Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
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: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 28 of 167
Found at i:8169847 original size:18 final size:17
Alignment explanation
Indices: 8169806--8169849 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 17
8169796 TTGTAAATAC
8169806 AATTTCTTTAATTTTTTT
1 AATTT-TTTAATTTTTTT
8169824 ACATTTTTTAACTTTTTTT
1 A-ATTTTTTAA-TTTTTTT
8169843 AATTTTT
1 AATTTTT
8169850 AAAAAATATG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 12 0.50
19 12 0.50
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (17 bp):
AATTTTTTAATTTTTTT
Found at i:8170011 original size:18 final size:18
Alignment explanation
Indices: 8169990--8170037 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
8169980 CTTTTTTAAG
*
8169990 TTTTATATTATTTCCTTA
1 TTTTATATTATTTACTTA
* * *
8170008 TTTTATTTTGTTTATTTA
1 TTTTATATTATTTACTTA
*
8170026 ATTTATATTATT
1 TTTTATATTATT
8170038 AATTTTAAAA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.71
Consensus pattern (18 bp):
TTTTATATTATTTACTTA
Found at i:8170031 original size:36 final size:36
Alignment explanation
Indices: 8169936--8170037 Score: 95
Period size: 38 Copynumber: 2.8 Consensus size: 36
8169926 CCACTTTTTT
* * *
8169936 TTTTACTTTTTTATTAAATTT-TATCT-TTTTCTTAA
1 TTTTATTTTTTTATTTAATTTATAT-TATTTCCTTAA
*
8169971 TTTT-TTTTTCTTTTTTAAGTTTTATATTATTTCCTT-A
1 TTTTATTTTT-TTATTTAA--TTTATATTATTTCCTTAA
8170008 TTTTATTTTGTTTATTTAATTTATATTATT
1 TTTTATTTT-TTTATTTAATTTATATTATT
8170038 AATTTTAAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
34 4 0.07
35 10 0.18
36 11 0.20
37 9 0.16
38 20 0.36
39 1 0.02
ACGTcount: A:0.21, C:0.06, G:0.02, T:0.72
Consensus pattern (36 bp):
TTTTATTTTTTTATTTAATTTATATTATTTCCTTAA
Found at i:8170512 original size:41 final size:41
Alignment explanation
Indices: 8170467--8170550 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
8170457 ATATATTAAC
8170467 TAGTAAATAATCAAATATATTCACTTTTATTATTATTGTTT
1 TAGTAAATAATCAAATATATTCACTTTTATTATTATTGTTT
8170508 TAGTAAATAATCAAATATATTCACTTTTATTATTATTGTTT
1 TAGTAAATAATCAAATATATTCACTTTTATTATTATTGTTT
8170549 TA
1 TA
8170551 ATAATATATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.37, C:0.07, G:0.05, T:0.51
Consensus pattern (41 bp):
TAGTAAATAATCAAATATATTCACTTTTATTATTATTGTTT
Found at i:8171337 original size:6 final size:6
Alignment explanation
Indices: 8171304--8171357 Score: 54
Period size: 6 Copynumber: 8.7 Consensus size: 6
8171294 GAAAAAAAAA
* * * *
8171304 TTATATT TTATAT ATATTT TTAATAT TTATAT TTATAT TTTTAT TTAAAT
1 TTATA-T TTATAT TTATAT TT-ATAT TTATAT TTATAT TTATAT TTATAT
8171354 TTAT
1 TTAT
8171358 TAATAGTCAC
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
6 28 0.74
7 10 0.26
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TTATAT
Found at i:8171338 original size:13 final size:13
Alignment explanation
Indices: 8171304--8171357 Score: 58
Period size: 13 Copynumber: 4.3 Consensus size: 13
8171294 GAAAAAAAAA
*
8171304 TTATATTTTATAT
1 TTATATTTAATAT
* *
8171317 ATATTTTTAATAT
1 TTATATTTAATAT
8171330 TTATATTT-ATAT
1 TTATATTTAATAT
*
8171342 TTTTATTTAA-AT
1 TTATATTTAATAT
8171354 TTAT
1 TTAT
8171358 TAATAGTCAC
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
12 16 0.48
13 17 0.52
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TTATATTTAATAT
Found at i:8171342 original size:21 final size:20
Alignment explanation
Indices: 8171306--8171346 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
8171296 AAAAAAAATT
8171306 ATATTTTATATATATTTTTA
1 ATATTTTATATATATTTTTA
*
8171326 ATATTTATATTTATATTTTTA
1 ATATTT-TATATATATTTTTA
8171347 TTTAAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
ATATTTTATATATATTTTTA
Found at i:8171506 original size:21 final size:22
Alignment explanation
Indices: 8171462--8171521 Score: 70
Period size: 21 Copynumber: 2.7 Consensus size: 22
8171452 AAAAGAATTT
8171462 AAAAATAATATTTAAAATTGTAA
1 AAAAAT-ATATTTAAAATTGTAA
8171485 AAAAATATATTATAAAA-T-TAA
1 AAAAATATATT-TAAAATTGTAA
* *
8171506 AAGAATATTTTTAAAA
1 AAAAATATATTTAAAA
8171522 ATAATAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 5 0.15
21 12 0.35
22 6 0.18
23 11 0.32
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (22 bp):
AAAAATATATTTAAAATTGTAA
Found at i:8171543 original size:22 final size:21
Alignment explanation
Indices: 8171514--8171559 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
8171504 AAAAGAATAT
8171514 TTTTAAAAATAATA-ATTAAAA
1 TTTTAAAAAT-ATACATTAAAA
*
8171535 TTTTAAAAATATACATTACAA
1 TTTTAAAAATATACATTAAAA
8171556 TTTT
1 TTTT
8171560 TTTAAAGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (21 bp):
TTTTAAAAATATACATTAAAA
Found at i:8171593 original size:16 final size:15
Alignment explanation
Indices: 8171572--8171632 Score: 50
Period size: 17 Copynumber: 3.7 Consensus size: 15
8171562 TAAAGTTAAT
*
8171572 AATAAAAAATAAACAA
1 AATAAAAAAGAAA-AA
8171588 AATAAAATAAGAAAAA
1 AATAAAA-AAGAAAAA
*
8171604 AATCAAAAAGGTAAAAA
1 AAT-AAAAAAG-AAAAA
*
8171621 AAAATAAAAAGA
1 AATA-AAAAAGA
8171633 CAATTTATTA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
16 16 0.43
17 21 0.57
ACGTcount: A:0.79, C:0.03, G:0.07, T:0.11
Consensus pattern (15 bp):
AATAAAAAAGAAAAA
Found at i:8171629 original size:17 final size:16
Alignment explanation
Indices: 8171572--8171683 Score: 54
Period size: 16 Copynumber: 7.0 Consensus size: 16
8171562 TAAAGTTAAT
*
8171572 AATAAAA-AATAAACAA
1 AATAAAATAAGAAA-AA
8171588 AATAAAATAAGAAAAA
1 AATAAAATAAGAAAAA
* **
8171604 AATCAAA-AAGGTAAA
1 AATAAAATAAGAAAAA
*
8171619 AA-AAAATAA-AAAGAC
1 AATAAAATAAGAAA-AA
** *
8171634 AATTTATTAAGAAATAA
1 AATAAAATAAGAAA-AA
8171651 AATAAAA-AAGTAAAAA
1 AATAAAATAAG-AAAAA
* *
8171667 AAAAGAAATATGAAAAA
1 AATA-AAATAAGAAAAA
8171684 TAAAAGGACA
Statistics
Matches: 70, Mismatches: 18, Indels: 15
0.68 0.17 0.15
Matches are distributed among these distances:
14 4 0.06
15 13 0.19
16 27 0.39
17 24 0.34
18 2 0.03
ACGTcount: A:0.75, C:0.03, G:0.07, T:0.15
Consensus pattern (16 bp):
AATAAAATAAGAAAAA
Found at i:8172512 original size:6 final size:6
Alignment explanation
Indices: 8172479--8172532 Score: 54
Period size: 6 Copynumber: 8.7 Consensus size: 6
8172469 GAAAAAAAAA
* * * *
8172479 TTATATT TTATAT ATATTT TTAATAT TTATAT TTATAT TTTTAT TTAAAT
1 TTATA-T TTATAT TTATAT TT-ATAT TTATAT TTATAT TTATAT TTATAT
8172529 TTAT
1 TTAT
8172533 TAATAGTCAC
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
6 28 0.74
7 10 0.26
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TTATAT
Found at i:8172513 original size:13 final size:13
Alignment explanation
Indices: 8172479--8172532 Score: 58
Period size: 13 Copynumber: 4.3 Consensus size: 13
8172469 GAAAAAAAAA
*
8172479 TTATATTTTATAT
1 TTATATTTAATAT
* *
8172492 ATATTTTTAATAT
1 TTATATTTAATAT
8172505 TTATATTT-ATAT
1 TTATATTTAATAT
*
8172517 TTTTATTTAA-AT
1 TTATATTTAATAT
8172529 TTAT
1 TTAT
8172533 TAATAGTCAC
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
12 16 0.48
13 17 0.52
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TTATATTTAATAT
Found at i:8172517 original size:21 final size:20
Alignment explanation
Indices: 8172481--8172521 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
8172471 AAAAAAAATT
8172481 ATATTTTATATATATTTTTA
1 ATATTTTATATATATTTTTA
*
8172501 ATATTTATATTTATATTTTTA
1 ATATTT-TATATATATTTTTA
8172522 TTTAAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
ATATTTTATATATATTTTTA
Found at i:8172681 original size:21 final size:22
Alignment explanation
Indices: 8172637--8172696 Score: 70
Period size: 21 Copynumber: 2.7 Consensus size: 22
8172627 AAAAGAATTT
8172637 AAAAATAATATTTAAAATTGTAA
1 AAAAAT-ATATTTAAAATTGTAA
8172660 AAAAATATATTATAAAA-T-TAA
1 AAAAATATATT-TAAAATTGTAA
* *
8172681 AAGAATATTTTTAAAA
1 AAAAATATATTTAAAA
8172697 ATAATAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 5 0.15
21 12 0.35
22 6 0.18
23 11 0.32
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (22 bp):
AAAAATATATTTAAAATTGTAA
Found at i:8172718 original size:22 final size:21
Alignment explanation
Indices: 8172689--8172734 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
8172679 AAAAGAATAT
8172689 TTTTAAAAATAATA-ATTAAAA
1 TTTTAAAAAT-ATACATTAAAA
*
8172710 TTTTAAAAATATACATTACAA
1 TTTTAAAAATATACATTAAAA
8172731 TTTT
1 TTTT
8172735 TTTAAAGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (21 bp):
TTTTAAAAATATACATTAAAA
Found at i:8172768 original size:16 final size:15
Alignment explanation
Indices: 8172747--8172807 Score: 50
Period size: 17 Copynumber: 3.7 Consensus size: 15
8172737 TAAAGTTAAT
*
8172747 AATAAAAAATAAACAA
1 AATAAAAAAGAAA-AA
8172763 AATAAAATAAGAAAAA
1 AATAAAA-AAGAAAAA
*
8172779 AATCAAAAAGGTAAAAA
1 AAT-AAAAAAG-AAAAA
*
8172796 AAAATAAAAAGA
1 AATA-AAAAAGA
8172808 CAATTTATTA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
16 16 0.43
17 21 0.57
ACGTcount: A:0.79, C:0.03, G:0.07, T:0.11
Consensus pattern (15 bp):
AATAAAAAAGAAAAA
Found at i:8172804 original size:17 final size:16
Alignment explanation
Indices: 8172747--8172858 Score: 54
Period size: 16 Copynumber: 7.0 Consensus size: 16
8172737 TAAAGTTAAT
*
8172747 AATAAAA-AATAAACAA
1 AATAAAATAAGAAA-AA
8172763 AATAAAATAAGAAAAA
1 AATAAAATAAGAAAAA
* **
8172779 AATCAAA-AAGGTAAA
1 AATAAAATAAGAAAAA
*
8172794 AA-AAAATAA-AAAGAC
1 AATAAAATAAGAAA-AA
** *
8172809 AATTTATTAAGAAATAA
1 AATAAAATAAGAAA-AA
8172826 AATAAAA-AAGTAAAAA
1 AATAAAATAAG-AAAAA
* *
8172842 AAAAGAAATATGAAAAA
1 AATA-AAATAAGAAAAA
8172859 TAAAAGGACA
Statistics
Matches: 70, Mismatches: 18, Indels: 15
0.68 0.17 0.15
Matches are distributed among these distances:
14 4 0.06
15 13 0.19
16 27 0.39
17 24 0.34
18 2 0.03
ACGTcount: A:0.75, C:0.03, G:0.07, T:0.15
Consensus pattern (16 bp):
AATAAAATAAGAAAAA
Found at i:8175897 original size:19 final size:20
Alignment explanation
Indices: 8175875--8175913 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
8175865 AATCGTGCTG
8175875 AAAATATATT-TTAATAATT
1 AAAATATATTATTAATAATT
*
8175894 AAAATATATTATTTATAATT
1 AAAATATATTATTAATAATT
8175914 GTAATTATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AAAATATATTATTAATAATT
Found at i:8178199 original size:16 final size:15
Alignment explanation
Indices: 8178178--8178228 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 15
8178168 TCGATGCCAA
8178178 TAAAAAAAAGTTTATG
1 TAAAAAAAA-TTTATG
8178194 TAAAAATAAATTTA--
1 TAAAAA-AAATTTATG
8178208 TAAAAAAAA-TTATG
1 TAAAAAAAATTTATG
*
8178222 TTAAAAA
1 TAAAAAA
8178229 CATCTGTAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
12 3 0.10
13 3 0.10
14 12 0.39
16 10 0.32
17 3 0.10
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (15 bp):
TAAAAAAAATTTATG
Found at i:8184277 original size:39 final size:39
Alignment explanation
Indices: 8184223--8184302 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
8184213 AAAAGAGTCA
*
8184223 TTAAACTATTTAAAAAAATTCATTTAAGTCACTATTCTG
1 TTAAACTATTTAAAAAAATTCATTTAAGTCACTACTCTG
8184262 TTAAACTATTTAAAAAAATTCATTTAAGTCACTACTCTG
1 TTAAACTATTTAAAAAAATTCATTTAAGTCACTACTCTG
8184301 TT
1 TT
8184303 GTATGTCCAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.40, C:0.14, G:0.05, T:0.41
Consensus pattern (39 bp):
TTAAACTATTTAAAAAAATTCATTTAAGTCACTACTCTG
Found at i:8197557 original size:21 final size:21
Alignment explanation
Indices: 8197522--8197562 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
8197512 TAGTTATGTT
*
8197522 AATAATTAATGTTTATTATTAA
1 AATAATTAATATTTA-TATTAA
8197544 AATAA-TAATATTTATATTA
1 AATAATTAATATTTATATTA
8197563 TATATATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 8 0.44
22 5 0.28
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
AATAATTAATATTTATATTAA
Found at i:8197570 original size:9 final size:9
Alignment explanation
Indices: 8197556--8197590 Score: 61
Period size: 9 Copynumber: 3.8 Consensus size: 9
8197546 TAATAATATT
8197556 TATATTATA
1 TATATTATA
8197565 TATATTATA
1 TATATTATA
8197574 TATATTATA
1 TATATTATA
8197583 TATTATTA
1 TA-TATTA
8197591 AAATATAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 20 0.80
10 5 0.20
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
TATATTATA
Found at i:8200307 original size:127 final size:125
Alignment explanation
Indices: 8200001--8200565 Score: 634
Period size: 127 Copynumber: 4.5 Consensus size: 125
8199991 CCCAAACGAT
* * * ** * * * *
8200001 AAATCGAAACCCAACACGATTGGGCACGATTTATCGAATTTCCAAATACGAAACATTGCCTCATT
1 AAATTGAAACCCAGCACGATTGGGCACGACTTCCCAAACTTCCAAACACGAAATATTGCCTCATT
* * *** * *
8200066 TTAATTTGAGAAAACATGGATGAAATTTCAAAAGGATATTTTGTATTTTAGTCGAATGGA
66 TTATTTTAAGAAAACATGGATGAAATTTCAAAAGGATATTCCATATTTTAGCCGAATGAA
* *
8200126 AAATTGAAGCCCA-CACGATTGGGCATGACTTCCCAAACTTCCAAACACGAAATATTGCCTCATT
1 AAATTGAAACCCAGCACGATTGGGCACGACTTCCCAAACTTCCAAACACGAAATATTGCCTCATT
* * *
8200190 TTATTTTAAGAAAATATGGATGAAATTTCAAAAAAGGATATTTCATATTTTAGCCGAATGGA
66 TTATTTTAAGAAAACATGGATGAAATTTC--AAAAGGATATTCCATATTTTAGCCGAATGAA
* *
8200252 AAATTGAAGCCCAGCACGATTGGGCACGACTTCCCAAACTTCCAAACACGAAATATTGCCTCGTT
1 AAATTGAAACCCAGCACGATTGGGCACGACTTCCCAAACTTCCAAACACGAAATATTGCCTCATT
* * * *
8200317 TTATTTTAAGAACACGTGGATGAAATTTCAAAAAAAGGATATTCCATATCTTAGTCGAATGAAA
66 TTATTTTAAGAAAACATGGATGAAATTTC---AAAAGGATATTCCATATTTTAGCCGAATG-AA
* * * *
8200381 AAAATGAAACCCAGCACGATTGGGCACGA-TCTCTCAAACTCCCCAAATACGAAATATTGCCTCA
1 AAATTGAAACCCAGCACGATTGGGCACGACT-TCCCAAACT-TCCAAACACGAAATATTGCCTCA
* * * * * *
8200445 TTTTAATTTTAAAAAAAACATGGACGAAATTTCCAAAGGATATTCCGTATTTTAGCTGAACGAA
64 TTTT-ATTTT-AAGAAAACATGGATGAAATTTCAAAAGGATATTCCATATTTTAGCCGAATGAA
* * *
8200509 AAATCGAAACCCAGCACGATTGGGCACGAC-CCCTCGAA-TTCCCAAACACGAAATATT
1 AAATTGAAACCCAGCACGATTGGGCACGACTTCC-CAAACTT-CCAAACACGAAATATT
8200566 TCCTTATGTC
Statistics
Matches: 380, Mismatches: 48, Indels: 22
0.84 0.11 0.05
Matches are distributed among these distances:
124 69 0.18
125 11 0.03
126 41 0.11
127 92 0.24
128 61 0.16
129 59 0.16
130 24 0.06
131 5 0.01
132 18 0.05
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.27
Consensus pattern (125 bp):
AAATTGAAACCCAGCACGATTGGGCACGACTTCCCAAACTTCCAAACACGAAATATTGCCTCATT
TTATTTTAAGAAAACATGGATGAAATTTCAAAAGGATATTCCATATTTTAGCCGAATGAA
Found at i:8200524 original size:257 final size:249
Alignment explanation
Indices: 8199995--8200565 Score: 671
Period size: 257 Copynumber: 2.2 Consensus size: 249
8199985 ATTCGGCCCA
* * * ** * *
8199995 AACGATAAATCGAAACCCAACACGATTGGGCACGATTTATCGAATTTCCAAATACGAAACATTGC
1 AACGAAAAATCGAAACCCAGCACGATTGGGCACGACTTCCCGAA-TTCCAAACACGAAATATTGC
* *** * *
8200060 CTCATTTTAATTTGAGAAAACATGGATGAAATTTCAAAAGGATATTTTGTATTTTAGTCGAATGG
65 CTCATTTTAATTTAAGAAAACATGGATGAAATTTCAAAAGGATATTCCATATCTTAGTCGAATGA
* * * *
8200125 AAAATTGAAGCCCACACGATTGGGCATGACTTCCCAAACTTCCAAACACGAAATATTGCCTCATT
130 AAAAATGAAACCCACACGATTGGGCACGACTTCCCAAACTCCCAAACACGAAATATTGCCTCATT
* * * *
8200190 TTATTTTAAGAAAATATGGATGAAATTTCAAAAAAGGATATTTCATATTTTAGCCG
195 TTATTTTAAAAAAACATGGACGAAATTTC-AAAAAGGATATTCCATATTTTAGCCG
* * * * *
8200246 AATGGAAAATTGAAGCCCAGCACGATTGGGCACGACTTCCCAAACTTCCAAACACGAAATATTGC
1 AACGAAAAATCGAAACCCAGCACGATTGGGCACGACTTCCCGAA-TTCCAAACACGAAATATTGC
* * * *
8200311 CTCGTTTTATTTTAAGAACACGTGGATGAAATTTCAAAAAAAGGATATTCCATATCTTAGTCGAA
65 CTCATTTTAATTTAAGAAAACATGGATGAAATTTC---AAAAGGATATTCCATATCTTAGTCGAA
* *
8200376 TGAAAAAAATGAAACCCAGCACGATTGGGCACGA-TCTCTCAAACTCCCCAAATACGAAATATTG
127 TG-AAAAAATGAAACCCA-CACGATTGGGCACGACT-TCCCAAACT-CCCAAACACGAAATATTG
* * *
8200440 CCTCATTTTAATTTTAAAAAAAACATGGACGAAATTTC-CAAAGGATATTCCGTATTTTAGCTG
188 CCTCATTTT-ATTTT-AAAAAAACATGGACGAAATTTCAAAAAGGATATTCCATATTTTAGCCG
*
8200503 AACGAAAAATCGAAACCCAGCACGATTGGGCACGAC-CCCTCGAATTCCCAAACACGAAATATT
1 AACGAAAAATCGAAACCCAGCACGATTGGGCACGACTTCC-CGAATT-CCAAACACGAAATATT
8200566 TCCTTATGTC
Statistics
Matches: 267, Mismatches: 42, Indels: 16
0.82 0.13 0.05
Matches are distributed among these distances:
251 82 0.31
254 25 0.09
255 13 0.05
256 26 0.10
257 97 0.36
258 5 0.02
259 19 0.07
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.27
Consensus pattern (249 bp):
AACGAAAAATCGAAACCCAGCACGATTGGGCACGACTTCCCGAATTCCAAACACGAAATATTGCC
TCATTTTAATTTAAGAAAACATGGATGAAATTTCAAAAGGATATTCCATATCTTAGTCGAATGAA
AAAATGAAACCCACACGATTGGGCACGACTTCCCAAACTCCCAAACACGAAATATTGCCTCATTT
TATTTTAAAAAAACATGGACGAAATTTCAAAAAGGATATTCCATATTTTAGCCG
Found at i:8202026 original size:2 final size:2
Alignment explanation
Indices: 8202019--8202048 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
8202009 CCCTGGTAAG
8202019 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
8202049 GTGCTATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:8205493 original size:22 final size:22
Alignment explanation
Indices: 8205464--8205531 Score: 84
Period size: 22 Copynumber: 3.0 Consensus size: 22
8205454 TGCACAAACG
8205464 AACAGAGAGCACTAAAGTGCTA
1 AACAGAGAGCACTAAAGTGCTA
* *
8205486 TACAGAGAGCAC-AGATGTGCTA
1 AACAGAGAGCACTA-AAGTGCTA
*
8205508 AACAGAGAGCACTTAACGTGCTA
1 AACAGAGAGCAC-TAAAGTGCTA
8205531 A
1 A
8205532 TAATAGTACA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
21 1 0.03
22 29 0.74
23 8 0.21
24 1 0.03
ACGTcount: A:0.41, C:0.19, G:0.24, T:0.16
Consensus pattern (22 bp):
AACAGAGAGCACTAAAGTGCTA
Found at i:8205909 original size:7 final size:7
Alignment explanation
Indices: 8205899--8205992 Score: 52
Period size: 7 Copynumber: 13.3 Consensus size: 7
8205889 TTCTTATGTT
8205899 TTATATA
1 TTATATA
8205906 TTATAT-
1 TTATATA
8205912 TATATTATA
1 T-TA-TATA
*
8205921 TAATATA
1 TTATATA
*
8205928 TAATAATA
1 TTAT-ATA
*
8205936 TAATATA
1 TTATATA
8205943 TTATATA
1 TTATATA
8205950 TTA-ATA
1 TTATATA
*
8205956 CTTAAATA
1 -TTATATA
8205964 TTA-AGT-
1 TTATA-TA
*
8205970 TAATATA
1 TTATATA
*
8205977 ATATATA
1 TTATATA
*
8205984 ATATATA
1 TTATATA
8205991 TT
1 TT
8205993 TTTATATAAA
Statistics
Matches: 72, Mismatches: 6, Indels: 18
0.75 0.06 0.19
Matches are distributed among these distances:
6 8 0.11
7 49 0.68
8 14 0.19
9 1 0.01
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (7 bp):
TTATATA
Found at i:8205926 original size:15 final size:14
Alignment explanation
Indices: 8205899--8205992 Score: 53
Period size: 12 Copynumber: 7.1 Consensus size: 14
8205889 TTCTTATGTT
8205899 TTATAT-AT-TATA
1 TTATATAATATATA
8205911 TTATAT--TATATA
1 TTATATAATATATA
*
8205923 ATATATAATA-ATA
1 TTATATAATATATA
* *
8205936 TAATATATTATATA
1 TTATATAATATATA
* *
8205950 TTA-ATACTTAAATA
1 TTATATA-ATATATA
8205964 TTA-AGTTAATATA-A
1 TTATA--TAATATATA
8205978 -TATATAATATATA
1 TTATATAATATATA
8205991 TT
1 TT
8205993 TTTATATAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 18
0.71 0.09 0.20
Matches are distributed among these distances:
11 1 0.02
12 22 0.34
13 16 0.25
14 20 0.31
15 3 0.05
16 2 0.03
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (14 bp):
TTATATAATATATA
Found at i:8221266 original size:15 final size:15
Alignment explanation
Indices: 8221241--8221298 Score: 89
Period size: 15 Copynumber: 3.8 Consensus size: 15
8221231 TCATATATAT
8221241 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
8221257 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
8221272 AATAATTTCAATCAA
1 TATAAATTCAATCAA
8221287 TATAAATTCAAT
1 TATAAATTCAAT
8221299 AAATTCATCG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
15 34 0.89
16 4 0.11
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:8222506 original size:17 final size:16
Alignment explanation
Indices: 8222482--8222515 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
8222472 AATTTTCCCT
8222482 TTTCTCCCTTTCTTTC
1 TTTCTCCCTTTCTTTC
8222498 TTTCTTCCCTTTCTTTC
1 TTTC-TCCCTTTCTTTC
8222515 T
1 T
8222516 CCCCTGTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTCTCCCTTTCTTTC
Found at i:8222529 original size:13 final size:13
Alignment explanation
Indices: 8222493--8222526 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
8222483 TTCTCCCTTT
*
8222493 CTTTCTTTCTTCC
1 CTTTCTTTCTCCC
8222506 CTTTCTTTCTCCC
1 CTTTCTTTCTCCC
8222519 CTGTTCTT
1 CT-TTCTT
8222527 CTCTGTTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.00, C:0.38, G:0.03, T:0.59
Consensus pattern (13 bp):
CTTTCTTTCTCCC
Found at i:8222586 original size:5 final size:5
Alignment explanation
Indices: 8222576--8222631 Score: 67
Period size: 5 Copynumber: 10.6 Consensus size: 5
8222566 TTACTTATTT
* *
8222576 ATATA ATATAA TATATA ATATA ATATA CTATA ATATA ATAATA ATATC
1 ATATA ATAT-A -ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA
8222624 ATATA ATA
1 ATATA ATA
8222632 ACAATTTCTT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
5 33 0.75
6 7 0.16
7 4 0.09
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:8222592 original size:12 final size:12
Alignment explanation
Indices: 8222575--8222628 Score: 65
Period size: 12 Copynumber: 4.3 Consensus size: 12
8222565 TTTACTTATT
8222575 TATATAATATAA
1 TATATAATATAA
8222587 TATATAATATAATA
1 TATATAATAT-A-A
8222601 TACTATAATATAA
1 TA-TATAATATAA
*
8222614 TA-ATAATATCA
1 TATATAATATAA
8222625 TATA
1 TATA
8222629 ATAACAATTT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
11 10 0.27
12 11 0.30
13 4 0.11
14 4 0.11
15 8 0.22
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.41
Consensus pattern (12 bp):
TATATAATATAA
Found at i:8222763 original size:21 final size:22
Alignment explanation
Indices: 8222724--8222776 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
8222714 CATACAATTG
*
8222724 TTAAAATAATATTATAATATCA
1 TTAAAATAATATTACAATATCA
*
8222746 TTAATATAA-ATTACAATAT-A
1 TTAAAATAATATTACAATATCA
*
8222766 ATAAAATAATA
1 TTAAAATAATA
8222777 ATATAGTCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 8 0.31
21 10 0.38
22 8 0.31
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (22 bp):
TTAAAATAATATTACAATATCA
Found at i:8222963 original size:19 final size:22
Alignment explanation
Indices: 8222939--8222985 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 22
8222929 ATCCTTTCCA
8222939 CTAATTACT-CTTAATT-AAG-
1 CTAATTACTACTTAATTGAAGT
*
8222958 CTAATT-TTACTTAATTGAAGT
1 CTAATTACTACTTAATTGAAGT
8222979 CTAATTA
1 CTAATTA
8222986 ACCACTCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
18 1 0.04
19 13 0.57
20 3 0.13
21 6 0.26
ACGTcount: A:0.36, C:0.13, G:0.06, T:0.45
Consensus pattern (22 bp):
CTAATTACTACTTAATTGAAGT
Found at i:8226157 original size:28 final size:27
Alignment explanation
Indices: 8226094--8226245 Score: 232
Period size: 27 Copynumber: 5.6 Consensus size: 27
8226084 ATATTAAGTC
* *
8226094 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
8226121 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
*
8226149 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
8226176 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
* *
8226204 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
8226231 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
8226246 GCACAATTTA
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
27 66 0.55
28 53 0.45
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:8226178 original size:55 final size:55
Alignment explanation
Indices: 8226094--8226270 Score: 264
Period size: 55 Copynumber: 3.2 Consensus size: 55
8226084 ATATTAAGTC
* * *
8226094 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
8226149 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
* * * * *
8226204 CGCACACTTAGTGCTACATAGTCAATTCGCACACTTAGTGCTGCACAATTTAAACC
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAA-TCAAACT
8226260 CGCACACTTAG
1 CGCACACTTAG
8226271 CGCCAATCTC
Statistics
Matches: 111, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
55 95 0.86
56 16 0.14
ACGTcount: A:0.32, C:0.29, G:0.14, T:0.25
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:8229380 original size:39 final size:33
Alignment explanation
Indices: 8229308--8229395 Score: 97
Period size: 39 Copynumber: 2.5 Consensus size: 33
8229298 CTTATGTTTT
*
8229308 TATATTATATTATATA-TAATATAATATAATAA
1 TATAATATATTATATATTAATATAATATAATAA
8229340 TATAATATATTATATATTAATACTTAAATATTAAGTTAA
1 TATAATATATTATATATTAATA--T-AATA-TAA--TAA
*
8229379 TATAATATATAATATAT
1 TATAATATATTATATAT
8229396 ATTTTTATAT
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
32 15 0.32
33 5 0.11
35 1 0.02
36 4 0.09
37 3 0.06
39 19 0.40
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (33 bp):
TATAATATATTATATATTAATATAATATAATAA
Found at i:8230132 original size:41 final size:41
Alignment explanation
Indices: 8230086--8230168 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
8230076 AAATGTAAGA
8230086 ATAATGGTTCATGATGTTTATGTGACAATGAATAAATTGTG
1 ATAATGGTTCATGATGTTTATGTGACAATGAATAAATTGTG
*
8230127 ATAATGGTTCATGATGTTTATGTGATAATGAATAAATTGTG
1 ATAATGGTTCATGATGTTTATGTGACAATGAATAAATTGTG
8230168 A
1 A
8230169 ATAAGAATTG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.35, C:0.04, G:0.22, T:0.40
Consensus pattern (41 bp):
ATAATGGTTCATGATGTTTATGTGACAATGAATAAATTGTG
Found at i:8236163 original size:19 final size:20
Alignment explanation
Indices: 8236141--8236187 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
8236131 TAGTTCAAAT
8236141 TTAAGGTTT-GACTTCAA-GA
1 TTAAGGTTTGGA-TTCAATGA
* *
8236160 TTAAGATTTGGATTCAATGT
1 TTAAGGTTTGGATTCAATGA
8236180 TTAAGGTT
1 TTAAGGTT
8236188 AAAAAATATG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.30, C:0.06, G:0.21, T:0.43
Consensus pattern (20 bp):
TTAAGGTTTGGATTCAATGA
Found at i:8244668 original size:13 final size:13
Alignment explanation
Indices: 8244652--8244693 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
8244642 AACGTTTTTT
*
8244652 TATTTATTTACAA
1 TATTTATTTAAAA
8244665 TATTTAAATTTAAAA
1 TATTT--ATTTAAAA
8244680 T-TTTATTTAAAA
1 TATTTATTTAAAA
8244692 TA
1 TA
8244694 ATTTTAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
12 9 0.36
13 5 0.20
14 3 0.12
15 8 0.32
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (13 bp):
TATTTATTTAAAA
Found at i:8246082 original size:20 final size:21
Alignment explanation
Indices: 8246057--8246095 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
8246047 TATAATACAT
*
8246057 TAATAT-AAATAACTAAAATA
1 TAATATAAAATAAATAAAATA
8246077 TAATATAAAATAAATAAAA
1 TAATATAAAATAAATAAAA
8246096 GCGATTGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (21 bp):
TAATATAAAATAAATAAAATA
Found at i:8254537 original size:20 final size:20
Alignment explanation
Indices: 8254501--8254538 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
8254491 GTTTTGAAAT
*
8254501 AGTTTATAATGATAAAATAA
1 AGTTTATAATGAGAAAATAA
8254521 AGTTT-TAATTGAGAAAAT
1 AGTTTATAA-TGAGAAAAT
8254539 TAGTTCAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (20 bp):
AGTTTATAATGAGAAAATAA
Found at i:8255053 original size:35 final size:36
Alignment explanation
Indices: 8254989--8255113 Score: 130
Period size: 35 Copynumber: 3.5 Consensus size: 36
8254979 CATGGCAAAG
* **
8254989 TGTGAAACATAAGGTATAATATTAA-CCATACTGAGT
1 TGTGAAACGT-AGGTATGGTATTAATCCATACTGAGT
* * * *
8255025 TATAAAACGTAGGTATGGTA-TCATCCATACCGAGT
1 TGTGAAACGTAGGTATGGTATTAATCCATACTGAGT
* *
8255060 TGTGAAACATAGGTATGGTATTAAT-CATATTGAGT
1 TGTGAAACGTAGGTATGGTATTAATCCATACTGAGT
*
8255095 TGCGAAACGTAGGTATGGT
1 TGTGAAACGTAGGTATGGT
8255114 TAATCGGATC
Statistics
Matches: 72, Mismatches: 15, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
34 2 0.03
35 60 0.83
36 10 0.14
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.31
Consensus pattern (36 bp):
TGTGAAACGTAGGTATGGTATTAATCCATACTGAGT
Found at i:8256081 original size:24 final size:24
Alignment explanation
Indices: 8256049--8256094 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
8256039 AACACCCTTA
* *
8256049 ACCCACATCCTTCACTGTAACATG
1 ACCCACATCCATCACCGTAACATG
8256073 ACCCACATCCATCACCGTAACA
1 ACCCACATCCATCACCGTAACA
8256095 GGGTTACAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.33, C:0.41, G:0.07, T:0.20
Consensus pattern (24 bp):
ACCCACATCCATCACCGTAACATG
Found at i:8257285 original size:35 final size:35
Alignment explanation
Indices: 8257190--8257347 Score: 140
Period size: 35 Copynumber: 4.5 Consensus size: 35
8257180 ATCGAAATGC
** * *
8257190 CATACCTACATTTCACAACTCGGTATGGGA-AATGT
1 CATACCTATGTTTCACAACTCAGTAT-GGATAATAT
* * ** *
8257225 CATACCTACGATTCTTAACTAAGTATGGATAATAT
1 CATACCTATGTTTCACAACTCAGTATGGATAATAT
* * * *
8257260 CATACCTGTGTTTCACAACTCAGTATGGTTGATAC
1 CATACCTATGTTTCACAACTCAGTATGGATAATAT
*
8257295 CATACCTATGTTTCACAACTCAGTATGGTTAATA-
1 CATACCTATGTTTCACAACTCAGTATGGATAATAT
*
8257329 CTATACCTTACGTTTCACA
1 C-ATACC-TATGTTTCACA
8257348 CTTTTCCATG
Statistics
Matches: 101, Mismatches: 19, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
34 4 0.04
35 87 0.86
36 10 0.10
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.34
Consensus pattern (35 bp):
CATACCTATGTTTCACAACTCAGTATGGATAATAT
Found at i:8260841 original size:26 final size:27
Alignment explanation
Indices: 8260812--8260865 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
8260802 ACAAGATTGA
8260812 ATTTTAATAA-AT-AATATTTTAAAATT
1 ATTTTAA-AATATAAATATTTTAAAATT
*
8260838 ATTTTAAAATATAAATATTTTAATATT
1 ATTTTAAAATATAAATATTTTAAAATT
8260865 A
1 A
8260866 CATGGTGTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 2 0.08
26 9 0.36
27 14 0.56
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
ATTTTAAAATATAAATATTTTAAAATT
Found at i:8261980 original size:19 final size:19
Alignment explanation
Indices: 8261956--8261992 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
8261946 ACCAACCATT
8261956 GTTTGGCCATATATGATAG
1 GTTTGGCCATATATGATAG
8261975 GTTTGGCCATATATGATA
1 GTTTGGCCATATATGATA
8261993 ATATACCTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.11, G:0.24, T:0.38
Consensus pattern (19 bp):
GTTTGGCCATATATGATAG
Found at i:8282430 original size:17 final size:18
Alignment explanation
Indices: 8282397--8282434 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
8282387 GGTTAGCCGT
8282397 AATTTAACTATAAATATA
1 AATTTAACTATAAATATA
*
8282415 AATTTAA-TATATATATA
1 AATTTAACTATAAATATA
8282432 AAT
1 AAT
8282435 AAATTTTACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
AATTTAACTATAAATATA
Found at i:8282553 original size:11 final size:11
Alignment explanation
Indices: 8282534--8282576 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
8282524 ATATATATAT
*
8282534 ATATGAATTTA
1 ATATAAATTTA
8282545 ATATAAATTTA
1 ATATAAATTTA
8282556 ATATATAATTTTA
1 ATATA-AA-TTTA
*
8282569 CTATAAAT
1 ATATAAAT
8282577 AAACTTGGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 16 0.57
12 4 0.14
13 8 0.29
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (11 bp):
ATATAAATTTA
Found at i:8285325 original size:9 final size:9
Alignment explanation
Indices: 8285305--8285337 Score: 50
Period size: 8 Copynumber: 3.7 Consensus size: 9
8285295 ATATATATAC
8285305 AAAATACATA
1 AAAATAC-TA
8285315 AAAATACTA
1 AAAATACTA
8285324 AAAATA-TA
1 AAAATACTA
8285332 AAAATA
1 AAAATA
8285338 AATATTTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.35
9 8 0.35
10 7 0.30
ACGTcount: A:0.73, C:0.06, G:0.00, T:0.21
Consensus pattern (9 bp):
AAAATACTA
Found at i:8289630 original size:16 final size:16
Alignment explanation
Indices: 8289609--8289639 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
8289599 TTTTGATGGC
*
8289609 ATAAACAGTCTGTCTG
1 ATAAACAATCTGTCTG
8289625 ATAAACAATCTGTCT
1 ATAAACAATCTGTCT
8289640 ATATGTTCAA
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:0.35, C:0.19, G:0.13, T:0.32
Consensus pattern (16 bp):
ATAAACAATCTGTCTG
Found at i:8293672 original size:17 final size:18
Alignment explanation
Indices: 8293630--8293674 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
8293620 CTTTATTTTA
8293630 TTATTTATTGTTCTAAAATT
1 TTATTTATTGTTCT--AATT
*
8293650 TAATTTATTGTTCT-ATT
1 TTATTTATTGTTCTAATT
8293667 TTATTTAT
1 TTATTTAT
8293675 CTTAGTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 10 0.43
20 13 0.57
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.64
Consensus pattern (18 bp):
TTATTTATTGTTCTAATT
Found at i:8299809 original size:20 final size:20
Alignment explanation
Indices: 8299784--8299833 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
8299774 CCTCAACAGT
*
8299784 AAAAAAAAAATTGAAAAAGA
1 AAAAAAAAAACTGAAAAAGA
* *
8299804 AAAAAAAACACTGAAAACGA
1 AAAAAAAAAACTGAAAAAGA
8299824 AAAAAAAAAA
1 AAAAAAAAAA
8299834 AAGGGTCATG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.80, C:0.06, G:0.08, T:0.06
Consensus pattern (20 bp):
AAAAAAAAAACTGAAAAAGA
Found at i:8300186 original size:26 final size:26
Alignment explanation
Indices: 8300130--8300195 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
8300120 GTTGTTAGTT
* * **
8300130 ATTAATATTGTTAGTAAAAAATCATT
1 ATTATTATTGTTAGTAAAAAACCACA
*
8300156 GTTATTATTGTTAGTAAAAAACCACA
1 ATTATTATTGTTAGTAAAAAACCACA
8300182 ATTATTATTAGTTA
1 ATTATTATT-GTTA
8300196 TTATTATTGT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 29 0.88
27 4 0.12
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.42
Consensus pattern (26 bp):
ATTATTATTGTTAGTAAAAAACCACA
Found at i:8305015 original size:72 final size:72
Alignment explanation
Indices: 8304891--8305024 Score: 232
Period size: 72 Copynumber: 1.9 Consensus size: 72
8304881 GATGATCCCG
* *
8304891 GGAAATTGTCATTGCCCGCCAAATCCGGATGATAAGAAGTATCAGCCGAATGTGAATGCGATAAC
1 GGAAATAGTCATTGCCCGCCAAATCCGGATGATAAGAAGTATCAGCCAAATGTGAATGCGATAAC
8304956 GAGCCCA
66 GAGCCCA
* *
8304963 GGAAATAGTCATTGCCTGCCAAATCCGGATGATAAGAAGTATCAGTCAAATGTGAATGCGAT
1 GGAAATAGTCATTGCCCGCCAAATCCGGATGATAAGAAGTATCAGCCAAATGTGAATGCGAT
8305025 CGCTCGGACT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 58 1.00
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.22
Consensus pattern (72 bp):
GGAAATAGTCATTGCCCGCCAAATCCGGATGATAAGAAGTATCAGCCAAATGTGAATGCGATAAC
GAGCCCA
Found at i:8307316 original size:146 final size:147
Alignment explanation
Indices: 8306895--8308097 Score: 1347
Period size: 146 Copynumber: 8.2 Consensus size: 147
8306885 ATAAGTAAAA
* * * *
8306895 TATTTTCGTATATT-TTT-TTTATATTATTTTAGCAAAAAATGTTTCAAATGTATTATGTAAGTG
1 TATTTTCGTATTTTATTTCTTTATATTATTTTAGC-CATAATGTTTCAAATGTATTATTTAAGTG
* *
8306958 TTTTTTTATATTAATTTAATAAATAACCCTGATTTTGGCACTTTCTTCGTATTTTTTTATTTTCG
65 -TTTTTTATATTAATTTAATAAATAACCCTGATTTTAGCACTTTATTCGTA---TTTTATTTTCG
8307023 TATCTTATTTTTTAAAATATAT
126 TATCTTATTTTTTAAAATATAT
*
8307045 TATTGTT-GTATTTTATTTCTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTAAGT
1 TATT-TTCGTATTTTATTTCTTTATATTATTTTAG-CCATAATGTTTCAAATGTATTATTTAAGT
** * *
8307109 GTTTTTTAT-TTTTTTTAATAAATAACCCTGATTTTAGCATTTTATTCGTA-TTT-TTTTCATAT
64 GTTTTTTATATTAATTTAATAAATAACCCTGATTTTAGCACTTTATTCGTATTTTATTTTCGTAT
8307171 CTTATTTTTTAAAATATAT
129 CTTATTTTTTAAAATATAT
* * * *
8307190 TATTTTCGTATTTTATTTCTTTATATTATTTTAGTCCATAATATCTCAAATCTATTATTTAAGTA
1 TATTTTCGTATTTTATTTCTTTATATTATTTTAG-CCATAATGTTTCAAATGTATTATTTAAGTG
** * *
8307255 TTTTTTATATTTTTTTAATAAATAACCCTGATTTTAGCACTTTATTCGTA-TTT-TTTTCATATA
65 TTTTTTATATTAATTTAATAAATAACCCTGATTTTAGCACTTTATTCGTATTTTATTTTCGTATC
**
8307318 TTATTTTTT-TCATATAT
130 TTATTTTTTAAAATATAT
* * * * * * *
8307335 TATTTTTGTATTTTATTTTTTTATTTTATTTTAGCAAAAAATATTTCAAATGTATTATGTAAGTG
1 TATTTTCGTATTTTATTTCTTTATATTATTTTAGC-CATAATGTTTCAAATGTATTATTTAAGTG
*
8307400 TTTTTTTATATTAATTTAATAAATAACCCTGATTTT-GACACTTTCTTCGTATTTTTATTTTCGT
65 -TTTTTTATATTAATTTAATAAATAACCCTGATTTTAG-CACTTTATTCGTA-TTTTATTTTCGT
8307464 ATCTTATTTTTTAAAATATAT
127 ATCTTATTTTTTAAAATATAT
* * *
8307485 TATTTTCGTATTTTATTTCTTCATATTATTTTAGTACATAATGTTTCAAATGTATTATTTAAGTA
1 TATTTTCGTATTTTATTTCTTTATATTATTTTAG-CCATAATGTTTCAAATGTATTATTTAAGTG
* * *
8307550 TTTTTTATATT-TTTTCAATAAATAACCCTGATTTTAGCACTTTATTCTTA-CTT-TTTTCGTAT
65 TTTTTTATATTAATTT-AATAAATAACCCTGATTTTAGCACTTTATTCGTATTTTATTTTCGTAT
*
8307612 ATTATTTTTTAAAATATAT
129 CTTATTTTTTAAAATATAT
* * * *
8307631 TATTTTCGTATTTTATGTT-TTTATATTATTTTAGCAAAAAATGTTTCAAATGTACTACTTAAGT
1 TATTTTCGTATTTTAT-TTCTTTATATTATTTTAGC-CATAATGTTTCAAATGTATTATTTAAGT
* * *
8307695 GTTTCTTTATATTAATATAATAAATAAACCTGATTTT-GACACTTTCTTCGTAATTTTTTTTATT
64 GTTT-TTTATATTAATTTAATAAATAACCCTGATTTTAG-CACTTTATTCGT-A----TTTTATT
8307759 TTCGTATCTTATTTTTTAAAATATAT
122 TTCGTATCTTATTTTTTAAAATATAT
* * *
8307785 TATTTTCGTATTTTATTTCTTTATATTATTTTAGTACTTAATGTTTCAAATGTATTATTTAAATG
1 TATTTTCGTATTTTATTTCTTTATATTATTTTAG-CCATAATGTTTCAAATGTATTATTTAAGTG
** * * *
8307850 TTTTTTATATTTTTTTAATAAATAACCCTAATTTTAGCACTTTATTC--A-TAT-TTTTCGTATA
65 TTTTTTATATTAATTTAATAAATAACCCTGATTTTAGCACTTTATTCGTATTTTATTTTCGTATC
*
8307911 TTATTTATTAAAATATAT
130 TTATTTTTTAAAATATAT
* ** * *
8307929 TATTTTCGTA---T-TTTGTTT-TAGCA---TA---A-AATCTTTCAAATGTATTATTTAAAT-T
1 TATTTTCGTATTTTATTTCTTTATATTATTTTAGCCATAATGTTTCAAATGTATTATTTAAGTGT
* * * * *
8307981 TTTTTATATTAATTTAATAAATAACCCTGACTTTGGCACCTTGTTCGTATTTTTTAATTTTCGAA
66 TTTTTATATTAATTTAATAAATAACCCTGATTTTAGCACTTTATTCGTA--TTTT-ATTTTCGTA
* *
8308046 TTTTATTTTTTAAAATATAC
128 TCTTATTTTTTAAAATATAT
*
8308066 TATTTTCATATTTTATTT-TTTATATTATTTTA
1 TATTTTCGTATTTTATTTCTTTATATTATTTTA
8308098 ACAAAAAATC
Statistics
Matches: 906, Mismatches: 101, Indels: 98
0.82 0.09 0.09
Matches are distributed among these distances:
130 40 0.04
131 24 0.03
132 1 0.00
135 2 0.00
136 2 0.00
137 33 0.04
139 3 0.00
140 10 0.01
141 7 0.01
144 41 0.05
145 155 0.17
146 194 0.21
147 40 0.04
148 9 0.01
149 58 0.06
150 108 0.12
151 13 0.01
152 41 0.05
153 40 0.04
154 85 0.09
ACGTcount: A:0.29, C:0.08, G:0.06, T:0.56
Consensus pattern (147 bp):
TATTTTCGTATTTTATTTCTTTATATTATTTTAGCCATAATGTTTCAAATGTATTATTTAAGTGT
TTTTTATATTAATTTAATAAATAACCCTGATTTTAGCACTTTATTCGTATTTTATTTTCGTATCT
TATTTTTTAAAATATAT
Found at i:8307324 original size:16 final size:16
Alignment explanation
Indices: 8307303--8307341 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
8307293 ACTTTATTCG
8307303 TATTTTTTTCATATAT
1 TATTTTTTTCATATAT
8307319 TATTTTTTTCATATAT
1 TATTTTTTTCATATAT
8307335 TATTTTT
1 TATTTTT
8307342 GTATTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (16 bp):
TATTTTTTTCATATAT
Found at i:8307350 original size:13 final size:13
Alignment explanation
Indices: 8307334--8307366 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
8307324 TTTTCATATA
8307334 TTATTTTTGTATT
1 TTATTTTTGTATT
*
8307347 TTATTTTTTTATT
1 TTATTTTTGTATT
8307360 TTATTTT
1 TTATTTT
8307367 AGCAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (13 bp):
TTATTTTTGTATT
Found at i:8307543 original size:295 final size:297
Alignment explanation
Indices: 8306895--8308097 Score: 1555
Period size: 295 Copynumber: 4.1 Consensus size: 297
8306885 ATAAGTAAAA
* * * * *
8306895 TATTTTCGTATATT-TTT-TTTATATTATTTTAGCAAAAAATGTTTCAAATGTATTATGTAAGTG
1 TATTTTCGTATTTTATTTCTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTAAGT-
* ** * *
8306958 TTTTTTTATATTAATTTAATAAATAACCCTGATTTTGGCACTTTCTTCGTATTTTTTTATTTTCG
65 ATTTTTTATATTTTTTTAATAAATAACCCTGATTTTAGCACTTTATTCGTA----TTT-TTTTCG
* * * * * *
8307023 TATCTTATTTTTTAAAATATATTATTGTTGTATTTTATTTCTTTATATTATTTTAGTACATAATG
125 TATATTATTTTTTAAAATATATTATTTTTGTATTTTATTTTTTTATATTATTTTAGCAAAAAATG
** *
8307088 TTTCAAATGTATTATTTAAGTG-TTTTTTAT-TTTTTTTAATAAATAACCCTGATTTT-AGCATT
190 TTTCAAATGTATTATTTAAGTGTTTTTTTATATTAATTTAATAAATAACCCTGATTTTGA-CACT
* *
8307150 TTATTCGTA---TTT-TTTTCATATCTTATTTTTTAAAATATAT
254 TTCTTCGTATTTTTTATTTTCGTATCTTATTTTTTAAAATATAT
* * * *
8307190 TATTTTCGTATTTTATTTCTTTATATTATTTTAGTCCATAATATCTCAAATCTATTATTTAAGTA
1 TATTTTCGTATTTTATTTCTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTAAGTA
*
8307255 TTTTTTATATTTTTTTAATAAATAACCCTGATTTTAGCACTTTATTCGTATTTTTTTCATATATT
66 TTTTTTATATTTTTTTAATAAATAACCCTGATTTTAGCACTTTATTCGTATTTTTTTCGTATATT
** * *
8307320 ATTTTTT-TCATATATTATTTTTGTATTTTATTTTTTTATTTTATTTTAGCAAAAAATATTTCAA
131 ATTTTTTAAAATATATTATTTTTGTATTTTATTTTTTTATATTATTTTAGCAAAAAATGTTTCAA
*
8307384 ATGTATTATGTAAGTGTTTTTTTATATTAATTTAATAAATAACCCTGATTTTGACACTTTCTTCG
196 ATGTATTATTTAAGTGTTTTTTTATATTAATTTAATAAATAACCCTGATTTTGACACTTTCTTCG
8307449 TA-TTTTTATTTTCGTATCTTATTTTTTAAAATATAT
261 TATTTTTTATTTTCGTATCTTATTTTTTAAAATATAT
*
8307485 TATTTTCGTATTTTATTTCTTCATATTATTTTAGTACATAATGTTTCAAATGTATTATTTAAGTA
1 TATTTTCGTATTTTATTTCTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTAAGTA
* * *
8307550 TTTTTTATATTTTTTCAATAAATAACCCTGATTTTAGCACTTTATTCTTACTTTTTTCGTATATT
66 TTTTTTATATTTTTTTAATAAATAACCCTGATTTTAGCACTTTATTCGTATTTTTTTCGTATATT
* *
8307615 ATTTTTTAAAATATATTATTTTCGTATTTTATGTTTTTATATTATTTTAGCAAAAAATGTTTCAA
131 ATTTTTTAAAATATATTATTTTTGTATTTTATTTTTTTATATTATTTTAGCAAAAAATGTTTCAA
* * * * *
8307680 ATGTACTACTTAAGTGTTTCTTTATATTAATATAATAAATAAACCTGATTTTGACACTTTCTTCG
196 ATGTATTATTTAAGTGTTTTTTTATATTAATTTAATAAATAACCCTGATTTTGACACTTTCTTCG
8307745 TAATTTTTTTTATTTTCGTATCTTATTTTTTAAAATATAT
261 T-A--TTTTTTATTTTCGTATCTTATTTTTTAAAATATAT
* * *
8307785 TATTTTCGTATTTTATTTCTTTATATTATTTTAGTACTTAATGTTTCAAATGTATTATTTAAATG
1 TATTTTCGTATTTTATTTCTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTAAGTA
* *
8307850 TTTTTTATATTTTTTTAATAAATAACCCTAATTTTAGCACTTTATTC--ATATTTTTCGTATATT
66 TTTTTTATATTTTTTTAATAAATAACCCTGATTTTAGCACTTTATTCGTATTTTTTTCGTATATT
* * * * *
8307913 ATTTATTAAAATATATTATTTTCG-----TA------T-T-TTGTTTTAGCATAAAATCTTTCAA
131 ATTTTTTAAAATATATTATTTTTGTATTTTATTTTTTTATATTATTTTAGCAAAAAATGTTTCAA
* * * * *
8307965 ATGTATTATTTAA--ATTTTTTTATATTAATTTAATAAATAACCCTGACTTTGGCACCTTGTTCG
196 ATGTATTATTTAAGTGTTTTTTTATATTAATTTAATAAATAACCCTGATTTTGACACTTTCTTCG
* * *
8308028 TATTTTTTAATTTTCGAATTTTATTTTTTAAAATATAC
261 TATTTTTT-ATTTTCGTATCTTATTTTTTAAAATATAT
*
8308066 TATTTTCATATTTTATTT-TTTATATTATTTTA
1 TATTTTCGTATTTTATTTCTTTATATTATTTTA
8308098 ACAAAAAATC
Statistics
Matches: 816, Mismatches: 78, Indels: 43
0.87 0.08 0.05
Matches are distributed among these distances:
280 20 0.02
281 43 0.05
282 1 0.00
283 43 0.05
285 32 0.04
286 1 0.00
287 1 0.00
290 63 0.08
291 25 0.03
292 38 0.05
293 3 0.00
294 3 0.00
295 168 0.21
296 160 0.20
297 38 0.05
298 37 0.05
300 140 0.17
ACGTcount: A:0.29, C:0.08, G:0.06, T:0.56
Consensus pattern (297 bp):
TATTTTCGTATTTTATTTCTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTAAGTA
TTTTTTATATTTTTTTAATAAATAACCCTGATTTTAGCACTTTATTCGTATTTTTTTCGTATATT
ATTTTTTAAAATATATTATTTTTGTATTTTATTTTTTTATATTATTTTAGCAAAAAATGTTTCAA
ATGTATTATTTAAGTGTTTTTTTATATTAATTTAATAAATAACCCTGATTTTGACACTTTCTTCG
TATTTTTTATTTTCGTATCTTATTTTTTAAAATATAT
Found at i:8308687 original size:3 final size:3
Alignment explanation
Indices: 8308668--8308726 Score: 59
Period size: 3 Copynumber: 20.0 Consensus size: 3
8308658 TCCTTCTCCC
* *
8308668 CTT CTT TTT CTTT CTT CTT CTT C-T CTT CTT CTC CTT CTT -TT CTT
1 CTT CTT CTT C-TT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
* *
8308712 TTT CTC CTT CTT CTT
1 CTT CTT CTT CTT CTT
8308727 TGTTCCCGAA
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
2 4 0.09
3 38 0.84
4 3 0.07
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
CTT
Found at i:8308696 original size:14 final size:14
Alignment explanation
Indices: 8308654--8308726 Score: 62
Period size: 14 Copynumber: 5.4 Consensus size: 14
8308644 CCTCCTTCTC
* **
8308654 CTTCTCCTTCTCCC
1 CTTCTTCTTCTCTT
*
8308668 CTTCTTTTTCT-TT
1 CTTCTTCTTCTCTT
8308681 CTTCTTCTTCTCTT
1 CTTCTTCTTCTCTT
* *
8308695 CTTCTCCTTCTTTT
1 CTTCTTCTTCTCTT
*
8308709 CTTTTTC-TC-CTT
1 CTTCTTCTTCTCTT
8308721 CTTCTT
1 CTTCTT
8308727 TGTTCCCGAA
Statistics
Matches: 47, Mismatches: 11, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
12 7 0.15
13 12 0.26
14 28 0.60
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (14 bp):
CTTCTTCTTCTCTT
Found at i:8308919 original size:19 final size:19
Alignment explanation
Indices: 8308895--8308939 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
8308885 CCATTTTTTA
* *
8308895 TTTTTTTTT-GTTTTCAGT
1 TTTTTTTTTCTTTTTCAAT
8308913 TTTTTTTTTCTTTTTCAAT
1 TTTTTTTTTCTTTTTCAAT
8308932 TTTTTTTT
1 TTTTTTTT
8308940 ACGGTTGAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.07, C:0.07, G:0.04, T:0.82
Consensus pattern (19 bp):
TTTTTTTTTCTTTTTCAAT
Found at i:8338066 original size:8 final size:8
Alignment explanation
Indices: 8338053--8338079 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
8338043 TTGCTTCCTT
8338053 TATTTCCA
1 TATTTCCA
8338061 TATTTCCA
1 TATTTCCA
8338069 TATTTCCA
1 TATTTCCA
8338077 TAT
1 TAT
8338080 CCATATCCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.26, C:0.22, G:0.00, T:0.52
Consensus pattern (8 bp):
TATTTCCA
Found at i:8338508 original size:10 final size:10
Alignment explanation
Indices: 8338493--8338517 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
8338483 ATATTTTTAA
8338493 ATTTTATTTC
1 ATTTTATTTC
8338503 ATTTTATTTC
1 ATTTTATTTC
8338513 ATTTT
1 ATTTT
8338518 TTTATATTTT
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:0.08, G:0.00, T:0.72
Consensus pattern (10 bp):
ATTTTATTTC
Found at i:8341795 original size:16 final size:15
Alignment explanation
Indices: 8341774--8341817 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 15
8341764 TTATTTATTA
8341774 AATAAAAATAATTTT
1 AATAAAAATAATTTT
*
8341789 AATTAAAATATTATTTT
1 AA-TAAAA-ATAATTTT
8341806 AAT-AAAATAATT
1 AATAAAAATAATT
8341818 AAATTTTACG
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
14 5 0.20
15 5 0.20
16 6 0.24
17 9 0.36
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AATAAAAATAATTTT
Found at i:8341806 original size:17 final size:16
Alignment explanation
Indices: 8341774--8341814 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
8341764 TTATTTATTA
8341774 AATAAAA-ATAATTTT
1 AATAAAATATAATTTT
*
8341789 AATTAAAATATTATTTT
1 AA-TAAAATATAATTTT
8341806 AATAAAATA
1 AATAAAATA
8341815 ATTAAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 2 0.09
16 12 0.52
17 9 0.39
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AATAAAATATAATTTT
Found at i:8341989 original size:21 final size:21
Alignment explanation
Indices: 8341950--8341989 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
8341940 ACTTGGAATA
*
8341950 TAAATTTATACATTTATTACT
1 TAAATTTATACATTCATTACT
8341971 TAAATTTAGTA-ATTCATTA
1 TAAATTTA-TACATTCATTA
8341990 TAATTTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (21 bp):
TAAATTTATACATTCATTACT
Found at i:8342844 original size:34 final size:34
Alignment explanation
Indices: 8342806--8342874 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
8342796 AGAATGGTGA
* *
8342806 TGCTTTAAATTTTTGAGTGTTTTAAAACTTTTTT
1 TGCTTTAAATTTTTGAGTGTTCTAAAAATTTTTT
*
8342840 TGCTTTAAATTTTTGGGTGTTCTAAAAATTTTTT
1 TGCTTTAAATTTTTGAGTGTTCTAAAAATTTTTT
8342874 T
1 T
8342875 TAAGGTTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.23, C:0.06, G:0.13, T:0.58
Consensus pattern (34 bp):
TGCTTTAAATTTTTGAGTGTTCTAAAAATTTTTT
Found at i:8343423 original size:14 final size:16
Alignment explanation
Indices: 8343404--8343437 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
8343394 TAAGCTTTTC
8343404 CTTTGTATA-TA-TTA
1 CTTTGTATAGTATTTA
8343418 CTTTGTATAGTATTTA
1 CTTTGTATAGTATTTA
8343434 CTTT
1 CTTT
8343438 TAATCTTCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.50
15 2 0.11
16 7 0.39
ACGTcount: A:0.24, C:0.09, G:0.09, T:0.59
Consensus pattern (16 bp):
CTTTGTATAGTATTTA
Found at i:8344992 original size:29 final size:29
Alignment explanation
Indices: 8344956--8345044 Score: 74
Period size: 29 Copynumber: 3.0 Consensus size: 29
8344946 TTAGTCTAAT
8344956 GTGCAATTTGATACATGAACTTTGATTTG
1 GTGCAATTTGATACATGAACTTTGATTTG
* * *
8344985 GTGCAATTAT-ACACATGAAATTTAAATTGTG
1 GTGCAATT-TGATACATGAACTTT-GATT-TG
* *
8345016 GTTC-ATATGTATACATGAAACTTTGATTT
1 GTGCAATTTG-ATACATG-AACTTTGATTT
8345045 TAATTCAATT
Statistics
Matches: 46, Mismatches: 8, Indels: 11
0.71 0.12 0.17
Matches are distributed among these distances:
29 20 0.43
30 7 0.15
31 14 0.30
32 5 0.11
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (29 bp):
GTGCAATTTGATACATGAACTTTGATTTG
Found at i:8346501 original size:17 final size:17
Alignment explanation
Indices: 8346479--8346514 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
8346469 GATAAAGGTA
8346479 TGTATAATCTTTAGACT
1 TGTATAATCTTTAGACT
8346496 TGTATAATCTTTAGACT
1 TGTATAATCTTTAGACT
8346513 TG
1 TG
8346515 AGATCACTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.47
Consensus pattern (17 bp):
TGTATAATCTTTAGACT
Found at i:8347902 original size:20 final size:20
Alignment explanation
Indices: 8347879--8347916 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
8347869 ACATTTTAGT
8347879 CACTTATGTTTGAAATGTAA
1 CACTTATGTTTGAAATGTAA
8347899 CACTTATGTTTGAAATGT
1 CACTTATGTTTGAAATGT
8347917 TACATTTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.42
Consensus pattern (20 bp):
CACTTATGTTTGAAATGTAA
Found at i:8347931 original size:29 final size:29
Alignment explanation
Indices: 8347899--8347966 Score: 127
Period size: 29 Copynumber: 2.3 Consensus size: 29
8347889 TGAAATGTAA
8347899 CACTTATGTTTGAAATGTTACATTTTAGT
1 CACTTATGTTTGAAATGTTACATTTTAGT
*
8347928 CACTTATGTTTGAAATGTTACGTTTTAGT
1 CACTTATGTTTGAAATGTTACATTTTAGT
8347957 CACTTATGTT
1 CACTTATGTT
8347967 ATGATTTTGT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.25, C:0.12, G:0.15, T:0.49
Consensus pattern (29 bp):
CACTTATGTTTGAAATGTTACATTTTAGT
Found at i:8359242 original size:19 final size:18
Alignment explanation
Indices: 8359213--8359253 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 18
8359203 GTGGATAATA
8359213 TTTTAATATTTTATATATTT
1 TTTTAATATTTTA-A-ATTT
8359233 TTTTAA-ATTTTAAATTT
1 TTTTAATATTTTAAATTT
8359250 TTTT
1 TTTT
8359254 CATGAATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.38
18 1 0.05
19 6 0.29
20 6 0.29
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTAATATTTTAAATTT
Found at i:8373952 original size:22 final size:22
Alignment explanation
Indices: 8373922--8373995 Score: 60
Period size: 22 Copynumber: 3.4 Consensus size: 22
8373912 TGAATACCGT
*
8373922 CTAATTATAAAAAGAAAAAGAA
1 CTAAATATAAAAAGAAAAAGAA
*** ** *
8373944 CTAAATATAATTCGAATACTG-T
1 CTAAATATAAAAAGAA-AAAGAA
*
8373966 CTAATTATAAAAAGAAAAAGAA
1 CTAAATATAAAAAGAAAAAGAA
8373988 CTAAATAT
1 CTAAATAT
8373996 GGTCCAAACC
Statistics
Matches: 35, Mismatches: 15, Indels: 4
0.65 0.28 0.07
Matches are distributed among these distances:
21 2 0.06
22 31 0.89
23 2 0.06
ACGTcount: A:0.58, C:0.08, G:0.08, T:0.26
Consensus pattern (22 bp):
CTAAATATAAAAAGAAAAAGAA
Found at i:8381681 original size:17 final size:17
Alignment explanation
Indices: 8381656--8381689 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
8381646 CTTAATATGT
8381656 ATGTATATTTTGATTTA
1 ATGTATATTTTGATTTA
* *
8381673 ATGTTTATTTTTATTTA
1 ATGTATATTTTGATTTA
8381690 TAATCTCTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.65
Consensus pattern (17 bp):
ATGTATATTTTGATTTA
Found at i:8382105 original size:20 final size:20
Alignment explanation
Indices: 8382068--8382106 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
8382058 TTTATCAGTT
* * *
8382068 AAATTTTAATTTTTAAATAA
1 AAATTTCAATATTAAAATAA
8382088 AAATTTCAATATTAAAATA
1 AAATTTCAATATTAAAATA
8382107 TCACGTATTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (20 bp):
AAATTTCAATATTAAAATAA
Found at i:8388201 original size:11 final size:11
Alignment explanation
Indices: 8388187--8388211 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
8388177 TCCGTTAGGC
8388187 GGTAGATTGTA
1 GGTAGATTGTA
8388198 GGTAGATTGTA
1 GGTAGATTGTA
8388209 GGT
1 GGT
8388212 GTTCCAAACG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.40, T:0.36
Consensus pattern (11 bp):
GGTAGATTGTA
Found at i:8392103 original size:8 final size:8
Alignment explanation
Indices: 8392090--8392114 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
8392080 AAAAGGTTGC
8392090 TCTTATTT
1 TCTTATTT
8392098 TCTTATTT
1 TCTTATTT
8392106 TCTTATTT
1 TCTTATTT
8392114 T
1 T
8392115 ATATTTTTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (8 bp):
TCTTATTT
Found at i:8393105 original size:17 final size:18
Alignment explanation
Indices: 8393072--8393105 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
8393062 TTTTTTCACA
8393072 TATTATACATATTTAAAC
1 TATTATACATATTTAAAC
*
8393090 TATTATTCAT-TTTAAA
1 TATTATACATATTTAAA
8393106 ATTTACATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TATTATACATATTTAAAC
Found at i:8399723 original size:19 final size:19
Alignment explanation
Indices: 8399696--8399752 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 19
8399686 ACTCATCCAG
*
8399696 TTTACTTAAATAATTATAA
1 TTTAATTAAATAATTATAA
* * **
8399715 TTTAATTAAAAAATAAATTT
1 TTTAATTAAATAAT-TATAA
8399735 TTTAATATAAATAATTAT
1 TTTAAT-TAAATAATTAT
8399753 TTTTAATAGT
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
19 12 0.41
20 10 0.34
21 7 0.24
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
TTTAATTAAATAATTATAA
Found at i:8399754 original size:20 final size:20
Alignment explanation
Indices: 8399702--8399760 Score: 59
Period size: 19 Copynumber: 3.0 Consensus size: 20
8399692 CCAGTTTACT
**
8399702 TAAATAATTATAATTTAAT-
1 TAAATAATTATTTTTTAATA
* *
8399721 TAAAAAATAAATTTTTTAATA
1 TAAATAAT-TATTTTTTAATA
8399742 TAAATAATTA-TTTTTAATA
1 TAAATAATTATTTTTTAATA
8399761 GTAGTTATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
19 16 0.50
20 9 0.28
21 7 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TAAATAATTATTTTTTAATA
Found at i:8403087 original size:19 final size:20
Alignment explanation
Indices: 8403046--8403087 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
8403036 TATGAATTCT
***
8403046 TTATTATTATTAATTATGTA
1 TTATTATTATTAATTACAAA
8403066 TTATTA-TATTAATTACAAA
1 TTATTATTATTAATTACAAA
8403085 TTA
1 TTA
8403088 GTAAATATCT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (20 bp):
TTATTATTATTAATTACAAA
Found at i:8404931 original size:25 final size:26
Alignment explanation
Indices: 8404888--8404936 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
8404878 TAGTAACACC
8404888 AATTTTTAATAGTAAAAAT-AAATGG
1 AATTTTTAATAGTAAAAATCAAATGG
*
8404913 AATTTTTACTAG-AATAAATCAAAT
1 AATTTTTAATAGTAA-AAATCAAAT
8404937 TACTCTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 2 0.10
25 15 0.71
26 4 0.19
ACGTcount: A:0.51, C:0.04, G:0.08, T:0.37
Consensus pattern (26 bp):
AATTTTTAATAGTAAAAATCAAATGG
Found at i:8407044 original size:21 final size:21
Alignment explanation
Indices: 8406994--8407033 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
8406984 TTTTTTATCT
*
8406994 ATAAACCTTAAATCTCAAACC
1 ATAAATCTTAAATCTCAAACC
8407015 ATAAATCTTAAATCTCAAA
1 ATAAATCTTAAATCTCAAA
8407034 TTTTAAATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.28
Consensus pattern (21 bp):
ATAAATCTTAAATCTCAAACC
Found at i:8407207 original size:33 final size:32
Alignment explanation
Indices: 8407151--8407251 Score: 107
Period size: 33 Copynumber: 3.0 Consensus size: 32
8407141 AGAATTGTAT
* *
8407151 AGTTCGAGTTTGGAGTTTGAGGTTTGAGGTTCA
1 AGTTCGAGCTTGGAATTT-AGGTTTGAGGTTCA
8407184 AGTTCAGAGCTTGGAATTTAGGTTTTG-GGTTCA
1 AGTTC-GAGCTTGGAATTTAGG-TTTGAGGTTCA
*
8407217 AGTTTGAGGCTTAGG-ATTTAGAGTTTGAGGTTCA
1 AGTTCGA-GCTT-GGAATTTAG-GTTTGAGGTTCA
8407251 A
1 A
8407252 TGTTAAAATT
Statistics
Matches: 59, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
32 2 0.03
33 32 0.54
34 25 0.42
ACGTcount: A:0.22, C:0.07, G:0.33, T:0.39
Consensus pattern (32 bp):
AGTTCGAGCTTGGAATTTAGGTTTGAGGTTCA
Found at i:8423363 original size:34 final size:35
Alignment explanation
Indices: 8423325--8423395 Score: 92
Period size: 34 Copynumber: 2.1 Consensus size: 35
8423315 TGCCAACCCC
* *
8423325 AAAATATATTATTATTGACCG-ATTATTCTTAA-TT
1 AAAATACAATATTATTGA-CGAATTATTCTTAACTT
*
8423359 AAAATACAATATTATTGAGGAATTATTCTTAACTT
1 AAAATACAATATTATTGACGAATTATTCTTAACTT
8423394 AA
1 AA
8423396 TTTGTATCGG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 1 0.03
34 27 0.84
35 4 0.12
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.42
Consensus pattern (35 bp):
AAAATACAATATTATTGACGAATTATTCTTAACTT
Found at i:8423494 original size:13 final size:13
Alignment explanation
Indices: 8423468--8423518 Score: 61
Period size: 13 Copynumber: 4.1 Consensus size: 13
8423458 AGGAGAGACT
8423468 ATATATAA-AAAA
1 ATATATAATAAAA
8423480 ATATATAATAAAA
1 ATATATAATAAAA
*
8423493 ATTTATAATAAAA
1 ATATATAATAAAA
* *
8423506 TTA-ATATTAAAA
1 ATATATAATAAAA
8423518 A
1 A
8423519 AAGCTAATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
12 16 0.48
13 17 0.52
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
ATATATAATAAAA
Found at i:8425346 original size:14 final size:15
Alignment explanation
Indices: 8425327--8425355 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
8425317 CCTTTAAAAA
8425327 AATCA-TATCAATTT
1 AATCATTATCAATTT
8425341 AATCATTATCAATTT
1 AATCATTATCAATTT
8425356 TAAAAATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.45
Consensus pattern (15 bp):
AATCATTATCAATTT
Found at i:8430935 original size:18 final size:19
Alignment explanation
Indices: 8430902--8430939 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
8430892 AATTATGTTA
*
8430902 TTATATAATTCTTGTAAAT
1 TTATATAATACTTGTAAAT
8430921 TTATA-AATACTTGTAAAT
1 TTATATAATACTTGTAAAT
8430939 T
1 T
8430940 ATTTTAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.50
Consensus pattern (19 bp):
TTATATAATACTTGTAAAT
Found at i:8436556 original size:25 final size:23
Alignment explanation
Indices: 8436504--8436561 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
8436494 TAATATTCCA
8436504 GGTGTGTTTGGGTTGGAAATTCT
1 GGTGTGTTTGGGTTGGAAATTCT
* *
8436527 GGTGTGTTTTGGTTGGATATTCT
1 GGTGTGTTTGGGTTGGAAATTCT
**
8436550 AATGTGTTTGGG
1 GGTGTGTTTGGG
8436562 AGGAATCTGC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.12, C:0.03, G:0.38, T:0.47
Consensus pattern (23 bp):
GGTGTGTTTGGGTTGGAAATTCT
Found at i:8436687 original size:18 final size:19
Alignment explanation
Indices: 8436666--8436706 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
8436656 AATGAAATGA
8436666 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
8436684 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
8436703 GAAA
1 GAAA
8436707 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:8439242 original size:25 final size:24
Alignment explanation
Indices: 8439206--8439252 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
8439196 CTTAAAAAAC
* *
8439206 TTTAAAATATAACAAATCAAATACA
1 TTTAAAACATAA-AAAACAAATACA
8439231 TTTAAAACATAAAAAACAAATA
1 TTTAAAACATAAAAAACAAATA
8439253 TTAAAACAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.64, C:0.11, G:0.00, T:0.26
Consensus pattern (24 bp):
TTTAAAACATAAAAAACAAATACA
Found at i:8442050 original size:58 final size:57
Alignment explanation
Indices: 8441955--8442178 Score: 274
Period size: 51 Copynumber: 4.1 Consensus size: 57
8441945 TGAGTACTCC
* *
8441955 TGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAATGACAGG
1 TGATAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAATGACA-G
*
8442013 TGATAAGTGATAAGTGATAAGTGGTAGTTTTAGCTACACTTATCTG----AT--CAG
1 TGATAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAATGACAG
* *
8442064 TGACAAGTGATAAATGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAATGAC--
1 TGATAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAATGACAG
* * *
8442119 ----AAGTGATAAGTGATAAGTGGTAGTTTTAACTACACTTATCTGATCAGTGACAAG
1 TGATAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAATGAC-AG
8442173 TGATAA
1 TGATAA
8442179 ATGTGATCAG
Statistics
Matches: 143, Mismatches: 10, Indels: 26
0.80 0.06 0.15
Matches are distributed among these distances:
51 91 0.64
52 2 0.01
54 2 0.01
55 2 0.01
57 1 0.01
58 45 0.31
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.32
Consensus pattern (57 bp):
TGATAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAATGACAG
Found at i:8442072 original size:51 final size:51
Alignment explanation
Indices: 8442012--8442178 Score: 289
Period size: 51 Copynumber: 3.3 Consensus size: 51
8442002 TCAATGACAG
*
8442012 GTGATAAGTGATAAGTGATAAGTGGTAGTTTTAGCTACACTTATCTGATCA
1 GTGACAAGTGATAAGTGATAAGTGGTAGTTTTAGCTACACTTATCTGATCA
* *
8442063 GTGACAAGTGATAAATGATAAGTGGTAGCTTTAGCTACACTTATCTGATCA
1 GTGACAAGTGATAAGTGATAAGTGGTAGTTTTAGCTACACTTATCTGATCA
* *
8442114 ATGACAAGTGATAAGTGATAAGTGGTAGTTTTAACTACACTTATCTGATCA
1 GTGACAAGTGATAAGTGATAAGTGGTAGTTTTAGCTACACTTATCTGATCA
8442165 GTGACAAGTGATAA
1 GTGACAAGTGATAA
8442179 ATGTGATCAG
Statistics
Matches: 108, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 108 1.00
ACGTcount: A:0.34, C:0.11, G:0.22, T:0.32
Consensus pattern (51 bp):
GTGACAAGTGATAAGTGATAAGTGGTAGTTTTAGCTACACTTATCTGATCA
Found at i:8442137 original size:102 final size:103
Alignment explanation
Indices: 8441960--8442181 Score: 356
Period size: 102 Copynumber: 2.1 Consensus size: 103
8441950 ACTCCTGATC
* *
8441960 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAATGACAGGTGATAAGTGATA
1 AGTGATAAATGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAATGAC----G--AAGTGATA
*
8442025 AGTGATAAGTGGTAGTTTTAGCTACACTTATCTGATCAGTGACA
60 AGTGATAAGTGGTAGTTTTAACTACACTTATCTGATCAGTGACA
8442069 AGTGATAAATGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAATGAC-AAGTGATAAGTGAT
1 AGTGATAAATGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAATGACGAAGTGATAAGTGAT
8442133 AAGTGGTAGTTTTAACTACACTTATCTGATCAGTGACA
66 AAGTGGTAGTTTTAACTACACTTATCTGATCAGTGACA
8442171 AGTGATAAATG
1 AGTGATAAATG
8442182 TGATCAGTGT
Statistics
Matches: 110, Mismatches: 3, Indels: 7
0.92 0.03 0.06
Matches are distributed among these distances:
102 62 0.56
109 48 0.44
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.32
Consensus pattern (103 bp):
AGTGATAAATGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAATGACGAAGTGATAAGTGAT
AAGTGGTAGTTTTAACTACACTTATCTGATCAGTGACA
Found at i:8445976 original size:20 final size:21
Alignment explanation
Indices: 8445946--8445991 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
8445936 TCAATAACAA
*
8445946 TTTTTCATTTTCTCTGTTCAC
1 TTTTTCATTTTCACTGTTCAC
* *
8445967 TTTTTC-TTTTCACTTTTGAC
1 TTTTTCATTTTCACTGTTCAC
8445987 TTTTT
1 TTTTT
8445992 ATATATTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.09, C:0.20, G:0.04, T:0.67
Consensus pattern (21 bp):
TTTTTCATTTTCACTGTTCAC
Found at i:8445978 original size:13 final size:14
Alignment explanation
Indices: 8445947--8445983 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
8445937 CAATAACAAT
8445947 TTTTCA-TTTTCTC
1 TTTTCACTTTTCTC
*
8445960 TGTTCACTTTT-TC
1 TTTTCACTTTTCTC
8445973 TTTTCACTTTT
1 TTTTCACTTTT
8445984 GACTTTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 17 0.81
14 4 0.19
ACGTcount: A:0.08, C:0.22, G:0.03, T:0.68
Consensus pattern (14 bp):
TTTTCACTTTTCTC
Found at i:8450419 original size:221 final size:222
Alignment explanation
Indices: 8450036--8450480 Score: 811
Period size: 221 Copynumber: 2.0 Consensus size: 222
8450026 TGGTCTACAA
* *
8450036 AATTCAAGAAAACGGGTTCAAGAGTTAGTTACGTACGAGGAAGGATTAACACCCTCGTAACGCCC
1 AATTCAAGAAAACGGGTTCAAGAGTCAGCTACGTACGAGGAAGGATTAACACCCTCGTAACGCCC
*
8450101 AAAATTGGTACCTAATTGATTAATTAATGTCTTAATGTTGGAAGTTGGAAAGCCGTAAAGAATTT
66 AAAATTGGTACCTAATTGATTAATTAATGTCTTAATGTTGGAAGTTGGAAAGCCATAAAGAATTT
* *
8450166 AAAACTATGATCCTCCTTTTTTATTAATGTTAATTTTAC-AAAAAAAATGTTTGATTAAATCAAA
131 AAAAATATGATCCTCCTTTTTTATTAATGTTAATTTTACAAAAAAAAATGTTTGAATAAATCAAA
*
8450230 GCGGATGCTAAAGACCTTTTTGTTCCG
196 GCGGATGCTAAAGACCTTTTTGTCCCG
**
8450257 AATTCAAGAAAACGGGTTCGGGAGTCAGCTACGTACGAGGAAGGATTAACACCCTCGTAACGCCC
1 AATTCAAGAAAACGGGTTCAAGAGTCAGCTACGTACGAGGAAGGATTAACACCCTCGTAACGCCC
8450322 AAAATTGGTACCTAATTGATTAATTAATGTCTTAATGTTGGAAGTTGGAAAGCCATAAAGAATTT
66 AAAATTGGTACCTAATTGATTAATTAATGTCTTAATGTTGGAAGTTGGAAAGCCATAAAGAATTT
8450387 AAAAATATGATCCTCCTTTTTTATTAATGTTAATTTTACAAAAAAAAATGTTTGAATAAATCAAA
131 AAAAATATGATCCTCCTTTTTTATTAATGTTAATTTTACAAAAAAAAATGTTTGAATAAATCAAA
8450452 GCGGATGCTAAAGACCTTTTTGTCCCG
196 GCGGATGCTAAAGACCTTTTTGTCCCG
8450479 AA
1 AA
8450481 GTAATAAAAT
Statistics
Matches: 215, Mismatches: 8, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
221 163 0.76
222 52 0.24
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (222 bp):
AATTCAAGAAAACGGGTTCAAGAGTCAGCTACGTACGAGGAAGGATTAACACCCTCGTAACGCCC
AAAATTGGTACCTAATTGATTAATTAATGTCTTAATGTTGGAAGTTGGAAAGCCATAAAGAATTT
AAAAATATGATCCTCCTTTTTTATTAATGTTAATTTTACAAAAAAAAATGTTTGAATAAATCAAA
GCGGATGCTAAAGACCTTTTTGTCCCG
Found at i:8451091 original size:25 final size:25
Alignment explanation
Indices: 8450988--8451098 Score: 84
Period size: 25 Copynumber: 4.4 Consensus size: 25
8450978 GTGAAACGAC
*
8450988 ATAATATATAAAGCAGTTTGAAATAA
1 ATAATATATAAAGCAGTTT-AAAAAA
* * *
8451014 ATAGTATA-AAA-CAATTTAAGATAA
1 ATAATATATAAAGCAGTTTAA-AAAA
* * * *
8451038 ATAGTATGTAAAACA-ATTAAAAAGA
1 ATAATATATAAAGCAGTTTAAAAA-A
*
8451063 ATAATATACAAAGCAGTTTAAAAAA
1 ATAATATATAAAGCAGTTTAAAAAA
*
8451088 ATAATACATAA
1 ATAATATATAA
8451099 GACAACTTAA
Statistics
Matches: 68, Mismatches: 12, Indels: 11
0.75 0.13 0.12
Matches are distributed among these distances:
23 2 0.03
24 18 0.26
25 32 0.47
26 16 0.24
ACGTcount: A:0.59, C:0.05, G:0.09, T:0.27
Consensus pattern (25 bp):
ATAATATATAAAGCAGTTTAAAAAA
Found at i:8451126 original size:75 final size:75
Alignment explanation
Indices: 8450988--8451144 Score: 169
Period size: 75 Copynumber: 2.1 Consensus size: 75
8450978 GTGAAACGAC
* * * * * *
8450988 ATAATATATAAAGCAGTTTGAAATAAATAGTATAAAACAATTTAAGATAAATAGTATGTAAAACA
1 ATAATATACAAAGCAGTTTGAAAAAAATAATATAAAACAACTTAAAATAAATAGTATGAAAAACA
8451053 ATTAAAA-AGA
66 ATTAAAATA-A
*
8451063 ATAATATACAAAGCAGTTT-AAAAAAATAATACATAAGACAACTTAAAAT-AATA-TATGAAAAA
1 ATAATATACAAAGCAGTTTGAAAAAAATAAT--ATAAAACAACTTAAAATAAATAGTATG-AAAA
**
8451125 ACGTTTAAAATAA
63 ACAATTAAAATAA
8451138 ATAATAT
1 ATAATAT
8451145 GTAGAAAGAA
Statistics
Matches: 69, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
74 13 0.19
75 41 0.59
76 15 0.22
ACGTcount: A:0.59, C:0.06, G:0.08, T:0.27
Consensus pattern (75 bp):
ATAATATACAAAGCAGTTTGAAAAAAATAATATAAAACAACTTAAAATAAATAGTATGAAAAACA
ATTAAAATAA
Found at i:8451166 original size:28 final size:28
Alignment explanation
Indices: 8451108--8451169 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
8451098 AGACAACTTA
*
8451108 AAATAATATATGAAAAAACGTTTAAAAT
1 AAATAATATATGAAAAAACGTTGAAAAT
* * *
8451136 AAATAATATGTAGAAAGAA-GTTGAAACT
1 AAATAATATAT-GAAAAAACGTTGAAAAT
8451164 AAATAA
1 AAATAA
8451170 AACAAAAAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 23 0.79
29 6 0.21
ACGTcount: A:0.60, C:0.03, G:0.11, T:0.26
Consensus pattern (28 bp):
AAATAATATATGAAAAAACGTTGAAAAT
Found at i:8452198 original size:5 final size:5
Alignment explanation
Indices: 8452153--8452192 Score: 55
Period size: 5 Copynumber: 8.0 Consensus size: 5
8452143 GGGTTTATTC
*
8452153 GAAAA -AAAA CGAAAA TAAAA GAAAA GAAAA GAAAA GAAAA
1 GAAAA GAAAA -GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA
8452193 ACAAAATCAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 4 0.13
5 23 0.74
6 4 0.13
ACGTcount: A:0.80, C:0.03, G:0.15, T:0.03
Consensus pattern (5 bp):
GAAAA
Found at i:8452902 original size:30 final size:31
Alignment explanation
Indices: 8452861--8452927 Score: 93
Period size: 30 Copynumber: 2.2 Consensus size: 31
8452851 AACTTAAATC
*
8452861 TAATAATTTAAATAAAAACTTTT-AAATAG-T
1 TAATAACTTAAATAAAAA-TTTTCAAATAGTT
*
8452891 TAATAACTTAAATGAAAATTTTCAAATAGTT
1 TAATAACTTAAATAAAAATTTTCAAATAGTT
8452922 TAATAA
1 TAATAA
8452928 TTATTTTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 4 0.12
30 22 0.67
31 7 0.21
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.39
Consensus pattern (31 bp):
TAATAACTTAAATAAAAATTTTCAAATAGTT
Found at i:8454956 original size:23 final size:23
Alignment explanation
Indices: 8454930--8454974 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
8454920 ATCTACGGTT
8454930 TTTGTTT-TTATGTTTTGTTGTGA
1 TTTGTTTCTTAT-TTTTGTTGTGA
*
8454953 TTTGTTTCTTCTTTTTGTTGTG
1 TTTGTTTCTTATTTTTGTTGTG
8454975 TGTGTGTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.04, C:0.04, G:0.20, T:0.71
Consensus pattern (23 bp):
TTTGTTTCTTATTTTTGTTGTGA
Found at i:8465851 original size:69 final size:68
Alignment explanation
Indices: 8465740--8465881 Score: 275
Period size: 69 Copynumber: 2.1 Consensus size: 68
8465730 TACCACGTAA
8465740 GATTGAATACAAATATTTTTGTTTTTGAAGCAGAGCTTTTTGGTATTTTTGTTCTTTTACAAAAA
1 GATTGAATACAAATATTTTTGTTTTTGAAGCAGAGCTTTTTGGTATTTTTGTTCTTTTAC-AAAA
8465805 AGAG
65 AGAG
8465809 GATTGAATACAAATATTTTTGTTTTTGAAGCAGAGCTTTTTGGTATTTTTGTTCTTTTACAAAAA
1 GATTGAATACAAATATTTTTGTTTTTGAAGCAGAGCTTTTTGGTATTTTTGTTCTTTTACAAAAA
8465874 GAG
66 GAG
8465877 GATTG
1 GATTG
8465882 GCAGTCCCAT
Statistics
Matches: 73, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
68 13 0.18
69 60 0.82
ACGTcount: A:0.30, C:0.07, G:0.18, T:0.45
Consensus pattern (68 bp):
GATTGAATACAAATATTTTTGTTTTTGAAGCAGAGCTTTTTGGTATTTTTGTTCTTTTACAAAAA
GAG
Found at i:8474181 original size:15 final size:15
Alignment explanation
Indices: 8474132--8474182 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
8474122 AATAGTCAGA
*
8474132 TTATATTTTAGTAAT
1 TTATATTTTAGTTAT
* * **
8474147 TTATGTTTGAAATA-
1 TTATATTTTAGTTAT
8474161 TTATATTTTAGTTAT
1 TTATATTTTAGTTAT
8474176 TTATATT
1 TTATATT
8474183 ATTATTTTGT
Statistics
Matches: 26, Mismatches: 9, Indels: 2
0.70 0.24 0.05
Matches are distributed among these distances:
14 10 0.38
15 16 0.62
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (15 bp):
TTATATTTTAGTTAT
Found at i:8475841 original size:49 final size:49
Alignment explanation
Indices: 8475788--8475886 Score: 180
Period size: 49 Copynumber: 2.0 Consensus size: 49
8475778 TTTTATAGGG
*
8475788 GTTGGTGTGGCGAATGCTGGGGTTGTCATCCAAGATTGGTGCGGCGAGT
1 GTTGGTGTGGCGAATGCTGGGGTTGTCATCCAAGATAGGTGCGGCGAGT
*
8475837 GTTGGTGTGGCGATTGCTGGGGTTGTCATCCAAGATAGGTGCGGCGAGT
1 GTTGGTGTGGCGAATGCTGGGGTTGTCATCCAAGATAGGTGCGGCGAGT
8475886 G
1 G
8475887 ATGGGGTAGC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.14, C:0.14, G:0.43, T:0.28
Consensus pattern (49 bp):
GTTGGTGTGGCGAATGCTGGGGTTGTCATCCAAGATAGGTGCGGCGAGT
Found at i:8483232 original size:11 final size:11
Alignment explanation
Indices: 8483216--8483240 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
8483206 ATTTAAAAAT
8483216 ATAAAGTATTA
1 ATAAAGTATTA
8483227 ATAAAGTATTA
1 ATAAAGTATTA
8483238 ATA
1 ATA
8483241 TATTTATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (11 bp):
ATAAAGTATTA
Found at i:8484031 original size:20 final size:18
Alignment explanation
Indices: 8483993--8484031 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
8483983 TTTCAAGAAA
8483993 TATAAATTTTAGAATTTT
1 TATAAATTTTAGAATTTT
*
8484011 TATAAATATTTTGAATATTT
1 TATAAAT-TTTAGAAT-TTT
8484031 T
1 T
8484032 TTATTTTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 7 0.39
20 4 0.22
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (18 bp):
TATAAATTTTAGAATTTT
Found at i:8490275 original size:21 final size:21
Alignment explanation
Indices: 8490249--8490289 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
8490239 AGACGAGCAA
* *
8490249 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
8490270 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
8490290 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:8492228 original size:16 final size:16
Alignment explanation
Indices: 8492195--8492228 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
8492185 GGAGATTGTT
* *
8492195 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
8492211 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
8492227 AA
1 AA
8492229 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:8494978 original size:18 final size:17
Alignment explanation
Indices: 8494937--8494980 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
8494927 TATAAAAATT
* *
8494937 ATTAAAAAAGAATAAAA
1 ATTAAAATAGAAGAAAA
*
8494954 ATAAAAATAGAAGACAAA
1 ATTAAAATAGAAGA-AAA
8494972 ATTAAAATA
1 ATTAAAATA
8494981 TAATTATCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.18
Consensus pattern (17 bp):
ATTAAAATAGAAGAAAA
Found at i:8499372 original size:2 final size:2
Alignment explanation
Indices: 8499365--8499405 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
8499355 AAGGTTACCG
* * *
8499365 TC TC TC TC TT TC TC TC TC TC TG TC TC TC TC TC TC TT TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
8499406 TTGTAATTGT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.41, G:0.02, T:0.56
Consensus pattern (2 bp):
TC
Found at i:8499382 original size:12 final size:12
Alignment explanation
Indices: 8499365--8499405 Score: 64
Period size: 12 Copynumber: 3.2 Consensus size: 12
8499355 AAGGTTACCG
8499365 TCTCTCTCTTTC
1 TCTCTCTCTTTC
8499377 TCTCTCTCTGTCTC
1 TCTCTCTCT-T-TC
8499391 TCTCTCTCTTTC
1 TCTCTCTCTTTC
8499403 TCT
1 TCT
8499406 TTGTAATTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 14 0.52
13 2 0.07
14 11 0.41
ACGTcount: A:0.00, C:0.41, G:0.02, T:0.56
Consensus pattern (12 bp):
TCTCTCTCTTTC
Found at i:8511305 original size:95 final size:95
Alignment explanation
Indices: 8511142--8511331 Score: 380
Period size: 95 Copynumber: 2.0 Consensus size: 95
8511132 CATTAAAGTT
8511142 TTATTTTAAATATATTATAAAATCGTACAAAAATTGCAGTGGCTAGGCAAAGCAATAAATGAAGA
1 TTATTTTAAATATATTATAAAATCGTACAAAAATTGCAGTGGCTAGGCAAAGCAATAAATGAAGA
8511207 AAATACAAAATACTAGTAATTAAGGAAATA
66 AAATACAAAATACTAGTAATTAAGGAAATA
8511237 TTATTTTAAATATATTATAAAATCGTACAAAAATTGCAGTGGCTAGGCAAAGCAATAAATGAAGA
1 TTATTTTAAATATATTATAAAATCGTACAAAAATTGCAGTGGCTAGGCAAAGCAATAAATGAAGA
8511302 AAATACAAAATACTAGTAATTAAGGAAATA
66 AAATACAAAATACTAGTAATTAAGGAAATA
8511332 ATATGTTGTG
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 95 1.00
ACGTcount: A:0.51, C:0.08, G:0.14, T:0.27
Consensus pattern (95 bp):
TTATTTTAAATATATTATAAAATCGTACAAAAATTGCAGTGGCTAGGCAAAGCAATAAATGAAGA
AAATACAAAATACTAGTAATTAAGGAAATA
Found at i:8513869 original size:18 final size:18
Alignment explanation
Indices: 8513846--8513889 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
8513836 AATTGATCGG
*
8513846 TTATTCAGTAACAGTGAA
1 TTATTCAGTAACAGTCAA
* *
8513864 TTATTCGGTAACAGTCAT
1 TTATTCAGTAACAGTCAA
8513882 TTATTCAG
1 TTATTCAG
8513890 AAATAATCAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.39
Consensus pattern (18 bp):
TTATTCAGTAACAGTCAA
Found at i:8514130 original size:53 final size:53
Alignment explanation
Indices: 8514015--8514135 Score: 181
Period size: 53 Copynumber: 2.3 Consensus size: 53
8514005 CCGGAACAGT
*
8514015 AACAGTAACAGTAGCAGTACGGTACACAGAGCACCTCATCGGAACAAATCTGA
1 AACAGTAACAGTAACAGTACGGTACACAGAGCACCTCATCGGAACAAATCTGA
* * *
8514068 AATAGTAACAGTAACATTACGGTACACAGAGTACCTCATCGGAACAAATCCT-A
1 AACAGTAACAGTAACAGTACGGTACACAGAGCACCTCATCGGAACAAAT-CTGA
*
8514121 AACAATAACAGTAAC
1 AACAGTAACAGTAAC
8514136 GGTAATAGTA
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
53 59 0.97
54 2 0.03
ACGTcount: A:0.43, C:0.23, G:0.17, T:0.17
Consensus pattern (53 bp):
AACAGTAACAGTAACAGTACGGTACACAGAGCACCTCATCGGAACAAATCTGA
Done.