Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012881.1 Corchorus olitorius cultivar O-4 contig12914, 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: 102734
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:520 original size:17 final size:17
Alignment explanation
Indices: 495--531 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
485 TTTGTTTTTC
* *
495 AATTTTTAATTATTATT
1 AATTATTAATTATAATT
512 AATTATTAATTATAATT
1 AATTATTAATTATAATT
529 AAT
1 AAT
532 AATAACAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
AATTATTAATTATAATT
Found at i:556 original size:22 final size:21
Alignment explanation
Indices: 523--580 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 21
513 ATTATTAATT
523 ATAATTAATAATAACAATTTAA
1 ATAATTAATAATAACAA-TTAA
*
545 ATTAA-TAATAATTAATAATTAA
1 A-TAATTAATAA-TAACAATTAA
567 ATAATTAATAATAA
1 ATAATTAATAATAA
581 TTTAAAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
21 6 0.19
22 18 0.56
23 8 0.25
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
ATAATTAATAATAACAATTAA
Found at i:562 original size:7 final size:7
Alignment explanation
Indices: 500--578 Score: 65
Period size: 7 Copynumber: 11.1 Consensus size: 7
490 TTTTCAATTT
*
500 TTAATTA
1 TTAATAA
*
507 TTATTAA
1 TTAATAA
*
514 TTATTAA
1 TTAATAA
521 TT-ATAA
1 TTAATAA
527 TTAATAA
1 TTAATAA
*
534 -TAACAA
1 TTAATAA
540 TTTAAATTAA
1 -TT-AA-TAA
550 -TAATAA
1 TTAATAA
556 TTAATAA
1 TTAATAA
563 TTAAATAA
1 TT-AATAA
571 TTAATAA
1 TTAATAA
578 T
1 T
579 AATTTAAAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
6 13 0.22
7 34 0.57
8 9 0.15
9 2 0.03
10 2 0.03
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (7 bp):
TTAATAA
Found at i:708 original size:12 final size:12
Alignment explanation
Indices: 691--715 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
681 CTACAAAATC
691 CGACATGATTTT
1 CGACATGATTTT
703 CGACATGATTTT
1 CGACATGATTTT
715 C
1 C
716 TTCAAGATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (12 bp):
CGACATGATTTT
Found at i:14377 original size:29 final size:28
Alignment explanation
Indices: 14338--14393 Score: 94
Period size: 29 Copynumber: 2.0 Consensus size: 28
14328 GTTATTTCAC
*
14338 GTTCTTTAGCGTTCTTGAAGATTAGAAAT
1 GTTCTTGAGCGTTCTTGAA-ATTAGAAAT
14367 GTTCTTGAGCGTTCTTGAAATTAGAAA
1 GTTCTTGAGCGTTCTTGAAATTAGAAA
14394 GTTTGAAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 8 0.31
29 18 0.69
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39
Consensus pattern (28 bp):
GTTCTTGAGCGTTCTTGAAATTAGAAAT
Found at i:15619 original size:10 final size:10
Alignment explanation
Indices: 15604--15654 Score: 102
Period size: 10 Copynumber: 5.1 Consensus size: 10
15594 GAGGTGCTTA
15604 TGGGCCGGGT
1 TGGGCCGGGT
15614 TGGGCCGGGT
1 TGGGCCGGGT
15624 TGGGCCGGGT
1 TGGGCCGGGT
15634 TGGGCCGGGT
1 TGGGCCGGGT
15644 TGGGCCGGGT
1 TGGGCCGGGT
15654 T
1 T
15655 TTTGCTTAGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 41 1.00
ACGTcount: A:0.00, C:0.20, G:0.59, T:0.22
Consensus pattern (10 bp):
TGGGCCGGGT
Found at i:29178 original size:15 final size:15
Alignment explanation
Indices: 29158--29190 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
29148 AGATTATCTC
29158 TTTATTTTATCATAA
1 TTTATTTTATCATAA
29173 TTTATTTTATCATAA
1 TTTATTTTATCATAA
29188 TTT
1 TTT
29191 GACCATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTATTTTATCATAA
Found at i:32360 original size:16 final size:17
Alignment explanation
Indices: 32334--32367 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
32324 AAACGACCGA
*
32334 TTGTAGGCAAACTCAAT
1 TTGTAGGCAAAATCAAT
32351 TTGT-GGCAAAATCAAT
1 TTGTAGGCAAAATCAAT
32367 T
1 T
32368 CCCATTGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (17 bp):
TTGTAGGCAAAATCAAT
Found at i:34451 original size:27 final size:27
Alignment explanation
Indices: 34414--34488 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 27
34404 TTCCAGCATT
*
34414 CAAGGGCAAAACTGTAATTTAGTCAAC
1 CAAGGGCAAAACTGTAATTTAGCCAAC
* * *
34441 CAGGGGTAAAA-TGGTAATTTTAGCCGAC
1 CAAGGGCAAAACT-GTAA-TTTAGCCAAC
*
34469 CAAGGGCAAAACAGTAATTT
1 CAAGGGCAAAACTGTAATTT
34489 TGACATCTTA
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
26 1 0.03
27 16 0.42
28 21 0.55
ACGTcount: A:0.39, C:0.16, G:0.23, T:0.23
Consensus pattern (27 bp):
CAAGGGCAAAACTGTAATTTAGCCAAC
Found at i:34797 original size:46 final size:46
Alignment explanation
Indices: 34730--34819 Score: 180
Period size: 46 Copynumber: 2.0 Consensus size: 46
34720 TAAGGGGCAT
34730 AATGGTAATTTTTATCGATCAAGAGTAACACGGTAATTTTACACGA
1 AATGGTAATTTTTATCGATCAAGAGTAACACGGTAATTTTACACGA
34776 AATGGTAATTTTTATCGATCAAGAGTAACACGGTAATTTTACAC
1 AATGGTAATTTTTATCGATCAAGAGTAACACGGTAATTTTACAC
34820 AAAAGAGTCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (46 bp):
AATGGTAATTTTTATCGATCAAGAGTAACACGGTAATTTTACACGA
Found at i:35362 original size:22 final size:22
Alignment explanation
Indices: 35311--35366 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
35301 TTTAATTTCC
* *
35311 TTATTTTCCTTTTTTTTGCCTT
1 TTATTTTTCTTTCTTTTGCCTT
35333 TT-TCTTTTCTTTCTTTT-CCTT
1 TTAT-TTTTCTTTCTTTTGCCTT
35354 TCTATTTTTCTTT
1 T-TATTTTTCTTT
35367 TCTATTTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
21 6 0.21
22 22 0.76
23 1 0.03
ACGTcount: A:0.04, C:0.20, G:0.02, T:0.75
Consensus pattern (22 bp):
TTATTTTTCTTTCTTTTGCCTT
Found at i:35368 original size:13 final size:13
Alignment explanation
Indices: 35331--35382 Score: 68
Period size: 13 Copynumber: 3.9 Consensus size: 13
35321 TTTTTTTGCC
*
35331 TTTTTCTTTTCTT
1 TTTTTCTTTTCTA
*
35344 TCTTTTCCTTTCTA
1 T-TTTTCTTTTCTA
35358 TTTTTCTTTTCTA
1 TTTTTCTTTTCTA
*
35371 TTTTTCTCTTCT
1 TTTTTCTTTTCT
35383 TCTTTTTTCT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
13 23 0.68
14 11 0.32
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75
Consensus pattern (13 bp):
TTTTTCTTTTCTA
Found at i:35388 original size:27 final size:27
Alignment explanation
Indices: 35330--35389 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
35320 TTTTTTTTGC
*
35330 CTTTTTCTTTTCTTTCTTTTCCTTTCT
1 CTTTTTCTTTTCTATCTTTTCCTTTCT
*
35357 ATTTTTCTTTTCTAT-TTTT-CTCTTCTT
1 CTTTTTCTTTTCTATCTTTTCCT-TTC-T
35384 CTTTTT
1 CTTTTT
35390 TCTCCCTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
25 2 0.07
26 7 0.25
27 19 0.68
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.75
Consensus pattern (27 bp):
CTTTTTCTTTTCTATCTTTTCCTTTCT
Found at i:35389 original size:15 final size:14
Alignment explanation
Indices: 35331--35393 Score: 60
Period size: 14 Copynumber: 4.5 Consensus size: 14
35321 TTTTTTTGCC
35331 TTTT-TCTTTTCTT
1 TTTTCTCTTTTCTT
* *
35344 TCTTT-TCCTTTCTA
1 T-TTTCTCTTTTCTT
35358 TTTT-TCTTTTCTAT
1 TTTTCTCTTTTCT-T
35372 TTTTCTCTTCTTCTT
1 TTTTCTCTT-TTCTT
35387 TTTTCTC
1 TTTTCTC
35394 CCTTTTTGGG
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
13 11 0.26
14 15 0.36
15 12 0.29
16 4 0.10
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTTCTCTTTTCTT
Found at i:36385 original size:19 final size:19
Alignment explanation
Indices: 36337--36376 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
36327 TTCTTCTTCT
36337 TACTTCCAATTTTAATTTA
1 TACTTCCAATTTTAATTTA
36356 TACTTCCAATTTTAATTTA
1 TACTTCCAATTTTAATTTA
36375 TA
1 TA
36377 GTATCAATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.53
Consensus pattern (19 bp):
TACTTCCAATTTTAATTTA
Found at i:42983 original size:636 final size:630
Alignment explanation
Indices: 41768--43020 Score: 2344
Period size: 636 Copynumber: 2.0 Consensus size: 630
41758 TTTATGCTCT
*
41768 ATTTTACCGTTTCTTAAATTGCCTATATTTTCTTGGTGGTTTGTGCTCTGTTTTGGTTTTATGAA
1 ATTTTACCATTTCTTAAATTGCCTATATTTTCTTGGTGGTTTGTGCTCTGTTTTGGTTTTATGAA
*
41833 ATAGGGGCAAACATAGCATTGATCTGCTGGGGAATTGTTCTGCTGAAGGATCACTATGTTGAGGA
66 ATAGGGGCAAACATAGCATCGATCTGCTGGGGAATTGTTCTGCTGAAGGATCACTATGTTGAGGA
41898 GGGAGCCCTTCTGCTAAAGATCGAGCTGCTGAGCCATATTCAGATCTCGTGCTCTGATGAGGCAA
131 GGGAGCCCTTCTGCTAAAGATCGAGCTGCTGAGCCATATTCAGATCTCGTGCTCTGATGAGGCAA
* *
41963 GCGTCGGTTCGAGCCTAACTCTTTGCTAAAAGAGATTTGGACCTAATCCATTAAACTTGATTCAG
196 ACGTCAGTTCGAGCCTAACTCTTTGCTAAAAGAGATTTGGACCTAATCCATTAAACTTGATTCAG
42028 GACTCAGATACTTGTGGGCCAGACTAGCCCTTATTCGAATATGCTAGAAGATCAAAATCTAGCTG
261 GACTCAGATACTTGTGGGCCAGACTAGCCCTTATTCGAATATGCTAGAAGATCAAAATCTAGCTG
42093 ACAACTCCAATCTCGAACTGACAAGGCGCCATATATGATCACCATAAAGGCCATGTCATCCCCAT
326 ACAACTCCAATCTCGAACTGACAAGGCGCCATATATGATCACCATAAAGGCCATGTCATCCCCAT
*
42158 CCCAAAAAGACCCCAACAGTCTGCTTATAATTATTTATATCCCCAGGACAAATTAGATCCCATGC
391 CCCAAAAAGACCCCAACAGTCTACTTATAATTATTTATATCCCCAGGACAAATTAGATCCCATGC
42223 ACTGAACGCTTTTCACCATATTATATACAAAACAATAAGAGGAGGAAGTGAAAAGACCAAAAAAC
456 ACTGAACGCTTTTCACCATATTATATACAAAACAATAAGAGGAGGAAGTGAAAAGACCAAAAAAC
*
42288 CGGTCTAAAGGTTTGACCTAGTTCATTTGGGCACTTTGGCCAGTTTTTTTTGTCATTTCAACATT
521 CGGTCTAAAGGTTTGACCTAATTCATTTGGGCACTTTGGCCAGTTTTTTTTGTCATTTCAACATT
42353 GGTATTTTTATTATTTGAGTTGACAACCAAGGCTCACTTCTTTCC
586 GGTATTTTTATTATTTGAGTTGACAACCAAGGCTCACTTCTTTCC
*
42398 ATTTTATCATTTCTTAAATTGCCTATATTTTCTTGGTGGTTTGTGCTCTGTTTTGGTTTTATGAA
1 ATTTTACCATTTCTTAAATTGCCTATATTTTCTTGGTGGTTTGTGCTCTGTTTTGGTTTTATGAA
*
42463 ATAGGGGCAAACATAGCATCGATCTGTTGGGGAATTGTTCTGCTGAAGGATCACTATGTTGAGGA
66 ATAGGGGCAAACATAGCATCGATCTGCTGGGGAATTGTTCTGCTGAAGGATCACTATGTTGAGGA
* *
42528 GGGAGCCCTTCTGCTAGAGATCGAGCTGTTGAGCCATATTCATATTCAGATCTCGTGCTCTGATG
131 GGGAGCCCTTCTGCTAAAGATCGAGCTGCTGAG-C-----CATATTCAGATCTCGTGCTCTGATG
42593 AGGCAAACGTCAGTTCGAGCCTAACTCTTTGCTAAAAGAGATTTGGACCTAATCCATTAAACTTG
190 AGGCAAACGTCAGTTCGAGCCTAACTCTTTGCTAAAAGAGATTTGGACCTAATCCATTAAACTTG
42658 ATTCAGGACTCAGATACTTGTGGGCCAGACTAGCCCTTATTCGAATATGCTAGAAGATCAAAATC
255 ATTCAGGACTCAGATACTTGTGGGCCAGACTAGCCCTTATTCGAATATGCTAGAAGATCAAAATC
42723 TAGCTGACAACTCCAATCTCGAACTGACAAGGCGCCATATATGATCACCATAAAGGCCATGTCAT
320 TAGCTGACAACTCCAATCTCGAACTGACAAGGCGCCATATATGATCACCATAAAGGCCATGTCAT
42788 CCCCATCCCAAAAAGACCCCAACAGTCTACTTATAATTATTTATATCCCCAGGACAAATTAGATC
385 CCCCATCCCAAAAAGACCCCAACAGTCTACTTATAATTATTTATATCCCCAGGACAAATTAGATC
42853 CCATGCACTGAACGCTTTTCACCATATTATATACAAAACAATAAGAGGAGGAAGTGAAAAGACCA
450 CCATGCACTGAACGCTTTTCACCATATTATATACAAAACAATAAGAGGAGGAAGTGAAAAGACCA
*
42918 AAAAACCGGTCTAGAGGTTTGACCTAATTCATTTGGGCACTTTGGCCAGTTTTTTTTGTCATTTC
515 AAAAACCGGTCTAAAGGTTTGACCTAATTCATTTGGGCACTTTGGCCAGTTTTTTTTGTCATTTC
*
42983 AACATTGGTATTTTTGTTATTTGAGTTGACAACCAAGG
580 AACATTGGTATTTTTATTATTTGAGTTGACAACCAAGG
43021 GCATTTTCAG
Statistics
Matches: 605, Mismatches: 12, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
630 157 0.26
631 1 0.00
636 447 0.74
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (630 bp):
ATTTTACCATTTCTTAAATTGCCTATATTTTCTTGGTGGTTTGTGCTCTGTTTTGGTTTTATGAA
ATAGGGGCAAACATAGCATCGATCTGCTGGGGAATTGTTCTGCTGAAGGATCACTATGTTGAGGA
GGGAGCCCTTCTGCTAAAGATCGAGCTGCTGAGCCATATTCAGATCTCGTGCTCTGATGAGGCAA
ACGTCAGTTCGAGCCTAACTCTTTGCTAAAAGAGATTTGGACCTAATCCATTAAACTTGATTCAG
GACTCAGATACTTGTGGGCCAGACTAGCCCTTATTCGAATATGCTAGAAGATCAAAATCTAGCTG
ACAACTCCAATCTCGAACTGACAAGGCGCCATATATGATCACCATAAAGGCCATGTCATCCCCAT
CCCAAAAAGACCCCAACAGTCTACTTATAATTATTTATATCCCCAGGACAAATTAGATCCCATGC
ACTGAACGCTTTTCACCATATTATATACAAAACAATAAGAGGAGGAAGTGAAAAGACCAAAAAAC
CGGTCTAAAGGTTTGACCTAATTCATTTGGGCACTTTGGCCAGTTTTTTTTGTCATTTCAACATT
GGTATTTTTATTATTTGAGTTGACAACCAAGGCTCACTTCTTTCC
Found at i:43942 original size:445 final size:441
Alignment explanation
Indices: 43090--44174 Score: 1404
Period size: 445 Copynumber: 2.5 Consensus size: 441
43080 ACTTCACTAG
* **
43090 TTGGATTATTTATCAAATGACCCCCATACTTTTCTACTTTATGTTATTTAG-TCATTTACAAATT
1 TTGGATTATTTATCAAATGA-CCTCATACTTTTCTACTTTATACTATTTAGTTC-TTTACAAATT
* * * * * *
43154 TTATCTTAATCGATTTAACGCTTTAGTTTTATTATTTTGATTTTCTGTTCTATTTGTCCGATTTA
64 CTATCTTAATCGATTTAACGCTTAAGCTTTATT-TTTT-ATTTTTTGTTCTATTTGTCCAATTAA
* * * *
43219 GGTGGTTCAGGTGTCTATTAAAAGCTAATTTCATGGTCTACAACTTTCATGAAAGACTCAAAAGC
127 GGTGATTCAGGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCATGAAGGACTCAAAAGC
** ** * * *
43284 CAA-TTTTTATGTTTCAATTCAAAACAAAACTTCTGAAATTTGGTTGTTTCGATTGTCGGTCTAT
192 CAATTTTTTATGCCTCAATTCAAAACAAAACTTCCCAAATTTGGTGGTTTCGATTGCCAGTCTAT
* * *
43348 TTAATATCATATAATTTTCGATCCACATGTCCGATTAAAGTTATTGATGAAGTGTCAGTGATAAT
257 TTAATATCATATAATTTTCGATCCACATGTCCGATTAAAGTTATT-ATCAAGTGTCAGTGAAAAG
** * * *
43413 GTTATTGCATGATCTACGACTTTTATGAAGGATCCGAAAGTTAAATTTGATCTACGAGTTGTATT
321 GTTATTGCATGATCTACGACTTGCATGAAGGATCCGAAAGCTAAATTTGATCTACAAGTTGTATG
* * * * *
43478 AAGGGTTCAAAATGAATTTTTATGTTTTAAGATCTCCATCAACAAACATTTTCTTAT
386 AAGAGTTCAAAAAGAATTTTTATGTTTCAAGATCTCCATCAA-AAACAATTTCCTAT
* * *
43535 TTGGATTATTTATCAAATGACCATCATA-TTTTCTACTTTACACTACTTAGTTCTTTACTAATTC
1 TTGGATTATTTATCAAATGACC-TCATACTTTTCTACTTTATACTATTTAGTTCTTTACAAATTC
* *
43599 TATTTTAATCGATTTAACGCTTAACCTTTATTTTTTAAAATTTTTTGTTCTATTTGTCCAATTAA
65 TATCTTAATCGATTTAACGCTTAAGCTTTATTTTTT---ATTTTTTGTTCTATTTGTCCAATTAA
* *
43664 GGTGATT-TGGTTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCATGACGGACTCAAAAG
127 GGTGATTCAGG-TGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCATGAAGGACTCAAAAG
43728 CCAATTTTTTATGCCTCAATTCAAAA-AAATACTTCCCAAATTTGGTGGTTTTCGATTGCCAGTC
191 CCAATTTTTTATGCCTCAATTCAAAACAAA-ACTTCCCAAATTTGGTGG-TTTCGATTGCCAGTC
* * *
43792 TATTTAATATCATATAGTTTTCGATCCACATGTCCGGTTAAAGTTA-T-TCAAGTGTCAGTTAAA
254 TATTTAATATCATATAATTTTCGATCCACATGTCCGATTAAAGTTATTATCAAGTGTCAGTGAAA
*
43855 AGGTTATTGCATGATCTACGAGTTGCATGAAGGA-CCAGAAAGCTAAATTTGATCTACAAGTT-T
319 AGGTTATTGCATGATCTACGACTTGCATGAAGGATCC-GAAAGCTAAATTTGATCTACAAGTTGT
*
43918 CATGAAGAGTTCAAAAGAGAATTTTTATGTTTCAAGATCTTCATCAAAAACAATTTCCTAT
383 -ATGAAGAGTTCAAAA-AGAATTTTTATGTTTCAAGATCTCCATCAAAAACAATTTCCTAT
* *
43979 TTGGATTATTTATCAAATGACTCTCATACTTTTCTATTTTATACTATTTAGTCCTTTACAAATTC
1 TTGGATTATTTATCAAATGAC-CTCATACTTTTCTACTTTATACTATTTAGTTCTTTACAAATTC
* * * * * * *
44044 AATCTTACTCGATTTAATGTTTCAGCTTTA--TTTT-TTTTTTATTCTATTTGTCCAATCAAGGT
65 TATCTTAATCGATTTAACGCTTAAGCTTTATTTTTTATTTTTTGTTCTATTTGTCCAATTAAGGT
* * * *
44106 AATTCAGGTGTCTATTAAAAGGT-ATTTCATGATATACAACTTTTATGAAGGACTCAAAAGCTAA
130 GATTCAGGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCATGAAGGACTCAAAAGCCAA
44170 TTTTT
195 TTTTT
44175 GTAAAAAACT
Statistics
Matches: 560, Mismatches: 66, Indels: 35
0.85 0.10 0.05
Matches are distributed among these distances:
438 42 0.08
439 44 0.08
440 2 0.00
443 11 0.02
444 176 0.31
445 193 0.34
446 35 0.06
447 57 0.10
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (441 bp):
TTGGATTATTTATCAAATGACCTCATACTTTTCTACTTTATACTATTTAGTTCTTTACAAATTCT
ATCTTAATCGATTTAACGCTTAAGCTTTATTTTTTATTTTTTGTTCTATTTGTCCAATTAAGGTG
ATTCAGGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCATGAAGGACTCAAAAGCCAAT
TTTTTATGCCTCAATTCAAAACAAAACTTCCCAAATTTGGTGGTTTCGATTGCCAGTCTATTTAA
TATCATATAATTTTCGATCCACATGTCCGATTAAAGTTATTATCAAGTGTCAGTGAAAAGGTTAT
TGCATGATCTACGACTTGCATGAAGGATCCGAAAGCTAAATTTGATCTACAAGTTGTATGAAGAG
TTCAAAAAGAATTTTTATGTTTCAAGATCTCCATCAAAAACAATTTCCTAT
Found at i:49379 original size:2 final size:2
Alignment explanation
Indices: 49372--49405 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
49362 ATCCATGGAC
49372 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
49406 CCATTCAACT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:51500 original size:29 final size:29
Alignment explanation
Indices: 51458--51514 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
51448 AATTATTGTC
*
51458 TTCAAATTAAATAGCTTGCTTAAGTAATT
1 TTCAAATCAAATAGCTTGCTTAAGTAATT
51487 TTCAAATCAAATAGCTTGCTTAAGTAAT
1 TTCAAATCAAATAGCTTGCTTAAGTAAT
51515 CATTTACCGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.39
Consensus pattern (29 bp):
TTCAAATCAAATAGCTTGCTTAAGTAATT
Found at i:51974 original size:22 final size:22
Alignment explanation
Indices: 51916--51974 Score: 82
Period size: 22 Copynumber: 2.7 Consensus size: 22
51906 GATTTCAATT
* * *
51916 TTTATTGCTGCTAGAAGTTAGA
1 TTTATTGCTGCCATAAGTCAGA
*
51938 TTTATTGCTGTCATAAGTCAGA
1 TTTATTGCTGCCATAAGTCAGA
51960 TTTATTGCTGCCATA
1 TTTATTGCTGCCATA
51975 GGGATACAGC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.42
Consensus pattern (22 bp):
TTTATTGCTGCCATAAGTCAGA
Found at i:53347 original size:3 final size:3
Alignment explanation
Indices: 53326--53361 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
53316 TCAATGTCAC
* *
53326 TAT TAT AAT TAT TAC TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
53362 CATCTGAAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:54560 original size:18 final size:18
Alignment explanation
Indices: 54537--54571 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
54527 ATTGAATTTA
*
54537 TAATTACTATATATATAT
1 TAATTACTACATATATAT
54555 TAATTACTACATATATA
1 TAATTACTACATATATA
54572 GTACCTATCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.46
Consensus pattern (18 bp):
TAATTACTACATATATAT
Found at i:55838 original size:74 final size:74
Alignment explanation
Indices: 55717--55864 Score: 235
Period size: 74 Copynumber: 2.0 Consensus size: 74
55707 CATGCAACAT
* *
55717 GTAGGTTTTGTGCTTATGTTAGTTTTGTTAGTTTAATTGTTACCTTCACTAAGGTTGCTTTATGT
1 GTAGGTTTTGTGCTTATGTGAGTTTTGTTAGTTTAATTATTACCTTCACTAAGGTTGCTTTATGT
55782 AGTTTCTTA
66 AGTTTCTTA
* * *
55791 GTAGGTTTTGTGCTTATGTGAGTTTTTTTAG-TTAATTTATTATCTTCATTAAGGTTGCTTTATG
1 GTAGGTTTTGTGCTTATGTGAGTTTTGTTAGTTTAA-TTATTACCTTCACTAAGGTTGCTTTATG
55855 TAGTTTCTTA
65 TAGTTTCTTA
55865 ATTAGTTTGT
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
73 4 0.06
74 64 0.94
ACGTcount: A:0.18, C:0.08, G:0.20, T:0.54
Consensus pattern (74 bp):
GTAGGTTTTGTGCTTATGTGAGTTTTGTTAGTTTAATTATTACCTTCACTAAGGTTGCTTTATGT
AGTTTCTTA
Found at i:59261 original size:21 final size:21
Alignment explanation
Indices: 59229--59272 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
59219 ATCTGTATTT
59229 ATAAATACTGAATAGTTACCA
1 ATAAATACTGAATAGTTACCA
*
59250 ATAAA-ACATGAATAGTTATCA
1 ATAAATAC-TGAATAGTTACCA
59271 AT
1 AT
59273 TCAAAAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.50, C:0.11, G:0.09, T:0.30
Consensus pattern (21 bp):
ATAAATACTGAATAGTTACCA
Found at i:68642 original size:39 final size:40
Alignment explanation
Indices: 68586--68666 Score: 128
Period size: 39 Copynumber: 2.0 Consensus size: 40
68576 TTTAATTCCT
*
68586 ATGTAATATATATAATAACTAAAATATTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
68626 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
68665 AT
1 AT
68667 TCTTAGGTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 30 0.79
40 8 0.21
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.38
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:69150 original size:199 final size:203
Alignment explanation
Indices: 68775--69181 Score: 750
Period size: 199 Copynumber: 2.0 Consensus size: 203
68765 TTCCTTAACA
* *
68775 ATAAATAAATCGGATTTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
1 ATAAATAAATCAGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
68840 AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATATAATAG
66 AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATATAATAG
68905 TAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATAATAACATT
131 TAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATAATAACATT
*
68970 CGCCATTG
196 CACCATTG
68978 ATAAATAAATCAGATCTTTAATATCTTTTATAATTTTGAAATTTT-TTTGACATTGATCTAATTT
1 ATAAATAAATCAGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
69042 AATTTAATAAATCAACCACTAATGTTCAACTAA-TTTTTTTGGTATAGTT-T-TATATATAATAG
66 AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATATAATAG
*
69104 TAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAATTAATAACATT
131 TAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATAATAACATT
69169 CACCATTG
196 CACCATTG
69177 ATAAA
1 ATAAA
69182 GTTATTAAGC
Statistics
Matches: 200, Mismatches: 4, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
199 88 0.44
200 1 0.00
201 16 0.08
202 52 0.26
203 43 0.22
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.44
Consensus pattern (203 bp):
ATAAATAAATCAGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATATAATAG
TAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATAATAACATT
CACCATTG
Found at i:69737 original size:36 final size:36
Alignment explanation
Indices: 69690--69759 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
69680 GAGATTTTGG
* *
69690 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA
*
69726 AGAAATATGATAACCAAAATCACAAAAGATGTAA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAA
69760 GGTTATTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.60, C:0.09, G:0.10, T:0.21
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATCACAAAAAATGTAATA
Found at i:72121 original size:19 final size:21
Alignment explanation
Indices: 72099--72138 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
72089 CCTTATACTA
72099 TATAA-ATTTTT-ATAACCTT
1 TATAACATTTTTAATAACCTT
*
72118 TATAACTTTTTTAATAACCTT
1 TATAACATTTTTAATAACCTT
72139 AAAGAAGAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 5 0.28
21 8 0.44
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.53
Consensus pattern (21 bp):
TATAACATTTTTAATAACCTT
Found at i:76443 original size:15 final size:14
Alignment explanation
Indices: 76423--76475 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
76413 ATATATTTCT
76423 AAATTTACATTATTA
1 AAATTTA-ATTATTA
* *
76438 AAATTTATTTGTTA
1 AAATTTAATTATTA
*
76452 AAAATTAATTA-TA
1 AAATTTAATTATTA
76465 AAATTTCAATT
1 AAATTT-AATT
76476 TAAAACGAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
13 7 0.23
14 17 0.55
15 7 0.23
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (14 bp):
AAATTTAATTATTA
Found at i:77066 original size:24 final size:22
Alignment explanation
Indices: 76898--77080 Score: 84
Period size: 22 Copynumber: 8.2 Consensus size: 22
76888 CTCCGTGTGC
* * *
76898 TTATCAAAATTTCATAAGATGG
1 TTATTAAAATTTCATAGGAAGG
**
76920 TTATTATGATTTCATGAGG-AGG
1 TTATTAAAATTTCAT-AGGAAGG
** * * *
76942 TTAACAAATTTTCATAGTATGG
1 TTATTAAAATTTCATAGGAAGG
** *
76964 TTACCAGAATTTCATATGGAA-G
1 TTATTAAAATTTCATA-GGAAGG
* * *
76986 TTATCAAAATTTTATGGGAAGG
1 TTATTAAAATTTCATAGGAAGG
* * * * *
77008 TTATCACATTTTCATAGTG-TGA
1 TTATTAAAATTTCATAG-GAAGG
**
77030 TTACCAAAATTTCATAGGATCAGG
1 TTATTAAAATTTCATAGGA--AGG
*
77054 TTATTAAAATTTCTTAGGAAGG
1 TTATTAAAATTTCATAGGAAGG
77076 TTATT
1 TTATT
77081 GAAACTTCGT
Statistics
Matches: 118, Mismatches: 35, Indels: 16
0.70 0.21 0.09
Matches are distributed among these distances:
21 7 0.06
22 89 0.75
23 5 0.04
24 17 0.14
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.39
Consensus pattern (22 bp):
TTATTAAAATTTCATAGGAAGG
Found at i:77079 original size:22 final size:23
Alignment explanation
Indices: 77035--77080 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
77025 TGTGATTACC
77035 AAAATTTCATAGGATCAGGTTATT
1 AAAATTTCATAGGA-CAGGTTATT
*
77059 AAAATTTCTTAGGA-AGGTTATT
1 AAAATTTCATAGGACAGGTTATT
77081 GAAACTTCGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 8 0.38
24 13 0.62
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.39
Consensus pattern (23 bp):
AAAATTTCATAGGACAGGTTATT
Found at i:77156 original size:22 final size:22
Alignment explanation
Indices: 77128--77169 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
77118 GGTTATCAAA
77128 GAGATTACTAA-AATGTCATAGT
1 GAGATTA-TAAGAATGTCATAGT
*
77150 GAGATTATAAGAATTTCATA
1 GAGATTATAAGAATGTCATA
77170 CTATGGTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.43, C:0.07, G:0.17, T:0.33
Consensus pattern (22 bp):
GAGATTATAAGAATGTCATAGT
Found at i:77191 original size:44 final size:43
Alignment explanation
Indices: 77137--77524 Score: 121
Period size: 44 Copynumber: 8.7 Consensus size: 43
77127 AGAGATTACT
* * * *
77137 AAAATGTCATAGTGAGATTATAAGAATTTCATACTATGGTTAAC
1 AAAATTTCATAGTGAGGTTATAA-AATTTCATACGAAGGTTAAC
* ** *
77181 AAAATTTCATAAG-GAGGTTACTAATATTTCATGGGAAGGTTATC
1 AAAATTTCAT-AGTGAGGTTA-TAAAATTTCATACGAAGGTTAAC
** * *
77225 AAAATTTCATAGTGAGGTTATCAAAATTTTTTA-G-TGTGATTATC
1 AAAATTTCATAGTGAGGTTAT-AAAATTTCATACGAAG-G-TTAAC
* * * * *
77269 AAAATTTCATA-TGAAGGTTATAAAAGTCTCAATTTCATAAGGAGTACC
1 AAAATTTCATAGTG-AGGTTATAAAA-TTTC-A-TAC-GAAGG-TTAAC
* * * * * **
77317 ACAATTTGATAG-AAGGTTATCAAATCTCATA-G-AGTGATTATT
1 AAAATTTCATAGTGAGGTTATAAAATTTCATACGAAG-G-TTAAC
* * * * * *
77359 GAAATTTCATAGAGATCGGATTATCAAACTTT-ATAGGAAGATTATC
1 AAAATTTCATAGTGA--GG-TTAT-AAAATTTCATACGAAGGTTAAC
** * *
77405 AAAATTTCATAGTGTTGTTATCAAAATTTCAAAGCG-AGGTTATC
1 AAAATTTCATAGTGAGGTTAT-AAAATTTCATA-CGAAGGTTAAC
* * * * * * *
77449 AAAATTACACAATGTGATTATCAAAATTTCATA-GAGGGTCAAC
1 AAAATTTCATAGTGAGGTTAT-AAAATTTCATACGAAGGTTAAC
* *
77492 AAAATTTTATAGAGAGGTTATCAAAATTTCATA
1 AAAATTTCATAGTGAGGTTAT-AAAATTTCATA
77525 AAGAGGTTAT
Statistics
Matches: 256, Mismatches: 63, Indels: 51
0.69 0.17 0.14
Matches are distributed among these distances:
41 2 0.01
42 15 0.06
43 54 0.21
44 116 0.45
45 9 0.04
46 28 0.11
47 15 0.06
48 16 0.06
49 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (43 bp):
AAAATTTCATAGTGAGGTTATAAAATTTCATACGAAGGTTAAC
Found at i:77199 original size:22 final size:21
Alignment explanation
Indices: 77174--77533 Score: 86
Period size: 22 Copynumber: 16.2 Consensus size: 21
77164 TTCATACTAT
77174 GGTTAACAAAATTTCATAAGGA
1 GGTTAACAAAATTTCAT-AGGA
* *
77196 GGTT-ACTAATATTTCATGGGAA
1 GGTTAAC-AAAATTTCATAGG-A
*
77218 GGTTATCAAAATTTCATAGTGA
1 GGTTAACAAAATTTCATAG-GA
* ** *
77240 GGTTATCAAAATTTTTTAGTGT
1 GGTTAACAAAATTTCATAG-GA
* * *
77262 GATTATCAAAATTTCATATGAA
1 GGTTAACAAAATTTCATA-GGA
*
77284 GGTTATAAAAGTCTCAATTTCATAAGGA
1 GGTTA-ACAA-----AATTTCAT-AGGA
* * * *
77312 -G-TACCACAATTTGATAGAA
1 GGTTAACAAAATTTCATAGGA
* *
77331 GGTTATC-AAATCTCATA-GA
1 GGTTAACAAAATTTCATAGGA
***
77350 GTGATTATTGAAATTTCATAGAGA
1 G-G-TTAACAAAATTTCATAG-GA
* *
77374 TCGGATTATCAAACTTT-ATAGGAA
1 --GG-TTAACAAAATTTCATAGG-A
* * *
77398 GATTATCAAAATTTCATAGTGT
1 GGTTAACAAAATTTCATAG-GA
* * *
77420 TGTTATCAAAATTTCAAAGCGA
1 GGTTAACAAAATTTCATAG-GA
* * * * *
77442 GGTTATCAAAATTACACAATGT
1 GGTTAACAAAATTTCA-TAGGA
* *
77464 GATTATCAAAATTTCATA-GA
1 GGTTAACAAAATTTCATAGGA
* *
77484 GGGTCAACAAAATTTTATAGAGA
1 -GGTTAACAAAATTTCATAG-GA
* *
77507 GGTTATCAAAATTTCATAAAGA
1 GGTTAACAAAATTTCAT-AGGA
77529 GGTTA
1 GGTTA
77534 TTTAATTTTC
Statistics
Matches: 253, Mismatches: 56, Indels: 58
0.69 0.15 0.16
Matches are distributed among these distances:
19 5 0.02
20 17 0.07
21 37 0.15
22 148 0.58
23 12 0.05
24 7 0.03
25 12 0.05
26 3 0.01
27 1 0.00
28 10 0.04
29 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (21 bp):
GGTTAACAAAATTTCATAGGA
Found at i:77495 original size:87 final size:87
Alignment explanation
Indices: 77404--77569 Score: 217
Period size: 87 Copynumber: 1.9 Consensus size: 87
77394 GGAAGATTAT
* ** * *
77404 CAAAATTTCATAGTGTTGTTATCAAAATTTCA-AAGCGAGGTTATCAAAATTACACAATGTGATT
1 CAAAATTTCATAGAGAGGTTATCAAAATTTCATAA-AGAGGTTATCAAAATTACAAAATGTGATT
*
77468 ATCAAAATTTCATAGAGGGTCAA
65 ACCAAAATTTCATAGAGGGTCAA
* ** * *
77491 CAAAATTTTATAGAGAGGTTATCAAAATTTCATAAAGAGGTTATTTAATTTTCAAAATGTGATTA
1 CAAAATTTCATAGAGAGGTTATCAAAATTTCATAAAGAGGTTATCAAAATTACAAAATGTGATTA
77556 CCAAAATTTCATAG
66 CCAAAATTTCATAG
77570 TGGTATTTCT
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
87 65 0.97
88 2 0.03
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (87 bp):
CAAAATTTCATAGAGAGGTTATCAAAATTTCATAAAGAGGTTATCAAAATTACAAAATGTGATTA
CCAAAATTTCATAGAGGGTCAA
Found at i:77534 original size:22 final size:22
Alignment explanation
Indices: 77400--77534 Score: 112
Period size: 22 Copynumber: 6.2 Consensus size: 22
77390 TATAGGAAGA
** **
77400 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAAAGAGG
*
77422 TTATCAAAATTTCA-AAGCGAGG
1 TTATCAAAATTTCATAA-AGAGG
* * * * *
77444 TTATCAAAATTACACAATGTGA
1 TTATCAAAATTTCATAAAGAGG
*
77466 TTATCAAAATTTCATAGAG-GG
1 TTATCAAAATTTCATAAAGAGG
* * * *
77487 TCAACAAAATTTTATAGAGAGG
1 TTATCAAAATTTCATAAAGAGG
77509 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAAAGAGG
77531 TTAT
1 TTAT
77535 TTAATTTTCA
Statistics
Matches: 90, Mismatches: 20, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
21 18 0.20
22 70 0.78
23 2 0.02
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (22 bp):
TTATCAAAATTTCATAAAGAGG
Found at i:77695 original size:22 final size:22
Alignment explanation
Indices: 77667--77946 Score: 134
Period size: 22 Copynumber: 12.6 Consensus size: 22
77657 TTTCAGGGGA
77667 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
* **
77689 TATCAAAATTTAATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * *
77711 TTTCAAAATTTCATAAGAGGGT
1 TATCAAAATTTCATATGAAGGT
* *
77733 TATCAAAATTTCATAT-TATGT
1 TATCAAAATTTCATATGAAGGT
*
77754 AGATCAAAATTTCATAT-ATAGGGAGAT
1 -TATCAAAATTTCATATGA-A--G-G-T
* *
77781 TAACAAAATTTCATAATG-AGAT
1 TATCAAAATTTCAT-ATGAAGGT
* * *
77803 TATCAGAAA-ATCATAGGGAGGT
1 TATCA-AAATTTCATATGAAGGT
*
77825 TATCAAAA--T--T-TGCA-GT
1 TATCAAAATTTCATATGAAGGT
* *
77841 TATCAAGATTTCATAAGAAGGT
1 TATCAAAATTTCATATGAAGGT
* *
77863 TATCAAAATTTTATAGGAAGGTT
1 TATCAAAATTTCATATGAAGG-T
* **
77886 TATCAAAATTTTACAGGAAAAAGGT
1 TATCAAAA-TTT-CA-TATGAAGGT
*
77911 TCATCAAAATTTCATAGTGAA-AT
1 T-ATCAAAATTTCATA-TGAAGGT
77934 TATCAAAATTTCA
1 TATCAAAATTTCA
77947 AAGTGTGATT
Statistics
Matches: 194, Mismatches: 40, Indels: 48
0.69 0.14 0.17
Matches are distributed among these distances:
16 9 0.05
17 2 0.01
18 2 0.01
20 2 0.01
21 9 0.05
22 109 0.56
23 18 0.09
24 8 0.04
25 6 0.03
26 26 0.13
27 3 0.02
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:78036 original size:23 final size:22
Alignment explanation
Indices: 78020--78103 Score: 71
Period size: 22 Copynumber: 3.8 Consensus size: 22
78010 TCATAGTGTT
*
78020 AGTTATCAAAATTTCATTGGGA
1 AGTTATCAAAATTTCATAGGGA
**
78042 AGTTATCAAAATTTCATACTGA
1 AGTTATCAAAATTTCATAGGGA
* * *
78064 GGTCT-TCAAAATTCCTTAGGGA
1 AGT-TATCAAAATTTCATAGGGA
* * *
78086 GGTTAACAAATTTTCATA
1 AGTTATCAAAATTTCATA
78104 AAAAGATTTA
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
21 1 0.02
22 46 0.96
23 1 0.02
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (22 bp):
AGTTATCAAAATTTCATAGGGA
Found at i:93226 original size:27 final size:27
Alignment explanation
Indices: 93193--93264 Score: 99
Period size: 27 Copynumber: 2.7 Consensus size: 27
93183 AGTGATCCTA
93193 AAATGACCAAAATGCCCCTGAACATGC
1 AAATGACCAAAATGCCCCTGAACATGC
* * **
93220 AAATGACCAAAATGCTCCTGGATGTGC
1 AAATGACCAAAATGCCCCTGAACATGC
*
93247 AAATGACTAAAATGCCCC
1 AAATGACCAAAATGCCCC
93265 CTAGGTGACC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.39, C:0.26, G:0.17, T:0.18
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGAACATGC
Found at i:94736 original size:59 final size:59
Alignment explanation
Indices: 94662--94789 Score: 188
Period size: 59 Copynumber: 2.2 Consensus size: 59
94652 TCTAGGGATA
* * *
94662 AAAGTTTCAAATTAAAAGTTCAAGGGAAAAATTCTTCTGA-TTTTGATAGTTT-AAGGGTG
1 AAAGTTTCAAATTAAAAGTTCAAGGG-AAAATTATTCTGACTTTAG-TAGTTTAAAGAGTG
*
94721 AAAGTTTCAAATTAAAAGTTCAAGGGAAAATTATTCTGACTTTAGTAGTTTAAAGATTG
1 AAAGTTTCAAATTAAAAGTTCAAGGGAAAATTATTCTGACTTTAGTAGTTTAAAGAGTG
94780 AAAGTTTCAA
1 AAAGTTTCAA
94790 TTTATAGGTT
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
58 18 0.29
59 45 0.71
ACGTcount: A:0.40, C:0.07, G:0.18, T:0.35
Consensus pattern (59 bp):
AAAGTTTCAAATTAAAAGTTCAAGGGAAAATTATTCTGACTTTAGTAGTTTAAAGAGTG
Found at i:96139 original size:30 final size:30
Alignment explanation
Indices: 96103--96163 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
96093 TATTTTTACC
96103 TATTAATTTTATGGTGAAATAATAACATGA
1 TATTAATTTTATGGTGAAATAATAACATGA
96133 TATTAATTTTATGGTGAAATAATAACATGA
1 TATTAATTTTATGGTGAAATAATAACATGA
96163 T
1 T
96164 CTTATTGGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.43, C:0.03, G:0.13, T:0.41
Consensus pattern (30 bp):
TATTAATTTTATGGTGAAATAATAACATGA
Found at i:100312 original size:16 final size:17
Alignment explanation
Indices: 100291--100323 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
100281 AAGAATTAAG
100291 ATAATATATAA-AATAA
1 ATAATATATAATAATAA
100307 ATAATATATAATAATAA
1 ATAATATATAATAATAA
100324 CTCTCATTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATAATATATAATAATAA
Found at i:101823 original size:20 final size:22
Alignment explanation
Indices: 101777--101823 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 22
101767 ACTAATCTTC
101777 TTATATAAGATTACTAAAAAAG
1 TTATATAAGATTACTAAAAAAG
* * *
101799 CTATAT-AGATTA-TGAAAATG
1 TTATATAAGATTACTAAAAAAG
101819 TTATA
1 TTATA
101824 CTCTTATCAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 10 0.48
21 6 0.29
22 5 0.24
ACGTcount: A:0.49, C:0.04, G:0.11, T:0.36
Consensus pattern (22 bp):
TTATATAAGATTACTAAAAAAG
Found at i:101993 original size:18 final size:19
Alignment explanation
Indices: 101946--101996 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 19
101936 TTCACATCTA
101946 ATAAGGTTACTAAAAAAACT
1 ATAAGGTTA-TAAAAAAACT
101966 ATAGAGGTTATATAAAAAA-T
1 ATA-AGGTTATA-AAAAAACT
101986 -TAAGGTTATAA
1 ATAAGGTTATAA
101997 CTTCAGCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
17 1 0.03
18 8 0.28
19 2 0.07
20 6 0.21
21 12 0.41
ACGTcount: A:0.53, C:0.04, G:0.14, T:0.29
Consensus pattern (19 bp):
ATAAGGTTATAAAAAAACT
Found at i:102708 original size:2 final size:2
Alignment explanation
Indices: 102701--102733 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
102691 TCTCTTTGTG
102701 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
102734 T
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.