Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1558.1
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: 416758
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 2633 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:287125 original size:16 final size:16
Alignment explanation
Indices: 287100--287130 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
287090 TTTAGGATGA
*
287100 GATGTTATGCAATCAT
1 GATGTCATGCAATCAT
287116 GATGTCATGCAATCA
1 GATGTCATGCAATCA
287131 AAACAAAAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Consensus pattern (16 bp):
GATGTCATGCAATCAT
Found at i:288125 original size:78 final size:78
Alignment explanation
Indices: 287996--288151 Score: 294
Period size: 78 Copynumber: 2.0 Consensus size: 78
287986 ACGTTAGGGT
*
287996 ACAATTCCTCATAATCCCCAAACTTGAATATCACTTTTATTATATACGAAAATCTTTATTTTGAG
1 ACAATTCCTCATAATCCCCAAACTTGAATATCACTTTTATTATATACGAAAATCTTCATTTTGAG
288061 AAAGTAACATGCC
66 AAAGTAACATGCC
*
288074 ACAATTCCTCATAATCCCCAAACTTGAATATCACTTTTATTTTATACGAAAATCTTCATTTTGAG
1 ACAATTCCTCATAATCCCCAAACTTGAATATCACTTTTATTATATACGAAAATCTTCATTTTGAG
288139 AAAGTAACATGCC
66 AAAGTAACATGCC
288152 GCACCCAATA
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 76 1.00
ACGTcount: A:0.37, C:0.21, G:0.08, T:0.35
Consensus pattern (78 bp):
ACAATTCCTCATAATCCCCAAACTTGAATATCACTTTTATTATATACGAAAATCTTCATTTTGAG
AAAGTAACATGCC
Found at i:289568 original size:10 final size:9
Alignment explanation
Indices: 289553--289595 Score: 50
Period size: 10 Copynumber: 4.6 Consensus size: 9
289543 TTGTTATCTT
289553 AAATGAAATA
1 AAATGAAA-A
289563 AAATGAAAA
1 AAATGAAAA
*
289572 TAAAGGAAAA
1 -AAATGAAAA
*
289582 AAATAAAAA
1 AAATGAAAA
289591 AAATG
1 AAATG
289596 CAAACAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
9 12 0.43
10 16 0.57
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.14
Consensus pattern (9 bp):
AAATGAAAA
Found at i:291671 original size:34 final size:34
Alignment explanation
Indices: 291628--291696 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
291618 TTTAGGAAAC
291628 TATGTTTCTTATATTTGCTCCACATGTAACCTAA
1 TATGTTTCTTATATTTGCTCCACATGTAACCTAA
291662 TATGTTTCTTATATTTGCTCCACATGTAACCTAA
1 TATGTTTCTTATATTTGCTCCACATGTAACCTAA
291696 T
1 T
291697 GGTTCATAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.26, C:0.20, G:0.09, T:0.45
Consensus pattern (34 bp):
TATGTTTCTTATATTTGCTCCACATGTAACCTAA
Found at i:294191 original size:9 final size:9
Alignment explanation
Indices: 294158--294196 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
294148 AGTAAATTTT
294158 ATTTTTAAA
1 ATTTTTAAA
294167 A-TTTTAAA
1 ATTTTTAAA
*
294175 ATTGTTAAA
1 ATTTTTAAA
294184 ATTTTTAATA
1 ATTTTTAA-A
294194 ATT
1 ATT
294197 AAAAAATAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
8 8 0.31
9 14 0.54
10 4 0.15
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (9 bp):
ATTTTTAAA
Found at i:294276 original size:27 final size:28
Alignment explanation
Indices: 294237--294293 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 28
294227 ATCTTTTCTA
* *
294237 TTTTAGTAATTTTTAATTTTAAATAAAT
1 TTTTAGTAATTTTTAATTCTAAAAAAAT
* *
294265 TTTTA-TATTTTTTCATTCTAAAAAAAT
1 TTTTAGTAATTTTTAATTCTAAAAAAAT
294292 TT
1 TT
294294 AGGGTTTTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 20 0.80
28 5 0.20
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.58
Consensus pattern (28 bp):
TTTTAGTAATTTTTAATTCTAAAAAAAT
Found at i:294794 original size:24 final size:24
Alignment explanation
Indices: 294754--294803 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
294744 GTGGCGCTAT
294754 TTTCTTTTAAGATATATATAT-ATA
1 TTTCTTTTAAGATATAT-TATCATA
294778 TTTCATTTTAAGA-ATATTATCATA
1 TTTC-TTTTAAGATATATTATCATA
294802 TT
1 TT
294804 AACGGATGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 3 0.12
24 13 0.54
25 8 0.33
ACGTcount: A:0.36, C:0.06, G:0.04, T:0.54
Consensus pattern (24 bp):
TTTCTTTTAAGATATATTATCATA
Found at i:295034 original size:21 final size:22
Alignment explanation
Indices: 295010--295057 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
295000 TAATAAAATA
295010 TTTAAATA-TTT-TAATTGATAT
1 TTTAAATATTTTGTAATTGA-AT
*
295031 TTTATATATTTTGTAATTGAAT
1 TTTAAATATTTTGTAATTGAAT
295053 TTTAA
1 TTTAA
295058 TTAATTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 7 0.30
22 9 0.39
23 7 0.30
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (22 bp):
TTTAAATATTTTGTAATTGAAT
Found at i:311665 original size:18 final size:18
Alignment explanation
Indices: 311651--311685 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
311641 CCAAAAGGAG
311651 CTGCGAGTGTCAAAGCAA
1 CTGCGAGTGTCAAAGCAA
* *
311669 CTGTGAGTGTCGAAGCA
1 CTGCGAGTGTCAAAGCA
311686 CCTACAGTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.20, G:0.31, T:0.20
Consensus pattern (18 bp):
CTGCGAGTGTCAAAGCAA
Found at i:311675 original size:201 final size:198
Alignment explanation
Indices: 311329--311843 Score: 712
Period size: 201 Copynumber: 2.6 Consensus size: 198
311319 GAGTGTTGAG
311329 GCACCTACGGTTAATGAAGTTGATGATGGCT-GCTCAAGCATTACCAGTGGTAAGTTGAGGAGAA
1 GCACCTACGGTTAATGAAGTTGAT-A-GG-TGGCTCAAGCATTA-CAGTGGTAAGTTGAGGAGAA
* * *
311393 GGACATGCTATGAGTGTGGACAAAAGGGCCATATTTCTTCTGCTTGCCCAAAAGGATCTGTGAGT
62 GGACATGCTACGAGTGTGGACAAAAGGGCCATATTTCTTCTGCTTGCCCAAAAGGAGCTGCGAGT
* ** * * * *
311458 GTCGAAGCGCCTGTGAGTGTTGAAGCACCTACAGTTAATGAAGTTGGTAACAGTGGTTCGATGGT
127 GTCAAAGCAACTGTGAGTGTCGAAGCACCTACAGTTAATGAAGTTGGCAACAGTGGTTCAACGGT
311523 TAATGAA
192 TAATGAA
* *
311530 GCACCTACAGTTAATGAAGTTGATAACGGTGGCTCAAGCATTACTAGTGGTAAGTTGAGGAGGAG
1 GCACCTACGGTTAATGAAGTTGAT-A-GGTGGCTCAAGCATTAC-AGTGGTAAGTTGAGGAGAAG
*
311595 GACATGCTACGAGTGTGGACAAAAGGGCCATATTTCTTCTGCTTGTCCAAAAGGAGCTGCGAGTG
63 GACATGCTACGAGTGTGGACAAAAGGGCCATATTTCTTCTGCTTGCCCAAAAGGAGCTGCGAGTG
*
311660 TCAAAGCAACTGTGAGTGTCGAAGCACCTACAGTTAGTGAAGTTGGCAACAGTGGTTCAACGGTT
128 TCAAAGCAACTGTGAGTGTCGAAGCACCTACAGTTAATGAAGTTGGCAACAGTGGTTCAACGGTT
311725 AATGAA
193 AATGAA
* * * * * * *
311731 GCACCTACGGTTAACGAAGTTGCT-GATGGCTC-GGCTGTTAGCAGTGGGAAATTGAGGAGAAGG
1 GCACCTACGGTTAATGAAGTTGATAGGTGGCTCAAGC-ATTA-CAGTGGTAAGTTGAGGAGAAGG
* * *
311794 ACATGCTACGAGTGCGGACAAAAGGGTCATATCTCTTCTGCTTGCCCAAA
64 ACATGCTACGAGTGTGGACAAAAGGGCCATATTTCTTCTGCTTGCCCAAA
311844 TAAGAAATCT
Statistics
Matches: 281, Mismatches: 29, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
197 2 0.01
198 74 0.26
199 1 0.00
200 2 0.01
201 202 0.72
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.25
Consensus pattern (198 bp):
GCACCTACGGTTAATGAAGTTGATAGGTGGCTCAAGCATTACAGTGGTAAGTTGAGGAGAAGGAC
ATGCTACGAGTGTGGACAAAAGGGCCATATTTCTTCTGCTTGCCCAAAAGGAGCTGCGAGTGTCA
AAGCAACTGTGAGTGTCGAAGCACCTACAGTTAATGAAGTTGGCAACAGTGGTTCAACGGTTAAT
GAA
Found at i:312735 original size:21 final size:21
Alignment explanation
Indices: 312711--312765 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
312701 TAATTTTAGT
312711 TTTTTAGTGGAAAA-CTTGGAA
1 TTTTTAGTGGAAAAGCTT-GAA
*
312732 -TTTTAGAGGAAAAGCTTGAA
1 TTTTTAGTGGAAAAGCTTGAA
*
312752 TTTTTATTGGAAAA
1 TTTTTAGTGGAAAA
312766 ATTATTATCT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.36, C:0.04, G:0.22, T:0.38
Consensus pattern (21 bp):
TTTTTAGTGGAAAAGCTTGAA
Found at i:317728 original size:15 final size:15
Alignment explanation
Indices: 317708--317737 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
317698 TTCCGAAGAA
*
317708 GGAAAGAGGCTAAAC
1 GGAAAGAAGCTAAAC
317723 GGAAAGAAGCTAAAC
1 GGAAAGAAGCTAAAC
317738 ATTTCAGAAG
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:0.50, C:0.13, G:0.30, T:0.07
Consensus pattern (15 bp):
GGAAAGAAGCTAAAC
Found at i:318811 original size:36 final size:36
Alignment explanation
Indices: 318771--318901 Score: 138
Period size: 36 Copynumber: 3.6 Consensus size: 36
318761 AATAGAAGTG
*
318771 ATAATTACAAATTTAAAAATAAATAGAATTTAAATT
1 ATAATTATAAATTTAAAAATAAATAGAATTTAAATT
* * * * *
318807 ATAATTATTAA-TTAAAAATTTGAAATAAAATTGAAGTG
1 ATAATTATAAATTTAAAAA--T-AAATAGAATTTAAATT
*
318845 ATAATTATAGATTTAAAAATAAATAGAATTTAAATT
1 ATAATTATAAATTTAAAAATAAATAGAATTTAAATT
* * *
318881 ATATTTATTAATTAAAAAATA
1 ATAATTATAAATTTAAAAATA
318902 CATGTTAATT
Statistics
Matches: 75, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
35 7 0.09
36 38 0.51
37 2 0.03
38 21 0.28
39 7 0.09
ACGTcount: A:0.56, C:0.01, G:0.05, T:0.38
Consensus pattern (36 bp):
ATAATTATAAATTTAAAAATAAATAGAATTTAAATT
Found at i:318833 original size:74 final size:74
Alignment explanation
Indices: 318705--318898 Score: 280
Period size: 74 Copynumber: 2.6 Consensus size: 74
318695 TTAAATTCAC
* * * *
318705 ATTTAAAAATAATTATAATGTTTAATTTAGAATTATTAATTAAAAAGTTAAAATAAAATAGAAGT
1 ATTTAAAAATAAATAGAA--TTTAAATTATAATTATTAATTAAAAAGTTAAAATAAAATAGAAGT
318770 GATAATTACAA
64 GATAATTACAA
* * *
318781 ATTTAAAAATAAATAGAATTTAAATTATAATTATTAATTAAAAATTTGAAATAAAATTGAAGTGA
1 ATTTAAAAATAAATAGAATTTAAATTATAATTATTAATTAAAAAGTTAAAATAAAATAGAAGTGA
* *
318846 TAATTATAG
66 TAATTACAA
*
318855 ATTTAAAAATAAATAGAATTTAAATTATATTTATTAATTAAAAA
1 ATTTAAAAATAAATAGAATTTAAATTATAATTATTAATTAAAAA
318899 ATACATGTTA
Statistics
Matches: 108, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
74 92 0.85
76 16 0.15
ACGTcount: A:0.55, C:0.01, G:0.07, T:0.38
Consensus pattern (74 bp):
ATTTAAAAATAAATAGAATTTAAATTATAATTATTAATTAAAAAGTTAAAATAAAATAGAAGTGA
TAATTACAA
Found at i:324097 original size:28 final size:28
Alignment explanation
Indices: 324050--324119 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 28
324040 TTCAGAGAAA
* * *
324050 AATTTT-AA-AAAAAATTAAGAATTGAG
1 AATTTTGAATAAAAAATCAAGAATTAAC
324076 AATTTTGAATAAAAAATCAAGAATTAAC
1 AATTTTGAATAAAAAATCAAGAATTAAC
**
324104 AATTGAGAATAAAAAA
1 AATTTTGAATAAAAAA
324120 AATTTGAGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 6 0.16
27 2 0.05
28 29 0.78
ACGTcount: A:0.60, C:0.03, G:0.10, T:0.27
Consensus pattern (28 bp):
AATTTTGAATAAAAAATCAAGAATTAAC
Found at i:326348 original size:17 final size:17
Alignment explanation
Indices: 326312--326349 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
326302 ATCATCGGTT
*
326312 AAATTTTAAATTTACCA
1 AAATTTTAAATTTACAA
*
326329 AAATTTTAAATTTAGAA
1 AAATTTTAAATTTACAA
326346 AAAT
1 AAAT
326350 ATATCATAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (17 bp):
AAATTTTAAATTTACAA
Found at i:338992 original size:23 final size:22
Alignment explanation
Indices: 338952--338995 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
338942 TTTAAAAAAT
338952 ATATTTATATTATATTATTTTA
1 ATATTTATATTATATTATTTTA
* *
338974 ATATTTAATATTTTTTTATTTT
1 ATATTT-ATATTATATTATTTT
338996 TTGAAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
ATATTTATATTATATTATTTTA
Found at i:340351 original size:7 final size:7
Alignment explanation
Indices: 340339--340368 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
340329 AAAGTCAATT
340339 ATTTAAA
1 ATTTAAA
340346 ATTTAAA
1 ATTTAAA
340353 ATTTAAA
1 ATTTAAA
340360 ATTTAAA
1 ATTTAAA
340367 AT
1 AT
340369 AGATAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
ATTTAAA
Found at i:341515 original size:18 final size:18
Alignment explanation
Indices: 341460--341515 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
341450 GATAAAAATG
* *
341460 ATTATTTTATAAAATAAA
1 ATTATTTCATTAAATAAA
* *
341478 CTTAATTTCTTCTAAA-AAA
1 ATT-ATTTCAT-TAAATAAA
341497 ATTATTTCATTAAATAAA
1 ATTATTTCATTAAATAAA
341515 A
1 A
341516 ATTCTAATTT
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
17 4 0.14
18 12 0.41
19 10 0.34
20 3 0.10
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTATTTCATTAAATAAA
Found at i:347610 original size:366 final size:366
Alignment explanation
Indices: 346938--348037 Score: 2191
Period size: 366 Copynumber: 3.0 Consensus size: 366
346928 AAGCTTGTTT
*
346938 AACTGGTCCAAACACATAAGAGTGGACCAACTCTAATGGTTTCTTCGCTTTAAATTTGGACTCTT
1 AACTGGTCCAAACACATCAGAGTGGACCAACTCTAATGGTTTCTTCGCTTTAAATTTGGACTCTT
347003 CGTACGGTAACTGGTGTGCTTTTCCATTCTGACAGCCTGCACACACAGTGTCTTTTCTCACTTCA
66 CGTACGGTAACTGGTGTGCTTTTCCATTCTGACAGCCTGCACACACAGTGTCTTTTCTCACTTCA
347068 AGTTGTGGAAGTCCCTTCAACATTGAGCTCTTCATCATCACATCTAATTTGGAATAGCTAACGTG
131 AGTTGTGGAAGTCCCTTCAACATTGAGCTCTTCATCATCACATCTAATTTGGAATAGCTAACGTG
347133 ACCTAGCCGCATTTGCCACACATCTGTCATTTCATTCCTTCTTGTCTTGTCTACGTATGCGGTTT
196 ACCTAGCCGCATTTGCCACACATCTGTCATTTCATTCCTTCTTGTCTTGTCTACGTATGCGGTTT
347198 CTGCAGACATTACATAGACTGATTCCAACCTCTGTCCCTTCATCACTGGTTCTTCTATAACTTCA
261 CTGCAGACATTACATAGACTGATTCCAACCTCTGTCCCTTCATCACTGGTTCTTCTATAACTTCA
347263 GGTTCTGATACACCTTTACATCTTGTGGACCAAAGAGAACA
326 GGTTCTGATACACCTTTACATCTTGTGGACCAAAGAGAACA
347304 AACTGGTCCAAACACATCAGAGTGGACCAACTCTAATGGTTTCTTCGCTTTAAATTTGGACTCTT
1 AACTGGTCCAAACACATCAGAGTGGACCAACTCTAATGGTTTCTTCGCTTTAAATTTGGACTCTT
347369 CGTACGGTAACTGGTGTGCTTTTCCATTCTGACAGCCTGCACACACAGTGTCTTTTCTCACTTCA
66 CGTACGGTAACTGGTGTGCTTTTCCATTCTGACAGCCTGCACACACAGTGTCTTTTCTCACTTCA
347434 AGTTGTGGAAGTCCCTTCAACATTGAGCTCTTCATCATCACATCTAATTTGGAATAGCTAACGTG
131 AGTTGTGGAAGTCCCTTCAACATTGAGCTCTTCATCATCACATCTAATTTGGAATAGCTAACGTG
347499 ACCTAGCCGCATTTGCCACACATCTGTCATTTCATTCCTTCTTGTCTTGTCTACGTATGCGGTTT
196 ACCTAGCCGCATTTGCCACACATCTGTCATTTCATTCCTTCTTGTCTTGTCTACGTATGCGGTTT
347564 CTGCAGACATTACATAGACTGATTCCAACCTCTGTCCCTTCATCACTGGTTCTTCTATAACTTCA
261 CTGCAGACATTACATAGACTGATTCCAACCTCTGTCCCTTCATCACTGGTTCTTCTATAACTTCA
347629 GGTTCTGATACACCTTTACATCTTGTGGACCAAAGAGAACA
326 GGTTCTGATACACCTTTACATCTTGTGGACCAAAGAGAACA
347670 AACTGGTCCAAACACATCAGAGTGGACCAACTCTAATGGTTTCTTCGCTTTAAATTTGGACTCTT
1 AACTGGTCCAAACACATCAGAGTGGACCAACTCTAATGGTTTCTTCGCTTTAAATTTGGACTCTT
347735 CGTACGGTAACTGGTGTGCTTTTCCATTCTGACAGCCTGCACACACAGTGTCTTTTCTCACTTCA
66 CGTACGGTAACTGGTGTGCTTTTCCATTCTGACAGCCTGCACACACAGTGTCTTTTCTCACTTCA
347800 AGTTGTGGAAGTCCCTTCAACATTGAGCTCTTCATCATCACATCTAATTTGGAATAGCTAACGTG
131 AGTTGTGGAAGTCCCTTCAACATTGAGCTCTTCATCATCACATCTAATTTGGAATAGCTAACGTG
347865 ACCTAGCCGCATTTGCCACACATCTGTCATTTCATTCCTTCTTGTCTTGTCTACGTATGCGGTTT
196 ACCTAGCCGCATTTGCCACACATCTGTCATTTCATTCCTTCTTGTCTTGTCTACGTATGCGGTTT
347930 CTGCAGACATTACATAGACTGATTCCAACCTCTGTCCCTTCATCACTGGTTCTTCTATAACTTCA
261 CTGCAGACATTACATAGACTGATTCCAACCTCTGTCCCTTCATCACTGGTTCTTCTATAACTTCA
347995 GGTTCTGATACACCTTTACATCTTGTGGACCAAAGAGAACA
326 GGTTCTGATACACCTTTACATCTTGTGGACCAAAGAGAACA
348036 AA
1 AA
348038 ATGGCTAGAA
Statistics
Matches: 733, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
366 733 1.00
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (366 bp):
AACTGGTCCAAACACATCAGAGTGGACCAACTCTAATGGTTTCTTCGCTTTAAATTTGGACTCTT
CGTACGGTAACTGGTGTGCTTTTCCATTCTGACAGCCTGCACACACAGTGTCTTTTCTCACTTCA
AGTTGTGGAAGTCCCTTCAACATTGAGCTCTTCATCATCACATCTAATTTGGAATAGCTAACGTG
ACCTAGCCGCATTTGCCACACATCTGTCATTTCATTCCTTCTTGTCTTGTCTACGTATGCGGTTT
CTGCAGACATTACATAGACTGATTCCAACCTCTGTCCCTTCATCACTGGTTCTTCTATAACTTCA
GGTTCTGATACACCTTTACATCTTGTGGACCAAAGAGAACA
Found at i:359778 original size:5 final size:5
Alignment explanation
Indices: 359768--359796 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
359758 GCATGCTTGG
359768 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
359797 CCCAATTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:359971 original size:14 final size:15
Alignment explanation
Indices: 359946--359975 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
359936 TTTAATCTAA
359946 ATTTTAAATTGATTT
1 ATTTTAAATTGATTT
359961 ATTTT-AATTGATTT
1 ATTTTAAATTGATTT
359975 A
1 A
359976 AGTCTTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (15 bp):
ATTTTAAATTGATTT
Found at i:363909 original size:19 final size:19
Alignment explanation
Indices: 363887--363925 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
363877 GAAGCTCATC
*
363887 TTTCGAATTAAACCGAGTT
1 TTTCGAAATAAACCGAGTT
*
363906 TTTCGAAATAAATCGAGTT
1 TTTCGAAATAAACCGAGTT
363925 T
1 T
363926 AGACAACTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTCGAAATAAACCGAGTT
Found at i:367314 original size:14 final size:15
Alignment explanation
Indices: 367289--367317 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
367279 GCAAAATTAA
367289 TAACACAATTTAACT
1 TAACACAATTTAACT
367304 TAACA-AATTTAACT
1 TAACACAATTTAACT
367318 ATTACCATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.34
Consensus pattern (15 bp):
TAACACAATTTAACT
Found at i:370001 original size:33 final size:33
Alignment explanation
Indices: 369974--370053 Score: 106
Period size: 33 Copynumber: 2.4 Consensus size: 33
369964 TCCTCTTCAT
* *
369974 TAGAGTCTCCTTCTTCCACTAGATCCTCCCTAC
1 TAGAGTCTCCTTCTTCCACTAAATCCTCTCTAC
* * *
370007 TAGAGTCTCATTCTTTCATTAAATCCTCTCTAC
1 TAGAGTCTCCTTCTTCCACTAAATCCTCTCTAC
*
370040 TAAAGTCTCCTTCT
1 TAGAGTCTCCTTCT
370054 AGCATAAAAG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.21, C:0.33, G:0.07, T:0.39
Consensus pattern (33 bp):
TAGAGTCTCCTTCTTCCACTAAATCCTCTCTAC
Found at i:388291 original size:19 final size:20
Alignment explanation
Indices: 388249--388298 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
388239 ATTACAAAAT
*
388249 AATTCAAAATAATTTTTAAA
1 AATTCAAAATAAATTTTAAA
*
388269 AATTTAAAATAAATTTT-AA
1 AATTCAAAATAAATTTTAAA
388288 AATTCAAAATA
1 AATTCAAAATA
388299 TCAAACAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (20 bp):
AATTCAAAATAAATTTTAAA
Found at i:394344 original size:52 final size:51
Alignment explanation
Indices: 394216--394418 Score: 175
Period size: 52 Copynumber: 4.0 Consensus size: 51
394206 TGACAGAAAA
* * * **
394216 GATGTGATATATGTTTCCGTATAAGACCATAGCCGAGCTATGGCATCGGTAC
1 GATGTGATATGTG-TTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGT
* * * *
394268 AATGTGATTTGCGTTCCCGCATAAGACCATAGCTGGGCTAT-GCATCGGTGT
1 GATGTGATATGTGTT-CCGTATAAGACCATAGCTGGGCTATGGCATCGGTGT
** *
394319 GATGTGATAATGTGATTCCGTATAAGACCATATTTGGGATATGGCATC-G-GT
1 GATGTGAT-ATGTG-TTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGT
* * * * *
394370 -A--TGATATGTGATCCGTGTAAGACCATGGCAGGGCTATGGCTTCGGTGT
1 GATGTGATATGTGTTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGT
394418 G
1 G
394419 TGATGTGTGA
Statistics
Matches: 120, Mismatches: 24, Indels: 17
0.75 0.15 0.11
Matches are distributed among these distances:
46 25 0.21
47 6 0.05
48 6 0.05
50 1 0.01
51 19 0.16
52 56 0.47
53 7 0.06
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (51 bp):
GATGTGATATGTGTTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGT
Found at i:403527 original size:56 final size:56
Alignment explanation
Indices: 403441--403626 Score: 354
Period size: 56 Copynumber: 3.3 Consensus size: 56
403431 CACTTATTCA
403441 TGGCACAAGGAACTTATGATGAATAGTAATGATAATAATGATAGAAGTTGTTTTTC
1 TGGCACAAGGAACTTATGATGAATAGTAATGATAATAATGATAGAAGTTGTTTTTC
403497 TGGCACAAGGAACTTATGATGAATAGTAATGATAATAATGATAGAAGTTGTTTTTC
1 TGGCACAAGGAACTTATGATGAATAGTAATGATAATAATGATAGAAGTTGTTTTTC
*
403553 TGGCACAAGGAACTTATGATGAATAGTAATGATAATAATGATAGAAGTTGTTTTCC
1 TGGCACAAGGAACTTATGATGAATAGTAATGATAATAATGATAGAAGTTGTTTTTC
*
403609 TGGCACAAGCAACTTATG
1 TGGCACAAGGAACTTATG
403627 GGATTCGTCC
Statistics
Matches: 128, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 128 1.00
ACGTcount: A:0.37, C:0.09, G:0.22, T:0.32
Consensus pattern (56 bp):
TGGCACAAGGAACTTATGATGAATAGTAATGATAATAATGATAGAAGTTGTTTTTC
Found at i:405507 original size:29 final size:30
Alignment explanation
Indices: 405464--405522 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
405454 GAATTGGATC
* *
405464 AAATCAAAATTTCATGTATAAAATTGCACA
1 AAATCAAAAGTTCATGTATAAAATTACACA
*
405494 AAATC-AAAGTTCATGTATACAATTACACA
1 AAATCAAAAGTTCATGTATAAAATTACACA
405523 TTAAACCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 21 0.81
30 5 0.19
ACGTcount: A:0.49, C:0.15, G:0.07, T:0.29
Consensus pattern (30 bp):
AAATCAAAAGTTCATGTATAAAATTACACA
Found at i:405541 original size:31 final size:29
Alignment explanation
Indices: 405474--405543 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 29
405464 AAATCAAAAT
* *
405474 TTCATGTATAAAATTGCACAAAATCAAAG
1 TTCATGTATAAAATTACACAAAACCAAAG
*
405503 TTCATGTATACAATTACACATTAAACCATAA-
1 TTCATGTATAAAATTACACA--AAACCA-AAG
405534 TTCATGTATA
1 TTCATGTATA
405544 GTTTTAGTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 18 0.51
31 15 0.43
32 2 0.06
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (29 bp):
TTCATGTATAAAATTACACAAAACCAAAG
Found at i:406139 original size:13 final size:13
Alignment explanation
Indices: 406118--406151 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
406108 ATGTGAAGAA
406118 TATTATTTAAAAT
1 TATTATTTAAAAT
*
406131 TATTTTTTAAAATT
1 TATTATTTAAAA-T
406145 TATTATT
1 TATTATT
406152 AAATTAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TATTATTTAAAAT
Found at i:412425 original size:18 final size:18
Alignment explanation
Indices: 412388--412430 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
412378 GAAAACATCA
* *
412388 TTCAACCCAAACAATGAT
1 TTCAAACCAAACAATAAT
*
412406 TTCAAACCAAACATTAAT
1 TTCAAACCAAACAATAAT
*
412424 TTTAAAC
1 TTCAAAC
412431 TAGGATTTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.47, C:0.23, G:0.02, T:0.28
Consensus pattern (18 bp):
TTCAAACCAAACAATAAT
Found at i:413593 original size:3 final size:3
Alignment explanation
Indices: 413585--413780 Score: 392
Period size: 3 Copynumber: 65.3 Consensus size: 3
413575 ATAAAGAAAG
413585 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
413633 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
413681 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
413729 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
413777 AAT A
1 AAT A
413781 CTAAATGATA
Statistics
Matches: 193, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 193 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Done.