Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397282.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_25.0, 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: 1368273
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.33
Warning! 33278 characters in sequence are not A, C, G, or T
File 2 of 4
Found at i:320970 original size:189 final size:190
Alignment explanation
Indices: 320650--321033 Score: 743
Period size: 189 Copynumber: 2.0 Consensus size: 190
320640 CCTTAGAAAG
320650 TTTTTGCGGCAGTCACTGCCGCTTTATATTCATCGGTAGAGTATCTCCGACGTTTCGACTTTCAC
1 TTTTTGCGGCAGTCACTGCCGCTTTATATTCATCGGTAGAGTATCTCCGACGTTTCGACTTTCAC
320715 TCGTTGCAGATAAATTGAAAAAATTAATTAAATTCTGAAAATTTTAATTTTAAAAAATTTAAATA
66 TCGTTGCAGATAAATTGAAAAAATTAATTAAATTCTGAAAATTTTAATTTTAAAAAATTTAAATA
*
320780 TTGAGAACATTTTTAATTGAATATTTTGTAAAATTTGAATACTGAATTTAATTGAAT-TT
131 TTGAGAACATTTTTAATTGAATATTTTGTAAAATTTGAACACTGAATTTAATTGAATATT
*
320839 TTTTTGCGGCTGTCACTGCCGCTTTATATTCATCGGTAGAGTATCTCCGACGTTTCGACTTTCAC
1 TTTTTGCGGCAGTCACTGCCGCTTTATATTCATCGGTAGAGTATCTCCGACGTTTCGACTTTCAC
320904 TCGTTGCAGATAAATTGAAAAAATTAATTAAATTCTGAAAATTTTAATTTTAAAAAATTTAAATA
66 TCGTTGCAGATAAATTGAAAAAATTAATTAAATTCTGAAAATTTTAATTTTAAAAAATTTAAATA
320969 TTGAGAACATTTTTAATTGAATATTTTGTAAAATTTGAACACTGAATTTAATTGAATATT
131 TTGAGAACATTTTTAATTGAATATTTTGTAAAATTTGAACACTGAATTTAATTGAATATT
321029 TTTTT
1 TTTTT
321034 ATATTACTTT
Statistics
Matches: 192, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
189 185 0.96
190 7 0.04
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.41
Consensus pattern (190 bp):
TTTTTGCGGCAGTCACTGCCGCTTTATATTCATCGGTAGAGTATCTCCGACGTTTCGACTTTCAC
TCGTTGCAGATAAATTGAAAAAATTAATTAAATTCTGAAAATTTTAATTTTAAAAAATTTAAATA
TTGAGAACATTTTTAATTGAATATTTTGTAAAATTTGAACACTGAATTTAATTGAATATT
Found at i:323871 original size:496 final size:493
Alignment explanation
Indices: 322796--324293 Score: 2162
Period size: 496 Copynumber: 3.0 Consensus size: 493
322786 GTTGTATGAC
* * * ** * *
322796 TTAAAAGAAACAGATAGGCCTATCAAACGAT-AAGAAATACAATGCAATAGCTGAACAAACTTTA
1 TTAAAAGAAACAGAGAAGCCTATTAGTCGATAAAGAAATACAATGCAATAGCTTAACAAACTATA
* * **
322860 TTGAGAAGAGG-GCCTGAGGGTGCCAACTATTATCCGTTAAACTTATGGTTGTTTGCTTCATTTA
66 TTGAGAAGAGGACCCTGA-GGTGCCAAC---TA----TT--A-TTATGTTTGTTTGCTTCATCAA
* *
322924 TCATTTCTGGCTTTAGTTGATATGGTTTAACTTTAATTTATT-TGTACTGGCTTACAGTGAATCA
120 TCATTTCTGGCTTCAGTTGATTTGGTTTAACTTTAATTTATTCT-TACTGGCTTACAGTGAATCA
* *
322988 GGTGTCAGGAATGAAGAAACACAGAAGCTTGTGCTTGGTGTTGATGATGGTATGCCAAAGAAGAA
184 GTTGTCAGGAATGAAGAAACACAAAAGCTTGTGCTTGGTGTTGATGATGGTATGCCAAAGAAGAA
* * *
323053 AAGAGAAGTGCCGGTAAAGGAGGAAAGATTTTCTGAAGATGATCATGGCATGACTGGAAAAACAG
249 AAGAGAAGTGCTGGTCAAGGAGGAAAGA-TTTCTGAAGATGATCATGGCATGACTGGAAAAGCAG
*
323118 TATTGGAACAAAATGAGCAAAATCAGAAGCTGGCCAGTAATGAGTGAGTGTTATTTTGCTTAAAA
313 TATTGGAACAAAATGAGCAAAATCAGAAGCT-GCCAGTAATGAGTGAGTGATATTTTGCTTAAAA
* *
323183 ATTTTCTTGTTTAATGAATTGTGCATTAGAGT-GTGGAAAATGACGTGGAGGAAAAAGCTAGGAA
377 ATTTTGTTGTTTAATGAATTGTGCATTGGA-TAGTGGAAAATGACGTGGAGGAAAAAGCTAGGAA
* * * * *
323247 GAAAATAGATAGAATGAGACTCAAGATAATGTTACAATTTTAGAAGGGAGTAA
441 GGAAATAGATAAAATGAGACTCAAGATAATGTTACAATGTCAGAAGGGACTAA
* * * * *
323300 TTAAACGAAACAGAGAAGCCTATTAGTCGATAATGGAATACAATGCTATAGCTTAGTC-AACTAT
1 TTAAAAGAAACAGAGAAGCCTATTAGTCGATAAAGAAATACAATGCAATAGCTTA-ACAAACTAT
*
323364 ATTGGGAAGAGGACCCTGAGGTGCCAACTATTATTATGTTTGTTTGCTTCATCAATCATTTCTGG
65 ATTGAGAAGAGGACCCTGAGGTGCCAACTATTATTATGTTTGTTTGCTTCATCAATCATTTCTGG
323429 CTTCCAGTTGATTTGGTTTAACTTTAATTTATTCTTACTGGCTTACAGTGAATCAGTTGTCAGGA
130 CTT-CAGTTGATTTGGTTTAACTTTAATTTATTCTTACTGGCTTACAGTGAATCAGTTGTCAGGA
*
323494 ATGAAGAAGCACAAAAGCTTGTGCTTGGTGTTGATGATGGTATGCCAAAGAAGAAAAGAGAAGTG
194 ATGAAGAAACACAAAAGCTTGTGCTTGGTGTTGATGATGGTATGCCAAAGAAGAAAAGAGAAGTG
* * * *
323559 CTGGTCAAGGAGGAAAGATTTCATGAAGCTGACCATGGCATGACTGGAAAGGCAGTATTAGAACA
259 CTGGTCAAGGAGGAAAGATTTC-TGAAGATGATCATGGCATGACTGGAAAAGCAGTATTGGAACA
*
323624 AAATGAGCAAAATCAGAAGCTGCCCAGTAATGAGTGAGTGATATTTTGCTTAAAAAATTTGTTGT
323 AAATGAGCAAAATCAGAAGCTG-CCAGTAATGAGTGAGTGATATTTTGCTTAAAAATTTTGTTGT
* * * * * *
323689 TTAAAGAATTATGCATTGGATAATGGAAAATGATGTCGAGGAAAAAGCTAAGAAGGAAATAGATA
387 TTAATGAATTGTGCATTGGATAGTGGAAAATGACGTGGAGGAAAAAGCTAGGAAGGAAATAGATA
*
323754 AAATGAGACTCAAGATAATGTTACAATGTCAGAAAGGACTAA
452 AAATGAGACTCAAGATAATGTTACAATGTCAGAAGGGACTAA
* *
323796 TTAAAAGAAACAGAGAAGCCTATTAGTTGATAAAGAAATACAATGCAACAGCTTAACAAACTATA
1 TTAAAAGAAACAGAGAAGCCTATTAGTCGATAAAGAAATACAATGCAATAGCTTAACAAACTATA
**
323861 TTGAGAAGAGGACATTGAGGTGCCAACTATTATTATGTTTGTTTGCTTCATCAATCATTTCTGGC
66 TTGAGAAGAGGACCCTGAGGTGCCAACTATTATTATGTTTGTTTGCTTCATCAATCATTTCTGGC
* **
323926 TTGCAGTTGATTTGGTTTAACTTTAATTTATTCGTACTGGCTTACAGTGAATCAGTTGTCCCGAA
131 TT-CAGTTGATTTGGTTTAACTTTAATTTATTCTTACTGGCTTACAGTGAATCAGTTGTCAGGAA
* *
323991 TGAAGAAACACAAAAACTTGTGCTTGGTGTTGATGATGGTATGCCAAAGAAGAAACGAGAAGTGC
195 TGAAGAAACACAAAAGCTTGTGCTTGGTGTTGATGATGGTATGCCAAAGAAGAAAAGAGAAGTGC
*
324056 TGGTCAAGGAGGAAAGATTTCCTGAAGTTGATCATGGCATGACTGGAAAAGCAGTATTGGAACAA
260 TGGTCAAGGAGGAAAGATTT-CTGAAGATGATCATGGCATGACTGGAAAAGCAGTATTGGAACAA
* *
324121 AATGAGCAAAATCAGAAGCTTGCCAGTGATGAGTGAGTGATATTTTGC-CAAAAATTTTGTTGTT
324 AATGAGCAAAATCAGAAGC-TGCCAGTAATGAGTGAGTGATATTTTGCTTAAAAATTTTGTTGTT
* * * * *
324185 GAATGATTTGTGCATTGAATAGTGGAAAAGTCAACATGGAGGAAAAAGCTAGGAAGGAAATAGAT
388 TAATGAATTGTGCATTGGATAGTGGAAAA-T-GACGTGGAGGAAAAAGCTAGGAAGGAAATAGAT
* *
324250 AAAATGAGATTGAAGATAATGTTACAATGTCAGAAGGGACTAA
451 AAAATGAGACTCAAGATAATGTTACAATGTCAGAAGGGACTAA
324293 T
1 T
324294 GCTGCACTAG
Statistics
Matches: 898, Mismatches: 83, Indels: 33
0.89 0.08 0.03
Matches are distributed among these distances:
495 76 0.08
496 670 0.75
497 73 0.08
498 2 0.00
502 2 0.00
504 25 0.03
505 44 0.05
506 6 0.01
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (493 bp):
TTAAAAGAAACAGAGAAGCCTATTAGTCGATAAAGAAATACAATGCAATAGCTTAACAAACTATA
TTGAGAAGAGGACCCTGAGGTGCCAACTATTATTATGTTTGTTTGCTTCATCAATCATTTCTGGC
TTCAGTTGATTTGGTTTAACTTTAATTTATTCTTACTGGCTTACAGTGAATCAGTTGTCAGGAAT
GAAGAAACACAAAAGCTTGTGCTTGGTGTTGATGATGGTATGCCAAAGAAGAAAAGAGAAGTGCT
GGTCAAGGAGGAAAGATTTCTGAAGATGATCATGGCATGACTGGAAAAGCAGTATTGGAACAAAA
TGAGCAAAATCAGAAGCTGCCAGTAATGAGTGAGTGATATTTTGCTTAAAAATTTTGTTGTTTAA
TGAATTGTGCATTGGATAGTGGAAAATGACGTGGAGGAAAAAGCTAGGAAGGAAATAGATAAAAT
GAGACTCAAGATAATGTTACAATGTCAGAAGGGACTAA
Found at i:334805 original size:11 final size:11
Alignment explanation
Indices: 334786--334821 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
334776 TCAATGCTTG
334786 TTTTGAAATAA
1 TTTTGAAATAA
*
334797 TTTTAAAATAA
1 TTTTGAAATAA
334808 TTTTGAAATAA
1 TTTTGAAATAA
334819 TTT
1 TTT
334822 ATTTCAAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (11 bp):
TTTTGAAATAA
Found at i:335781 original size:27 final size:28
Alignment explanation
Indices: 335751--335808 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
335741 TTATTTCACC
*
335751 AAATAATGG-TAGACTCATTTGAATTTG
1 AAATAATGGAAAGACTCATTTGAATTTG
** *
335778 AAATTTTGGAAAGATTCATTTGAATTTG
1 AAATAATGGAAAGACTCATTTGAATTTG
335806 AAA
1 AAA
335809 CATCTTTATC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 7 0.27
28 19 0.73
ACGTcount: A:0.40, C:0.05, G:0.17, T:0.38
Consensus pattern (28 bp):
AAATAATGGAAAGACTCATTTGAATTTG
Found at i:340365 original size:24 final size:25
Alignment explanation
Indices: 340332--340382 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
340322 GTTGGAAAAG
*
340332 AATTTCCAAC-CAAATTCTGTTGGA
1 AATTTCCAACACAAATTCCGTTGGA
* *
340356 AATTTTCAACAGAAATTCCGTTGGA
1 AATTTCCAACACAAATTCCGTTGGA
340381 AA
1 AA
340383 AGAATTTCCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 9 0.39
25 14 0.61
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (25 bp):
AATTTCCAACACAAATTCCGTTGGA
Found at i:342434 original size:31 final size:31
Alignment explanation
Indices: 342368--342443 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
342358 TATACATGAA
* **
342368 AATGAAAGAGCACGAATCTTATTTGACAATT
1 AATGAAAGAGCACGAATCTCATTTGACAAGC
342399 AATGAAAGAGCACGAATCTCA-TTG-CTACAGC
1 AATGAAAGAGCACGAATCTCATTTGAC-A-AGC
342430 AATGAAAGAGCACG
1 AATGAAAGAGCACG
342444 TTGTCATCTG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
29 1 0.03
30 4 0.10
31 35 0.88
ACGTcount: A:0.42, C:0.17, G:0.20, T:0.21
Consensus pattern (31 bp):
AATGAAAGAGCACGAATCTCATTTGACAAGC
Found at i:345675 original size:21 final size:19
Alignment explanation
Indices: 345639--345680 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
345629 ACATGTTGAA
345639 TAGTTAATTTAAGTTATTT
1 TAGTTAATTTAAGTTATTT
*
345658 TAGTTCAATTTTATGTTATTT
1 TAGTT-AA-TTTAAGTTATTT
345679 TA
1 TA
345681 TTTTAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 2 0.10
21 13 0.65
ACGTcount: A:0.29, C:0.02, G:0.10, T:0.60
Consensus pattern (19 bp):
TAGTTAATTTAAGTTATTT
Found at i:348092 original size:15 final size:15
Alignment explanation
Indices: 348072--348101 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
348062 GAATATGTTA
348072 AATTTATAATTATAT
1 AATTTATAATTATAT
*
348087 AATTTATATTTATAT
1 AATTTATAATTATAT
348102 TTTCTTTTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
AATTTATAATTATAT
Found at i:356223 original size:21 final size:23
Alignment explanation
Indices: 356199--356244 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
356189 GATGAAAAGA
356199 TTAAAAATT-TT-TTATATTATT
1 TTAAAAATTATTATTATATTATT
* *
356220 TTAAAATTTATTATTATATTTTT
1 TTAAAAATTATTATTATATTATT
356243 TT
1 TT
356245 TAATAAAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 8 0.38
22 2 0.10
23 11 0.52
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
TTAAAAATTATTATTATATTATT
Found at i:356683 original size:29 final size:28
Alignment explanation
Indices: 356649--356766 Score: 96
Period size: 27 Copynumber: 4.2 Consensus size: 28
356639 TTATCAAATC
*
356649 AATTTTTTCATCATAACATGTAACAATTA
1 AATTTTTTAAT-ATAACATGTAACAATTA
*
356678 AATTTTTTAATATAACGTGTAACAATTA
1 AATTTTTTAATATAACATGTAACAATTA
* ** * * *
356706 AA-TATCCAACATAGCGTGTAACAATTA
1 AATTTTTTAATATAACATGTAACAATTA
* * * *
356733 AA-TATTCAATATAACGTGTAATAATTA
1 AATTTTTTAATATAACATGTAACAATTA
*
356760 AACTTTT
1 AATTTTT
356767 AGTTTGACGT
Statistics
Matches: 76, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
27 45 0.59
28 21 0.28
29 10 0.13
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.38
Consensus pattern (28 bp):
AATTTTTTAATATAACATGTAACAATTA
Found at i:356807 original size:27 final size:27
Alignment explanation
Indices: 356661--356803 Score: 135
Period size: 27 Copynumber: 5.3 Consensus size: 27
356651 TTTTTTCATC
* *
356661 ATAACATGTAACAATTAAATTTTTTAAT
1 ATAACGTGTAACAATTAAA-TATTTAAT
** *
356689 ATAACGTGTAACAATTAAATATCCAAC
1 ATAACGTGTAACAATTAAATATTTAAT
* *
356716 ATAGCGTGTAACAATTAAATATTCAAT
1 ATAACGTGTAACAATTAAATATTTAAT
* *
356743 ATAACGTGTAATAATTAAACT-TTTAGT
1 ATAACGTGTAACAATTAAA-TATTTAAT
* * * * *
356770 TTGACGTATAACAACTAAATCTTTAAT
1 ATAACGTGTAACAATTAAATATTTAAT
356797 ATAACGT
1 ATAACGT
356804 ATAATTATAA
Statistics
Matches: 93, Mismatches: 20, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
26 1 0.01
27 73 0.78
28 19 0.20
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.36
Consensus pattern (27 bp):
ATAACGTGTAACAATTAAATATTTAAT
Found at i:357602 original size:9 final size:9
Alignment explanation
Indices: 357584--357628 Score: 53
Period size: 9 Copynumber: 5.4 Consensus size: 9
357574 TTTAAAAGAA
357584 TTTA-AATT
1 TTTATAATT
357592 TTTATAATT
1 TTTATAATT
357601 TTTATAA--
1 TTTATAATT
357608 TTTATAA-T
1 TTTATAATT
*
357616 TTTATCATT
1 TTTATAATT
357625 TTTA
1 TTTA
357629 AACGGTTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
7 7 0.21
8 10 0.30
9 16 0.48
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (9 bp):
TTTATAATT
Found at i:357618 original size:24 final size:24
Alignment explanation
Indices: 357582--357628 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
357572 GATTTAAAAG
357582 AATTTAAATTTTTATAATTTTTAT
1 AATTTAAATTTTTATAATTTTTAT
*
357606 AATTTATAA-TTTTATCATTTTTA
1 AATTTA-AATTTTTATAATTTTTA
357629 AACGGTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 19 0.90
25 2 0.10
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (24 bp):
AATTTAAATTTTTATAATTTTTAT
Found at i:358912 original size:37 final size:37
Alignment explanation
Indices: 358871--358948 Score: 147
Period size: 37 Copynumber: 2.1 Consensus size: 37
358861 AGAAGAGAAA
*
358871 AATTGTGAATAAGGTGGAGAAAGACTAAGTAATATAG
1 AATTGTGAATAAGGTGGAGAAAGACTAAGTAATAGAG
358908 AATTGTGAATAAGGTGGAGAAAGACTAAGTAATAGAG
1 AATTGTGAATAAGGTGGAGAAAGACTAAGTAATAGAG
358945 AATT
1 AATT
358949 AAGGAAAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.46, C:0.03, G:0.27, T:0.24
Consensus pattern (37 bp):
AATTGTGAATAAGGTGGAGAAAGACTAAGTAATAGAG
Found at i:376120 original size:12 final size:12
Alignment explanation
Indices: 376085--376120 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
376075 CTTTCTTTTA
*
376085 ATTAATAAAAAA
1 ATTAATAAAAAT
*
376097 ATTAATTAAAAT
1 ATTAATAAAAAT
376109 ATTAATAAAAAT
1 ATTAATAAAAAT
376121 GATATAATAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
ATTAATAAAAAT
Found at i:379643 original size:29 final size:26
Alignment explanation
Indices: 379582--379638 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
379572 AGAGTAAGGT
379582 ATCATATACTAAGTAGTAAAAAATAA
1 ATCATATACTAAGTAGTAAAAAATAA
379608 ATCATATACTAAGTAGTAAAAAATAA
1 ATCATATACTAAGTAGTAAAAAATAA
379634 ATCAT
1 ATCAT
379639 CATATGATTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.56, C:0.09, G:0.07, T:0.28
Consensus pattern (26 bp):
ATCATATACTAAGTAGTAAAAAATAA
Found at i:384744 original size:19 final size:18
Alignment explanation
Indices: 384715--384766 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
384705 TAAATTTTAA
*
384715 AAAATTCTTTAAAAAAAT
1 AAAATTTTTTAAAAAAAT
** *
384733 AACTTTTTTTTAAAAAAT
1 AAAATTTTTTAAAAAAAT
384751 AAAATTTTTTAAAAAA
1 AAAATTTTTTAAAAAA
384767 GAGCTTTAGG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (18 bp):
AAAATTTTTTAAAAAAAT
Found at i:393358 original size:12 final size:14
Alignment explanation
Indices: 393330--393361 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
393320 TGAATAAGAC
393330 ATTTTTTAGAATAA
1 ATTTTTTAGAATAA
393344 ATTTTTTA-AAT-A
1 ATTTTTTAGAATAA
393356 ATTTTT
1 ATTTTT
393362 AATTAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.39
13 3 0.17
14 8 0.44
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (14 bp):
ATTTTTTAGAATAA
Found at i:394039 original size:23 final size:23
Alignment explanation
Indices: 394008--394062 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
393998 TAGGGTTTAA
* *
394008 CATTGCGTGACTGGTTGATAAGT
1 CATTGCGTGACTGATTGATAAAT
* *
394031 CATTACGTGACTTATTGATAAAT
1 CATTGCGTGACTGATTGATAAAT
394054 CATTGCGTG
1 CATTGCGTG
394063 CCAGAATAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (23 bp):
CATTGCGTGACTGATTGATAAAT
Found at i:395932 original size:26 final size:26
Alignment explanation
Indices: 395871--395938 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 26
395861 AACATTGTTC
* *
395871 TGTATCATCTCCAAATTATTCTTTGT
1 TGTATCATTTACAAATTATTCTTTGT
* *
395897 TGTATTATTTACAAA-TATTTCTTTTT
1 TGTATCATTTACAAATTA-TTCTTTGT
395923 TGTATCATTTAACAAA
1 TGTATCATTT-ACAAA
395939 GAGAAGGGCA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
25 2 0.06
26 28 0.80
27 5 0.14
ACGTcount: A:0.29, C:0.13, G:0.06, T:0.51
Consensus pattern (26 bp):
TGTATCATTTACAAATTATTCTTTGT
Found at i:396264 original size:23 final size:23
Alignment explanation
Indices: 396224--396308 Score: 98
Period size: 23 Copynumber: 3.7 Consensus size: 23
396214 CAAGTATTTG
* * *
396224 ATATGGAATCATGCGACTACTAA
1 ATATGGAATCACGTGACTAGTAA
* *
396247 ATTTGGAATCACGTGACTAGTTA
1 ATATGGAATCACGTGACTAGTAA
*
396270 ATATAGAATCACGTGACTAGTAA
1 ATATGGAATCACGTGACTAGTAA
* *
396293 ATATGAAATCGCGTGA
1 ATATGGAATCACGTGA
396309 ACCGTTAAGA
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (23 bp):
ATATGGAATCACGTGACTAGTAA
Found at i:396460 original size:23 final size:23
Alignment explanation
Indices: 396380--396689 Score: 144
Period size: 23 Copynumber: 13.5 Consensus size: 23
396370 AATGACGTTT
* * *
396380 CTAGTTTTTATGGAATTGAATGA
1 CTAGTTATTATGGAATCGCATGA
* **
396403 CTAGTTATTA-GAAAATCGTGTGA
1 CTAGTTATTATG-GAATCGCATGA
* * * *
396426 ATAGTAAATATGGAGTCGCATGA
1 CTAGTTATTATGGAATCGCATGA
396449 CTAGTTATTATGGAATCGCATGA
1 CTAGTTATTATGGAATCGCATGA
* ** *
396472 TTAGTTATTATAAAATTG-ATTGA
1 CTAGTTATTATGGAATCGCA-TGA
* * * * * *
396495 GTAGTAAATATGGAGTCGCGTAA
1 CTAGTTATTATGGAATCGCATGA
* *
396518 CTAGTTATTATGGAATTGCGTGA
1 CTAGTTATTATGGAATCGCATGA
* * *
396541 CTAGTTGA-TATTGAGTCGCGTGA
1 CTAGTT-ATTATGGAATCGCATGA
* * * * * * *
396564 GTAGTAAATATGGAGTGGCGTTA
1 CTAGTTATTATGGAATCGCATGA
*
396587 CTAGTTATTATGGAATCGCACGA
1 CTAGTTATTATGGAATCGCATGA
** *
396610 CTAGTTATTATAAAATTGCATGA
1 CTAGTTATTATGGAATCGCATGA
* * * * * *
396633 GTAGTAAATAT-GAAGTCACGTAA
1 CTAGTTATTATGGAA-TCGCATGA
* *
396656 CTAGTT-TATATGGAATCACGTGA
1 CTAGTTAT-TATGGAATCGCATGA
396679 CTAGTTATTAT
1 CTAGTTATTAT
396690 AAAATTAAGT
Statistics
Matches: 210, Mismatches: 67, Indels: 20
0.71 0.23 0.07
Matches are distributed among these distances:
22 5 0.02
23 199 0.95
24 6 0.03
ACGTcount: A:0.33, C:0.09, G:0.23, T:0.35
Consensus pattern (23 bp):
CTAGTTATTATGGAATCGCATGA
Found at i:396748 original size:69 final size:69
Alignment explanation
Indices: 396353--396887 Score: 438
Period size: 69 Copynumber: 7.8 Consensus size: 69
396343 ATAGAGGCAC
* * ** * ** *
396353 GTGAGTAGTAAAAATGGAAT-GACGTTTCTAGTTTTTATGGAATTGAATGACTAGTTATTAGAAA
1 GTGAGTAGTAAATATGGAGTCG-CGTGACTAGTTATTATGGAATTGCGTGACTAGTTATTATAAA
* *
396417 ATCGT
65 ATTGA
* * * * *
396422 GTGAATAGTAAATATGGAGTCGCATGACTAGTTATTATGGAATCGCATGATTAGTTATTATAAAA
1 GTGAGTAGTAAATATGGAGTCGCGTGACTAGTTATTATGGAATTGCGTGACTAGTTATTATAAAA
396487 TTGA
66 TTGA
* * **
396491 TTGAGTAGTAAATATGGAGTCGCGTAACTAGTTATTATGGAATTGCGTGACTAGTTGA-TATTGA
1 GTGAGTAGTAAATATGGAGTCGCGTGACTAGTTATTATGGAATTGCGTGACTAGTT-ATTATAAA
* * *
396555 GTCGC
65 ATTGA
* * * **
396560 GTGAGTAGTAAATATGGAGTGGCGTTACTAGTTATTATGGAATCGCACGACTAGTTATTATAAAA
1 GTGAGTAGTAAATATGGAGTCGCGTGACTAGTTATTATGGAATTGCGTGACTAGTTATTATAAAA
396625 TTGCA
66 TTG-A
* * * **
396630 -TGAGTAGTAAATATGAAGTCACGTAACTAGTT-TATATGGAATCACGTGACTAGTTATTATAAA
1 GTGAGTAGTAAATATGGAGTCGCGTGACTAGTTAT-TATGGAATTGCGTGACTAGTTATTATAAA
*
396693 ATTAA
65 ATTGA
* * * * **
396698 GTGAGTAATAAATATTGAGTCGCGTGACTAGTTATTATGGAATTGTGTGACTAATTATTATGGAA
1 GTGAGTAGTAAATATGGAGTCGCGTGACTAGTTATTATGGAATTGCGTGACTAGTTATTATAAAA
396763 TT-A
66 TTGA
* ** * * * * * *
396766 CGTGATTAGTTGATATTGAGTCGCGTGAGTAG-TATATATAG-AGTGATGTTACTAGTTATTATA
1 -GTGAGTAGTAAATATGGAGTCGCGTGACTAGTTAT-TATGGAATTG-CGTGACTAGTTATTATA
* *
396829 AAATCGT
63 AAATTGA
* ** * * *
396836 GTGACTAGTTGATATGGAATCACGTGACTAGTTGA-TATGGAATTACGTGACT
1 GTGAGTAGTAAATATGGAGTCGCGTGACTAGTT-ATTATGGAATTGCGTGACT
396888 TTTTGATATG
Statistics
Matches: 374, Mismatches: 78, Indels: 28
0.78 0.16 0.06
Matches are distributed among these distances:
68 10 0.03
69 357 0.95
70 6 0.02
71 1 0.00
ACGTcount: A:0.33, C:0.08, G:0.24, T:0.35
Consensus pattern (69 bp):
GTGAGTAGTAAATATGGAGTCGCGTGACTAGTTATTATGGAATTGCGTGACTAGTTATTATAAAA
TTGA
Found at i:396856 original size:23 final size:22
Alignment explanation
Indices: 396433--396887 Score: 158
Period size: 23 Copynumber: 19.8 Consensus size: 22
396423 TGAATAGTAA
* *
396433 ATATGGAGTCGCATGACTAGTT
1 ATATGGAATCGCGTGACTAGTT
* *
396455 ATTATGGAATCGCATGATTAGTT
1 A-TATGGAATCGCGTGACTAGTT
** * ** * *
396478 ATTATAAAATTGATTGAGTAGTAA
1 A-TATGGAATCGCGTGACTAGT-T
* *
396502 ATATGGAGTCGCGTAACTAGTT
1 ATATGGAATCGCGTGACTAGTT
*
396524 ATTATGGAATTGCGTGACTAGTT
1 A-TATGGAATCGCGTGACTAGTT
* * * *
396547 GATATTGAGTCGCGTGAGTAGTAA
1 -ATATGGAATCGCGTGACTAGT-T
* * *
396571 ATATGGAGTGGCGTTACTAGTT
1 ATATGGAATCGCGTGACTAGTT
**
396593 ATTATGGAATCGCACGACTAGTT
1 A-TATGGAATCGCGTGACTAGTT
** * * * *
396616 ATTATAAAATTGCATGAGTAGTAA
1 A-TATGGAATCGCGTGACTAGT-T
* *
396640 ATAT-GAAGTCACGTAACTAGTTT
1 ATATGGAA-TCGCGTGACTAG-TT
*
396663 ATATGGAATCACGTGACTAGTT
1 ATATGGAATCGCGTGACTAGTT
** *** * * *
396685 ATTATAAAATTAAGTGAGTAATAA
1 A-TATGGAATCGCGTGACTAGT-T
* *
396709 ATATTGAGTCGCGTGACTAGTT
1 ATATGGAATCGCGTGACTAGTT
* * *
396731 ATTATGGAATTGTGTGACTAATT
1 A-TATGGAATCGCGTGACTAGTT
** *
396754 ATTATGGAATTACGTGATTAGTT
1 A-TATGGAATCGCGTGACTAGTT
* * *
396777 GATATTGAGTCGCGTGAGTAGTAT
1 -ATATGGAATCGCGTGACTAGT-T
* * * *
396801 ATATAGAGT-GATGTTACTAGTT
1 ATATGGAATCG-CGTGACTAGTT
** *
396823 ATTATAAAATCGTGTGACTAGTT
1 A-TATGGAATCGCGTGACTAGTT
*
396846 GATATGGAATCACGTGACTAGTT
1 -ATATGGAATCGCGTGACTAGTT
**
396869 GATATGGAATTACGTGACT
1 -ATATGGAATCGCGTGACT
396888 TTTTGATATG
Statistics
Matches: 322, Mismatches: 92, Indels: 37
0.71 0.20 0.08
Matches are distributed among these distances:
22 12 0.04
23 298 0.93
24 12 0.04
ACGTcount: A:0.32, C:0.09, G:0.24, T:0.35
Consensus pattern (22 bp):
ATATGGAATCGCGTGACTAGTT
Found at i:396885 original size:92 final size:91
Alignment explanation
Indices: 396655--396885 Score: 241
Period size: 92 Copynumber: 2.5 Consensus size: 91
396645 AAGTCACGTA
* * *
396655 ACTAGTTTATATGGAATCACGTGACTAGTT-ATTATAAAATTAAGTGAGTAATAAATATTGAGTC
1 ACTAG-TTATATGGAATCACGTGACTAGTTGA-TATAGAATTACGTGAGTAATAAATATAGAGTC
** *
396719 GCGTGACTAGTTATTATGGAATTGTGTG
64 GCGTGACTAGTTATTATAAAATCGTGTG
* * * * * ** * *
396747 ACTAATTATTATGGAATTACGTGATTAGTTGATATTGAGTCGCGTGAGTAGTATATATAGAGT-G
1 ACTAGTTA-TATGGAATCACGTGACTAGTTGATATAGAATTACGTGAGTAATAAATATAGAGTCG
* *
396811 ATGTTACTAGTTATTATAAAATCGTGTG
65 -CGTGACTAGTTATTATAAAATCGTGTG
*
396839 ACTAGTTGATATGGAATCACGTGACTAGTTGATATGGAATTACGTGA
1 ACTAGTT-ATATGGAATCACGTGACTAGTTGATATAGAATTACGTGA
396886 CTTTTTGATA
Statistics
Matches: 111, Mismatches: 24, Indels: 8
0.78 0.17 0.06
Matches are distributed among these distances:
91 4 0.04
92 105 0.95
93 2 0.02
ACGTcount: A:0.32, C:0.08, G:0.23, T:0.37
Consensus pattern (91 bp):
ACTAGTTATATGGAATCACGTGACTAGTTGATATAGAATTACGTGAGTAATAAATATAGAGTCGC
GTGACTAGTTATTATAAAATCGTGTG
Found at i:396893 original size:23 final size:23
Alignment explanation
Indices: 396836--396910 Score: 114
Period size: 23 Copynumber: 3.3 Consensus size: 23
396826 ATAAAATCGT
*
396836 GTGACTAGTTGATATGGAATCAC
1 GTGACTAGTTGATATGGAATTAC
396859 GTGACTAGTTGATATGGAATTAC
1 GTGACTAGTTGATATGGAATTAC
** *
396882 GTGACTTTTTGATATGGGATTAC
1 GTGACTAGTTGATATGGAATTAC
396905 GTGACT
1 GTGACT
396911 CGCTTATTGT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.27, C:0.11, G:0.27, T:0.36
Consensus pattern (23 bp):
GTGACTAGTTGATATGGAATTAC
Found at i:402632 original size:2 final size:2
Alignment explanation
Indices: 402627--402659 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
402617 TTATATAGAA
*
402627 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
402660 CATACTTGCC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:403334 original size:12 final size:12
Alignment explanation
Indices: 403317--403341 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
403307 ATAAAAAATG
403317 ATTAAATATAAA
1 ATTAAATATAAA
403329 ATTAAATATAAA
1 ATTAAATATAAA
403341 A
1 A
403342 AAATGTATCG
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATTAAATATAAA
Found at i:422935 original size:45 final size:46
Alignment explanation
Indices: 422871--422962 Score: 177
Period size: 45 Copynumber: 2.0 Consensus size: 46
422861 AAGAAAATCC
422871 TCATAAATGTTTTAAAGTTAATCTT-AAAGAAAGATGAATTGAATA
1 TCATAAATGTTTTAAAGTTAATCTTAAAAGAAAGATGAATTGAATA
422916 TCATAAATGTTTTAAAGTTAATCTTAAAAGAAAGATGAATTGAATA
1 TCATAAATGTTTTAAAGTTAATCTTAAAAGAAAGATGAATTGAATA
422962 T
1 T
422963 ACTTTGAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
45 25 0.54
46 21 0.46
ACGTcount: A:0.47, C:0.04, G:0.13, T:0.36
Consensus pattern (46 bp):
TCATAAATGTTTTAAAGTTAATCTTAAAAGAAAGATGAATTGAATA
Found at i:434439 original size:2 final size:2
Alignment explanation
Indices: 434432--434465 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
434422 AAGCATGCTA
434432 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
434466 GATTCCTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:436925 original size:42 final size:42
Alignment explanation
Indices: 436879--436970 Score: 166
Period size: 42 Copynumber: 2.2 Consensus size: 42
436869 ACCCACTTTT
*
436879 CCTCCAAAGTTTTTAATTCAAAGTATTCCCCCAAAAGATTTC
1 CCTCCAAAGTTTTCAATTCAAAGTATTCCCCCAAAAGATTTC
*
436921 CCTCCAAAGTTTTCAATTCAAAGTATTCCCCCCAAAGATTTC
1 CCTCCAAAGTTTTCAATTCAAAGTATTCCCCCAAAAGATTTC
436963 CCTCCAAA
1 CCTCCAAA
436971 ACATTTGGGA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.33, C:0.30, G:0.07, T:0.30
Consensus pattern (42 bp):
CCTCCAAAGTTTTCAATTCAAAGTATTCCCCCAAAAGATTTC
Found at i:437096 original size:35 final size:35
Alignment explanation
Indices: 437057--437123 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
437047 GGGCTGGCAC
437057 CCTCTTGGGCCTCCTGGCGGGTCCGGACTGTGTCA
1 CCTCTTGGGCCTCCTGGCGGGTCCGGACTGTGTCA
* *
437092 CCTCTTGGGCCTCCTGGTGGGTCTGGACTGTG
1 CCTCTTGGGCCTCCTGGCGGGTCCGGACTGTG
437124 GCCCGTGACA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.04, C:0.31, G:0.36, T:0.28
Consensus pattern (35 bp):
CCTCTTGGGCCTCCTGGCGGGTCCGGACTGTGTCA
Found at i:442149 original size:14 final size:14
Alignment explanation
Indices: 442132--442228 Score: 63
Period size: 14 Copynumber: 6.9 Consensus size: 14
442122 CCCCACCCAC
442132 TTTTCCCTCCAAAG
1 TTTTCCCTCCAAAG
*** *
442146 TTTTTAATTCAAAG
1 TTTTCCCTCCAAAG
* *
442160 TATTCCCCCCAAAAG
1 TTTTCCCTCC-AAAG
*
442175 ATTTCCCTCCAAAG
1 TTTTCCCTCCAAAG
**
442189 TTTTCAAT-CAAAG
1 TTTTCCCTCCAAAG
*
442202 TATTCCC-CCAAAAG
1 TTTTCCCTCC-AAAG
*
442216 ATTTCCCTCCAAA
1 TTTTCCCTCCAAA
442229 ACATTTGGGA
Statistics
Matches: 58, Mismatches: 21, Indels: 8
0.67 0.24 0.09
Matches are distributed among these distances:
13 10 0.17
14 35 0.60
15 13 0.22
ACGTcount: A:0.32, C:0.30, G:0.06, T:0.32
Consensus pattern (14 bp):
TTTTCCCTCCAAAG
Found at i:442222 original size:41 final size:43
Alignment explanation
Indices: 442133--442228 Score: 169
Period size: 41 Copynumber: 2.3 Consensus size: 43
442123 CCCACCCACT
*
442133 TTTCCCTCCAAAGTTTTTAATTCAAAGTATTCCCCCCAAAAGA
1 TTTCCCTCCAAAGTTTTCAATTCAAAGTATTCCCCCCAAAAGA
442176 TTTCCCTCCAAAGTTTTCAA-TCAAAGTATT-CCCCCAAAAGA
1 TTTCCCTCCAAAGTTTTCAATTCAAAGTATTCCCCCCAAAAGA
442217 TTTCCCTCCAAA
1 TTTCCCTCCAAA
442229 ACATTTGGGA
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
41 23 0.44
42 10 0.19
43 19 0.37
ACGTcount: A:0.32, C:0.30, G:0.06, T:0.31
Consensus pattern (43 bp):
TTTCCCTCCAAAGTTTTCAATTCAAAGTATTCCCCCCAAAAGA
Found at i:442489 original size:15 final size:16
Alignment explanation
Indices: 442458--442490 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
442448 AAAAACTTAA
*
442458 AAACAAAAGCATACAT
1 AAACAAAAACATACAT
442474 AAACAAAAAC-TACAT
1 AAACAAAAACATACAT
442489 AA
1 AA
442491 GAATAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.67, C:0.18, G:0.03, T:0.12
Consensus pattern (16 bp):
AAACAAAAACATACAT
Found at i:449272 original size:18 final size:19
Alignment explanation
Indices: 449232--449274 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
449222 AACTAAAAAT
*
449232 AAAAAATGTGTTTTTACTC
1 AAAAAATGTGTATTTACTC
* *
449251 AAAAAAT-TGTATTTCCTG
1 AAAAAATGTGTATTTACTC
449269 AAAAAA
1 AAAAAA
449275 AAACCCATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.35
Consensus pattern (19 bp):
AAAAAATGTGTATTTACTC
Found at i:450884 original size:20 final size:17
Alignment explanation
Indices: 450849--450892 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
450839 AATGTTATGC
450849 TTATTTTTTTAATTTTG
1 TTATTTTTTTAATTTTG
450866 TTATTATTTATTAATTTT-
1 TTATT-TTT-TTAATTTTG
450884 TATATTTTT
1 T-TATTTTT
450893 GTAGGAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 5 0.21
18 7 0.29
19 12 0.50
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (17 bp):
TTATTTTTTTAATTTTG
Found at i:455878 original size:25 final size:25
Alignment explanation
Indices: 455850--455907 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
455840 CTTTACTATT
*
455850 GTGTTGAGCTTAGAGGATACCCTAG
1 GTGTTGAGCCTAGAGGATACCCTAG
455875 GTGTTGAGCCTAGAGGATACCCTAG
1 GTGTTGAGCCTAGAGGATACCCTAG
455900 GTGTTGAG
1 GTGTTGAG
455908 ATCGAGACTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.22, C:0.16, G:0.34, T:0.28
Consensus pattern (25 bp):
GTGTTGAGCCTAGAGGATACCCTAG
Found at i:459659 original size:29 final size:30
Alignment explanation
Indices: 459592--459659 Score: 70
Period size: 29 Copynumber: 2.3 Consensus size: 30
459582 TTAGCTAGGA
* *
459592 AATTACCTATGCTATGCCATATAGTTCAAG
1 AATTGCCTATACTATGCCATATAGTTCAAG
* *
459622 AATTG-CTATACTATGCCTTGTAGATT-AAG
1 AATTGCCTATACTATGCCATATAG-TTCAAG
459651 AA-TGCCTAT
1 AATTGCCTAT
459660 TCCGTATAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
28 2 0.06
29 24 0.75
30 6 0.19
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (30 bp):
AATTGCCTATACTATGCCATATAGTTCAAG
Found at i:469537 original size:19 final size:20
Alignment explanation
Indices: 469508--469546 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
469498 ATGTAATGAC
*
469508 AAATATTAAAATTAAAAAAT
1 AAATATTAAAAGTAAAAAAT
469528 AAAT-TTAAAAGTAAAAAAT
1 AAATATTAAAAGTAAAAAAT
469547 TTTAAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (20 bp):
AAATATTAAAAGTAAAAAAT
Found at i:469552 original size:16 final size:15
Alignment explanation
Indices: 469508--469567 Score: 50
Period size: 19 Copynumber: 3.7 Consensus size: 15
469498 ATGTAATGAC
*
469508 AAATATTAAAATTAAA
1 AAATTTTAAAA-TAAA
469524 AAATAAATTTAAAAGTAAA
1 AAAT---TTTAAAA-TAAA
469543 AAATTTTAAAA-AATA
1 AAATTTTAAAATAA-A
469558 AAATTTTAAA
1 AAATTTTAAA
469568 TCATAACTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
14 2 0.05
15 11 0.29
16 11 0.29
19 14 0.37
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (15 bp):
AAATTTTAAAATAAA
Found at i:469573 original size:15 final size:15
Alignment explanation
Indices: 469519--469567 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
469509 AATATTAAAA
469519 TTAAAAAAT-AAA-T
1 TTAAAAAATAAAATT
469532 TTAAAAGTAA-AAAATT
1 TTAAAA--AATAAAATT
469548 TTAAAAAATAAAATT
1 TTAAAAAATAAAATT
469563 TTAAA
1 TTAAA
469568 TCATAACTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
13 6 0.19
14 2 0.06
15 16 0.52
16 7 0.23
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (15 bp):
TTAAAAAATAAAATT
Found at i:470435 original size:7 final size:7
Alignment explanation
Indices: 470389--470455 Score: 55
Period size: 8 Copynumber: 8.9 Consensus size: 7
470379 AAGAAAAGTC
470389 ATAAATAA
1 ATAAA-AA
470397 ATAAAAA
1 ATAAAAA
470404 ACT-AAAA
1 A-TAAAAA
*
470411 ATGAAAAT
1 AT-AAAAA
*
470419 AGAAACAA
1 ATAAA-AA
470427 ATAAAAA
1 ATAAAAA
470434 ATTAAAAA
1 A-TAAAAA
470442 TATAAAAA
1 -ATAAAAA
470450 ATAAAA
1 ATAAAA
470456 TTAAATTTCA
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
6 1 0.02
7 20 0.41
8 27 0.55
9 1 0.02
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (7 bp):
ATAAAAA
Found at i:470440 original size:23 final size:23
Alignment explanation
Indices: 470395--470455 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
470385 AGTCATAAAT
*
470395 AAATA-AAAAACT-AAAAATG-A
1 AAATAGAAAAAATAAAAAATGAA
*
470415 AAATAGAAACAAATAAAAAATTAA
1 AAATAGAAA-AAATAAAAAATGAA
*
470439 AAATATAAAAAATAAAA
1 AAATAGAAAAAATAAAA
470456 TTAAATTTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 5 0.15
21 3 0.09
22 3 0.09
23 14 0.41
24 9 0.26
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.16
Consensus pattern (23 bp):
AAATAGAAAAAATAAAAAATGAA
Found at i:473771 original size:2 final size:2
Alignment explanation
Indices: 473764--473795 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
473754 ATGTGAGGTC
473764 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
473796 GTAGATGCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:485695 original size:29 final size:27
Alignment explanation
Indices: 485650--485712 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 27
485640 TAGATTGTTA
*
485650 ATTATGTTTAAAAAATATGAA-TATTAT
1 ATTATATTTAAAAAATAT-AATTATTAT
485677 ATTATATTATAAAGAAATATAATTATTAT
1 ATTATATT-TAAA-AAATATAATTATTAT
485706 ATATATA
1 AT-TATA
485713 ACTTTATTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
27 7 0.23
28 6 0.19
29 14 0.45
30 4 0.13
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (27 bp):
ATTATATTTAAAAAATATAATTATTAT
Found at i:485711 original size:15 final size:16
Alignment explanation
Indices: 485691--485729 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
485681 TATTATAAAG
485691 AAATATAA-TTATTAT
1 AAATATAACTTATTAT
*
485706 ATATATAACTTTATTAT
1 AAATATAAC-TTATTAT
485723 AAATATA
1 AAATATA
485730 TTTACTTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 7 0.35
17 13 0.65
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (16 bp):
AAATATAACTTATTAT
Found at i:486070 original size:2 final size:2
Alignment explanation
Indices: 486065--486099 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
486055 TGTGTGTGTC
486065 TA 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 TA T
486100 GTACAACATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:489246 original size:17 final size:18
Alignment explanation
Indices: 489224--489257 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
489214 CCATTTATCA
489224 AATAAAAA-AAAAGAAAG
1 AATAAAAACAAAAGAAAG
489241 AATAAAAACAAAAGAAA
1 AATAAAAACAAAAGAAA
489258 ATGTAAAGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.82, C:0.03, G:0.09, T:0.06
Consensus pattern (18 bp):
AATAAAAACAAAAGAAAG
Found at i:489743 original size:27 final size:27
Alignment explanation
Indices: 489699--489754 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
489689 AATTAATTTT
* *
489699 TTATTAATTAATATATAAATTGATAAA
1 TTATTAATTAATATATAAACTAATAAA
*
489726 TTATTAATTTAT-TGATAAACTAATAAA
1 TTATTAATTAATAT-ATAAACTAATAAA
489753 TT
1 TT
489755 TTCATAGTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 1 0.04
27 24 0.96
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (27 bp):
TTATTAATTAATATATAAACTAATAAA
Found at i:489752 original size:35 final size:35
Alignment explanation
Indices: 489683--489754 Score: 85
Period size: 35 Copynumber: 2.1 Consensus size: 35
489673 AAAGAATATT
* *
489683 TTGATAAATTAATTTTTTATTAATTAATATATAAA
1 TTGATAAATTAATTATTTATTAATAAATATATAAA
*
489718 TTGATAAATT-ATTAATTTATTGATAAACTA-ATAAA
1 TTGATAAATTAATT-ATTTATTAATAAA-TATATAAA
489753 TT
1 TT
489755 TTCATAGTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
34 3 0.09
35 27 0.84
36 2 0.06
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (35 bp):
TTGATAAATTAATTATTTATTAATAAATATATAAA
Found at i:509591 original size:21 final size:21
Alignment explanation
Indices: 509565--509618 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
509555 AGACACAACC
*
509565 ATAGTCGATCCTATAAAAGCT
1 ATAGTCAATCCTATAAAAGCT
509586 ATAGTCAATCCTATAAAAGCT
1 ATAGTCAATCCTATAAAAGCT
509607 ATAGTCAATCCT
1 ATAGTCAATCCT
509619 TAGGCAATGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (21 bp):
ATAGTCAATCCTATAAAAGCT
Found at i:510262 original size:33 final size:32
Alignment explanation
Indices: 510211--510319 Score: 103
Period size: 33 Copynumber: 3.2 Consensus size: 32
510201 TTAAGCTCGG
* *
510211 TAAAAGCCAATTTATGGGTTGTGCTTGTTCTTGT
1 TAAAAGGC-ATTTATGGGTTATGCTTGTTC-TGT
510245 TAAAAGGCATTTATGGGTTATGCTTGCTTCTGT
1 TAAAAGGCATTTATGGGTTATGCTTG-TTCTGT
** *
510278 TGCAAGGCA-TTATGAGGGTTATTGCTTGTTCATGA
1 TAAAAGGCATTTAT--GGGTTA-TGCTTGTTC-TGT
510313 TAAAAGG
1 TAAAAGG
510320 TATTATGAGA
Statistics
Matches: 63, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
32 4 0.06
33 27 0.43
34 19 0.30
35 13 0.21
ACGTcount: A:0.24, C:0.11, G:0.26, T:0.39
Consensus pattern (32 bp):
TAAAAGGCATTTATGGGTTATGCTTGTTCTGT
Found at i:512184 original size:18 final size:16
Alignment explanation
Indices: 512163--512196 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
512153 ACAATAAAAG
512163 GACAAAAGAGAATAGAAA
1 GACAAAA-AGAA-AGAAA
512181 GACAAAAAGAAAGAAA
1 GACAAAAAGAAAGAAA
512197 TGGAAAGAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 4 0.25
18 7 0.44
ACGTcount: A:0.71, C:0.06, G:0.21, T:0.03
Consensus pattern (16 bp):
GACAAAAAGAAAGAAA
Found at i:512405 original size:62 final size:63
Alignment explanation
Indices: 512287--512405 Score: 186
Period size: 63 Copynumber: 1.9 Consensus size: 63
512277 TATTCTTTAT
* *
512287 TTGTATTAATAATTTAAGAAAAAATTATTTTAAGGGCCCATTAAAATATATGTATAAAACATA
1 TTGTATTAATAATTTAAGAAAAAATTATTTTAAGGACCCATTAAAATATATATATAAAACATA
* * *
512350 TTGTATTAATAATTTAATAAAAAATTATTTTAA-GACTCATTAATATATATATATAA
1 TTGTATTAATAATTTAAGAAAAAATTATTTTAAGGACCCATTAAAATATATATATAA
512406 TATAGAAATT
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
62 19 0.37
63 32 0.63
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.40
Consensus pattern (63 bp):
TTGTATTAATAATTTAAGAAAAAATTATTTTAAGGACCCATTAAAATATATATATAAAACATA
Found at i:515436 original size:30 final size:30
Alignment explanation
Indices: 515400--515458 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
515390 TTTATTAAAA
*
515400 TAATATTCA-AATGTTAATAA-TTCAATAATC
1 TAATATT-ATAATATTAATAACTT-AATAATC
515430 TAATATTATAATATTAATAACTTAATAAT
1 TAATATTATAATATTAATAACTTAATAAT
515459 AATTTTTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 1 0.04
30 23 0.88
31 2 0.08
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (30 bp):
TAATATTATAATATTAATAACTTAATAATC
Found at i:520937 original size:19 final size:19
Alignment explanation
Indices: 520915--520953 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
520905 CTTTAGGATG
*
520915 ATTTATTAAGATATTATTA
1 ATTTAATAAGATATTATTA
**
520934 ATTTAATAATTTATTATTA
1 ATTTAATAAGATATTATTA
520953 A
1 A
520954 AACATTAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (19 bp):
ATTTAATAAGATATTATTA
Found at i:534472 original size:19 final size:19
Alignment explanation
Indices: 534422--534473 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
534412 CTAGGAAGAA
* **
534422 TTGATTCCCAATAATGCTC
1 TTGATTCCAAATGCTGCTC
534441 TTGATTCCAAATGCTGCTC
1 TTGATTCCAAATGCTGCTC
534460 TTGATTCCAAATGC
1 TTGATTCCAAATGC
534474 CAGAAGTGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.25, C:0.25, G:0.13, T:0.37
Consensus pattern (19 bp):
TTGATTCCAAATGCTGCTC
Found at i:541031 original size:21 final size:20
Alignment explanation
Indices: 540997--541038 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
540987 TAATTTAAAA
540997 TAAAATAACATAAAATTTAAC
1 TAAAATAACAT-AAATTTAAC
**
541018 TAAAATAATTTAAA-TTAAC
1 TAAAATAACATAAATTTAAC
541037 TA
1 TA
541039 CTTAACATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 7 0.37
20 3 0.16
21 9 0.47
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (20 bp):
TAAAATAACATAAATTTAAC
Found at i:541349 original size:17 final size:17
Alignment explanation
Indices: 541324--541362 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
541314 CATCACTATA
*
541324 TATTGAAGCTTCCCACC
1 TATTTAAGCTTCCCACC
541341 TATTTAAGCTTCCCACC
1 TATTTAAGCTTCCCACC
541358 TATTT
1 TATTT
541363 TGAAGACTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.23, C:0.31, G:0.08, T:0.38
Consensus pattern (17 bp):
TATTTAAGCTTCCCACC
Found at i:548013 original size:12 final size:12
Alignment explanation
Indices: 547974--548018 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
547964 ATGATCAATC
547974 AAAAAAG-AAGA
1 AAAAAAGAAAGA
*
547985 AAAAAGAGATAAAA
1 AAAAA-AGA-AAGA
547999 AAAAAAGAAAGA
1 AAAAAAGAAAGA
548011 AAAAAAGA
1 AAAAAAGA
548019 NNNNNNNNNN
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
11 5 0.17
12 13 0.45
13 3 0.10
14 8 0.28
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (12 bp):
AAAAAAGAAAGA
Found at i:559919 original size:18 final size:17
Alignment explanation
Indices: 559896--559930 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
559886 GTTTTTTCCT
*
559896 TTTTTATTTTATTTATTA
1 TTTTTATATTA-TTATTA
559914 TTTTTATATTATTATTA
1 TTTTTATATTATTATTA
559931 AAAATAAGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTTATATTATTATTA
Found at i:560327 original size:20 final size:20
Alignment explanation
Indices: 560302--560345 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
560292 TAGAGCTTAA
560302 AACTCTTTTTGTGTCAATGT
1 AACTCTTTTTGTGTCAATGT
560322 AACTCTTTTTGTGTCAATGT
1 AACTCTTTTTGTGTCAATGT
560342 AACT
1 AACT
560346 GGACTTATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.23, C:0.16, G:0.14, T:0.48
Consensus pattern (20 bp):
AACTCTTTTTGTGTCAATGT
Found at i:560546 original size:123 final size:123
Alignment explanation
Indices: 560325--561065 Score: 740
Period size: 123 Copynumber: 6.0 Consensus size: 123
560315 TCAATGTAAC
* * * * * **
560325 TCTTTTTGTGTCAATGTAACT-GGACTTATACATCTTGGATGTCAGTTAAATTGGATTTAAACTC
1 TCTTTTTGTGCCAACGTAGCTAGG-CTTAAACATCTTGGATGCCAGTTAAATTGGGCTTAAACTC
* * * * * * *
560389 CTTATGTGTCAACATAACTGGATTTATACATCTTGGATGCTAGCTAAATTAGGCTTAAA
65 CTTTTGTGCCAACGTAACTGGACTTATACTTCTTGGATGCCAGCTAAATTGGGCTTAAA
* * * *
560448 TCTTTTTATGCCAACATAGCTAGGCTTAAACATCTTGGATG-CTGTCTAAATTGGGTTTAAACTC
1 TCTTTTTGTGCCAACGTAGCTAGGCTTAAACATCTTGGATGCCAGT-TAAATTGGGCTTAAACTC
* *
560512 CTTTTGTGCCAACGTAGCCGGACTTATACTTCTTGGATGCCAGCTAAATTGGGCTTGAACA
65 CTTTTGTGCCAACGTAACTGGACTTATACTTCTTGGATGCCAGCTAAATTGGGCTT-AA-A
* * * * * * * *
560573 TC-TTTTGTGCCAACGTAACTAGACTTATACTTCTTGGACGCCAATTTAATTGGGCTT-AACTCT
1 TCTTTTTGTGCCAACGTAGCTAGGCTTAAACATCTTGGATGCCAGTTAAATTGGGCTTAAACTCC
* * * * * * *
560636 TTTTGTGCCAACGTAGCT-AAGTTTAAACATCTTGGATGCTAGATAAATTGGGCTTAAA
66 TTTTGTGCCAACGTAACTGGA-CTTATACTTCTTGGATGCCAGCTAAATTGGGCTTAAA
* ** * ** * * *
560694 CTCCTTTTGTGCCATTGTAGAT-GGACTTATTCTTCTTGGATGCCAGCTAAATTGAGCTTAAACA
1 -TCTTTTTGTGCCAACGTAGCTAGG-CTTAAACATCTTGGATGCCAGTTAAATTGGGCTTAAAC-
* * * * * *
560758 T-TTTTTGTGCTAATGTAACTGGACTTATACTTCTTGGATACCAGTTTAATTGGGCTTAAA
63 TCCTTTTGTGCCAACGTAACTGGACTTATACTTCTTGGATGCCAGCTAAATTGGGCTTAAA
* * *
560818 TCTTTTTGTGCCAACGTAGTTAGGCTTAAAAATCTTGGATGCTAGTTAAATTGGGCTTAAACTCC
1 TCTTTTTGTGCCAACGTAGCTAGGCTTAAACATCTTGGATGCCAGTTAAATTGGGCTTAAACTCC
* * * *
560883 TTTTGTGCCAACGTAACTGGACTTATATTTCTTGGATGTCAGTTTAATTGGGCTTAAA
66 TTTTGTGCCAACGTAACTGGACTTATACTTCTTGGATGCCAGCTAAATTGGGCTTAAA
* * * * * * * *
560941 TCTTTTTATACGAACGTACCTAGGCTTCAACATCTTGGATGCTAGCTAAATTGGGCTTAAAATCC
1 TCTTTTTGTGCCAACGTAGCTAGGCTTAAACATCTTGGATGCCAGTTAAATTGGGCTTAAACTCC
* * * *
561006 TCTTGTGCCCACGTAACGGGACTTATACTTCTTGGATGCCAGGTAAATTGGGCTTAAA
66 TTTTGTGCCAACGTAACTGGACTTATACTTCTTGGATGCCAGCTAAATTGGGCTTAAA
561064 TC
1 TC
561066 CTCTCATGTT
Statistics
Matches: 513, Mismatches: 91, Indels: 28
0.81 0.14 0.04
Matches are distributed among these distances:
121 1 0.00
122 10 0.02
123 399 0.78
124 96 0.19
125 7 0.01
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (123 bp):
TCTTTTTGTGCCAACGTAGCTAGGCTTAAACATCTTGGATGCCAGTTAAATTGGGCTTAAACTCC
TTTTGTGCCAACGTAACTGGACTTATACTTCTTGGATGCCAGCTAAATTGGGCTTAAA
Found at i:560647 original size:185 final size:185
Alignment explanation
Indices: 560322--561067 Score: 808
Period size: 185 Copynumber: 4.0 Consensus size: 185
560312 GTGTCAATGT
* * * * * * **
560322 AACTCTTTTTGTGTCAATGTAACTGGACTTATACATCTTGGATGTCAGTTAAATTGGATTTAAAC
1 AACTCCTTTTGTGCCAACGTAACTGGACTTATACTTCTTGGATGCCAGCTAAATTGGGCTTAAAC
* * * * * * * * *
560387 -TCCTTATGTGTCAACATAACTGGATTTATACATCTTGGATGCTAGCTAAATTAGGCTTAAATCT
66 AT-CTTTTGTGCCAACGTAACTGGACTTATACTTCTTGGATGCCAGTTTAATTGGGCTTAAATCT
* * *
560451 TTTTATGCCAACATAGCTAGGCTTAAACATCTTGGATGCT-GTCTAAATTGGGTTTA
130 TTTTGTGCCAACGTAGCTAGGCTTAAACATCTTGGATGCTAGT-TAAATTGGGCTTA
* * *
560507 AACTCCTTTTGTGCCAACGTAGCCGGACTTATACTTCTTGGATGCCAGCTAAATTGGGCTTGAAC
1 AACTCCTTTTGTGCCAACGTAACTGGACTTATACTTCTTGGATGCCAGCTAAATTGGGCTTAAAC
* * * *
560572 ATCTTTTGTGCCAACGTAACTAGACTTATACTTCTTGGACGCCAATTTAATTGGGCTTAACTCTT
66 ATCTTTTGTGCCAACGTAACTGGACTTATACTTCTTGGATGCCAGTTTAATTGGGCTTAAATCTT
* * *
560637 TTTGTGCCAACGTAGCTAAGTTTAAACATCTTGGATGCTAGATAAATTGGGCTTA
131 TTTGTGCCAACGTAGCTAGGCTTAAACATCTTGGATGCTAGTTAAATTGGGCTTA
** * *
560692 AACTCCTTTTGTGCCATTGTAGA-TGGACTTATTCTTCTTGGATGCCAGCTAAATTGAGCTTAAA
1 AACTCCTTTTGTGCCAACGTA-ACTGGACTTATACTTCTTGGATGCCAGCTAAATTGGGCTTAAA
* * * *
560756 CATTTTTTGTGCTAATGTAACTGGACTTATACTTCTTGGATACCAGTTTAATTGGGCTTAAATCT
65 CATCTTTTGTGCCAACGTAACTGGACTTATACTTCTTGGATGCCAGTTTAATTGGGCTTAAATCT
* *
560821 TTTTGTGCCAACGTAGTTAGGCTTAAAAATCTTGGATGCTAGTTAAATTGGGCTTA
130 TTTTGTGCCAACGTAGCTAGGCTTAAACATCTTGGATGCTAGTTAAATTGGGCTTA
* * * *
560877 AACTCCTTTTGTGCCAACGTAACTGGACTTATATTTCTTGGATGTCAGTTTAATTGGGCTT-AA-
1 AACTCCTTTTGTGCCAACGTAACTGGACTTATACTTCTTGGATGCCAGCTAAATTGGGCTTAAAC
* * * * * * * *
560940 ATCTTTTTATACGAACGTACCTAGG-CTTCA-ACATCTTGGATGCTAGCTAAATTGGGCTTAAAA
66 ATC-TTTTGTGCCAACGTAACT-GGACTT-ATACTTCTTGGATGCCAGTTTAATTGGGCTT-AAA
* * * * * * * * *
561003 TCCTCTTGTGCCCACGTAAC-GGGACTTATACTTCTTGGATGCCAGGTAAATTGGGCTTA
127 TCTTTTTGTGCCAACGTAGCTAGG-CTTAAACATCTTGGATGCTAGTTAAATTGGGCTTA
561062 AA-TCCT
1 AACTCCT
561068 CTCATGTTTG
Statistics
Matches: 472, Mismatches: 80, Indels: 19
0.83 0.14 0.03
Matches are distributed among these distances:
183 2 0.00
184 49 0.10
185 419 0.89
186 2 0.00
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (185 bp):
AACTCCTTTTGTGCCAACGTAACTGGACTTATACTTCTTGGATGCCAGCTAAATTGGGCTTAAAC
ATCTTTTGTGCCAACGTAACTGGACTTATACTTCTTGGATGCCAGTTTAATTGGGCTTAAATCTT
TTTGTGCCAACGTAGCTAGGCTTAAACATCTTGGATGCTAGTTAAATTGGGCTTA
Found at i:561057 original size:62 final size:62
Alignment explanation
Indices: 560328--561067 Score: 617
Period size: 62 Copynumber: 12.0 Consensus size: 62
560318 ATGTAACTCT
* * * * ** *
560328 TTTTGTGTCAATGTAACTGGACTTATACATCTTGGATGTCAGTTAAATTGGATTTAAACTCC
1 TTTTGTGCCAACGTAACTGGACTTATACATCTTGGATGCCAGCTAAATTGGGCTTAAAATCC
* * * * * * *
560390 TTATGTGTCAACATAACTGGATTTATACATCTTGGATGCTAGCTAAATTAGGCTT-AAATCT
1 TTTTGTGCCAACGTAACTGGACTTATACATCTTGGATGCCAGCTAAATTGGGCTTAAAATCC
* * * * * * *
560451 TTTTATGCCAACATAGCTAGG-CTTAAACATCTTGGATG-CTGTCTAAATTGGGTTTAAACTCC
1 TTTTGTGCCAACGTAACT-GGACTTATACATCTTGGATGCCAG-CTAAATTGGGCTTAAAATCC
* * * *
560513 TTTTGTGCCAACGTAGCCGGACTTATACTTCTTGGATGCCAGCTAAATTGGGCTTGAACAT-C
1 TTTTGTGCCAACGTAACTGGACTTATACATCTTGGATGCCAGCTAAATTGGGCTT-AAAATCC
* * * ** * * *
560575 TTTTGTGCCAACGTAACTAGACTTATACTTCTTGGACGCCAATTTAATTGGGCTT-AACTCT
1 TTTTGTGCCAACGTAACTGGACTTATACATCTTGGATGCCAGCTAAATTGGGCTTAAAATCC
* * * * * * *
560636 TTTTGTGCCAACGTAGCT-AAGTTTAAACATCTTGGATGCTAGATAAATTGGGCTTAAACTCC
1 TTTTGTGCCAACGTAACTGGA-CTTATACATCTTGGATGCCAGCTAAATTGGGCTTAAAATCC
** * * * *
560698 TTTTGTGCCATTGTAGA-TGGACTTATTCTTCTTGGATGCCAGCTAAATTGAGCTTAAACAT-T
1 TTTTGTGCCAACGTA-ACTGGACTTATACATCTTGGATGCCAGCTAAATTGGGCTTAAA-ATCC
* * * * * * *
560760 TTTTGTGCTAATGTAACTGGACTTATACTTCTTGGATACCAGTTTAATTGGGCTT-AAATCT
1 TTTTGTGCCAACGTAACTGGACTTATACATCTTGGATGCCAGCTAAATTGGGCTTAAAATCC
** * * * * *
560821 TTTTGTGCCAACGTAGTTAGG-CTTAAAAATCTTGGATGCTAGTTAAATTGGGCTTAAACTCC
1 TTTTGTGCCAACGTAACT-GGACTTATACATCTTGGATGCCAGCTAAATTGGGCTTAAAATCC
** * * * *
560883 TTTTGTGCCAACGTAACTGGACTTATATTTCTTGGATGTCAGTTTAATTGGGCTT-AAATCT
1 TTTTGTGCCAACGTAACTGGACTTATACATCTTGGATGCCAGCTAAATTGGGCTTAAAATCC
* * * * *
560944 TTTTATACGAACGTACCTAGG-CTTCA-ACATCTTGGATGCTAGCTAAATTGGGCTTAAAATCC
1 TTTTGTGCCAACGTAACT-GGACTT-ATACATCTTGGATGCCAGCTAAATTGGGCTTAAAATCC
* * * * *
561006 TCTTGTGCCCACGTAACGGGACTTATACTTCTTGGATGCCAGGTAAATTGGGCTT-AAATCC
1 TTTTGTGCCAACGTAACTGGACTTATACATCTTGGATGCCAGCTAAATTGGGCTTAAAATCC
561067 T
1 T
561068 CTCATGTTTG
Statistics
Matches: 539, Mismatches: 117, Indels: 45
0.77 0.17 0.06
Matches are distributed among these distances:
60 6 0.01
61 191 0.35
62 335 0.62
63 7 0.01
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (62 bp):
TTTTGTGCCAACGTAACTGGACTTATACATCTTGGATGCCAGCTAAATTGGGCTTAAAATCC
Found at i:569571 original size:20 final size:20
Alignment explanation
Indices: 569546--569587 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
569536 ATCGGAGTAA
*
569546 AAAATTA-ATAATTTTAAAAT
1 AAAATTATAT-ATTATAAAAT
569566 AAAATTATATATTATAAAAT
1 AAAATTATATATTATAAAAT
569586 AA
1 AA
569588 TCAACACTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 18 0.90
21 2 0.10
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAATTATATATTATAAAAT
Found at i:577479 original size:16 final size:17
Alignment explanation
Indices: 577457--577495 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
577447 TGAAATGCCC
577457 AATATATTTAT-AATAA
1 AATATATTTATAAATAA
* *
577473 TATATATTTTTAAATAA
1 AATATATTTATAAATAA
577490 AATATA
1 AATATA
577496 CATTTTTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
AATATATTTATAAATAA
Found at i:582855 original size:24 final size:24
Alignment explanation
Indices: 582828--582874 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
582818 AAATGAATAG
582828 ACAAAATGATTAAAACAGAACAAA
1 ACAAAATGATTAAAACAGAACAAA
* * * *
582852 ACAACATTATTCAATCAGAACAA
1 ACAAAATGATTAAAACAGAACAA
582875 GAGCATATTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.60, C:0.17, G:0.06, T:0.17
Consensus pattern (24 bp):
ACAAAATGATTAAAACAGAACAAA
Found at i:584846 original size:13 final size:13
Alignment explanation
Indices: 584828--584853 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
584818 AAAAAGAAAA
584828 AAAGCTTTAACTT
1 AAAGCTTTAACTT
584841 AAAGCTTTAACTT
1 AAAGCTTTAACTT
584854 TTTGATTTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (13 bp):
AAAGCTTTAACTT
Found at i:587098 original size:15 final size:16
Alignment explanation
Indices: 587078--587112 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
587068 AGTATTCAAG
587078 ATTTAAAGTAAA-TTT
1 ATTTAAAGTAAATTTT
*
587093 ATTTAAATTAAATTTT
1 ATTTAAAGTAAATTTT
587109 ATTT
1 ATTT
587113 TAAAACATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (16 bp):
ATTTAAAGTAAATTTT
Found at i:599814 original size:3 final size:3
Alignment explanation
Indices: 599806--599862 Score: 55
Period size: 3 Copynumber: 19.0 Consensus size: 3
599796 AACATCAATC
* * *
599806 ATA ATA ATA ATT ATA ATA ATA ATA ACA ATA GTA ATTA ATGA ATA A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA AT-A ATA ATA
599852 ATA A-A ATA ATA
1 ATA ATA ATA ATA
599863 TTACAAATAT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
2 4 0.09
3 34 0.77
4 6 0.14
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:606371 original size:47 final size:47
Alignment explanation
Indices: 606315--606422 Score: 144
Period size: 47 Copynumber: 2.3 Consensus size: 47
606305 AGTTGTGTAG
* *
606315 CCTCGTTTAAAGATAAGGAGCTTTTCCAATCATTTTAAGTTGCATAA
1 CCTCATTTAAAGATAAGGAGCTTTTACAATCATTTTAAGTTGCATAA
* * ** * *
606362 TCTCATTTAAAAAGGAGGAGCTTTTACAATCATTTTAAGTTGTATAG
1 CCTCATTTAAAGATAAGGAGCTTTTACAATCATTTTAAGTTGCATAA
606409 CCTCATTTAAAGAT
1 CCTCATTTAAAGAT
606423 GGAGAGTTTT
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (47 bp):
CCTCATTTAAAGATAAGGAGCTTTTACAATCATTTTAAGTTGCATAA
Found at i:606520 original size:48 final size:47
Alignment explanation
Indices: 606444--606647 Score: 128
Period size: 47 Copynumber: 4.3 Consensus size: 47
606434 CCACCCAATT
* * * * * *
606444 TTAAAATTATTGAAAAAGCTCCCTATCTCAAAATAAGGCCACGTAAC
1 TTAAAATGATTGGAAAAGTTCCCAATCTCAAAACAAGGCCACGCAAC
* * ** *
606491 TTAAAAATGATTGGAATAGTTCCCAATCTCTAAACGGGGCTACGCAAC
1 TT-AAAATGATTGGAAAAGTTCCCAATCTCAAAACAAGGCCACGCAAC
** ** *
606539 TTAAAATGATTGGAAAAGTTCCTC-ATCTCTAAATGAA-GTTATGCAAC
1 TTAAAATGATTGGAAAAGTTCC-CAATCTC-AAAACAAGGCCACGCAAC
* * ** ** *
606586 TTAAAATGATTAGG-AAAGTTCTTC-ATCTCTAAATGAGGTTACACAAC
1 TTAAAATGATT-GGAAAAGTTC-CCAATCTCAAAACAAGGCCACGCAAC
606633 TTAAAATGATTGGAA
1 TTAAAATGATTGGAA
606648 GAGCTCTTCA
Statistics
Matches: 124, Mismatches: 26, Indels: 14
0.76 0.16 0.09
Matches are distributed among these distances:
46 5 0.04
47 78 0.63
48 41 0.33
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (47 bp):
TTAAAATGATTGGAAAAGTTCCCAATCTCAAAACAAGGCCACGCAAC
Found at i:606559 original size:47 final size:46
Alignment explanation
Indices: 606488--606781 Score: 241
Period size: 47 Copynumber: 6.2 Consensus size: 46
606478 AAGGCCACGT
* ** *
606488 AACTTAAAAATGATTGGAATAGTTCCCAATCTCTAAACGGGGCTACGC
1 AACTT-AAAATGATTGGAAAAGTTCCC-ATCTCTAAACGAAGCTACAC
* * **
606536 AACTTAAAATGATTGGAAAAGTTCCTCATCTCTAAATGAAGTTATGC
1 AACTTAAAATGATTGGAAAAGTTCC-CATCTCTAAACGAAGCTACAC
* * * *
606583 AACTTAAAATGATTAGG-AAAGTTCTTCATCTCTAAATGAGGTTACAC
1 AACTTAAAATGATT-GGAAAAGTTC-CCATCTCTAAACGAAGCTACAC
* * * *
606630 AACTTAAAATGATTGGAAGAGCTCTTCATCTCTAAACGAAGCTATAC
1 AACTTAAAATGATTGGAAAAGTTC-CCATCTCTAAACGAAGCTACAC
* * *
606677 AACTTTAAAAATGATTGAAAAAGCTCCCCATCTCTGAATC-AAGCTACAC
1 AAC-TT-AAAATGATTGGAAAAG-TTCCCATCTCT-AAACGAAGCTACAC
* * * * * * *
606726 AACTTAAAATGATTGTAAAAGCTCCTCCTTTCTAAATGAGGCTACAT
1 AACTTAAAATGATTGGAAAAGTTCC-CATCTCTAAACGAAGCTACAC
606773 AACTTAAAA
1 AACTTAAAA
606782 ACAATTGGAA
Statistics
Matches: 204, Mismatches: 32, Indels: 21
0.79 0.12 0.08
Matches are distributed among these distances:
46 6 0.03
47 150 0.74
48 12 0.06
49 32 0.16
50 4 0.02
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.29
Consensus pattern (46 bp):
AACTTAAAATGATTGGAAAAGTTCCCATCTCTAAACGAAGCTACAC
Found at i:606633 original size:94 final size:93
Alignment explanation
Indices: 606488--606814 Score: 332
Period size: 94 Copynumber: 3.4 Consensus size: 93
606478 AAGGCCACGT
* * *
606488 AACTTAAAAATGATTGGAATAGTTCCCAATCTCTAAACGGGGCTACGCAACTTAAAATGATTGGA
1 AACTTAAAAATGATTGGAA-AGTTCCC-ATCTCTAAATGAGGCTACACAACTTAAAATGATTGGA
* * *
606553 AAAGTTCCTCATCTCTAAATGAAGTTATGC
64 AAAGCTCCTCATCTCTAAATGAAGCTATAC
* *
606583 AACTT-AAAATGATTAGGAAAGTTCTTCATCTCTAAATGAGGTTACACAACTTAAAATGATTGGA
1 AACTTAAAAATGATT-GGAAAGTTC-CCATCTCTAAATGAGGCTACACAACTTAAAATGATTGGA
* * *
606647 AGAGCTCTTCATCTCTAAACGAAGCTATAC
64 AAAGCTCCTCATCTCTAAATGAAGCTATAC
* * * * * *
606677 AACTTTAAAAATGATTGAAAAAGCTCCCCATCTCTGAATCAAGCTACACAACTTAAAATGATTGT
1 AAC-TTAAAAATGATTG-GAAAG-TTCCCATCTCTAAATGAGGCTACACAACTTAAAATGATTGG
* * * * *
606742 AAAAGCTCCTCCTTTCTAAATGAGGCTACAT
63 AAAAGCTCCTCATCTCTAAATGAAGCTATAC
** **
606773 AACTTAAAAACAATTGGAAACACTCCTCATCTCTAAATGAGG
1 AACTTAAAAATGATTGGAAA-GTTCC-CATCTCTAAATGAGG
606815 TTTGAGATGG
Statistics
Matches: 188, Mismatches: 36, Indels: 16
0.78 0.15 0.07
Matches are distributed among these distances:
94 79 0.42
95 36 0.19
96 71 0.38
97 2 0.01
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (93 bp):
AACTTAAAAATGATTGGAAAGTTCCCATCTCTAAATGAGGCTACACAACTTAAAATGATTGGAAA
AGCTCCTCATCTCTAAATGAAGCTATAC
Found at i:606734 original size:143 final size:141
Alignment explanation
Indices: 606444--606781 Score: 340
Period size: 143 Copynumber: 2.4 Consensus size: 141
606434 CCACCCAATT
* * * * * ** *
606444 TTAAAATTATTGAAAAAGCTCC-CTATCTCAAAATAAGGCCACGTAACTTAAAAATGATTGGAAT
1 TTAAAATGATTGTAAAAGCTCCTC-ATCTCTAAATGAGGCTACACAACTT-AAAATGATTGGAAG
* ** * * * *
606508 AGTTCCCAATCTCTAAACGGGGCTACGCAACTTAAAATGATTGGAAAAGTTCCTCATCTCTAAAT
64 AGCTCCCAATCTCTAAACGAAGCTACACAACTTAAAATGATTGAAAAAGCTCCCCATCTCTAAAT
* * **
606573 GAAGTTATGCAAC
129 CAAGCTACACAAC
* * * *
606586 TTAAAATGATTAG-GAAAGTTCTTCATCTCTAAATGAGGTTACACAACTTAAAATGATTGGAAGA
1 TTAAAATGATT-GTAAAAGCTCCTCATCTCTAAATGAGGCTACACAACTTAAAATGATTGGAAGA
* * *
606650 GCTCTTC-ATCTCTAAACGAAGCTATACAACTTTAAAAATGATTGAAAAAGCTCCCCATCTCTGA
65 GCTC-CCAATCTCTAAACGAAGCTACACAAC-TT-AAAATGATTGAAAAAGCTCCCCATCTCTAA
606714 ATCAAGCTACACAAC
127 ATCAAGCTACACAAC
* * *
606729 TTAAAATGATTGTAAAAGCTCCTCCTTTCTAAATGAGGCTACATAACTTAAAA
1 TTAAAATGATTGTAAAAGCTCCTCATCTCTAAATGAGGCTACACAACTTAAAA
606782 ACAATTGGAA
Statistics
Matches: 158, Mismatches: 32, Indels: 11
0.79 0.16 0.05
Matches are distributed among these distances:
141 36 0.23
142 39 0.25
143 83 0.53
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (141 bp):
TTAAAATGATTGTAAAAGCTCCTCATCTCTAAATGAGGCTACACAACTTAAAATGATTGGAAGAG
CTCCCAATCTCTAAACGAAGCTACACAACTTAAAATGATTGAAAAAGCTCCCCATCTCTAAATCA
AGCTACACAAC
Found at i:606892 original size:48 final size:48
Alignment explanation
Indices: 606840--606934 Score: 129
Period size: 48 Copynumber: 2.0 Consensus size: 48
606830 TTTTTTAATT
606840 ATTTTAAAGTTAAGTAGCCTCATTAAGAGATG-GAGAGCTTTTCCAATC
1 ATTTTAAAGTTAAGTAGCCTCATTAAGAGATGAG-GAGCTTTTCCAATC
** * * *
606888 ATTTTAAAGTTGCGTAGCCTTATTTAGAGATGAGGAGCTTTTTCAAT
1 ATTTTAAAGTTAAGTAGCCTCATTAAGAGATGAGGAGCTTTTCCAAT
606935 TATGTTGCGT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
48 40 0.98
49 1 0.02
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.37
Consensus pattern (48 bp):
ATTTTAAAGTTAAGTAGCCTCATTAAGAGATGAGGAGCTTTTCCAATC
Found at i:606970 original size:40 final size:42
Alignment explanation
Indices: 606896--606978 Score: 116
Period size: 40 Copynumber: 2.0 Consensus size: 42
606886 TCATTTTAAA
* *
606896 GTTGCGTAGCCTTATTTAGAGATGAGGAGCTTTTTC-AATTAT
1 GTTGCGTAACCTCATTTA-AGATGAGGAGCTTTTTCTAATTAT
*
606938 GTTGCGTAACCTCATTT-AGATGAGGAGTTTTTTCTAATTAT
1 GTTGCGTAACCTCATTTAAGATGAGGAGCTTTTTCTAATTAT
606979 TTTTAGAGCT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
40 16 0.43
41 6 0.16
42 15 0.41
ACGTcount: A:0.24, C:0.12, G:0.22, T:0.42
Consensus pattern (42 bp):
GTTGCGTAACCTCATTTAAGATGAGGAGCTTTTTCTAATTAT
Found at i:618422 original size:1 final size:1
Alignment explanation
Indices: 618416--618445 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
618406 GCATTTGAGA
618416 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
618446 AGACAATGTC
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:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:621823 original size:33 final size:33
Alignment explanation
Indices: 621786--621853 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
621776 GAGAGTTTGG
621786 CTTGGTGGCTCAGATATGAAGATAGTTAAGAGT
1 CTTGGTGGCTCAGATATGAAGATAGTTAAGAGT
621819 CTTGGTGGCTCAGATATGAAGATAGTTAAGAGT
1 CTTGGTGGCTCAGATATGAAGATAGTTAAGAGT
621852 CT
1 CT
621854 CTTAACCTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.29, C:0.10, G:0.29, T:0.31
Consensus pattern (33 bp):
CTTGGTGGCTCAGATATGAAGATAGTTAAGAGT
Found at i:621942 original size:29 final size:29
Alignment explanation
Indices: 621898--621983 Score: 127
Period size: 29 Copynumber: 3.0 Consensus size: 29
621888 TTTTTCCTTA
* *
621898 TTCTCTTATTCTTGTTCATGTACAGCTTT
1 TTCTCTTATACCTGTTCATGTACAGCTTT
621927 TTCTCTTATACCTGTTCATGTACAGCTTT
1 TTCTCTTATACCTGTTCATGTACAGCTTT
* **
621956 TTCTCTTACACCTGTTCACATACAGCTT
1 TTCTCTTATACCTGTTCATGTACAGCTT
621984 CCTTTCTTGT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.17, C:0.26, G:0.09, T:0.48
Consensus pattern (29 bp):
TTCTCTTATACCTGTTCATGTACAGCTTT
Found at i:629114 original size:26 final size:27
Alignment explanation
Indices: 629069--629123 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 27
629059 AAGGATGAAA
**
629069 TAATCTCCTTCATGTCAAGTT-AGAGT
1 TAATCTCCTTCATGAAAAGTTGAGAGT
*
629095 TAATCTCCTTGATGAAAAGTTGAGAGT
1 TAATCTCCTTCATGAAAAGTTGAGAGT
629122 TA
1 TA
629124 TCTTTTGGCC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 18 0.72
27 7 0.28
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (27 bp):
TAATCTCCTTCATGAAAAGTTGAGAGT
Found at i:645651 original size:21 final size:21
Alignment explanation
Indices: 645622--645661 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
645612 TAACTAAGTA
645622 TTGTCTTAATTAAGACAAGAG
1 TTGTCTTAATTAAGACAAGAG
* *
645643 TTGTTTTAATTTAGACAAG
1 TTGTCTTAATTAAGACAAG
645662 GTGCGTATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.40
Consensus pattern (21 bp):
TTGTCTTAATTAAGACAAGAG
Found at i:649357 original size:43 final size:43
Alignment explanation
Indices: 649304--649385 Score: 146
Period size: 43 Copynumber: 1.9 Consensus size: 43
649294 AGATGGACTA
*
649304 ATGAACAGATTTTCATAGAAAGGCTTGCTTGGGCCCAATAGGC
1 ATGAACAGATTTTCATAGAAAGGCTTGCTTAGGCCCAATAGGC
*
649347 ATGAATAGATTTTCATAGAAAGGCTTGCTTAGGCCCAAT
1 ATGAACAGATTTTCATAGAAAGGCTTGCTTAGGCCCAAT
649386 GGGGTATGCC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (43 bp):
ATGAACAGATTTTCATAGAAAGGCTTGCTTAGGCCCAATAGGC
Found at i:652072 original size:33 final size:33
Alignment explanation
Indices: 652027--652093 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
652017 AGGTCCTTGA
* *
652027 AGCTTCCGTTGGATGAGAAACGTTATCCTGATT
1 AGCTTCCATTGGATGAGAAACGCTATCCTGATT
*
652060 AGCTTCCATTGGATGAGAAATGCTATCCTGATT
1 AGCTTCCATTGGATGAGAAACGCTATCCTGATT
652093 A
1 A
652094 TAGACTAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (33 bp):
AGCTTCCATTGGATGAGAAACGCTATCCTGATT
Found at i:655197 original size:22 final size:23
Alignment explanation
Indices: 655172--655214 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
655162 TTTCATTTTT
*
655172 ATTT-TTTATTATTAAAATATTA
1 ATTTATTTATTATAAAAATATTA
*
655194 ATTTATTTTTTATAAAAATAT
1 ATTTATTTATTATAAAAATAT
655215 AAATAATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
ATTTATTTATTATAAAAATATTA
Found at i:657672 original size:6 final size:7
Alignment explanation
Indices: 657653--657698 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
657643 CTGCACCAAT
657653 AAGAAAC
1 AAGAAAC
657660 AAGAAAC
1 AAGAAAC
657667 -AGAAAC
1 AAGAAAC
657673 AAGAAA-
1 AAGAAAC
*
657679 ATAGAAAG
1 A-AGAAAC
*
657687 AAGAAAG
1 AAGAAAC
657694 AAGAA
1 AAGAA
657699 GAAAAAGATA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
6 7 0.19
7 28 0.78
8 1 0.03
ACGTcount: A:0.72, C:0.07, G:0.20, T:0.02
Consensus pattern (7 bp):
AAGAAAC
Found at i:657672 original size:13 final size:13
Alignment explanation
Indices: 657654--657692 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
657644 TGCACCAATA
657654 AGAAACAAGAAAC
1 AGAAACAAGAAAC
*
657667 AGAAACAAGAAAAT
1 AGAAACAAG-AAAC
*
657681 AGAAAGAAGAAA
1 AGAAACAAGAAA
657693 GAAGAAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.72, C:0.08, G:0.18, T:0.03
Consensus pattern (13 bp):
AGAAACAAGAAAC
Found at i:667190 original size:3 final size:3
Alignment explanation
Indices: 667182--667206 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
667172 TATAAGTATG
667182 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
667207 CATGATGCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:668140 original size:19 final size:20
Alignment explanation
Indices: 668106--668147 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
668096 CTATTTCAAG
*
668106 TTTCCATTTTTATTTTT-AA
1 TTTCCATTTTCATTTTTGAA
*
668125 TTTCCATTTTCCTTTTTGAA
1 TTTCCATTTTCATTTTTGAA
668145 TTT
1 TTT
668148 TCAATTTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.17, C:0.14, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTCCATTTTCATTTTTGAA
Found at i:669775 original size:70 final size:70
Alignment explanation
Indices: 669695--669835 Score: 282
Period size: 70 Copynumber: 2.0 Consensus size: 70
669685 TTATTCTATA
669695 GAATTTATTTTATTAGTTAATAATAATTATAAACATAAAGATAAAGATATACCTTTTATTAAAAT
1 GAATTTATTTTATTAGTTAATAATAATTATAAACATAAAGATAAAGATATACCTTTTATTAAAAT
669760 CAAAT
66 CAAAT
669765 GAATTTATTTTATTAGTTAATAATAATTATAAACATAAAGATAAAGATATACCTTTTATTAAAAT
1 GAATTTATTTTATTAGTTAATAATAATTATAAACATAAAGATAAAGATATACCTTTTATTAAAAT
669830 CAAAT
66 CAAAT
669835 G
1 G
669836 CTTAGAGTAA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 71 1.00
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.40
Consensus pattern (70 bp):
GAATTTATTTTATTAGTTAATAATAATTATAAACATAAAGATAAAGATATACCTTTTATTAAAAT
CAAAT
Found at i:670921 original size:16 final size:16
Alignment explanation
Indices: 670900--670934 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
670890 ATATGCATAC
* *
670900 ATGTATGTGTATGTGT
1 ATGTATATGTATATGT
670916 ATGTATATGTATATGT
1 ATGTATATGTATATGT
670932 ATG
1 ATG
670935 CATTAGATGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.49
Consensus pattern (16 bp):
ATGTATATGTATATGT
Found at i:677897 original size:10 final size:10
Alignment explanation
Indices: 677882--677935 Score: 58
Period size: 10 Copynumber: 5.6 Consensus size: 10
677872 CTGCATAAAT
*
677882 CATACATATA
1 CATACACATA
677892 CAT--ACATA
1 CATACACATA
* *
677900 TATACGCATA
1 CATACACATA
*
677910 CATACGCATA
1 CATACACATA
677920 CATACACATA
1 CATACACATA
677930 CATACA
1 CATACA
677936 TATGTATATG
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
8 6 0.16
10 31 0.84
ACGTcount: A:0.46, C:0.26, G:0.04, T:0.24
Consensus pattern (10 bp):
CATACACATA
Found at i:677919 original size:20 final size:20
Alignment explanation
Indices: 677882--677934 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
677872 CTGCATAAAT
*
677882 CATACATATACATA--CATA
1 CATACACATACATACGCATA
* *
677900 TATACGCATACATACGCATA
1 CATACACATACATACGCATA
677920 CATACACATACATAC
1 CATACACATACATAC
677935 ATATGTATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
18 11 0.39
20 17 0.61
ACGTcount: A:0.45, C:0.26, G:0.04, T:0.25
Consensus pattern (20 bp):
CATACACATACATACGCATA
Found at i:677959 original size:18 final size:18
Alignment explanation
Indices: 677936--677972 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
677926 CATACATACA
*
677936 TATGTATATGTATGTATG
1 TATGTATATATATGTATG
*
677954 TATGTATTTATATGTATG
1 TATGTATATATATGTATG
677972 T
1 T
677973 GTGTCTAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.27, C:0.00, G:0.19, T:0.54
Consensus pattern (18 bp):
TATGTATATATATGTATG
Found at i:683880 original size:110 final size:108
Alignment explanation
Indices: 683661--683990 Score: 455
Period size: 109 Copynumber: 3.0 Consensus size: 108
683651 ATTTGAAAAC
* * *
683661 CTTAAATACAATAAGCAAAAAATATGATCAGTGTAGAATGAAATGTAAATAACATCAACAAATAA
1 CTTAAATACAATAAGCAAAAAATATGATCAATGCAGAATGAAATGTAAATAACATCAAAAAATAA
* * *
683726 ATATTACATAGCAAAATATTAAGGTGATAATTTAAAACTCTAAA
66 AGATTACACAGCAAAA-ATTAAGGTGATAATTCAAAACTCTAAA
*
683770 CTTAAATACAATAAGCAAAAAATATGATCAATGCAGAATGAAATGTAAATAATATCAAAAAAATA
1 CTTAAATACAATAAGCAAAAAATATGATCAATGCAGAATGAAATGTAAATAACATC-AAAAAATA
*
683835 AAGATTACGCAGCCAAAAATTAAGGTGATAATTCAAAACTCTAAA
65 AAGATTACACAG-CAAAAATTAAGGTGATAATTCAAAACTCTAAA
* * * * * * *
683880 CTTAAATACAATAAAC-GAAAATATGATCAATACAGGATGAAATGTAAATAGCATTAATAAATAA
1 CTTAAATACAATAAGCAAAAAATATGATCAATGCAGAATGAAATGTAAATAACATCAAAAAATAA
* * *
683944 AGATTACACAGTAAAAAATTTAGGTGTTAATTCAAAACTCTAAA
66 AGATTACACAG-CAAAAATTAAGGTGATAATTCAAAACTCTAAA
683988 CTT
1 CTT
683991 TATGAAATTT
Statistics
Matches: 198, Mismatches: 21, Indels: 5
0.88 0.09 0.02
Matches are distributed among these distances:
108 50 0.25
109 86 0.43
110 57 0.29
111 5 0.03
ACGTcount: A:0.53, C:0.11, G:0.11, T:0.26
Consensus pattern (108 bp):
CTTAAATACAATAAGCAAAAAATATGATCAATGCAGAATGAAATGTAAATAACATCAAAAAATAA
AGATTACACAGCAAAAATTAAGGTGATAATTCAAAACTCTAAA
Found at i:697121 original size:19 final size:21
Alignment explanation
Indices: 697097--697137 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
697087 TTTTTTCAAC
697097 AATGATC-C-AAATTCAACTG
1 AATGATCACTAAATTCAACTG
*
697116 AATGATCACTAATTTCAACTG
1 AATGATCACTAAATTCAACTG
697137 A
1 A
697138 TTGAAAGGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 1 0.05
21 11 0.58
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (21 bp):
AATGATCACTAAATTCAACTG
Found at i:701354 original size:92 final size:91
Alignment explanation
Indices: 701231--701517 Score: 305
Period size: 98 Copynumber: 3.0 Consensus size: 91
701221 AGTCAAGATG
* * **
701231 AAGCTGAGAAACCAAGTAAAGAAGTAAAAAAAAGGTAACAAAGAGAAGGTGAAGGAATGAAAGCA
1 AAGCTGAGAAACCCAGTGAAGAAGTAAAAAAAAATTAACAAAGAGAAGGTGAAGGAATGAAAGC-
*
701296 TGCCCCTGACACTCAGTCCTCTTAAGC
65 TGCCCCTGACACTCAATCCTCTTAAGC
* * *
701323 CAGCTGAGAAACCCAGTGAAGAAGTAAAAAAAAATTAACAAAGAGAAGAGGGTGAAGGACTCAAA
1 AAGCTGAGAAACCCAGTGAAGAAGTAAAAAAAAATTAACAAAGAG-A-A-GGTGAAGGAATGAAA
701388 GCT-CACCC-GACACTCAATCCT-TTAAAGC
63 GCTGC-CCCTGACACTCAATCCTCTT-AAGC
* *
701416 AAGCTGAGAAACTCGGTGAAGAAGTTAAAAAAAAAAAAATTAACAAAGAGAAGAAAGTGAAGGAA
1 AAGCTGAGAAACCCAGTGAAGAAG-T----AAAAAAAAATTAACAAAGAGAAG---GTGAAGGAA
*
701481 TG--AGCTTGCCCATGACACTCAATCCTCTTAAGC
58 TGAAAGC-TGCCCCTGACACTCAATCCTCTTAAGC
701514 AAGC
1 AAGC
701518 ATCACAGGTG
Statistics
Matches: 164, Mismatches: 14, Indels: 28
0.80 0.07 0.14
Matches are distributed among these distances:
92 42 0.26
93 39 0.24
94 6 0.04
95 16 0.10
96 4 0.02
97 4 0.02
98 51 0.31
99 2 0.01
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (91 bp):
AAGCTGAGAAACCCAGTGAAGAAGTAAAAAAAAATTAACAAAGAGAAGGTGAAGGAATGAAAGCT
GCCCCTGACACTCAATCCTCTTAAGC
Found at i:705721 original size:115 final size:115
Alignment explanation
Indices: 705519--705748 Score: 415
Period size: 115 Copynumber: 2.0 Consensus size: 115
705509 GGATCAATCA
* * *
705519 ATAAACTATTGTTGCATTATGTTGGTACAATAGTAGTAAAGCAATTAATATTTTTCAACAAAATG
1 ATAAACTATTGTTGCATGATGTTGGTACAACAGTAGTAAAGCAATTAATATTTTTCAACAAAAAG
*
705584 TTTTTCCTTATTTTGTCAAATTGCAATGTTAATTATGGTACTTAATTATT
66 TTTTTCCTTATTTTGTCAAATTGCAATGTTAATTACGGTACTTAATTATT
705634 ATAAACTATTGTTGCATGATGTTGGTACAACAGTAGTAAAGCAATTAATATTTTTCAACAAAAAG
1 ATAAACTATTGTTGCATGATGTTGGTACAACAGTAGTAAAGCAATTAATATTTTTCAACAAAAAG
*
705699 TTTTTCCTTATTTTGTCAAATTGCAATGTTAATTACGGTATTTAATTATT
66 TTTTTCCTTATTTTGTCAAATTGCAATGTTAATTACGGTACTTAATTATT
705749 TATTTAAGTG
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
115 110 1.00
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.43
Consensus pattern (115 bp):
ATAAACTATTGTTGCATGATGTTGGTACAACAGTAGTAAAGCAATTAATATTTTTCAACAAAAAG
TTTTTCCTTATTTTGTCAAATTGCAATGTTAATTACGGTACTTAATTATT
Found at i:709964 original size:14 final size:13
Alignment explanation
Indices: 709940--709978 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
709930 AGAAAAAAAA
709940 CTCTTTTTTTCTT
1 CTCTTTTTTTCTT
709953 CTCTTCTTTTTCTT
1 CTCTT-TTTTTCTT
*
709967 CACTTTTCTTTC
1 CTCTTTT-TTTC
709979 AATCCAGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 7 0.30
14 16 0.70
ACGTcount: A:0.03, C:0.28, G:0.00, T:0.69
Consensus pattern (13 bp):
CTCTTTTTTTCTT
Found at i:714032 original size:15 final size:15
Alignment explanation
Indices: 714012--714046 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
714002 TTTATAGCCA
*
714012 ATTTCCCTCCAAAAT
1 ATTTCCCTCCAAAAC
714027 ATTTCCCTCCAAAAC
1 ATTTCCCTCCAAAAC
714042 ATTTC
1 ATTTC
714047 AAAAGGAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.31, C:0.34, G:0.00, T:0.34
Consensus pattern (15 bp):
ATTTCCCTCCAAAAC
Found at i:721148 original size:31 final size:31
Alignment explanation
Indices: 721110--721171 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
721100 AACTAACAAG
721110 AAGTAGGTTGCACCAAATCAATGATCACCTT
1 AAGTAGGTTGCACCAAATCAATGATCACCTT
* *
721141 AAGTAGGTTGCACCAAATCAATTATTACCTT
1 AAGTAGGTTGCACCAAATCAATGATCACCTT
721172 TAATTTCCTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (31 bp):
AAGTAGGTTGCACCAAATCAATGATCACCTT
Found at i:723792 original size:17 final size:18
Alignment explanation
Indices: 723760--723793 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
723750 TTTTATAGTA
723760 GTTTTCGATGATGATAGC
1 GTTTTCGATGATGATAGC
*
723778 GTTTTGGAT-ATGATAG
1 GTTTTCGATGATGATAG
723794 GATATATGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.24, C:0.06, G:0.29, T:0.41
Consensus pattern (18 bp):
GTTTTCGATGATGATAGC
Found at i:738952 original size:9 final size:10
Alignment explanation
Indices: 738928--738952 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
738918 AGATTAGTTT
738928 ATTTTTGTTA
1 ATTTTTGTTA
738938 ATTTTTGTTA
1 ATTTTTGTTA
738948 ATTTT
1 ATTTT
738953 ATGCATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.08, T:0.72
Consensus pattern (10 bp):
ATTTTTGTTA
Found at i:751483 original size:16 final size:16
Alignment explanation
Indices: 751462--751495 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
751452 TGACCCTGTA
751462 GATTTAAAGATAAGTG
1 GATTTAAAGATAAGTG
*
751478 GATTTAAAGATGAGTG
1 GATTTAAAGATAAGTG
751494 GA
1 GA
751496 AGGAATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.29, T:0.29
Consensus pattern (16 bp):
GATTTAAAGATAAGTG
Found at i:754998 original size:15 final size:15
Alignment explanation
Indices: 754970--755037 Score: 82
Period size: 15 Copynumber: 4.5 Consensus size: 15
754960 AAGTTTCCCC
**
754970 AAATATTTTTCTCCA
1 AAATATTTCCCTCCA
*
754985 AAATGTTTCCCTCCA
1 AAATATTTCCCTCCA
**
755000 AAGCATTTCCCTCCA
1 AAATATTTCCCTCCA
755015 AAATATTTCCCTCCA
1 AAATATTTCCCTCCA
*
755030 AAACATTT
1 AAATATTT
755038 GGGAGGGAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 44 1.00
ACGTcount: A:0.32, C:0.29, G:0.03, T:0.35
Consensus pattern (15 bp):
AAATATTTCCCTCCA
Found at i:755016 original size:30 final size:30
Alignment explanation
Indices: 754980--755037 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
754970 AAATATTTTT
* *
754980 CTCCAAAATGTTTCCCTCCAAAGCATTTCC
1 CTCCAAAATATTTCCCTCCAAAACATTTCC
755010 CTCCAAAATATTTCCCTCCAAAACATTT
1 CTCCAAAATATTTCCCTCCAAAACATTT
755038 GGGAGGGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.34, G:0.03, T:0.31
Consensus pattern (30 bp):
CTCCAAAATATTTCCCTCCAAAACATTTCC
Found at i:755076 original size:34 final size:34
Alignment explanation
Indices: 755033--755102 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 34
755023 CCCTCCAAAA
755033 CATTTGGGAGGGAAAGCT-AAAGTTTCTAGAAGCT
1 CATTTGGGAGGGAAAGCTGAAAGTTTC-AGAAGCT
* *
755067 CATTTGGGAGGGAAAGCTGAAATTTTCAGCAGCT
1 CATTTGGGAGGGAAAGCTGAAAGTTTCAGAAGCT
755101 CA
1 CA
755103 ATACATGGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
34 26 0.79
35 7 0.21
ACGTcount: A:0.31, C:0.14, G:0.29, T:0.26
Consensus pattern (34 bp):
CATTTGGGAGGGAAAGCTGAAAGTTTCAGAAGCT
Found at i:755314 original size:15 final size:15
Alignment explanation
Indices: 755266--755325 Score: 57
Period size: 15 Copynumber: 4.0 Consensus size: 15
755256 CGAGCCATCT
*
755266 TGCGTGCTGCGTACC
1 TGCGTGCCGCGTACC
* * * *
755281 TGTGTGCCACGCACT
1 TGCGTGCCGCGTACC
755296 TGCGTGCCGCGTACC
1 TGCGTGCCGCGTACC
* *
755311 TGCGCGCCGTGTACC
1 TGCGTGCCGCGTACC
755326 CATGGCGTGC
Statistics
Matches: 34, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.08, C:0.37, G:0.32, T:0.23
Consensus pattern (15 bp):
TGCGTGCCGCGTACC
Found at i:755943 original size:15 final size:15
Alignment explanation
Indices: 755920--755972 Score: 70
Period size: 15 Copynumber: 3.5 Consensus size: 15
755910 TTTCCCTCTC
* *
755920 AAATGTTTTGGAGGA
1 AAATATTTTGGAGGG
755935 AAATATTTTGGAGGG
1 AAATATTTTGGAGGG
**
755950 AAATGCTTTGGAGGG
1 AAATATTTTGGAGGG
755965 AAATATTT
1 AAATATTT
755973 GAGGAAACTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.34, C:0.02, G:0.30, T:0.34
Consensus pattern (15 bp):
AAATATTTTGGAGGG
Found at i:768336 original size:13 final size:13
Alignment explanation
Indices: 768318--768342 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
768308 GAGTTTACTC
768318 CTATTTTCTCTCT
1 CTATTTTCTCTCT
768331 CTATTTTCTCTC
1 CTATTTTCTCTC
768343 CTCAACTGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.32, G:0.00, T:0.60
Consensus pattern (13 bp):
CTATTTTCTCTCT
Found at i:770963 original size:2 final size:2
Alignment explanation
Indices: 770956--770980 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
770946 ATCTCCTTTT
770956 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
770981 GTCGCTTGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:780434 original size:42 final size:42
Alignment explanation
Indices: 780334--780462 Score: 127
Period size: 42 Copynumber: 3.1 Consensus size: 42
780324 GGGACTGCTG
* *
780334 AGCCTGCCCCAACAAGTGTTCAGCCAGACG-CCGAGGT-TACAA
1 AGCCTGCCTCAACAAGTGTTCCGCCAGA-GACCGAGGTCT-CAA
* ** *
780376 AGCCTGCGTCTGCAAGTGTTCCTCCAGAGACCGAGGTCTCAA
1 AGCCTGCCTCAACAAGTGTTCCGCCAGAGACCGAGGTCTCAA
* * * * *
780418 AGCCTGCTTCAACAAGTGGTCCGCCAGACACTGAGGCCTCAA
1 AGCCTGCCTCAACAAGTGTTCCGCCAGAGACCGAGGTCTCAA
780460 AGC
1 AGC
780463 ACATTGGTTC
Statistics
Matches: 71, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
41 1 0.01
42 69 0.97
43 1 0.01
ACGTcount: A:0.26, C:0.33, G:0.25, T:0.17
Consensus pattern (42 bp):
AGCCTGCCTCAACAAGTGTTCCGCCAGAGACCGAGGTCTCAA
Found at i:790055 original size:16 final size:16
Alignment explanation
Indices: 790034--790070 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
790024 ACATATAAAT
790034 ATTGAGAATGAGT-TAA
1 ATTGAGAATG-GTATAA
790050 ATTGAGAATGGTATAA
1 ATTGAGAATGGTATAA
790066 ATTGA
1 ATTGA
790071 TGCCAATGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 2 0.10
16 18 0.90
ACGTcount: A:0.43, C:0.00, G:0.24, T:0.32
Consensus pattern (16 bp):
ATTGAGAATGGTATAA
Found at i:804801 original size:14 final size:13
Alignment explanation
Indices: 804763--804801 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
804753 GTTTGTAAGC
*
804763 CAATAAACAATAA
1 CAATAAACAAAAA
804776 CAATAAAGCAAAAA
1 CAATAAA-CAAAAA
804790 CACATAAACAAA
1 CA-ATAAACAAA
804802 GACCAAACGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 7 0.30
14 11 0.48
15 5 0.22
ACGTcount: A:0.69, C:0.18, G:0.03, T:0.10
Consensus pattern (13 bp):
CAATAAACAAAAA
Found at i:805706 original size:14 final size:13
Alignment explanation
Indices: 805685--805726 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 13
805675 CATGTTTCTC
805685 ATTTTATTTATTT
1 ATTTTATTTATTT
805698 ATGTTTATTTATTTT
1 AT-TTTATTTA-TTT
805713 ATTTTATTTTATTT
1 ATTTTA-TTTATTT
805727 TCTATACAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 2 0.08
14 15 0.58
15 9 0.35
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.76
Consensus pattern (13 bp):
ATTTTATTTATTT
Found at i:805715 original size:5 final size:5
Alignment explanation
Indices: 805685--805727 Score: 56
Period size: 5 Copynumber: 9.0 Consensus size: 5
805675 CATGTTTCTC
805685 ATTTT A-TTT A-TTT ATGTTT A-TTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT AT-TTT ATTTT ATTTT ATTTT ATTTT ATTTT
805728 CTATACAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
4 12 0.34
5 19 0.54
6 4 0.11
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (5 bp):
ATTTT
Found at i:805755 original size:10 final size:11
Alignment explanation
Indices: 805734--805768 Score: 54
Period size: 10 Copynumber: 3.2 Consensus size: 11
805724 TTTTCTATAC
805734 AAATGAAAAATA
1 AAAT-AAAAATA
805746 AAAT-AAAATA
1 AAATAAAAATA
805756 AAATAAAAATA
1 AAATAAAAATA
805767 AA
1 AA
805769 GTTTTGTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.45
11 8 0.36
12 4 0.18
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (11 bp):
AAATAAAAATA
Found at i:813390 original size:35 final size:37
Alignment explanation
Indices: 813345--813413 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
813335 GAAAATCGTT
*
813345 TGATCTCGTG-AAAAG-CAAGTGT-AAAGGTTATCACC
1 TGATCGCGTGAAAAAGTCAA-TGTAAAAGGTTATCACC
813380 TGATCGCGTGAAAAAGTCAATGTAAAAGGTTATC
1 TGATCGCGTGAAAAAGTCAATGTAAAAGGTTATC
813414 GGTTTATCGT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
35 9 0.30
36 8 0.27
37 13 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.26
Consensus pattern (37 bp):
TGATCGCGTGAAAAAGTCAATGTAAAAGGTTATCACC
Done.