACTCGTAAAAATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCAC
GCTTTTAATATCGAGTTTTCATATTTTCCAAATTAATTTATAATTAAATCGAAACAAGATTTAGA
TGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTT
CAAGGAGTCTCGACGCCAAAAATCATGCAAAACTGAGCTGGGACCCCGAAACGCCTTTTTAGCAA
AAAACCATGATGGTTAGTACTCGATTTCGGCTAAAATTTTGCAAAAATTGACCCAAAAAATTTTC
CCA
Found at i:42603 original size:15 final size:16
Alignment explanation
Indices: 42583--42612 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
42573 ACTATTGATA
42583 ATATTATAAT-TAAAT
1 ATATTATAATCTAAAT
42598 ATATTATAATCTAAA
1 ATATTATAATCTAAA
42613 AATAATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATTATAATCTAAAT
Done.