Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold44
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: 3265628
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.28
Warning! 491382 characters in sequence are not A, C, G, or T
File 13 of 17
Found at i:2456902 original size:43 final size:43
Alignment explanation
Indices: 2456841--2457028 Score: 198
Period size: 43 Copynumber: 4.1 Consensus size: 43
2456831 TTAGAGGTGG
*
2456841 TAAAGGTGCCAATATGCTGATTCAAGGCCAGTGGTATTGGACT
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGTGATATTGGACT
* * * *
2456884 TAAAGGTGTCAATGTGCTGATTCAAAGCCAGCGACT-TTGGACT
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGTGA-TATTGGACT
*
2456927 TAAAGATGACAAATGCACCAATATGTTGATTCAAGGCCAGTGATATTGGACT
1 TAAAG--G-----TG--CCAATATGCTGATTCAAGGCCAGTGATATTGGACT
* *
2456979 TAAAGGTGCCAATATGCTGATTCAAGGCCAGTGACATTGGGCT
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGTGATATTGGACT
2457022 TAGAAGG
1 TA-AAGG
2457029 AGATGCCACC
Statistics
Matches: 120, Mismatches: 13, Indels: 23
0.77 0.08 0.15
Matches are distributed among these distances:
43 75 0.62
44 5 0.04
45 3 0.03
50 3 0.03
51 1 0.01
52 33 0.28
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (43 bp):
TAAAGGTGCCAATATGCTGATTCAAGGCCAGTGATATTGGACT
Found at i:2457143 original size:32 final size:31
Alignment explanation
Indices: 2457034--2457153 Score: 123
Period size: 32 Copynumber: 3.7 Consensus size: 31
2457024 GAAGGAGATG
*
2457034 CCACCAACTTGTGTGGGCTTTTGAAAGGGTTA
1 CCACCAACTTGTGTGGGC-TTTGAGAGGGTTA
* * * * *
2457066 CCACCGACTTATGTAGGCTTTAAGAAAGGTTA
1 CCACCAACTTGTGTGGGCTTTGAG-AGGGTTA
* * *
2457098 CCAACCAGCTTGTGTGGGCTTTGAGGGGGCTTG
1 CC-ACCAACTTGTGTGGGCTTTGAGAGGG-TTA
2457131 CCACCAACTTGTGTGGGCTTTGA
1 CCACCAACTTGTGTGGGCTTTGA
2457154 AGAAGGTTTC
Statistics
Matches: 70, Mismatches: 15, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
31 4 0.06
32 45 0.64
33 21 0.30
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (31 bp):
CCACCAACTTGTGTGGGCTTTGAGAGGGTTA
Found at i:2457150 original size:65 final size:65
Alignment explanation
Indices: 2457036--2457161 Score: 157
Period size: 65 Copynumber: 1.9 Consensus size: 65
2457026 AGGAGATGCC
*
2457036 ACCAACTTGTGTGGGCTTTTGAAAGGGTTACCACCGACTTATGTAGGCTTT-AAGAAAGGTTACC
1 ACCAACTTGTGTGGGCTTTTGAAAGGGTTACCACCAACTTATGTAGGCTTTGAAG-AAGGTTACC
2457100 A
65 A
* ** * * *
2457101 ACCAGCTTGTGTGGGC-TTTGAGGGGGCTTGCCACCAACTTGTGTGGGCTTTGAAGAAGGTT
1 ACCAACTTGTGTGGGCTTTTGAAAGGG-TTACCACCAACTTATGTAGGCTTTGAAGAAGGTT
2457162 TCTCCACTGG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
64 8 0.15
65 41 0.79
66 3 0.06
ACGTcount: A:0.22, C:0.18, G:0.30, T:0.29
Consensus pattern (65 bp):
ACCAACTTGTGTGGGCTTTTGAAAGGGTTACCACCAACTTATGTAGGCTTTGAAGAAGGTTACCA
Found at i:2458766 original size:21 final size:20
Alignment explanation
Indices: 2458740--2458807 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 20
2458730 TTTTTTTCCC
2458740 TTTTTTTGTTTGTTGTTGTTT
1 TTTTTTTGTTT-TTGTTGTTT
*
2458761 TTTTTTTGTGTTTTTTTG-TT
1 TTTTTTTGT-TTTTGTTGTTT
*
2458781 TGTTTTTGTTTTGTGTTTGTTT
1 TTTTTTTGTTTT-TG-TTGTTT
2458803 TTTTT
1 TTTTT
2458808 AAAAGAAGGA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
19 3 0.08
20 11 0.28
21 17 0.44
22 8 0.21
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (20 bp):
TTTTTTTGTTTTTGTTGTTT
Found at i:2458767 original size:31 final size:31
Alignment explanation
Indices: 2458729--2458792 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
2458719 CATCTGGACC
2458729 TTTTTTTTCCCTTTTTTTGTTTGTTGTTGTT
1 TTTTTTTTCCCTTTTTTTGTTTGTTGTTGTT
*** *
2458760 TTTTTTTTGTGTTTTTTTGTTTGTTTTTGTT
1 TTTTTTTTCCCTTTTTTTGTTTGTTGTTGTT
2458791 TT
1 TT
2458793 GTGTTTGTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.00, C:0.05, G:0.14, T:0.81
Consensus pattern (31 bp):
TTTTTTTTCCCTTTTTTTGTTTGTTGTTGTT
Found at i:2458774 original size:11 final size:11
Alignment explanation
Indices: 2458740--2458804 Score: 51
Period size: 11 Copynumber: 5.6 Consensus size: 11
2458730 TTTTTTTCCC
2458740 TTTTTTTGT-T
1 TTTTTTTGTGT
* * *
2458750 TGTTGTTGTTT
1 TTTTTTTGTGT
2458761 TTTTTTTGTGT
1 TTTTTTTGTGT
*
2458772 TTTTTTGTTTGTT
1 TTTTTT-TGTG-T
2458785 TTTGTTTTGTGT
1 TTT-TTTTGTGT
2458797 TTGTTTTT
1 TT-TTTTT
2458805 TTTAAAAGAA
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
10 7 0.16
11 15 0.35
12 10 0.23
13 8 0.19
14 3 0.07
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (11 bp):
TTTTTTTGTGT
Found at i:2458800 original size:31 final size:30
Alignment explanation
Indices: 2458740--2458807 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 30
2458730 TTTTTTTCCC
* *
2458740 TTTTTTTGTTTGTTGTTGTTTTTTTTTTGT
1 TTTTTTTGTTTGTTGTTGTTTTGTGTTTGT
*
2458770 GTTTTTTTGTTTGTTTTTGTTTTGTGTTTGT
1 -TTTTTTTGTTTGTTGTTGTTTTGTGTTTGT
2458801 TTTTTTT
1 TTTTTTT
2458808 AAAAGAAGGA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 7 0.21
31 27 0.79
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (30 bp):
TTTTTTTGTTTGTTGTTGTTTTGTGTTTGT
Found at i:2458804 original size:17 final size:17
Alignment explanation
Indices: 2458741--2458801 Score: 74
Period size: 17 Copynumber: 3.8 Consensus size: 17
2458731 TTTTTTCCCT
2458741 TTTTTTGTTTGTTGTTG
1 TTTTTTGTTTGTTGTTG
*
2458758 TTTTTTTTTTG-TG-T-
1 TTTTTTGTTTGTTGTTG
*
2458772 TTTTTTGTTTGTTTTTG
1 TTTTTTGTTTGTTGTTG
*
2458789 TTTTGTGTTTGTT
1 TTTTTTGTTTGTT
2458802 TTTTTTAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
14 10 0.27
15 2 0.05
16 3 0.08
17 22 0.59
ACGTcount: A:0.00, C:0.00, G:0.20, T:0.80
Consensus pattern (17 bp):
TTTTTTGTTTGTTGTTG
Found at i:2463595 original size:13 final size:13
Alignment explanation
Indices: 2463577--2463602 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2463567 CAATTTTTTG
2463577 TGTATCGATACAT
1 TGTATCGATACAT
2463590 TGTATCGATACAT
1 TGTATCGATACAT
2463603 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2463667 original size:21 final size:20
Alignment explanation
Indices: 2463641--2463717 Score: 91
Period size: 21 Copynumber: 3.8 Consensus size: 20
2463631 CTGCCAAGAA
2463641 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACAT-TTTTTT
*****
2463662 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTTTTTT
2463682 ATGTATCGATACATTTTTTT
1 ATGTATCGATACATTTTTTT
2463702 CATGTATCGATACATT
1 -ATGTATCGATACATT
2463718 GCAACATGTA
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTTT
Found at i:2463687 original size:20 final size:20
Alignment explanation
Indices: 2463662--2463734 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
2463652 CATCTTTTTT
2463662 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
2463682 ATGTATCGATACATTTTTTTC
1 ATGTATCGATACA-TTGCAAC
2463703 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
2463723 ATGTATCGATAC
1 ATGTATCGATAC
2463735 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:2463701 original size:41 final size:41
Alignment explanation
Indices: 2463641--2463734 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
2463631 CTGCCAAGAA
*
2463641 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
*
2463682 ATGTATCGATACATTTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
2463723 ATGTATCGATAC
1 ATGTATCGATAC
2463735 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:2464343 original size:48 final size:48
Alignment explanation
Indices: 2464288--2464383 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
2464278 AAATTTTACG
2464288 AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
1 AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
2464336 AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
1 AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
2464384 TTATCTCCCC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.25, C:0.29, G:0.08, T:0.38
Consensus pattern (48 bp):
AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
Found at i:2466242 original size:13 final size:13
Alignment explanation
Indices: 2466224--2466261 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
2466214 ATAAACACCC
2466224 TGTATCGATACAG
1 TGTATCGATACAG
*
2466237 TGTATCGATACAT
1 TGTATCGATACAG
2466250 TGTATCGATACA
1 TGTATCGATACA
2466262 AATAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:2472451 original size:13 final size:13
Alignment explanation
Indices: 2472433--2472458 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2472423 CAATTTTTTG
2472433 TGTATCGATACAT
1 TGTATCGATACAT
2472446 TGTATCGATACAT
1 TGTATCGATACAT
2472459 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2472523 original size:21 final size:20
Alignment explanation
Indices: 2472497--2472573 Score: 91
Period size: 21 Copynumber: 3.8 Consensus size: 20
2472487 CTGCCAAGAA
2472497 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACAT-TTTTTT
*****
2472518 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTTTTTT
2472538 ATGTATCGATACATTTTTTT
1 ATGTATCGATACATTTTTTT
2472558 CATGTATCGATACATT
1 -ATGTATCGATACATT
2472574 GCAACATGTA
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTTT
Found at i:2472543 original size:20 final size:20
Alignment explanation
Indices: 2472518--2472590 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
2472508 CATCTTTTTT
2472518 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
2472538 ATGTATCGATACATTTTTTTC
1 ATGTATCGATACA-TTGCAAC
2472559 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
2472579 ATGTATCGATAC
1 ATGTATCGATAC
2472591 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:2472557 original size:41 final size:41
Alignment explanation
Indices: 2472497--2472590 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
2472487 CTGCCAAGAA
*
2472497 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
*
2472538 ATGTATCGATACATTTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
2472579 ATGTATCGATAC
1 ATGTATCGATAC
2472591 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:2476486 original size:13 final size:13
Alignment explanation
Indices: 2476468--2476493 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2476458 CAATTTTTTG
2476468 TGTATCGATACAT
1 TGTATCGATACAT
2476481 TGTATCGATACAT
1 TGTATCGATACAT
2476494 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2476558 original size:21 final size:20
Alignment explanation
Indices: 2476532--2476608 Score: 91
Period size: 21 Copynumber: 3.8 Consensus size: 20
2476522 CTGCCAAGAA
2476532 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACAT-TTTTTT
*****
2476553 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTTTTTT
2476573 ATGTATCGATACATTTTTTT
1 ATGTATCGATACATTTTTTT
2476593 CATGTATCGATACATT
1 -ATGTATCGATACATT
2476609 GCAACATGTA
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTTT
Found at i:2476578 original size:20 final size:20
Alignment explanation
Indices: 2476553--2476625 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
2476543 CATCTTTTTT
2476553 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
2476573 ATGTATCGATACATTTTTTTC
1 ATGTATCGATACA-TTGCAAC
2476594 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
2476614 ATGTATCGATAC
1 ATGTATCGATAC
2476626 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:2476592 original size:41 final size:41
Alignment explanation
Indices: 2476532--2476625 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
2476522 CTGCCAAGAA
*
2476532 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
*
2476573 ATGTATCGATACATTTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
2476614 ATGTATCGATAC
1 ATGTATCGATAC
2476626 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:2477235 original size:48 final size:48
Alignment explanation
Indices: 2477180--2477275 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
2477170 AAATTTTACG
2477180 AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
1 AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
2477228 AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
1 AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
2477276 TTATCTCCCC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.25, C:0.29, G:0.08, T:0.38
Consensus pattern (48 bp):
AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
Found at i:2479135 original size:13 final size:13
Alignment explanation
Indices: 2479117--2479154 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
2479107 ATAAACACCC
2479117 TGTATCGATACAG
1 TGTATCGATACAG
*
2479130 TGTATCGATACAT
1 TGTATCGATACAG
2479143 TGTATCGATACA
1 TGTATCGATACA
2479155 AATAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:2481254 original size:15 final size:15
Alignment explanation
Indices: 2481234--2481264 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2481224 ATTTCGTTTG
*
2481234 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
2481249 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
2481264 G
1 G
2481265 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:2485344 original size:13 final size:13
Alignment explanation
Indices: 2485326--2485351 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2485316 CAATTTTTTG
2485326 TGTATCGATACAT
1 TGTATCGATACAT
2485339 TGTATCGATACAT
1 TGTATCGATACAT
2485352 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2485416 original size:21 final size:20
Alignment explanation
Indices: 2485390--2485466 Score: 91
Period size: 21 Copynumber: 3.8 Consensus size: 20
2485380 CTGCCAAGAA
2485390 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACAT-TTTTTT
*****
2485411 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTTTTTT
2485431 ATGTATCGATACATTTTTTT
1 ATGTATCGATACATTTTTTT
2485451 CATGTATCGATACATT
1 -ATGTATCGATACATT
2485467 GCAACATGTA
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTTT
Found at i:2485436 original size:20 final size:20
Alignment explanation
Indices: 2485411--2485483 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
2485401 CATCTTTTTT
2485411 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
2485431 ATGTATCGATACATTTTTTTC
1 ATGTATCGATACA-TTGCAAC
2485452 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
2485472 ATGTATCGATAC
1 ATGTATCGATAC
2485484 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:2485450 original size:41 final size:41
Alignment explanation
Indices: 2485390--2485483 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
2485380 CTGCCAAGAA
*
2485390 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
*
2485431 ATGTATCGATACATTTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
2485472 ATGTATCGATAC
1 ATGTATCGATAC
2485484 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:2495198 original size:20 final size:20
Alignment explanation
Indices: 2495173--2495407 Score: 150
Period size: 20 Copynumber: 10.7 Consensus size: 20
2495163 TTTAACTAGG
2495173 TGTATCGATACATTGAAAAA
1 TGTATCGATACATTGAAAAA
2495193 TGTATCGATACATCTAGGAAAAAAGA
1 TGTATCGATACAT-T--G--AAAA-A
*
2495219 TAGAAGGTATCAATACATT-AAAGAA
1 T-----GTATCGATACATTGAAA-AA
* *
2495244 TGTATCGATACATTTG-TACA
1 TGTATCGATACA-TTGAAAAA
*
2495264 TGAATCGATACATTGAAAAA
1 TGTATCGATACATTGAAAAA
2495284 TGTATCGATACATCTGGGTAAAAAGATAGAA
1 TGTATCGATACAT-T--G-----A-A-A-AA
* * *
2495315 TGTATCGATACATTCATACA
1 TGTATCGATACATTGAAAAA
2495335 TGTATCGATACATTGAAAAA
1 TGTATCGATACATTGAAAAA
* * *
2495355 TGTATCGATACATTCATACA
1 TGTATCGATACATTGAAAAA
2495375 TGTATCGATACATTGAAAAA
1 TGTATCGATACATTGAAAAA
2495395 TGTATCGATACAT
1 TGTATCGATACAT
2495408 CTGGGTAAAA
Statistics
Matches: 169, Mismatches: 20, Indels: 52
0.70 0.08 0.22
Matches are distributed among these distances:
19 3 0.02
20 114 0.67
21 6 0.04
23 3 0.02
25 9 0.05
26 3 0.02
28 1 0.01
29 1 0.01
30 3 0.02
31 26 0.15
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (20 bp):
TGTATCGATACATTGAAAAA
Found at i:2495286 original size:40 final size:40
Alignment explanation
Indices: 2495231--2495478 Score: 196
Period size: 40 Copynumber: 6.7 Consensus size: 40
2495221 GAAGGTATCA
**
2495231 ATACATT-AAAGAATGTATCGATACATTTGTACATGAATCG
1 ATACATTGAAA-AATGTATCGATACATTCATACATGAATCG
***
2495271 ATACATTGAAAAATGTATCGATACA-TC-TGGGT-AA---
1 ATACATTGAAAAATGTATCGATACATTCATACATGAATCG
* *
2495305 A-A-A--GATAGAATGTATCGATACATTCATACATGTATCG
1 ATACATTGA-AAAATGTATCGATACATTCATACATGAATCG
*
2495342 ATACATTGAAAAATGTATCGATACATTCATACATGTATCG
1 ATACATTGAAAAATGTATCGATACATTCATACATGAATCG
***
2495382 ATACATTGAAAAATGTATCGATACA-TC-TGGGT-AA---
1 ATACATTGAAAAATGTATCGATACATTCATACATGAATCG
*
2495416 A-A-A--GACAAAATGTATCGATACATTCATACATGTATCG
1 ATACATTGA-AAAATGTATCGATACATTCATACATGAATCG
* *
2495453 ATACATTAAAAAATATATCGATACAT
1 ATACATTGAAAAATGTATCGATACAT
2495479 CTGGGTAAAA
Statistics
Matches: 165, Mismatches: 20, Indels: 46
0.71 0.09 0.20
Matches are distributed among these distances:
30 4 0.02
31 31 0.19
32 6 0.04
33 6 0.04
34 4 0.02
37 5 0.03
38 6 0.04
39 5 0.03
40 92 0.56
41 6 0.04
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.30
Consensus pattern (40 bp):
ATACATTGAAAAATGTATCGATACATTCATACATGAATCG
Found at i:2495338 original size:91 final size:91
Alignment explanation
Indices: 2495176--2495387 Score: 284
Period size: 91 Copynumber: 2.3 Consensus size: 91
2495166 AACTAGGTGT
2495176 ATCGATACATTGAAAAATGTATCGATACATCTAGGAAAAAAGATAGAAGGTATCAATACATTAAA
1 ATCGATACATTGAAAAATGTATCGATACATCTAGGAAAAAAGATAGAAGGTATCAATACATTAAA
* *
2495241 GAATGTATCGATACATTTG-TACATGA
66 GAATGTATCGATACA-TTGAAAAATGA
* * * * *
2495267 ATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGATAGAATGTATCGATACATTCAT
1 ATCGATACATTGAAAAATGTATCGATACATCTAGGAAAAAAGATAGAAGGTATCAATACATT-AA
* *
2495332 A-CATGTATCGATACATTGAAAAATGT
65 AGAATGTATCGATACATTGAAAAATGA
* * *
2495358 ATCGATACATTCATACATGTATCGATACAT
1 ATCGATACATTGAAAAATGTATCGATACAT
2495388 TGAAAAATGT
Statistics
Matches: 107, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
90 3 0.03
91 102 0.95
92 2 0.02
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (91 bp):
ATCGATACATTGAAAAATGTATCGATACATCTAGGAAAAAAGATAGAAGGTATCAATACATTAAA
GAATGTATCGATACATTGAAAAATGA
Found at i:2495367 original size:111 final size:110
Alignment explanation
Indices: 2495225--2495478 Score: 418
Period size: 111 Copynumber: 2.3 Consensus size: 110
2495215 AAGATAGAAG
* **
2495225 GTATCAATACATTAAAGAATGTATCGATACATTTGTACATGAATCGATACATTGAAAAATGTATC
1 GTATCGATACATTAAA-AATGTATCGATACATTCATACATGAATCGATACATTGAAAAATGTATC
* *
2495290 GATACATCTGGGTAAAAAGATAGAATGTATCGATACATTCATACAT
65 GATACATCTGGGTAAAAAGACAAAATGTATCGATACATTCATACAT
*
2495336 GTATCGATACATTGAAAAATGTATCGATACATTCATACATGTATCGATACATTGAAAAATGTATC
1 GTATCGATACATT-AAAAATGTATCGATACATTCATACATGAATCGATACATTGAAAAATGTATC
2495401 GATACATCTGGGTAAAAAGACAAAATGTATCGATACATTCATACAT
65 GATACATCTGGGTAAAAAGACAAAATGTATCGATACATTCATACAT
*
2495447 GTATCGATACATTAAAAAATATATCGATACAT
1 GTATCGATACATT-AAAAATGTATCGATACAT
2495479 CTGGGTAAAA
Statistics
Matches: 134, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
111 131 0.98
112 3 0.02
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.30
Consensus pattern (110 bp):
GTATCGATACATTAAAAATGTATCGATACATTCATACATGAATCGATACATTGAAAAATGTATCG
ATACATCTGGGTAAAAAGACAAAATGTATCGATACATTCATACAT
Found at i:2495426 original size:71 final size:71
Alignment explanation
Indices: 2495351--2495489 Score: 260
Period size: 71 Copynumber: 2.0 Consensus size: 71
2495341 GATACATTGA
* *
2495351 AAAATGTATCGATACATTCATACATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAA
1 AAAATGTATCGATACATTCATACATGTATCGATACATTAAAAAATATATCGATACATCTGGGTAA
2495416 AAAGAC
66 AAAGAC
2495422 AAAATGTATCGATACATTCATACATGTATCGATACATTAAAAAATATATCGATACATCTGGGTAA
1 AAAATGTATCGATACATTCATACATGTATCGATACATTAAAAAATATATCGATACATCTGGGTAA
2495487 AAA
66 AAA
2495490 TATGACTTTT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 66 1.00
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.29
Consensus pattern (71 bp):
AAAATGTATCGATACATTCATACATGTATCGATACATTAAAAAATATATCGATACATCTGGGTAA
AAAGAC
Found at i:2495450 original size:20 final size:20
Alignment explanation
Indices: 2495422--2495478 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
2495412 GTAAAAAGAC
*
2495422 AAAATGTATCGATACATTCA
1 AAAATGTATCGATACATTAA
* *
2495442 TACATGTATCGATACATTAA
1 AAAATGTATCGATACATTAA
*
2495462 AAAATATATCGATACAT
1 AAAATGTATCGATACAT
2495479 CTGGGTAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.32
Consensus pattern (20 bp):
AAAATGTATCGATACATTAA
Found at i:2496263 original size:48 final size:47
Alignment explanation
Indices: 2496201--2496471 Score: 307
Period size: 46 Copynumber: 5.8 Consensus size: 47
2496191 AGAGGAGTGC
** * *
2496201 CAATGTGCCAATTCAAGGCTAATGACATCGAGCTAAGGGAAAAGTGGA
1 CAATGTGCTGATTCAAGGCCAATGACATTGAGCTAA-GGAAAAGTGGA
* ** * * *
2496249 CAATGTGTTGATTCAAGGCCAGCGATAGTGAGTTAAGGGAAAAGTGGA
1 CAATGTGCTGATTCAAGGCCAATGACATTGAGCTAA-GGAAAAGTGGA
*
2496297 CAATGTGCTGATTCAAGGCC-GTGACATTGAGCTAAGAGAAAAGTGGA
1 CAATGTGCTGATTCAAGGCCAATGACATTGAGCTAAG-GAAAAGTGGA
* * *
2496344 CAATGTGCTGATTCAAGGCCAATGAAATTGAGCTAA-TAAAGGTGGA
1 CAATGTGCTGATTCAAGGCCAATGACATTGAGCTAAGGAAAAGTGGA
* *
2496390 CAATGTGCTGATTCAAGGCCAACGACATTGAGCTAA--TAAAGATGGA
1 CAATGTGCTGATTCAAGGCCAATGACATTGAGCTAAGGAAAAG-TGGA
* * *
2496436 CAATGTGCTGATTCAAAGCTAGTGACATTGAGCTAA
1 CAATGTGCTGATTCAAGGCCAATGACATTGAGCTAA
2496472 TAAAGGTGCT
Statistics
Matches: 193, Mismatches: 27, Indels: 8
0.85 0.12 0.04
Matches are distributed among these distances:
45 3 0.02
46 79 0.41
47 41 0.21
48 70 0.36
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (47 bp):
CAATGTGCTGATTCAAGGCCAATGACATTGAGCTAAGGAAAAGTGGA
Found at i:2496466 original size:92 final size:94
Alignment explanation
Indices: 2496201--2496501 Score: 315
Period size: 95 Copynumber: 3.2 Consensus size: 94
2496191 AGAGGAGTGC
** * * * * * *
2496201 CAATGTGCCAATTCAAGGCTAATGACATCGAGCTAAGGGAAAAGTGGACAATGTGTTGATTCAAG
1 CAATGTGCTGATTCAAGGCCAACGACATTGAGCTAAGAGAAAAGTGGACAATGTGCTGATTCAAA
** * * * * *
2496266 GCCAGCGATAGTGAGTTAAGGGAAAAGTGGA
66 GCCAATGAAATTGAGCTAA--TAAAGGTGGA
** *
2496297 CAATGTGCTGATTCAAGGCC-GTGACATTGAGCTAAGAGAAAAGTGGACAATGTGCTGATTCAAG
1 CAATGTGCTGATTCAAGGCCAACGACATTGAGCTAAGAGAAAAGTGGACAATGTGCTGATTCAAA
2496361 GCCAATGAAATTGAGCTAATAAAGGTGGA
66 GCCAATGAAATTGAGCTAATAAAGGTGGA
* *
2496390 CAATGTGCTGATTCAAGGCCAACGACATTGAGCTAATA-AAGA-TGGACAATGTGCTGATTCAAA
1 CAATGTGCTGATTCAAGGCCAACGACATTGAGCTAAGAGAAAAGTGGACAATGTGCTGATTCAAA
* * *
2496453 GCTAGTGACATTGAGCTAATAAAGGT-G-
66 GCCAATGAAATTGAGCTAATAAAGGTGGA
* *
2496480 CTAATATGCTGATTCAATGCCA
1 C-AATGTGCTGATTCAAGGCCA
2496502 GCGATATCGG
Statistics
Matches: 179, Mismatches: 24, Indels: 9
0.84 0.11 0.04
Matches are distributed among these distances:
90 1 0.01
91 19 0.11
92 43 0.24
93 31 0.17
94 14 0.08
95 54 0.30
96 17 0.09
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (94 bp):
CAATGTGCTGATTCAAGGCCAACGACATTGAGCTAAGAGAAAAGTGGACAATGTGCTGATTCAAA
GCCAATGAAATTGAGCTAATAAAGGTGGA
Found at i:2496476 original size:23 final size:21
Alignment explanation
Indices: 2496413--2496476 Score: 56
Period size: 21 Copynumber: 2.9 Consensus size: 21
2496403 CAAGGCCAAC
2496413 GACATTGAGCTAATAAAGATG
1 GACATTGAGCTAATAAAGATG
* * * *
2496434 GACAATGTGCTGATTCAAAGCTAG
1 GACATTGAGCT-AAT-AAAGAT-G
2496458 TGACATTGAGCTAATAAAG
1 -GACATTGAGCTAATAAAG
2496477 GTGCTAATAT
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
21 9 0.28
22 2 0.06
23 9 0.28
24 3 0.09
25 9 0.28
ACGTcount: A:0.39, C:0.12, G:0.23, T:0.25
Consensus pattern (21 bp):
GACATTGAGCTAATAAAGATG
Found at i:2496680 original size:28 final size:28
Alignment explanation
Indices: 2496619--2497269 Score: 730
Period size: 28 Copynumber: 22.5 Consensus size: 28
2496609 CACCGACTTG
2496619 TGTGGGCTTTGAAAGGGGATGCCACTGACT
1 TGTGGGCTTTGAAA-GGG-TGCCACTGACT
* *
2496649 TGTGGGCTTTGAAGGGGTACCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
2496677 TGTGGGCTGTGAAAGGGTGCTACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
2496705 TGTGGGCTTTAAAAAGGTGCCATTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
2496733 TGTGGGCTTTGGAAGGGTGCCACTGATTT
1 TGTGGGCTTTGAAAGGGTGCCACTGA-CT
* *
2496762 GTGTGGGCTTTAAAAGGGTGCCACTCACT
1 -TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
2496791 TGTGGGCTTTGGAAGGGTGCCACTGATTT
1 TGTGGGCTTTGAAAGGGTGCCACTGA-CT
2496820 GTGTGGGCTTTGAAAGGGTATGCCACTGACT
1 -TGTGGGCTTTGAAAGGG--TGCCACTGACT
* *
2496851 TGTCGGCTTTAAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
2496879 TGTGGGCTTTAAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
2496907 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
2496935 TGTGGGCTTTGGAAGGGTGCCACTGATTT
1 TGTGGGCTTTGAAAGGGTGCCACTGA-CT
*
2496964 GTGTGGGCTTTGAAAAGGTGCCACTGACT
1 -TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
2496993 TGTGGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
2497021 TATGGTCTTTTG-AAGAGATGCCACTGACT
1 TGTGGGC-TTTGAAAG-GGTGCCACTGACT
*
2497050 TGTGGGCTTTGAAAAGAGTTGCCACTGACT
1 TGTGGGCTTTG-AAAG-GGTGCCACTGACT
* *
2497080 TGAGTGGACTTTGAAAGGGTGCCACCGACT
1 T--GTGGGCTTTGAAAGGGTGCCACTGACT
* *
2497110 TGTGGGCTTTGAAAAGAGTTGCCACCGACT
1 TGTGGGCTTTG-AAAG-GGTGCCACTGACT
* *
2497140 TGAGTGGACTTTGAAAGGGTGCCACCGACT
1 T--GTGGGCTTTGAAAGGGTGCCACTGACT
**
2497170 TGTGGGCTTTGAAACGATATGCCACTGACT
1 TGTGGGCTTTGAAA-G-GGTGCCACTGACT
* *
2497200 TGTGGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
** *
2497228 TGTGTTCTTTTG-AAGAGATGCCACTGACT
1 TGTGGGC-TTTGAAAG-GGTGCCACTGACT
2497257 TGTGGGCTTTGAA
1 TGTGGGCTTTGAA
2497270 GAGATGAACG
Statistics
Matches: 536, Mismatches: 62, Indels: 47
0.83 0.10 0.07
Matches are distributed among these distances:
28 273 0.51
29 57 0.11
30 170 0.32
31 9 0.02
32 27 0.05
ACGTcount: A:0.21, C:0.17, G:0.32, T:0.30
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGGTGCCACTGACT
Found at i:2496681 original size:58 final size:56
Alignment explanation
Indices: 2496619--2497269 Score: 730
Period size: 58 Copynumber: 11.2 Consensus size: 56
2496609 CACCGACTTG
* *
2496619 TGTGGGCTTTGAAAGGGGATGCCACTGACTTGTGGGCTTTGAAGGGGTACCACTGACT
1 TGTGGGCTTTGAAA-GGG-TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * *
2496677 TGTGGGCTGTGAAAGGGTGCTACTGACTTGTGGGCTTTAAAAAGGTGCCATTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
2496733 TGTGGGCTTTGGAAGGGTGCCACTGATTTGTGTGGGCTTTAAAAGGGTGCCACTCACT
1 TGTGGGCTTTGAAAGGGTGCCACTGA-CT-TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
2496791 TGTGGGCTTTGGAAGGGTGCCACTGATTTGTGTGGGCTTTGAAAGGGTATGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGA-CT-TGTGGGCTTTGAAAGGG--TGCCACTGACT
* * *
2496851 TGTCGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACT
* *
2496907 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGGAAGGGTGCCACTGATTT
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGA-CT
* * *
2496964 GTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTAACT
1 -TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
2497021 TATGGTCTTTTG-AAGAGATGCCACTGACTTGTGGGCTTTGAAAAGAGTTGCCACTGACT
1 TGTGGGC-TTTGAAAG-GGTGCCACTGACTTGTGGGCTTTG-AAAG-GGTGCCACTGACT
* * * *
2497080 TGAGTGGACTTTGAAAGGGTGCCACCGACTTGTGGGCTTTGAAAAGAGTTGCCACCGACT
1 T--GTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAG-GGTGCCACTGACT
* * **
2497140 TGAGTGGACTTTGAAAGGGTGCCACCGACTTGTGGGCTTTGAAACGATATGCCACTGACT
1 T--GTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAA-G-GGTGCCACTGACT
* * ** *
2497200 TGTGGGCTTTGAAAGGATGCCACTAACTTGTGTTCTTTTG-AAGAGATGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC-TTTGAAAG-GGTGCCACTGACT
2497257 TGTGGGCTTTGAA
1 TGTGGGCTTTGAA
2497270 GAGATGAACG
Statistics
Matches: 526, Mismatches: 52, Indels: 31
0.86 0.09 0.05
Matches are distributed among these distances:
56 124 0.24
57 60 0.11
58 184 0.35
59 20 0.04
60 131 0.25
61 7 0.01
ACGTcount: A:0.21, C:0.17, G:0.32, T:0.30
Consensus pattern (56 bp):
TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACT
Found at i:2496908 original size:202 final size:202
Alignment explanation
Indices: 2496607--2497266 Score: 827
Period size: 202 Copynumber: 3.3 Consensus size: 202
2496597 GGGCTTTGAA
* * * * *
2496607 GCCACCGACTTGTGTGGGC-TTTGAAAGGGGATGCCACTGACTTGTGGGCTTTGAAGGGGTACCA
1 GCCACTGACTTGTGTGGGCTTTTG-AA-GAGATGCCACTGACTTGTGGGCTTTAAAAGGGTGCCA
* * *
2496671 CTGACTTGTGGGCTGTGAAAGGGTGCTACTGACTTGTGGGCTTTAAAAAGGTGCCATTGACTTGT
64 CTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTAAAAAGGTGCCACTGACTTGT
*
2496736 GGGCTTTGGAAGGGTGCCACTGATTTGTGTGGGCTTT-AAAAGGGTGCCACTCACTTGTGGGCTT
129 GGGCTTTGGAAGGGTGCCACTGATTTGTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTT
* *
2496800 TGGAAGGGT
194 TGAAAGGAT
* * *
2496809 GCCACTGATTTGTGTGGGC-TTTGAAAGGGTATGCCACTGACTTGTCGGCTTTAAAAGGGTGCCA
1 GCCACTGACTTGTGTGGGCTTTTG-AAGAG-ATGCCACTGACTTGTGGGCTTTAAAAGGGTGCCA
* * *
2496873 CTGACTTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGT
64 CTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTAAAAAGGTGCCACTGACTTGT
2496938 GGGCTTTGGAAGGGTGCCACTGATTTGTGTGGGCTTTGAAAA-GGTGCCACTGACTTGTGGGCTT
129 GGGCTTTGGAAGGGTGCCACTGATTTGTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTT
2497002 TGAAAGGAT
194 TGAAAGGAT
* * * *
2497011 GCCACTAAC-T-TATGGTCTTTTGAAGAGATGCCACTGACTTGTGGGCTTTGAAAAGAGTTGCCA
1 GCCACTGACTTGTGTGGGCTTTTGAAGAGATGCCACTGACTTGTGGGCTTT-AAAAG-GGTGCCA
* * * *
2497074 CTGACTTGAGTGGACTTTGAAAGGGTGCCACCGACTTGTGGGCTTTGAAAAGAGTTGCCACCGAC
64 CTGACTT--GTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTT-AAAA-AGGTGCCACTGAC
* * * * * **
2497139 TTGAGTGGACTTTGAAAGGGTGCCACCGA-CT-TGTGGGCTTTGAAACGATATGCCACTGACTTG
125 TT--GTGGGCTTTGGAAGGGTGCCACTGATTTGTGTGGGCTTTGAAAAG-GGTGCCACTGACTTG
2497202 TGGGCTTTGAAAGGAT
187 TGGGCTTTGAAAGGAT
* *
2497218 GCCACTAACTTGTGT--TCTTTTGAAGAGATGCCACTGACTTGTGGGCTTT
1 GCCACTGACTTGTGTGGGCTTTTGAAGAGATGCCACTGACTTGTGGGCTTT
2497267 GAAGAGATGA
Statistics
Matches: 406, Mismatches: 37, Indels: 25
0.87 0.08 0.05
Matches are distributed among these distances:
199 21 0.05
200 14 0.03
201 21 0.05
202 185 0.46
203 38 0.09
204 3 0.01
205 26 0.06
206 1 0.00
207 94 0.23
208 1 0.00
209 2 0.00
ACGTcount: A:0.20, C:0.18, G:0.32, T:0.30
Consensus pattern (202 bp):
GCCACTGACTTGTGTGGGCTTTTGAAGAGATGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACT
GACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTAAAAAGGTGCCACTGACTTGTGG
GCTTTGGAAGGGTGCCACTGATTTGTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTG
AAAGGAT
Found at i:2498543 original size:1 final size:1
Alignment explanation
Indices: 2498520--2498619 Score: 56
Period size: 1 Copynumber: 100.0 Consensus size: 1
2498510 TCTGGACCCC
* * * * * * * ** *
2498520 TTTTTTGTTTGTTTGTTTGTTTTTTTTTTGTTTTTTCTTTGTTTTTAGTTTTTTTTTTGTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
** *** *
2498585 TGGTTTTTTTTTTGGGTTTTTTTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2498620 GGTACGAAGG
Statistics
Matches: 74, Mismatches: 25, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 74 1.00
ACGTcount: A:0.01, C:0.01, G:0.14, T:0.84
Consensus pattern (1 bp):
T
Found at i:2498551 original size:11 final size:11
Alignment explanation
Indices: 2498520--2498619 Score: 101
Period size: 11 Copynumber: 8.4 Consensus size: 11
2498510 TCTGGACCCC
2498520 TTTTTTGTTTGT
1 TTTTTTGTTT-T
*
2498532 TTGTTTGTTTT
1 TTTTTTGTTTT
2498543 TTTTTTGTTTT
1 TTTTTTGTTTT
*
2498554 TTCTTTGTTTTT
1 TTTTTTG-TTTT
*
2498566 AGTTTTTTTTTTGT
1 --TTTTTTGTTT-T
2498580 TTTTTTGGTTTT
1 TTTTTT-GTTTT
2498592 TTTTTTGGGTTTT
1 TTTTTT--GTTTT
2498605 TTTTTTGTTTT
1 TTTTTTGTTTT
2498616 TTTT
1 TTTT
2498620 GGTACGAAGG
Statistics
Matches: 76, Mismatches: 6, Indels: 13
0.80 0.06 0.14
Matches are distributed among these distances:
11 26 0.34
12 26 0.34
13 18 0.24
14 6 0.08
ACGTcount: A:0.01, C:0.01, G:0.14, T:0.84
Consensus pattern (11 bp):
TTTTTTGTTTT
Found at i:2498560 original size:22 final size:23
Alignment explanation
Indices: 2498520--2498619 Score: 105
Period size: 25 Copynumber: 4.2 Consensus size: 23
2498510 TCTGGACCCC
*
2498520 TTTTTTGTTTGTTTGTTTGTTTT
1 TTTTTTGTTTGTTTTTTTGTTTT
*
2498543 TTTTTTGTTT-TTTCTTTGTTTTT
1 TTTTTTGTTTGTTTTTTTG-TTTT
*
2498566 AGTTTTTTTTTTGTTTTTTTGGTTTT
1 --TTTTTTGTTTGTTTTTTT-GTTTT
2498592 TTTTTTGGGTTT-TTTTTTTGTTTT
1 TTTTTT--GTTTGTTTTTTTGTTTT
2498616 TTTT
1 TTTT
2498620 GGTACGAAGG
Statistics
Matches: 66, Mismatches: 4, Indels: 13
0.80 0.05 0.16
Matches are distributed among these distances:
22 7 0.11
23 14 0.21
24 15 0.23
25 16 0.24
26 13 0.20
27 1 0.02
ACGTcount: A:0.01, C:0.01, G:0.14, T:0.84
Consensus pattern (23 bp):
TTTTTTGTTTGTTTTTTTGTTTT
Found at i:2498615 original size:20 final size:18
Alignment explanation
Indices: 2498520--2498616 Score: 80
Period size: 18 Copynumber: 5.7 Consensus size: 18
2498510 TCTGGACCCC
*
2498520 TTTTTTGTTTGTTTG-TTT
1 TTTTTTGTTT-TTAGTTTT
*
2498538 GTTTTT-TTTTT-GTTTT
1 TTTTTTGTTTTTAGTTTT
*
2498554 TTCTTTGTTTTTAGTTTT
1 TTTTTTGTTTTTAGTTTT
**
2498572 TTTTTTGTTTTT--TTGG
1 TTTTTTGTTTTTAGTTTT
**
2498588 TTTTTT-TTTTGGGTTTT
1 TTTTTTGTTTTTAGTTTT
2498605 TTTTTTGTTTTT
1 TTTTTTGTTTTT
2498617 TTTGGTACGA
Statistics
Matches: 63, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
15 5 0.08
16 17 0.27
17 16 0.25
18 25 0.40
ACGTcount: A:0.01, C:0.01, G:0.14, T:0.84
Consensus pattern (18 bp):
TTTTTTGTTTTTAGTTTT
Found at i:2504151 original size:19 final size:19
Alignment explanation
Indices: 2504123--2504185 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 19
2504113 AGCGATACAT
2504123 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
*
2504142 TGTATTGAT---ACA--T-
1 TGTATCGATACAACACTTA
*
2504155 TGTATTGATACAACACTTA
1 TGTATCGATACAACACTTA
2504174 TGTATCGATACA
1 TGTATCGATACA
2504186 GTTACTGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 9 0.25
14 1 0.03
16 6 0.17
18 1 0.03
19 19 0.53
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.37
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:2504157 original size:32 final size:32
Alignment explanation
Indices: 2504110--2504185 Score: 125
Period size: 32 Copynumber: 2.4 Consensus size: 32
2504100 GCAGTAGCTT
*
2504110 TGTAGCGATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
* *
2504142 TGTATTGATACATTGTATTGATACAACACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
2504174 TGTATCGATACA
1 TGTATCGATACA
2504186 GTTACTGTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATTGTATCGATACAACACTTA
Found at i:2504160 original size:13 final size:13
Alignment explanation
Indices: 2504142--2504166 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2504132 ACAACACTTA
2504142 TGTATTGATACAT
1 TGTATTGATACAT
2504155 TGTATTGATACA
1 TGTATTGATACA
2504167 ACACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (13 bp):
TGTATTGATACAT
Found at i:2510869 original size:78 final size:79
Alignment explanation
Indices: 2510705--2510904 Score: 287
Period size: 78 Copynumber: 2.5 Consensus size: 79
2510695 TTGACTATGG
* *
2510705 AAAATCGGTGTTCTAGAAATAAAATCGGGGTTGGAGTATCCCCTTGAAAATAACAGGGTTGGAGT
1 AAAATTGGTGTTCTAGAAATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGT
*
2510770 ATCCCCAATTGTGA
66 ATCCCCAATTGTAA
* * *
2510784 AATATTGGTGTTCTGGAAATAAAA-CTGGGGTTGGAGTAT-CCCTCGAAAATAACGGGGTTGGAG
1 AAAATTGGTGTTCTAGAAATAAAATC-GGGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAG
2510847 TATCCCCAATTGTAA
65 TATCCCCAATTGTAA
* ** *
2510862 AAAATTGGTGTTTTAGAAATAAAATCAAGGCTGGAGTATCCCC
1 AAAATTGGTGTTCTAGAAATAAAATCGGGGTTGGAGTATCCCC
2510905 GATTGTGAGA
Statistics
Matches: 106, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
78 68 0.64
79 38 0.36
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (79 bp):
AAAATTGGTGTTCTAGAAATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGT
ATCCCCAATTGTAA
Found at i:2512532 original size:21 final size:21
Alignment explanation
Indices: 2512506--2512561 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
2512496 GTTGGGACCT
2512506 TGTATCGATACATTAAGGGCA
1 TGTATCGATACATTAAGGGCA
2512527 TGTATCGATACATTAAGGGCA
1 TGTATCGATACATTAAGGGCA
2512548 TGTATCGATACATT
1 TGTATCGATACATT
2512562 TTGGCAAAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.32
Consensus pattern (21 bp):
TGTATCGATACATTAAGGGCA
Found at i:2513166 original size:61 final size:61
Alignment explanation
Indices: 2513094--2514621 Score: 1834
Period size: 61 Copynumber: 25.1 Consensus size: 61
2513084 TCCTCCTTGG
* ** * *
2513094 GGACTAGAAGGTGCCACCAACTTGTATGGGCTTTGCAAGGAGAAA-GCATCCTGCTCTTTGA
1 GGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA-AAAGGCGTCCCGCTCTTTGA
* *
2513155 GGACTAGAAGGTGCTACCAACTTGTGTGGGCTTTAAAA-GAAAATGGCGTCCTGCTAC-TTGA
1 GGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA-GGCGTCCCGCT-CTTTGA
* **
2513216 GGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTACT-TCTTGA
1 GGACTAG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCCGCTCT-TTGA
* *
2513277 GGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCCGCTCTTTGA
1 GGACTAG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCCGCTCTTTGA
* *** *
2513338 GGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTGTCCTATTCTTTAA
1 GGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCCGCTCTTTGA
* * **
2513399 GGACT-GAAGATGCCACCAGCTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTACTCTTTGA
1 GGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCCGCTCTTTGA
* ** * * * *
2513459 AGACTAGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAAGCGTCCTGCTCCTTAA
1 GGACTAG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCCGCTCTTTGA
*
2513521 GGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCCGCTCTTTGA
1 GGACTAG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCCGCTCTTTGA
* * * *
2513582 GGACTAGAAGGTGCCACCAATTTGTGTGGGCTTTAAAAGGAAAATGC-ACCCTGCTCTTTAA
1 GGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCC-GCTCTTTGA
*
2513643 GGACTA-AAGGTGCCACCAGCTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCCGCTCTTTGA
1 GGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCCGCTCTTTGA
** ** * *
2513703 GGACTAGAAGGTGCCACGTACTTCAGTGGGCTTTAAAAGGAAAATGCGTCCCACTCTTTGA
1 GGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCCGCTCTTTGA
* * * *
2513764 GGACTA-AAGAGTGCTACCAACTTGTGTGGGTTTTAAAAGGAAAAGACTGTCCCACTCTTTGA
1 GGACTAGAAG-GTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC-GTCCCGCTCTTTGA
* * * * ** * *
2513826 GGACTAGAAAGTGCCACCAACTAGTTTGGGCTTTAAAAGGAAAAGGCATCTTGCTCCTTAA
1 GGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCCGCTCTTTGA
* ** * **
2513887 GGACT-GAAAAGTGCCACCAGTTTGTGTGGGCTGTAAAAGGAAAAGGTATCCCGCTCTTTGA
1 GGACTAG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCCGCTCTTTGA
** * **
2513948 GGACTAGAAGGTGCCATGAACTTGTGTGGGCTTTAAAAGGAAAAAGGCATCTTGCTCTTTGA
1 GGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGG-AAAAGGCGTCCCGCTCTTTGA
* * *
2514010 GGACT-GAAGAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAGAGACATCCCGCTCTTTGA
1 GGACTAGAAG-GTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCCGCTCTTTGA
* * * *
2514071 AGACTAGAAGGTGCCACCAACTGGTGTGGGCTTTAAACGGAAAAGGCATCCCGCTCTTTGA
1 GGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCCGCTCTTTGA
* * * * *
2514132 GGACT-GAAGGTGCCACCAGCTTGTATGGGCTTTAGAAGGAAAATGCGTCCCACTCTTTGA
1 GGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCCGCTCTTTGA
* ** * *
2514192 GGACTAAAAGGTGCCATGAACTTGTGTGGGCTTTAAAAGGCAAAGGCATCCCGCTCTTTGA
1 GGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCCGCTCTTTGA
* ** * *
2514253 GGACT-GAAGAGGGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTACTCCTTAA
1 GGACTAGAAG-GTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCCGCTCTTTGA
* * * * * *
2514314 AGACT-GAAAAGTGCCACCAACTTCTGTGGGCTTTAGAAGGAAAAGGCATCCCGCTCTTTTA
1 GGACTAG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCCGCTCTTTGA
* *
2514375 GGACTTA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTGTCCTGCTCTTTGA
1 GGAC-TAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCCGCTCTTTGA
* * * *
2514436 GGACT-GAAGGTGCCACCAGCTTGTGTGGGTTTTAAAAGGAAAAGACGTCCCACTCTTTGA
1 GGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCCGCTCTTTGA
* * *
2514496 GAACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAATGAAAAGGCGTTCCGCTCTTTGA
1 GGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCCGCTCTTTGA
* * * *
2514557 GGACT-GAAGGTGCCACCAGCATGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCCTTGA
1 GGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCCGCTCTTTGA
2514617 GGACT
1 GGACT
2514622 GAAAAGTGAA
Statistics
Matches: 1267, Mismatches: 170, Indels: 61
0.85 0.11 0.04
Matches are distributed among these distances:
59 3 0.00
60 277 0.22
61 813 0.64
62 172 0.14
63 2 0.00
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (61 bp):
GGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCCGCTCTTTGA
Found at i:2515498 original size:16 final size:16
Alignment explanation
Indices: 2515477--2515516 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
2515467 TTTTTCTCTA
2515477 TTTTTTTTCTTTGTT-
1 TTTTTTTTCTTTGTTG
*
2515492 TTGTTTTTTTTTTGTTG
1 TT-TTTTTTCTTTGTTG
2515509 TTTTTTTT
1 TTTTTTTT
2515517 AAAAAGAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 2 0.09
16 18 0.82
17 2 0.09
ACGTcount: A:0.00, C:0.03, G:0.10, T:0.88
Consensus pattern (16 bp):
TTTTTTTTCTTTGTTG
Found at i:2515501 original size:19 final size:18
Alignment explanation
Indices: 2515477--2515516 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
2515467 TTTTTCTCTA
*
2515477 TTTTTTTTCT-TTGTTTT
1 TTTTTTTTTTGTTGTTTT
2515494 GTTTTTTTTTTGTTGTTTT
1 -TTTTTTTTTTGTTGTTTT
2515513 TTTT
1 TTTT
2515517 AAAAAGAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.00, C:0.03, G:0.10, T:0.88
Consensus pattern (18 bp):
TTTTTTTTTTGTTGTTTT
Found at i:2515513 original size:14 final size:15
Alignment explanation
Indices: 2515478--2515516 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 15
2515468 TTTTCTCTAT
2515478 TTTTTTTCTTTGTTTTG
1 TTTTTTT-TTTG-TTTG
2515495 TTTTTTTTTTG-TTG
1 TTTTTTTTTTGTTTG
2515509 TTTTTTTT
1 TTTTTTTT
2515517 AAAAAGAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 11 0.50
16 4 0.18
17 7 0.32
ACGTcount: A:0.00, C:0.03, G:0.10, T:0.87
Consensus pattern (15 bp):
TTTTTTTTTTGTTTG
Found at i:2516256 original size:33 final size:32
Alignment explanation
Indices: 2516196--2516263 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
2516186 CCTTAACTGT
* *
2516196 TTGTATCGATACACACAATATGTATCGATACA
1 TTGTATCGACACACACAAAATGTATCGATACA
*
2516228 TTGTATCGACACATCCCAAAATGTATCGATACA
1 TTGTATCGACACA-CACAAAATGTATCGATACA
2516261 TTG
1 TTG
2516264 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 12 0.38
33 20 0.62
ACGTcount: A:0.35, C:0.21, G:0.13, T:0.31
Consensus pattern (32 bp):
TTGTATCGACACACACAAAATGTATCGATACA
Found at i:2524295 original size:22 final size:22
Alignment explanation
Indices: 2524269--2524313 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
2524259 TGAAATTGTT
2524269 AAATTATTTGATTAAGGGGGAG
1 AAATTATTTGATTAAGGGGGAG
*
2524291 AAATTTTTTGATTAAGGGGGAG
1 AAATTATTTGATTAAGGGGGAG
2524313 A
1 A
2524314 GAAAAGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.31, T:0.33
Consensus pattern (22 bp):
AAATTATTTGATTAAGGGGGAG
Found at i:2524861 original size:13 final size:13
Alignment explanation
Indices: 2524843--2524867 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2524833 AGATTGCATA
2524843 GTATCGATACATT
1 GTATCGATACATT
2524856 GTATCGATACAT
1 GTATCGATACAT
2524868 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:2524986 original size:13 final size:13
Alignment explanation
Indices: 2524968--2524993 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2524958 ACACACAATA
2524968 TGTATCGATACAT
1 TGTATCGATACAT
2524981 TGTATCGATACAT
1 TGTATCGATACAT
2524994 CCCAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2525009 original size:33 final size:32
Alignment explanation
Indices: 2524948--2525015 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 32
2524938 CCTTAACTGT
*
2524948 TTGTATCGATACACACAATATGTATCGATACA
1 TTGTATCGATACACACAAAATGTATCGATACA
*
2524980 TTGTATCGATACATCCCAAAATGTATCGATACA
1 TTGTATCGATACA-CACAAAATGTATCGATACA
2525013 TTG
1 TTG
2525016 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 13 0.39
33 20 0.61
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.32
Consensus pattern (32 bp):
TTGTATCGATACACACAAAATGTATCGATACA
Found at i:2529059 original size:21 final size:21
Alignment explanation
Indices: 2529026--2529070 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2529016 TTGCAAGTTG
*
2529026 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
2529048 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
2529068 AAA
1 AAA
2529071 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:2530317 original size:299 final size:299
Alignment explanation
Indices: 2529773--2530376 Score: 983
Period size: 299 Copynumber: 2.0 Consensus size: 299
2529763 ATCACAAAAA
* * *
2529773 TGTCACGTAATTGATATTTGTAATAATAAAACGATTTTCTTAGGCCATAGAGAAGGGAACATTTA
1 TGTCACGTAACTGATACTTGTAATAATAAAACAATTTTCTTAGGCCATAGAGAAGGGAACATTTA
*
2529838 TGTTGTACATTTAGATGTTTTAAGTTCCCAAAATGTATGTTTTGTTGCCGACAACAATAACATAC
66 TGTTATACATTTAGATGTTTTAAGTTCCCAAAATGTATGTTTTGTTGCCGACAACAATAACATAC
* * * *
2529903 CTTGGCTATGGCATCGAAAATTAGGACACGCAAGTATGAGCGTAATTTCTAAATTGTCTAGGAAA
131 CTTGGCTATGGCACCGAAAACTAGGACACGCAAGTATGAGCGTAATCTCTAAATTATCTAGGAAA
2529968 AATCTCGTAATTGGATTACCTAAGGTCAAATTCGAGTGCGATAAAGTTTGTGATGCATGTGTTAA
196 AATCTCGTAATTGGATTACCTAAGGTCAAATTCGAGTGCGATAAAGTTTGTGATGCATGTGTTAA
*
2530033 AGGAAAACATAAAAGAAGCTCTTTTAAACCTATAAACAT
261 AGGAAAACATAAAAGAAACTCTTTTAAACCTATAAACAT
*
2530072 TGTCACGTAACTGATACTTGTAATAATAAAACAATTTTCTTAGGCCATAGTGAAGGGAACATTTA
1 TGTCACGTAACTGATACTTGTAATAATAAAACAATTTTCTTAGGCCATAGAGAAGGGAACATTTA
* * *
2530137 TGTTATACATTTAGATGTTTTAAGTTCCTAAAATGTATGTTTTGTTGCCGATAACAATGACATAC
66 TGTTATACATTTAGATGTTTTAAGTTCCCAAAATGTATGTTTTGTTGCCGACAACAATAACATAC
* * *
2530202 CTTGGCTATGGCACCGAAAACTAGGACACGTAAGTATGAGCGTACTCTCTAAGTTATCTAGGAAA
131 CTTGGCTATGGCACCGAAAACTAGGACACGCAAGTATGAGCGTAATCTCTAAATTATCTAGGAAA
* * * * * *
2530267 AATCTTGTAATTGGGTTACCTAAGGTCAAATTTGATTGTGATAGAGTTTGTGATGCATGTGTTAA
196 AATCTCGTAATTGGATTACCTAAGGTCAAATTCGAGTGCGATAAAGTTTGTGATGCATGTGTTAA
* * *
2530332 AGGTAAGCATAAAAGAAATTCTTTTAAACCTATAAACAT
261 AGGAAAACATAAAAGAAACTCTTTTAAACCTATAAACAT
2530371 TGTCAC
1 TGTCAC
2530377 AACTTCTAGA
Statistics
Matches: 280, Mismatches: 25, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
299 280 1.00
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (299 bp):
TGTCACGTAACTGATACTTGTAATAATAAAACAATTTTCTTAGGCCATAGAGAAGGGAACATTTA
TGTTATACATTTAGATGTTTTAAGTTCCCAAAATGTATGTTTTGTTGCCGACAACAATAACATAC
CTTGGCTATGGCACCGAAAACTAGGACACGCAAGTATGAGCGTAATCTCTAAATTATCTAGGAAA
AATCTCGTAATTGGATTACCTAAGGTCAAATTCGAGTGCGATAAAGTTTGTGATGCATGTGTTAA
AGGAAAACATAAAAGAAACTCTTTTAAACCTATAAACAT
Found at i:2531193 original size:15 final size:15
Alignment explanation
Indices: 2531173--2531203 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2531163 TAAAAATGTC
*
2531173 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
2531188 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
2531203 C
1 C
2531204 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:2533471 original size:20 final size:20
Alignment explanation
Indices: 2533428--2533472 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
2533418 AAATCTTTTG
2533428 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
2533449 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
2533469 CAAA
1 CAAA
2533473 CCAAAACAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.31, C:0.20, G:0.04, T:0.44
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:2535864 original size:13 final size:13
Alignment explanation
Indices: 2535846--2535871 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2535836 TAGAGTAAGT
2535846 ATGTATCGATACA
1 ATGTATCGATACA
2535859 ATGTATCGATACA
1 ATGTATCGATACA
2535872 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2537180 original size:13 final size:13
Alignment explanation
Indices: 2537162--2537188 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2537152 ATAGTAACCC
2537162 ATGTATCGATACA
1 ATGTATCGATACA
2537175 ATGTATCGATACA
1 ATGTATCGATACA
2537188 A
1 A
2537189 GGAATATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2552986 original size:7 final size:7
Alignment explanation
Indices: 2552974--2553006 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
2552964 AGAAGAGATA
2552974 AAAAAAC
1 AAAAAAC
2552981 AAAAAAAC
1 -AAAAAAC
2552989 AAAAAAC
1 AAAAAAC
2552996 AAAAAA-
1 AAAAAAC
2553002 AAAAA
1 AAAAA
2553007 CAACACAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 5 0.20
7 13 0.52
8 7 0.28
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:2552986 original size:8 final size:8
Alignment explanation
Indices: 2552973--2553016 Score: 56
Period size: 8 Copynumber: 5.5 Consensus size: 8
2552963 AAGAAGAGAT
2552973 AAAAAAAC
1 AAAAAAAC
2552981 AAAAAAAC
1 AAAAAAAC
2552989 -AAAAAAC
1 AAAAAAAC
2552996 AAAAAAA-
1 AAAAAAAC
2553003 AAAACAACAC
1 AAAA-AA-AC
2553013 AAAA
1 AAAA
2553017 GGTTCGAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
7 11 0.34
8 16 0.50
9 1 0.03
10 4 0.12
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:2552992 original size:15 final size:14
Alignment explanation
Indices: 2552973--2553016 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 14
2552963 AAGAAGAGAT
2552973 AAAAAAACAAAAAA
1 AAAAAAACAAAAAA
2552987 ACAAAAAACAAAAAA
1 A-AAAAAACAAAAAA
2553002 AAAAACAACACAAAA
1 AAAAA-AACA-AAAA
2553017 GGTTCGAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 5 0.19
15 18 0.67
16 4 0.15
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAAACAAAAAA
Found at i:2552999 original size:22 final size:22
Alignment explanation
Indices: 2552973--2553016 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2552963 AAGAAGAGAT
*
2552973 AAAAAAACAAAAAAACAAAAAAC
1 AAAAAAA-AAAACAACAAAAAAC
*
2552996 AAAAAAAAAAACAACACAAAA
1 AAAAAAAAAAACAACAAAAAA
2553017 GGTTCGAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (22 bp):
AAAAAAAAAAACAACAAAAAAC
Found at i:2554522 original size:28 final size:27
Alignment explanation
Indices: 2554447--2554574 Score: 143
Period size: 27 Copynumber: 4.6 Consensus size: 27
2554437 TTCCTCGCCC
*
2554447 CCTTCAAAGCCCACAAGTCAGTAGC-A
1 CCTTCAAAGCCCACAAGTCAGTGGCAA
*
2554473 CCTTTTTCAAAAGCCCACAAGTTAGTGGC-A
1 CC---TTC-AAAGCCCACAAGTCAGTGGCAA
*
2554503 CCTTTTCAAAGCCCACAAGTCAATGGCAA
1 CC--TTCAAAGCCCACAAGTCAGTGGCAA
*
2554532 CCTTCAAAGCCCACAAGGCAGTGGCAA
1 CCTTCAAAGCCCACAAGTCAGTGGCAA
2554559 CCTTCAAAAGCCCACA
1 CCTTC-AAAGCCCACA
2554575 CAAGTTGGTG
Statistics
Matches: 90, Mismatches: 6, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
26 2 0.02
27 28 0.31
28 28 0.31
29 11 0.12
30 21 0.23
ACGTcount: A:0.34, C:0.33, G:0.16, T:0.18
Consensus pattern (27 bp):
CCTTCAAAGCCCACAAGTCAGTGGCAA
Found at i:2554556 original size:55 final size:55
Alignment explanation
Indices: 2554447--2554574 Score: 145
Period size: 55 Copynumber: 2.3 Consensus size: 55
2554437 TTCCTCGCCC
* **
2554447 CCTTCAAAGCCCACAAGTCAGTAGCACCTTTTTCAAAAGCCCACAAGTTAGTGGC-A
1 CCTTCAAAGCCCACAAGTCAATAGCACC--TTTCAAAAGCCCACAAGGCAGTGGCAA
*
2554503 CCTTTTCAAAGCCCACAAGTCAATGGCAACC-TTC-AAAGCCCACAAGGCAGTGGCAA
1 CC--TTCAAAGCCCACAAGTCAATAGC-ACCTTTCAAAAGCCCACAAGGCAGTGGCAA
2554559 CCTTCAAAAGCCCACA
1 CCTTC-AAAGCCCACA
2554575 CAAGTTGGTG
Statistics
Matches: 63, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
54 3 0.05
55 28 0.44
56 8 0.13
58 21 0.33
59 3 0.05
ACGTcount: A:0.34, C:0.33, G:0.16, T:0.18
Consensus pattern (55 bp):
CCTTCAAAGCCCACAAGTCAATAGCACCTTTCAAAAGCCCACAAGGCAGTGGCAA
Found at i:2554769 original size:49 final size:49
Alignment explanation
Indices: 2554594--2555293 Score: 538
Period size: 52 Copynumber: 14.8 Consensus size: 49
2554584 GGCATATTCT
* * * * *
2554594 TTTAAGTCCAATATCACTGGCCTCGAATCAGCATATTGGCGCCTTTGTCATC
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC--T-TCATC
* * *
2554646 TTTAAGTCCAATGTCGCTGGCCTCGAATCAGCATATTGGCGCCTTTGTCATC
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC--T-TCATC
* *
2554698 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTAGCACCTTCACC
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
*
2554747 TTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCA----C--C
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
* * * *
2554790 TTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTTATC
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
*
2554839 TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA----C--C
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
* * * * *
2554882 TTTAAGTCTAATATCACTGGCCTTGAATCAGCATATTGGCACCTT-GTC
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
* *
2554930 TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATT---A---GCA-C
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
* *
2554972 ---AAGCCCAATATCGCTGGCCTTGAATCAGCACATTGG------CA-C
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
* * * *
2555011 ---AAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCGTCATC
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
* * * *
2555057 TTTAAGACCGATGTCGCTGGCCTAGAATCAGCACATCGGCACCTTAACTATC
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTT--C-ATC
* * * *
2555109 TTTAAGACCAATATCGCTGGCCTTGAATTAGTACATTGGCACCTTCATC
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
* * * ** * * *
2555158 TTTAAGTTCGATATCATTGGCTTTGAATCAGCATATTGGCATCTTTAACAT-
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-CCTT--CATC
* * * * *
2555209 TCTTAAGCCCAATGTCACTGGCCTT-ATCTCAGCACATTGG--CGTTCTTC
1 T-TTAAGTCCAATGTCGCTGGCCTTGA-ATCAGCACATTGGCACCTTCATC
* * *
2555257 TTCAAGTCTAATGTCGCTGGCCATGAATCAGCACATT
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATT
2555294 ATCATTCTTC
Statistics
Matches: 540, Mismatches: 73, Indels: 75
0.78 0.11 0.11
Matches are distributed among these distances:
39 70 0.13
42 1 0.00
43 75 0.14
45 4 0.01
46 1 0.00
47 30 0.06
48 35 0.06
49 154 0.29
50 5 0.01
51 3 0.01
52 162 0.30
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (49 bp):
TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
Found at i:2554791 original size:21 final size:21
Alignment explanation
Indices: 2554767--2554834 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 21
2554757 ATGTTGCTGG
2554767 CCTTGAATCAGCACATTGGCA
1 CCTTGAATCAGCACATTGGCA
* ** *
2554788 CCTTTAAGTCCAATATCGTTGG--
1 CCTTGAA-T-CAGCA-CATTGGCA
*
2554810 CCTTGAATCAGCATATTGGCA
1 CCTTGAATCAGCACATTGGCA
2554831 CCTT
1 CCTT
2554835 TATCTTTAAG
Statistics
Matches: 33, Mismatches: 9, Indels: 10
0.63 0.17 0.19
Matches are distributed among these distances:
19 4 0.12
20 3 0.09
21 11 0.33
22 7 0.21
23 3 0.09
24 5 0.15
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (21 bp):
CCTTGAATCAGCACATTGGCA
Found at i:2554794 original size:43 final size:43
Alignment explanation
Indices: 2554743--2555153 Score: 334
Period size: 43 Copynumber: 9.1 Consensus size: 43
2554733 TTAGCACCTT
* * *
2554743 CACCTTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGG
1 CACCTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGG
* * *
2554786 CACCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGG
1 CACCTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGG
*
2554829 CACCTTTATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGG
1 CA-C-----CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGG
* * * *
2554878 CACCTTTAAGTCTAATATCACTGGCCTTGAATCAGCATATTGG
1 CACCTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGG
* *
2554921 CACCTTGTCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTAG
1 CA-C----CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGG
*
2554969 CA-C---AAGCCCAATATCGCTGGCCTTGAATCAGCACATTGG
1 CACCTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGG
* *
2555008 CA-C---AAGCCCAATATCGCTGGCCTTGAATCAGCATATTGG
1 CACCTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGG
* * * *
2555047 CACCGTCATCTTTAAGACCGATGTCGCTGGCCTAGAATCAGCACATCGG
1 CA----C--CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGG
* *
2555096 CACCTTAACTATCTTTAAGACCAATATCGCTGGCCTTGAATTAGTACATTGG
1 ---C---AC---CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGG
2555148 CACCTT
1 CACCTT
2555154 CATCTTTAAG
Statistics
Matches: 305, Mismatches: 35, Indels: 56
0.77 0.09 0.14
Matches are distributed among these distances:
39 73 0.24
42 1 0.00
43 81 0.27
44 2 0.01
46 3 0.01
48 37 0.12
49 69 0.23
51 1 0.00
52 37 0.12
55 1 0.00
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (43 bp):
CACCTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGG
Found at i:2554858 original size:92 final size:92
Alignment explanation
Indices: 2554697--2555293 Score: 506
Period size: 92 Copynumber: 6.4 Consensus size: 92
2554687 CCTTTGTCAT
* * * * * *
2554697 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTAGCACCTTCACCTTTAAGTCCAATGTT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGACCAATGTC
2554762 GCTGGCCTTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
* *
2554789 CTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGACCAATGTC
2554854 GCTGGCCTTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
* * * *
2554881 CTTTAAGTCTAATATCACTGGCCTTGAATCAGCATATTGGCACC-TTGTCTTTAAGACCAATGTC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGACCAATGTC
*
2554945 GCTGGCCTTGAATCAGCACATTAGCA-
66 GCTGGCCTTGAATCAGCACATTGGCAC
* * *
2554971 C---AAGCCCAATATCGCTGGCCTTGAATCAGCACATTGG---C---A-C---AAGCCCAATATC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGACCAATGTC
*
2555023 GCTGGCCTTGAATCAGCATATTGGCACCGTC
66 GCTGGCCTTGAATCAGCACATTGGCA----C
* * * * *
2555054 ATCTTTAAGACCGATGTCGCTGGCCTAGAATCAGCACATCGGCACCTTAACTATCTTTAAGACCA
1 --CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTT---TATCTTTAAGACCA
* * *
2555119 ATATCGCTGGCCTTGAATTAGTACATTGGCACCTTC
61 ATGTCGCTGGCCTTGAATCAGCACATTGGCA----C
* * ** * * * * *
2555155 ATCTTTAAGTTCGATATCATTGGCTTTGAATCAGCATATTGGCATCTTTAACATTCTTAAGCCCA
1 --CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTATC--T-TTAAGACCA
* * *
2555220 ATGTCACTGGCCTT-ATCTCAGCACATTGGCGTTC
61 ATGTCGCTGGCCTTGA-ATCAGCACATTGGC--AC
* * * *
2555254 TTCTTCAAGTCTAATGTCGCTGGCCATGAATCAGCACATT
1 --CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATT
2555294 ATCATTCTTC
Statistics
Matches: 415, Mismatches: 61, Indels: 51
0.79 0.12 0.10
Matches are distributed among these distances:
78 34 0.08
81 1 0.00
84 1 0.00
85 1 0.00
87 32 0.08
88 31 0.07
90 1 0.00
91 45 0.11
92 125 0.30
97 1 0.00
98 4 0.01
99 30 0.07
100 2 0.00
101 107 0.26
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.30
Consensus pattern (92 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGACCAATGTC
GCTGGCCTTGAATCAGCACATTGGCAC
Found at i:2554883 original size:21 final size:21
Alignment explanation
Indices: 2554859--2554927 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
2554849 ATGTCGCTGG
2554859 CCTTGAATCAGCACATTGGCA
1 CCTTGAATCAGCACATTGGCA
* ** *
2554880 CCTTTAAGTCTAATATCACTGG--
1 CCTTGAA-TC-AGCA-CATTGGCA
*
2554902 CCTTGAATCAGCATATTGGCA
1 CCTTGAATCAGCACATTGGCA
2554923 CCTTG
1 CCTTG
2554928 TCTTTAAGAC
Statistics
Matches: 34, Mismatches: 9, Indels: 10
0.64 0.17 0.19
Matches are distributed among these distances:
19 4 0.12
20 2 0.06
21 13 0.38
22 8 0.24
23 2 0.06
24 5 0.15
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.30
Consensus pattern (21 bp):
CCTTGAATCAGCACATTGGCA
Found at i:2554991 original size:39 final size:39
Alignment explanation
Indices: 2554937--2555049 Score: 199
Period size: 39 Copynumber: 2.9 Consensus size: 39
2554927 GTCTTTAAGA
* *
2554937 CCAATGTCGCTGGCCTTGAATCAGCACATTAGCACAAGC
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACAAGC
2554976 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACAAGC
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACAAGC
*
2555015 CCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCAC
2555050 CGTCATCTTT
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 71 1.00
ACGTcount: A:0.27, C:0.30, G:0.20, T:0.22
Consensus pattern (39 bp):
CCAATATCGCTGGCCTTGAATCAGCACATTGGCACAAGC
Found at i:2555190 original size:101 final size:101
Alignment explanation
Indices: 2555015--2555249 Score: 260
Period size: 101 Copynumber: 2.3 Consensus size: 101
2555005 TGGCACAAGC
* * *
2555015 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCGTCATCTTTAAGACCGATGTCGCTGGCCT
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCGTCATCTTTAAGACCGATATCACTGGCCT
2555080 AGAATCAGCACATCGGCA-CCTTAAC-TATCTTTAAGA
66 AGAATCAGCACATCGGCATCCTTAACAT-TC-TTAAGA
* * * ** * *
2555116 CCAATATCGCTGGCCTTGAATTAGTACATTGGCACCTTCATCTTTAAGTTCGATATCATTGGCTT
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCGTCATCTTTAAGACCGATATCACTGGCCT
* * * * *
2555181 TGAATCAGCATATTGGCATCTTTAACATTCTTAAGC
66 AGAATCAGCACATCGGCATCCTTAACATTCTTAAGA
* * *
2555217 CCAATGTCACTGGCCTT-ATCTCAGCACATTGGC
1 CCAATATCGCTGGCCTTGA-ATCAGCACATTGGC
2555250 GTTCTTCTTC
Statistics
Matches: 111, Mismatches: 20, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
100 1 0.01
101 101 0.91
102 8 0.07
103 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (101 bp):
CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCGTCATCTTTAAGACCGATATCACTGGCCT
AGAATCAGCACATCGGCATCCTTAACATTCTTAAGA
Found at i:2556000 original size:21 final size:20
Alignment explanation
Indices: 2555970--2556008 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
2555960 CACATTTTTA
2555970 TCTAAATGTATCGATACATT
1 TCTAAATGTATCGATACATT
2555990 TCTAGAATGTATCGATACA
1 TCTA-AATGTATCGATACA
2556009 AGGTTCCAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (20 bp):
TCTAAATGTATCGATACATT
Found at i:2556072 original size:21 final size:19
Alignment explanation
Indices: 2556048--2556099 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
2556038 CAACAATTTA
2556048 TATCGATACAAACAGTAAATG
1 TATCGATACAAA-AGT-AATG
* **
2556069 TATCGATACATAAGTGTTG
1 TATCGATACAAAAGTAATG
2556088 TATCGATACAAA
1 TATCGATACAAA
2556100 GCTACCCTGC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 13 0.48
20 3 0.11
21 11 0.41
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.29
Consensus pattern (19 bp):
TATCGATACAAAAGTAATG
Found at i:2559675 original size:16 final size:15
Alignment explanation
Indices: 2559654--2559687 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
2559644 ATACCTAAAG
2559654 TTCTTTTTTTTTCTCT
1 TTCTTTTTTTTT-TCT
2559670 TTCTTTTTTTTTTCT
1 TTCTTTTTTTTTTCT
2559685 TTC
1 TTC
2559688 ATTCTTATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (15 bp):
TTCTTTTTTTTTTCT
Found at i:2559678 original size:15 final size:15
Alignment explanation
Indices: 2559658--2559687 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2559648 CTAAAGTTCT
2559658 TTTTTTTTCTCTTTC
1 TTTTTTTTCTCTTTC
*
2559673 TTTTTTTTTTCTTTC
1 TTTTTTTTCTCTTTC
2559688 ATTCTTATTG
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:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTTTTCTCTTTC
Found at i:2560543 original size:19 final size:19
Alignment explanation
Indices: 2560514--2560560 Score: 85
Period size: 19 Copynumber: 2.4 Consensus size: 19
2560504 AACAATCTCT
2560514 ATACATATAACCCTTGGTTA
1 ATAC-TATAACCCTTGGTTA
2560534 ATACTATAACCCTTGGTTA
1 ATACTATAACCCTTGGTTA
2560553 ATACTATA
1 ATACTATA
2560561 TACAATAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 23 0.85
20 4 0.15
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (19 bp):
ATACTATAACCCTTGGTTA
Found at i:2561031 original size:20 final size:20
Alignment explanation
Indices: 2561006--2561044 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2560996 ATTATAAAAA
2561006 GATTTTAATATTAAATATAT
1 GATTTTAATATTAAATATAT
*
2561026 GATTTTAGTATTAAATATA
1 GATTTTAATATTAAATATA
2561045 ATAAATATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.49
Consensus pattern (20 bp):
GATTTTAATATTAAATATAT
Found at i:2562185 original size:2 final size:2
Alignment explanation
Indices: 2562178--2562220 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
2562168 TGCTACTTTC
* *
2562178 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2562220 T
1 T
2562221 TATTAAATTA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2571325 original size:39 final size:42
Alignment explanation
Indices: 2571282--2571364 Score: 127
Period size: 42 Copynumber: 2.0 Consensus size: 42
2571272 TTCAAGGATG
**
2571282 GGTTCAGAAGGTTTAGA-G-G-TTTCTACAAGGGGTTCAAAA
1 GGTTCAGAAGGTTTAGATGTGAGCTCTACAAGGGGTTCAAAA
2571321 GGTTCAGAAGGTTTAGATGTGAGCTCTACAAGGGGTTCAAAA
1 GGTTCAGAAGGTTTAGATGTGAGCTCTACAAGGGGTTCAAAA
2571363 GG
1 GG
2571365 GTCAAGGGTG
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
39 17 0.44
40 1 0.03
41 1 0.03
42 20 0.51
ACGTcount: A:0.30, C:0.11, G:0.33, T:0.27
Consensus pattern (42 bp):
GGTTCAGAAGGTTTAGATGTGAGCTCTACAAGGGGTTCAAAA
Found at i:2573230 original size:26 final size:26
Alignment explanation
Indices: 2573191--2573240 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
2573181 CTCTAATACC
* *
2573191 ATGTTGAAAGAAAATAAGAGATTGAA
1 ATGTTGAAAGAAAAGAAGAAATTGAA
*
2573217 ATGTTGAAATAAAAGAAGAAATTG
1 ATGTTGAAAGAAAAGAAGAAATTG
2573241 TATTTATTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.54, C:0.00, G:0.22, T:0.24
Consensus pattern (26 bp):
ATGTTGAAAGAAAAGAAGAAATTGAA
Found at i:2586183 original size:45 final size:45
Alignment explanation
Indices: 2586133--2586228 Score: 108
Period size: 45 Copynumber: 2.1 Consensus size: 45
2586123 TTATTTATAT
2586133 TTAATT-TATAAATAAAT-ATTTAAACAATAT-TATTTATATATTAAA
1 TTAATTATATAAATAAATAATTT-AACAATATCTATTTA-AT-TTAAA
* * * *
2586178 TTAATTATGTAAATAATTAATTTACCCATATCTATTTAATTTAAA
1 TTAATTATATAAATAAATAATTTAACAATATCTATTTAATTTAAA
2586223 TTAATT
1 TTAATT
2586229 CTTATATTTG
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
45 17 0.39
46 17 0.39
47 10 0.23
ACGTcount: A:0.46, C:0.05, G:0.01, T:0.48
Consensus pattern (45 bp):
TTAATTATATAAATAAATAATTTAACAATATCTATTTAATTTAAA
Found at i:2587362 original size:31 final size:31
Alignment explanation
Indices: 2587324--2587386 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
2587314 TCTTTCTTCA
2587324 TATAAAATCCATTATATGCAACATTCTAAGG
1 TATAAAATCCATTATATGCAACATTCTAAGG
*
2587355 TATAAAATCCGTTATATGCAACATTCTAAGG
1 TATAAAATCCATTATATGCAACATTCTAAGG
2587386 T
1 T
2587387 CTAAGCATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (31 bp):
TATAAAATCCATTATATGCAACATTCTAAGG
Found at i:2587947 original size:21 final size:21
Alignment explanation
Indices: 2587921--2587997 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
2587911 AAATTATCCA
2587921 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
2587942 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
* * *
2587963 AATGTATTGATACA-TTCTACA
1 AATGTATCGATACATTTGTA-G
2587984 AATGTATCGATACA
1 AATGTATCGATACA
2587998 GGGTCCCAAC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
20 3 0.06
21 46 0.94
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:2588126 original size:13 final size:13
Alignment explanation
Indices: 2588108--2588133 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2588098 CATTTTTCTG
2588108 TGTATCGATACAT
1 TGTATCGATACAT
2588121 TGTATCGATACAT
1 TGTATCGATACAT
2588134 CTTTTCTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2588130 original size:33 final size:34
Alignment explanation
Indices: 2588088--2588154 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
2588078 GCCAAGGGAA
2588088 TGTATCGATACAT-TTTTCTGTGTATCGATACAT
1 TGTATCGATACATCTTTTCTGTGTATCGATACAT
*
2588121 TGTATCGATACATCTTTTCTTTGTATCGATACAT
1 TGTATCGATACATCTTTTCTGTGTATCGATACAT
2588155 CTAGGAAGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 13 0.41
34 19 0.59
ACGTcount: A:0.24, C:0.16, G:0.13, T:0.46
Consensus pattern (34 bp):
TGTATCGATACATCTTTTCTGTGTATCGATACAT
Found at i:2590567 original size:51 final size:52
Alignment explanation
Indices: 2590497--2590620 Score: 153
Period size: 51 Copynumber: 2.4 Consensus size: 52
2590487 CTCAATTCTC
** * * * *
2590497 CACAATCGGGGATATTCCAACTCTGATTTTATTTTC-AAAACACTAA-TTTT
1 CACAATCAAGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTT
*
2590547 CTATAATCAAGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTT
1 C-ACAATCAAGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTT
*
2590600 CACAATTAAGGATACTCCAAC
1 CACAATCAAGGATACTCCAAC
2590621 CTCGTTATTT
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
50 1 0.02
51 29 0.47
52 27 0.44
53 5 0.08
ACGTcount: A:0.35, C:0.23, G:0.08, T:0.33
Consensus pattern (52 bp):
CACAATCAAGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTT
Found at i:2590611 original size:52 final size:51
Alignment explanation
Indices: 2590506--2590620 Score: 151
Period size: 52 Copynumber: 2.2 Consensus size: 51
2590496 CCACAATCGG
* * * * *
2590506 GGATATTCCAACTCTGATTTTATTTTCAAAACACTAATTTTCTATAATCAA
1 GGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTCTACAATCAA
*
2590557 GGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTT-TCACAATTAA
1 GGATACTCCAACTCCGATTTTATTTCC-AAAACACCAATTTTCT-ACAATCAA
2590609 GGATACTCCAAC
1 GGATACTCCAAC
2590621 CTCGTTATTT
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
51 25 0.45
52 31 0.55
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.35
Consensus pattern (51 bp):
GGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTCTACAATCAA
Found at i:2591755 original size:20 final size:20
Alignment explanation
Indices: 2591730--2591781 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
2591720 TACAAGCCAA
** *
2591730 TGTATCGATACAATTTTTTG
1 TGTATCGATACAATACTTGG
2591750 TGTATCGATAC-ATACTTGG
1 TGTATCGATACAATACTTGG
2591769 TGTATCGATACAA
1 TGTATCGATACAA
2591782 GTTTGGCTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.40
Consensus pattern (20 bp):
TGTATCGATACAATACTTGG
Found at i:2591787 original size:19 final size:18
Alignment explanation
Indices: 2591730--2591787 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 18
2591720 TACAAGCCAA
*
2591730 TGTATCGATACAATTTTTTG
1 TGTATCGATACAA--TTTGG
*
2591750 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
2591769 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
2591788 CTACTGCCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
18 1 0.03
19 19 0.58
20 12 0.36
21 1 0.03
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.41
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:2591827 original size:21 final size:21
Alignment explanation
Indices: 2591801--2591854 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
2591791 CTGCCAAGAA
2591801 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
2591822 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
2591843 ATGTATCGATAC
1 ATGTATCGATAC
2591855 TTTGAATTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.11, T:0.44
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:2594331 original size:13 final size:13
Alignment explanation
Indices: 2594313--2594350 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
2594303 ATAATCACCC
2594313 TGTATCGATACAG
1 TGTATCGATACAG
*
2594326 TGTATCGATACAT
1 TGTATCGATACAG
2594339 TGTATCGATACA
1 TGTATCGATACA
2594351 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:2600534 original size:13 final size:13
Alignment explanation
Indices: 2600516--2600541 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2600506 CAATTTTTTG
2600516 TGTATCGATACAT
1 TGTATCGATACAT
2600529 TGTATCGATACAT
1 TGTATCGATACAT
2600542 ACTTGTTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2600628 original size:20 final size:19
Alignment explanation
Indices: 2600600--2600655 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 19
2600590 ACATCTTTTT
*
2600600 CATGCATCGATA-TATTGCAA
1 CATGTATCGATACT-TTG-AA
2600620 CATGTATCGATACTTTGAA
1 CATGTATCGATACTTTGAA
2600639 CTATGTATCGATACTTT
1 C-ATGTATCGATACTTT
2600656 TAAGGGTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
19 3 0.09
20 29 0.88
21 1 0.03
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (19 bp):
CATGTATCGATACTTTGAA
Found at i:2614434 original size:27 final size:27
Alignment explanation
Indices: 2614404--2614486 Score: 62
Period size: 27 Copynumber: 3.0 Consensus size: 27
2614394 TTGGTGGCAT
2614404 TTTCCAGTCCTCAAAGAGCAGGACACC
1 TTTCCAGTCCTCAAAGAGCAGGACACC
* * * * ** *
2614431 TTTCAAAGGCCACACAAGTTGGTGG-CA-T
1 TTTC-CAGTCCTCA-AAG-AGCAGGACACC
2614459 TTTCCAGTCCTCAAAGAGCAGGACACC
1 TTTCCAGTCCTCAAAGAGCAGGACACC
2614486 T
1 T
2614487 CTTAAAGCCC
Statistics
Matches: 37, Mismatches: 14, Indels: 10
0.61 0.23 0.16
Matches are distributed among these distances:
25 3 0.08
26 5 0.14
27 11 0.30
28 10 0.27
29 5 0.14
30 3 0.08
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (27 bp):
TTTCCAGTCCTCAAAGAGCAGGACACC
Found at i:2614592 original size:55 final size:55
Alignment explanation
Indices: 2614200--2614591 Score: 470
Period size: 55 Copynumber: 7.0 Consensus size: 55
2614190 GATGCCTTTT
* * *
2614200 CCTTTTAAAGCCCACACAAGTTGGTGGCAC-CTTCAGTCCTCAAAGAGCGGGACG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACG
* * *
2614254 CCTTTTCTTTTAAAGCCCACCCAAGTTGGTGGCACCTTT-AGTCCTCAAAGAGCAGGATG
1 CC-TTTC----AAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACG
* * *
2614313 CTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACC
1 C-----C-TTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACG
* *
2614374 CCTTTCGAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGACG
* *
2614429 CCTTTCAAAGGCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGACG
* *
2614484 CCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGATG
1 CCT-TTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACG
* *
2614539 CCTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAGGA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGA
2614592 TACACTTTAT
Statistics
Matches: 300, Mismatches: 22, Indels: 31
0.85 0.06 0.09
Matches are distributed among these distances:
54 7 0.02
55 192 0.64
56 6 0.02
59 42 0.14
60 29 0.10
61 18 0.06
64 6 0.02
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (55 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACG
Found at i:2615346 original size:21 final size:21
Alignment explanation
Indices: 2615320--2615396 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
2615310 AAATTATCCA
2615320 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
2615341 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
* *
2615362 AATGTATCGATACA-TTCTACA
1 AATGTATCGATACATTTGTA-G
2615383 AATGTATCGATACA
1 AATGTATCGATACA
2615397 GGGTCCCAAC
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 3 0.06
21 48 0.94
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:2617963 original size:51 final size:51
Alignment explanation
Indices: 2617864--2617986 Score: 142
Period size: 51 Copynumber: 2.4 Consensus size: 51
2617854 CTCAATTCTC
* * **
2617864 CACAATCGGGGATATTCCAACTCCAATTTTATTTTCAAAACAGTAA-TTTT
1 CACAATCGGGGATACTCCAACTCCAATTTTATTTCCAAAACAACAATTTTT
* *
2617914 CTATAATCGGGGATACTCCAACTCCGA-TTTATTTCCAAAAACAACAATTTTT
1 C-ACAATCGGGGATACTCCAACTCCAATTTTATTTCC-AAAACAACAATTTTT
* *
2617966 CACAATTGAGGATACTCCAAC
1 CACAATCGGGGATACTCCAAC
2617987 CTCATTATTT
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
50 9 0.15
51 47 0.77
52 5 0.08
ACGTcount: A:0.35, C:0.23, G:0.11, T:0.32
Consensus pattern (51 bp):
CACAATCGGGGATACTCCAACTCCAATTTTATTTCCAAAACAACAATTTTT
Found at i:2618146 original size:79 final size:79
Alignment explanation
Indices: 2618002--2618204 Score: 223
Period size: 79 Copynumber: 2.6 Consensus size: 79
2617992 TATTTCATCG
** *
2618002 GGGATACTCCAACCCCGTTACCTCCGAGGGAATACTCCAACCCCGGCTTTATTCCCAAAATATCG
1 GGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATATCG
* **
2618067 ATTTCTCATAATTA
66 ATTTCTCACAACCA
** *
2618081 GGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGATG-TTT-TTTTC-TAATCA
1 GGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCG--GCTTTATTCCCAAAAT-A
*
2618143 TCGATTTCTCACAACCG
63 TCGATTTCTCACAACCA
* * * * *
2618160 GGGATACTCCAGCCCCGTCATTTTCAAGGGGACACTCCAACCCCG
1 GGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCG
2618205 TTATTATCTC
Statistics
Matches: 106, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
78 3 0.03
79 99 0.93
80 3 0.03
81 1 0.01
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.26
Consensus pattern (79 bp):
GGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATATCG
ATTTCTCACAACCA
Found at i:2621804 original size:78 final size:78
Alignment explanation
Indices: 2621718--2622196 Score: 290
Period size: 78 Copynumber: 6.2 Consensus size: 78
2621708 TTTTCATCTT
* *
2621718 AGGGGATACTCCAACCTTGCTTTATTTCCAAAATATTAAAATTTTCATTTTGAGGATACTCCAAC
1 AGGGGATACTCCAACCATGCTTTATTTCCAAAATATTAAAATTTTCATCTTGAGGATACTCCAAC
** *
2621783 CTTA-CTATTTTTG
66 CCCATC-AATTTTG
* * * * * *
2621796 AGGGGATACTGCAATCCCAT--TTTATTTTCAAACTTTTAAAATTTCCATCTTGGGGATACTCCA
1 AGGGGATACTCCAA--CCATGCTTTATTTCCAAAATATTAAAATTTTCATCTTGAGGATACTCCA
*
2621859 ACCCCATCAATTTCG
64 ACCCCATCAATTTTG
* * ** * * *
2621874 AGAGGATACTCCAACCAAGCTTTTATTTCCAAAATGCTAAATTTTTCATCTT-AAGATACTTCAA
1 AGGGGATACTCCAACCATGC-TTTATTTCCAAAATATTAAAATTTTCATCTTGAGGATACTCCAA
*
2621938 CCCCATCAATTCTG
65 CCCCATCAATTTTG
* * * * * **
2621952 AGGGGATACTCCAACTC-TGTTTTATTTCCAAAATATT-AAATTTT--TCTCGGGGGTATTTTAA
1 AGGGGATACTCCAAC-CATGCTTTATTTCCAAAATATTAAAATTTTCATCTTGAGGATACTCCAA
* * *
2622013 CCCCGT-TATTTTCA
65 CCCCATCAATTTT-G
* ** * * * * *
2622027 AGGGGATACTCTC-GCCCCGTTTTGATTTCCAAAAATATT-GATTTTTCATC-TCAGGATACTTC
1 AGGGGATACTC-CAACCATGCTTT-ATTTCC-AAAATATTAAAATTTTCATCTTGAGGATACTCC
* ** *
2622089 TACCCTGT-TATTTTCG
63 AACCCCATCAATTTT-G
* * * * *
2622105 AAGGGATACTCCAACCCTAT-TTTTATTTCAAAAATATTAAATTTTTCATC-TCAGGATACTCCA
1 AGGGGATACTCCAA-CC-ATGCTTTATTTCCAAAATATTAAAATTTTCATCTTGAGGATACTCCA
*
2622168 ACCCCAT--ATTTCG
64 ACCCCATCAATTTTG
*
2622181 AGGGGACACTCCAACC
1 AGGGGATACTCCAACC
2622197 TTGCCTCTTT
Statistics
Matches: 314, Mismatches: 68, Indels: 41
0.74 0.16 0.10
Matches are distributed among these distances:
74 8 0.03
75 31 0.10
76 29 0.09
77 41 0.13
78 167 0.53
79 35 0.11
80 3 0.01
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.36
Consensus pattern (78 bp):
AGGGGATACTCCAACCATGCTTTATTTCCAAAATATTAAAATTTTCATCTTGAGGATACTCCAAC
CCCATCAATTTTG
Found at i:2625035 original size:19 final size:20
Alignment explanation
Indices: 2624990--2625041 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
2624980 TTACAAGCCA
**
2624990 ATGTATCGATACATTTTATG
1 ATGTATCGATACATACTATG
*
2625010 ATGTATCGATACATACTGTG
1 ATGTATCGATACATACTATG
2625030 -TGTATCGATACA
1 ATGTATCGATACA
2625042 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATACTATG
Found at i:2625132 original size:13 final size:13
Alignment explanation
Indices: 2625114--2625142 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
2625104 ACATTTGGTC
2625114 ATGTATCGATACA
1 ATGTATCGATACA
2625127 ATGTATCGATACA
1 ATGTATCGATACA
2625140 ATG
1 ATG
2625143 CAATCTGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2628918 original size:13 final size:13
Alignment explanation
Indices: 2628900--2628924 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2628890 CATTATGCTT
2628900 TGTATCGATACAA
1 TGTATCGATACAA
2628913 TGTATCGATACA
1 TGTATCGATACA
2628925 TGTTCATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2630599 original size:3 final size:3
Alignment explanation
Indices: 2630584--2630624 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
2630574 AACCGTCAAA
* *
2630584 GAT GAT GAA GAT GAT GAT GAT GAT GAT GAT GAT AAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
2630625 AGTTGACTCG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.39, C:0.00, G:0.32, T:0.29
Consensus pattern (3 bp):
GAT
Found at i:2636384 original size:27 final size:28
Alignment explanation
Indices: 2636313--2636373 Score: 106
Period size: 28 Copynumber: 2.2 Consensus size: 28
2636303 TTTTTGAAAA
*
2636313 TAAATTTTGGTATTTGACAAAGGGGGAG
1 TAAATTTTGGTATTTGACAAAGGGAGAG
2636341 TAAATTTTGGTATTTGACAAAGGGAGAG
1 TAAATTTTGGTATTTGACAAAGGGAGAG
2636369 -AAATT
1 TAAATT
2636374 ATTTTTTTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 5 0.16
28 27 0.84
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.33
Consensus pattern (28 bp):
TAAATTTTGGTATTTGACAAAGGGAGAG
Found at i:2637068 original size:13 final size:14
Alignment explanation
Indices: 2637037--2637074 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
2637027 ACCCTAGAAA
*
2637037 GTATCGATACACTT
1 GTATCGATACACAT
2637051 GTATCGATACA-AT
1 GTATCGATACACAT
*
2637064 GTATCGGTACA
1 GTATCGATACA
2637075 TTATGCTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (14 bp):
GTATCGATACACAT
Found at i:2637159 original size:13 final size:13
Alignment explanation
Indices: 2637141--2637167 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2637131 GATACATGGG
2637141 ACATTGTATCGAT
1 ACATTGTATCGAT
2637154 ACATTGTATCGAT
1 ACATTGTATCGAT
2637167 A
1 A
2637168 TATGGTGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (13 bp):
ACATTGTATCGAT
Found at i:2643755 original size:21 final size:20
Alignment explanation
Indices: 2643729--2643781 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
2643719 TTCTATAATT
2643729 TGTATCGATACAAATAGTGAA
1 TGTATCGATACAAA-AGTGAA
* *
2643750 TGTATCGAAACATAAGTGAA
1 TGTATCGATACAAAAGTGAA
2643770 TGTATCGATACA
1 TGTATCGATACA
2643782 TGTCTGAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.42, C:0.11, G:0.19, T:0.28
Consensus pattern (20 bp):
TGTATCGATACAAAAGTGAA
Found at i:2643769 original size:20 final size:21
Alignment explanation
Indices: 2643729--2643802 Score: 89
Period size: 21 Copynumber: 3.6 Consensus size: 21
2643719 TTCTATAATT
*
2643729 TGTATCGATACAAATAGTGAA
1 TGTATCGATACATATAGTGAA
*
2643750 TGTATCGAAACATA-AGTGAA
1 TGTATCGATACATATAGTGAA
* *
2643770 TGTATCGATACATGT-CTGAAA
1 TGTATCGATACATATAGTG-AA
2643791 TGTATCGATACA
1 TGTATCGATACA
2643803 GGACTATGTT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
20 20 0.43
21 26 0.57
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30
Consensus pattern (21 bp):
TGTATCGATACATATAGTGAA
Found at i:2643908 original size:51 final size:52
Alignment explanation
Indices: 2643839--2643977 Score: 208
Period size: 51 Copynumber: 2.7 Consensus size: 52
2643829 TCCGGAAAGA
* * * *
2643839 AAATGTATCAATACATTTTTCATTGTATCGATATATTTTGGGTTTTTG-CCC
1 AAATGTATCGATACATTTTTCATTGTATCGATACATTCTAGGTTTTTGACCC
* *
2643890 AAATATATCGATACATTTTTCATTGTATTGATACATTCTAGGTTTTTGACCC
1 AAATGTATCGATACATTTTTCATTGTATCGATACATTCTAGGTTTTTGACCC
*
2643942 AAATGTATCGATACATTTTTCAATGTATCGATACAT
1 AAATGTATCGATACATTTTTCATTGTATCGATACAT
2643978 GTAGGCTCTT
Statistics
Matches: 78, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
51 42 0.54
52 36 0.46
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.44
Consensus pattern (52 bp):
AAATGTATCGATACATTTTTCATTGTATCGATACATTCTAGGTTTTTGACCC
Found at i:2646454 original size:79 final size:79
Alignment explanation
Indices: 2646323--2646499 Score: 264
Period size: 79 Copynumber: 2.2 Consensus size: 79
2646313 ACCATTAAGG
* * * * *
2646323 ATACTCCAACCCCATTTTTATTTTCAAATTATCGATTTTTCATCATCAGGGATACTCCAACCCCA
1 ATACTCCAACCTCGTTTTTATTTCCAAAATATCGATTTTTCACCATCAGGGATACTCCAACCCCA
*
2646388 TCATTTCTGAGGGA
66 TCATTTCCGAGGGA
* *
2646402 ATACTCCAACATCGTTTTTATTTCCAAAATATCGATTTTTCACCATTAGGGATACTCCAACCCCA
1 ATACTCCAACCTCGTTTTTATTTCCAAAATATCGATTTTTCACCATCAGGGATACTCCAACCCCA
*
2646467 TCATTTCCGAGGGG
66 TCATTTCCGAGGGA
*
2646481 ATACTCCAACCTCGCTTTT
1 ATACTCCAACCTCGTTTTT
2646500 CAACCCAAAG
Statistics
Matches: 87, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
79 87 1.00
ACGTcount: A:0.27, C:0.28, G:0.11, T:0.34
Consensus pattern (79 bp):
ATACTCCAACCTCGTTTTTATTTCCAAAATATCGATTTTTCACCATCAGGGATACTCCAACCCCA
TCATTTCCGAGGGA
Found at i:2650345 original size:428 final size:428
Alignment explanation
Indices: 2649537--2650396 Score: 1418
Period size: 428 Copynumber: 2.0 Consensus size: 428
2649527 CTACCACTTA
** *
2649537 TGGGATTATAGGGAGGCACTTTTTACGTGCCACTGCTCATATTGCGTCAGCTTCAATGTCAGCAA
1 TGGGATTATAGGGAGGCACTTGCTACGTGCCACTACTCATATTGCGTCAGCTTCAATGTCAGCAA
* * * *
2649602 TTCACTCCATTCTTTGAAAACCTTAAGCATTAGGACTTTGAATATGGAGTAGCTAATTACAAAGT
66 TTCACTCCATTCTTTGAAAACCTCAAGCATTAGGACTTTAAATATGGAGAAGCTAATTACAAAGC
**
2649667 AAAAGTCCAATATGCTTTCCAAGCTTAGAAAAAAGTTCACTGTATGGAATGATATTGGAGAGGAA
131 AAAAGTCCAATATGCTTTCCAAGCTTAGAAAAAAGTTCACTGTATGGAACAATATTGGAGAGGAA
* * * *
2649732 GCTTTATGACTTCGGGGTATGAGGAATGGTGAATCCATCGCATCAACGATACTGTACCACCACCT
196 GCTCTATGACTTCGGGGTATGAGGAATGGCGAATCCATCGCATCAACAATACCGTACCACCACCT
2649797 AATTTTAGGACACTACAAATCCCAACAAAAGAGCCTCTTTTTGAAGCTGAACTACTTAGATGAGA
261 AATTTTAGGACACTACAAATCCCAACAAAAGAGCCTCTTTTTGAAGCTGAACTACTTAGATGAGA
*
2649862 ATTCAAGCAAGAAAGGGCATCGTACATCACAAAAATTGCTCGACTAAAAGAGGAAAAGGTCCAGT
326 ATTCAAGCAAAAAAGGGCATCGTACATCACAAAAATTGCTCGACTAAAAGAGGAAAAGGTCCAGT
*
2649927 TAGAGATACACATTTATCTTCGTGATGGTGAGATAAGT
391 TAGAGATACACATCTATCTTCGTGATGGTGAGATAAGT
* * *
2649965 TGGGATTATAGGGAGGCACTTGCTATGTGCCACTACTCGTATTGTGTCAGCTTCAATGTCAGCAA
1 TGGGATTATAGGGAGGCACTTGCTACGTGCCACTACTCATATTGCGTCAGCTTCAATGTCAGCAA
2650030 TTCACTCCATTCTTTGAAAACCTCAAGCATT-GGAACTTTAAATATGGAGAAGCTAATTACAAAG
66 TTCACTCCATTCTTTGAAAACCTCAAGCATTAGG-ACTTTAAATATGGAGAAGCTAATTACAAAG
*
2650094 CAAAAGTCCAATATGCTTTCCAAGCTTGGAAAAAAGTTCACTGTATGGAACAATATTGGAGAGGA
130 CAAAAGTCCAATATGCTTTCCAAGCTTAGAAAAAAGTTCACTGTATGGAACAATATTGGAGAGGA
* * * *
2650159 AGCTCTATGACTTTGGGGTATGAGGAATGGCGAATCCGTCGCATCAATAATACCGTGCCACCACC
195 AGCTCTATGACTTCGGGGTATGAGGAATGGCGAATCCATCGCATCAACAATACCGTACCACCACC
* *
2650224 TAATTTTGGGACACTACAAATCCCAACAAAAGAGCCTTTTTTTGAAGCTGAACTACTTAGATGAG
260 TAATTTTAGGACACTACAAATCCCAACAAAAGAGCCTCTTTTTGAAGCTGAACTACTTAGATGAG
* * * *
2650289 AATTCGAGTAAAAAAGGGCATCGTACATCACAAAAATTGC-CTGACTAGAGGAGGAAAAGGTCCA
325 AATTCAAGCAAAAAAGGGCATCGTACATCACAAAAATTGCTC-GACTAAAAGAGGAAAAGGTCCA
*
2650353 GTTAGAGATAGACATCTATCTTCGTGATGGTGAGATAAGT
389 GTTAGAGATACACATCTATCTTCGTGATGGTGAGATAAGT
2650393 TGGG
1 TGGG
2650397 TGGCTAAAGA
Statistics
Matches: 400, Mismatches: 30, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
427 3 0.01
428 397 0.99
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.27
Consensus pattern (428 bp):
TGGGATTATAGGGAGGCACTTGCTACGTGCCACTACTCATATTGCGTCAGCTTCAATGTCAGCAA
TTCACTCCATTCTTTGAAAACCTCAAGCATTAGGACTTTAAATATGGAGAAGCTAATTACAAAGC
AAAAGTCCAATATGCTTTCCAAGCTTAGAAAAAAGTTCACTGTATGGAACAATATTGGAGAGGAA
GCTCTATGACTTCGGGGTATGAGGAATGGCGAATCCATCGCATCAACAATACCGTACCACCACCT
AATTTTAGGACACTACAAATCCCAACAAAAGAGCCTCTTTTTGAAGCTGAACTACTTAGATGAGA
ATTCAAGCAAAAAAGGGCATCGTACATCACAAAAATTGCTCGACTAAAAGAGGAAAAGGTCCAGT
TAGAGATACACATCTATCTTCGTGATGGTGAGATAAGT
Found at i:2656882 original size:15 final size:15
Alignment explanation
Indices: 2656864--2656897 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
2656854 AAAATCATTT
2656864 AAAAAAAAGAAAAAG
1 AAAAAAAAGAAAAAG
*
2656879 AAAAAAGAGAAAAAG
1 AAAAAAAAGAAAAAG
2656894 AAAA
1 AAAA
2656898 GGGTCCAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAAAAAAGAAAAAG
Found at i:2658245 original size:28 final size:28
Alignment explanation
Indices: 2658210--2658927 Score: 555
Period size: 28 Copynumber: 25.3 Consensus size: 28
2658200 ATCTCTTTTC
*
2658210 AAAGCCCACAAGTCAGTGGCATCCTCTT
1 AAAGCCCACAAGTCAGTGGCACCCTCTT
* * * *
2658238 AAAGCCCAAAAGTCAGTGACACTCTCTC
1 AAAGCCCACAAGTCAGTGGCACCCTCTT
* * * * * *
2658266 GAAGCCCATAAGTCGGTGGCGTTCCCTATC
1 AAAGCCCACAAGTCAGTGGC--ACCCTCTT
*
2658296 AAAGCCCACAAGTCAGTGGCATCCT-TT
1 AAAGCCCACAAGTCAGTGGCACCCTCTT
* *
2658323 CAAAGCACACAAGTTAGTGGCACCCTCTT
1 -AAAGCCCACAAGTCAGTGGCACCCTCTT
* * * *
2658352 AGAGCCTATAAGTCAGTGGCACCCTCTC
1 AAAGCCCACAAGTCAGTGGCACCCTCTT
* ** * *
2658380 AAAGCCCACAAGTTAGTGGTGTCCCTATC
1 AAAGCCCACAAGTCAGTGG-CACCCTCTT
* *
2658409 AAAACCCACAAGTCAGTGGCACCCTCAT
1 AAAGCCCACAAGTCAGTGGCACCCTCTT
* * *
2658437 AAAGCCCATAAGTCAATGGCACCCTCTC
1 AAAGCCCACAAGTCAGTGGCACCCTCTT
* *
2658465 GAAGCCCACAAGTCGGTGGCATCCC-CTAT
1 AAAGCCCACAAGTCAGTGGCA-CCCTCT-T
* * * *
2658494 CAAAGCCCACAAGTTAATAGCACCCTTTT
1 -AAAGCCCACAAGTCAGTGGCACCCTCTT
*
2658523 AAAGCCCACAAGTTAGTGGCACCCTCTT
1 AAAGCCCACAAGTCAGTGGCACCCTCTT
* * * * *
2658551 AAAGCCCATAAATCAATGG-AACCTTTT
1 AAAGCCCACAAGTCAGTGGCACCCTCTT
* * * *
2658578 CGAAGCCCATAAGTCGGTGGCATCCTCTT
1 -AAAGCCCACAAGTCAGTGGCACCCTCTT
* * * *
2658607 AAAGCCCAAAAGTCAGTGACACTCTCTC
1 AAAGCCCACAAGTCAGTGGCACCCTCTT
* * * * * *
2658635 GAAGCCCATAAGTCGGTGGCGTTCCCTATC
1 AAAGCCCACAAGTCAGTGGC--ACCCTCTT
*
2658665 AAAGCCCACAAGTCAGTGGCATCCT-TT
1 AAAGCCCACAAGTCAGTGGCACCCTCTT
* *
2658692 CAAAGCACACAAGTTAGTGGCACCCTCTT
1 -AAAGCCCACAAGTCAGTGGCACCCTCTT
* * * *
2658721 AGAGCCTATAAGTCAGTGGCACCCTCTC
1 AAAGCCCACAAGTCAGTGGCACCCTCTT
* ** * *
2658749 AAAGCCCACAAGTTAGTGGTGTCCCTATC
1 AAAGCCCACAAGTCAGTGG-CACCCTCTT
* *
2658778 AAAACCCACAAGTCAGTGGCACCCTCAT
1 AAAGCCCACAAGTCAGTGGCACCCTCTT
* * *
2658806 AAAGCCCATAAGTCAATGGCACCCTCTC
1 AAAGCCCACAAGTCAGTGGCACCCTCTT
* * *
2658834 GAAGCCCACAAGTCGGTGGCGTCCC-CTAT
1 AAAGCCCACAAGTCAGTGGC-ACCCTCT-T
* * * *
2658863 CAAAGCCCACAAGTTAATAGCACCCTTTT
1 -AAAGCCCACAAGTCAGTGGCACCCTCTT
*
2658892 AAAGCCCACAAGTTAGTGGCACCCTCTT
1 AAAGCCCACAAGTCAGTGGCACCCTCTT
2658920 AAAGCCCA
1 AAAGCCCA
2658928 TAAATCAATC
Statistics
Matches: 534, Mismatches: 136, Indels: 40
0.75 0.19 0.06
Matches are distributed among these distances:
27 8 0.01
28 379 0.71
29 70 0.13
30 77 0.14
ACGTcount: A:0.30, C:0.32, G:0.18, T:0.21
Consensus pattern (28 bp):
AAAGCCCACAAGTCAGTGGCACCCTCTT
Done.