Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold198
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: 3915534
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 240068 characters in sequence are not A, C, G, or T
File 6 of 13
Found at i:1408485 original size:33 final size:33
Alignment explanation
Indices: 1408443--1408645 Score: 163
Period size: 33 Copynumber: 5.6 Consensus size: 33
1408433 AAAATATAGT
1408443 GGAATCAGCACTTAGCAACCACCAATGAATCGG
1 GGAATCAGCACTTAGCAACCACCAATGAATCGG
* *
1408476 GGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGG
1 GGAATCAGCACTTAGCAACCAC---CA-A--TGA-AT-CGG
* * *
1408517 TGGGATCAGCACTTAGCAACCACCAATGATTCAG
1 -GGAATCAGCACTTAGCAACCACCAATGAATCGG
* * *
1408551 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATATGG
1 GGAATCAGCACTTAGCAA-CCAC--CA-A--T-GAAT-CGG
1408592 TGGAATCAGCACTTAGCAACCACCAATGAATCGG
1 -GGAATCAGCACTTAGCAACCACCAATGAATCGG
*
1408626 GGAATCAACACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
1408646 CCTTGGGGGA
Statistics
Matches: 135, Mismatches: 17, Indels: 36
0.72 0.09 0.19
Matches are distributed among these distances:
33 57 0.42
34 7 0.05
35 4 0.03
36 7 0.05
37 2 0.01
38 2 0.01
39 7 0.05
40 4 0.03
41 7 0.05
42 38 0.28
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.20
Consensus pattern (33 bp):
GGAATCAGCACTTAGCAACCACCAATGAATCGG
Found at i:1408554 original size:75 final size:75
Alignment explanation
Indices: 1408362--1408649 Score: 432
Period size: 75 Copynumber: 3.8 Consensus size: 75
1408352 TATCCGTTAT
* * * *
1408362 TGGTGGATTCAACACTTAGCAACCACCAATGATTCGGGGAATCAAAACTTAGCAACCCCTTTTCA
1 TGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAACACTTAGCAACCCC-TTTCA
*
1408427 CATTCAAAAATA
65 CATT-TAAAATA
* *
1408439 TAGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTTCAC
1 TGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAACACTTAGCAACCCCTTTCAC
*
1408504 ATTTAAGATA
66 ATTTAAAATA
* * * * * *
1408514 CGGTGGGATCAGCACTTAGCAACCACCAATGATTCAGGGAATCAGCACTTAGCAACCCCCTTCAC
1 TGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAACACTTAGCAACCCCTTTCAC
1408579 ATTTAAAATA
66 ATTTAAAATA
1408589 TGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAACACTTAGCAACCCCTT
1 TGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAACACTTAGCAACCCCTT
1408650 GGGGGAAACT
Statistics
Matches: 190, Mismatches: 21, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
75 128 0.67
76 9 0.05
77 53 0.28
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.22
Consensus pattern (75 bp):
TGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAACACTTAGCAACCCCTTTCAC
ATTTAAAATA
Found at i:1412191 original size:20 final size:21
Alignment explanation
Indices: 1412168--1412223 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 21
1412158 GATACCAACT
* *
1412168 TAAAAATATCGATACT-TTTA
1 TAAAAATATCGATACTCATGA
* *
1412188 TAAAAATATTGGTACTCATGA
1 TAAAAATATCGATACTCATGA
1412209 -AAAAATATCGATACT
1 TAAAAATATCGATACT
1412224 GCTAGGGTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
20 27 0.93
21 2 0.07
ACGTcount: A:0.46, C:0.11, G:0.09, T:0.34
Consensus pattern (21 bp):
TAAAAATATCGATACTCATGA
Found at i:1423829 original size:16 final size:16
Alignment explanation
Indices: 1423810--1423847 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
1423800 GTTTTGTTCT
1423810 ATTATAACTCTATTCC
1 ATTATAACTCTATTCC
* *
1423826 ATTACAGCTCTATTCC
1 ATTATAACTCTATTCC
1423842 ATTATA
1 ATTATA
1423848 CTGAACCAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.32, C:0.24, G:0.03, T:0.42
Consensus pattern (16 bp):
ATTATAACTCTATTCC
Found at i:1427148 original size:43 final size:43
Alignment explanation
Indices: 1427101--1427188 Score: 133
Period size: 43 Copynumber: 2.0 Consensus size: 43
1427091 GTACACCTGT
*
1427101 TAGATCAGTTTACA-CACTCCTGTGAAAATGATAAATAGAGATC
1 TAGATCAGTTTA-ATCACTCCTGTGAAAATGATAAACAGAGATC
* *
1427144 TAGATCAGTTTAATCACTCCTGTTAAAATGATACACAGAGATC
1 TAGATCAGTTTAATCACTCCTGTGAAAATGATAAACAGAGATC
1427187 TA
1 TA
1427189 ACGTGAAATT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
42 1 0.02
43 40 0.98
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.30
Consensus pattern (43 bp):
TAGATCAGTTTAATCACTCCTGTGAAAATGATAAACAGAGATC
Found at i:1428310 original size:27 final size:26
Alignment explanation
Indices: 1428267--1428317 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
1428257 ACCACCAATA
*
1428267 TTTTTAATAAAATTTATTTTTTTATT
1 TTTTTAATAAAATTTATTTGTTTATT
1428293 TTTTTAA-AAATATATTATTTGTTTA
1 TTTTTAATAAA-AT-TTATTTGTTTA
1428318 GTGGTGCCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 3 0.14
26 9 0.41
27 10 0.45
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (26 bp):
TTTTTAATAAAATTTATTTGTTTATT
Found at i:1428692 original size:10 final size:11
Alignment explanation
Indices: 1428657--1428703 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
1428647 GTGTAGTTTG
*
1428657 TTTATTGTTAT
1 TTTAATGTTAT
* *
1428668 TTTTATGTTGTT
1 TTTAATGTT-AT
1428680 TTTAAT-TTAT
1 TTTAATGTTAT
1428690 TTTAATGTTAT
1 TTTAATGTTAT
1428701 TTT
1 TTT
1428704 GTTAGTTATT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
10 7 0.24
11 16 0.55
12 6 0.21
ACGTcount: A:0.19, C:0.00, G:0.09, T:0.72
Consensus pattern (11 bp):
TTTAATGTTAT
Found at i:1428724 original size:14 final size:15
Alignment explanation
Indices: 1428697--1428730 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1428687 TATTTTAATG
1428697 TTATTTTGTTAGTTA
1 TTATTTTGTTAGTTA
1428712 TTATTTT-TTAGTTA
1 TTATTTTGTTAGTTA
*
1428726 CTATT
1 TTATT
1428731 ATAAATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.21, C:0.03, G:0.09, T:0.68
Consensus pattern (15 bp):
TTATTTTGTTAGTTA
Found at i:1435453 original size:23 final size:23
Alignment explanation
Indices: 1435425--1435479 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
1435415 TGTTTTCTTT
* *
1435425 CTTTCTTTCTTCTTC-TTCTTTTC
1 CTTTCTTTCTTCTCCTTTC-TCTC
*
1435448 CTTTCTATCTTCTCCTTTCTCTC
1 CTTTCTTTCTTCTCCTTTCTCTC
1435471 CTTTCTTTC
1 CTTTCTTTC
1435480 CCTCTTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 24 0.89
24 3 0.11
ACGTcount: A:0.02, C:0.35, G:0.00, T:0.64
Consensus pattern (23 bp):
CTTTCTTTCTTCTCCTTTCTCTC
Found at i:1435478 original size:27 final size:26
Alignment explanation
Indices: 1435418--1435479 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
1435408 CTTTTTTTGT
* * *
1435418 TTTCTTTCTTTCTTTCTTCTTCTTCT
1 TTTCTTTCTATCTTTCCTCTTCTTCC
1435444 TTTCCTTTCTATCTTCTCCT-TTCTCTCC
1 TTT-CTTTCTATCTT-TCCTCTTCT-TCC
1435472 TTTCTTTC
1 TTTCTTTC
1435480 CCTCTTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
26 3 0.10
27 19 0.63
28 8 0.27
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (26 bp):
TTTCTTTCTATCTTTCCTCTTCTTCC
Found at i:1436469 original size:51 final size:51
Alignment explanation
Indices: 1436388--1436519 Score: 210
Period size: 51 Copynumber: 2.6 Consensus size: 51
1436378 TCTTGCACCA
* ** *
1436388 CTGAAATTATCTTCGTCTTTAGCCGGAAGGTTGCATTATTAAACTTTAATG
1 CTGAAATTATCTTCATCTTTAGCCAAAAGGTTGCATTATTAAACATTAATG
*
1436439 CTGAAATTATCTTCATCTTTTGCCAAAAGGTTGCATTATTAAACATTAATG
1 CTGAAATTATCTTCATCTTTAGCCAAAAGGTTGCATTATTAAACATTAATG
*
1436490 CTGAAATTATCTTTATCTTTAGCCAAAAGG
1 CTGAAATTATCTTCATCTTTAGCCAAAAGG
1436520 AAATTATAGT
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 74 1.00
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (51 bp):
CTGAAATTATCTTCATCTTTAGCCAAAAGGTTGCATTATTAAACATTAATG
Found at i:1447145 original size:13 final size:14
Alignment explanation
Indices: 1447127--1447155 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1447117 TTCTGGAGAC
1447127 AAATTTC-ATTTAA
1 AAATTTCAATTTAA
1447140 AAATTTCAATTTAA
1 AAATTTCAATTTAA
1447154 AA
1 AA
1447156 GTTTGAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (14 bp):
AAATTTCAATTTAA
Found at i:1448000 original size:43 final size:43
Alignment explanation
Indices: 1447939--1448025 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
1447929 GACTTGGGAA
*
1447939 AATGTTTGGGTGAGGGGGACCCAATGATGTAGTGGTGAATCAG
1 AATGTTTGGGTGAGGGGGACCCAATGATGCAGTGGTGAATCAG
1447982 AATGTTTGGGTGAGGGGGACCCAATGATGCAGTGGTGAATCAG
1 AATGTTTGGGTGAGGGGGACCCAATGATGCAGTGGTGAATCAG
1448025 A
1 A
1448026 CCCTTACTAG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.26, C:0.10, G:0.39, T:0.24
Consensus pattern (43 bp):
AATGTTTGGGTGAGGGGGACCCAATGATGCAGTGGTGAATCAG
Found at i:1454305 original size:39 final size:38
Alignment explanation
Indices: 1454189--1454305 Score: 126
Period size: 39 Copynumber: 3.0 Consensus size: 38
1454179 TTAAAACATG
* * * * *
1454189 TATTAAAGATGTCCTAAACTATGACATAATTAAAACCCT
1 TATTAATGATGTTC-AAATTATGACATAATTAAAACTCA
* * *
1454228 TATTAATGTTGTTTAGATTATGACATAATTAAAAACTCA
1 TATTAATGATGTTCAAATTATGACATAATT-AAAACTCA
*
1454267 TATTAATGATGTTCAAATTATAACATAATTAAAGACTCA
1 TATTAATGATGTTCAAATTATGACATAATTAAA-ACTCA
1454306 AACTAAATTA
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
38 17 0.27
39 47 0.73
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.36
Consensus pattern (38 bp):
TATTAATGATGTTCAAATTATGACATAATTAAAACTCA
Found at i:1456183 original size:18 final size:19
Alignment explanation
Indices: 1456162--1456217 Score: 69
Period size: 18 Copynumber: 2.9 Consensus size: 19
1456152 TTTCTTTCAA
1456162 TTTTTTTTCTCTCATTTC-
1 TTTTTTTTCTCTCATTTCT
*
1456180 TTTTTTATCTCTCAATTTCT
1 TTTTTTTTCTCTC-ATTTCT
*
1456200 TTTATTTTTCGCTCATTT
1 TTT-TTTTTCTCTCATTT
1456218 TCTCTTATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 12 0.38
19 5 0.16
20 7 0.22
21 8 0.25
ACGTcount: A:0.11, C:0.20, G:0.02, T:0.68
Consensus pattern (19 bp):
TTTTTTTTCTCTCATTTCT
Found at i:1457157 original size:13 final size:13
Alignment explanation
Indices: 1457139--1457168 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1457129 CAAAGTTGCT
*
1457139 AAATTTTTTTTTC
1 AAATTTTCTTTTC
1457152 AAATTTTCTTTTC
1 AAATTTTCTTTTC
1457165 AAAT
1 AAAT
1457169 ACAATCTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.10, G:0.00, T:0.60
Consensus pattern (13 bp):
AAATTTTCTTTTC
Found at i:1475007 original size:114 final size:112
Alignment explanation
Indices: 1474602--1475155 Score: 436
Period size: 115 Copynumber: 4.8 Consensus size: 112
1474592 TATGTTACAG
* * *
1474602 TTAGTGGCATTTAAGGGAAAACACCGCTAAAGCATAATATTAGCGGCG-TTTTGTGAGAAGCGCC
1 TTAGTGGC-GTTAAGGG-AAACGCCGCTAAAGCATACTATTAGCGGCGCTTTT-TGAGAAGCGCC
** *
1474666 GCAAAATAT-CTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATACAAGAA
63 GCAAAATATGC-TAACCAAAACGCAGAGTTTTTTCTTGAGGTATACTAGAA
** * **
1474716 TTAGTGGCGCAAAGGGAACACGCCGCT-AAGTCATACTATTAGCGACGCTTTCGGAGAAGCGCCG
1 TTAGTGGCGTTAAGGGAA-ACGCCGCTAAAG-CATACTATTAGCGGCGCTTTTTGAGAAGCGCCG
* * * * * *
1474780 CAATATTTGGC-AACCAAAATGCAGCGTTTTTTTGTCTTGATGTATAC-AGTTA
64 CAAAATAT-GCTAACCAAAACGCAGAG--TTTTT-TCTTGAGGTATACTAG-AA
** ** * * * **** *
1474832 TTAGTGGCGTATATTA-AAAAACATCGCTAAATCATAGTATTAGCGGCACTTGGAAAAAAGCGCC
1 TTAGTGGCGT-TA--AGGGAAACGCCGCTAAAGCATACTATTAGCGGCGCTTTTTGAGAAGCGCC
** * *
1474896 GCAAAATATGCCCACCAAAACGCAGAGTTTTTTCATGAGGTATATTAGAA
63 GCAAAATATGCTAACCAAAACGCAGAGTTTTTTCTTGAGGTATACTAGAA
* *
1474946 TTAGTGGCGCTTATGGGAGAACGCCGCTAAAGCATACTATTAGCGGCGCTTTTTGAGAAGCGCTG
1 TTAGTGGCG-TTAAGGGA-AACGCCGCTAAAGCATACTATTAGCGGCGCTTTTTGAGAAGCGCCG
* ** * * * * *
1475011 TAAAATATATTAACAAAAACGCAGTGTTTAATTCTTGATGTATACTGGAA
64 CAAAATATGCTAACCAAAACGCAGAGTTT-TTTCTTGAGGTATACTAGAA
* * * * *
1475061 TTAGTGGCGTCCACGAGAAATCGCCGCTAAAGCATAGTGTTAGCGGCGCTTTTTGAGAAGCGCCG
1 TTAGTGGCGT-TAAGGGAAA-CGCCGCTAAAGCATACTATTAGCGGCGCTTTTTGAGAAGCGCCG
* **
1475126 GAAAATATTTTAACCAAAACGCAGAGTTTT
64 CAAAATATGCTAACCAAAACGCAGAGTTTT
1475156 GGTCTTAACC
Statistics
Matches: 342, Mismatches: 77, Indels: 42
0.74 0.17 0.09
Matches are distributed among these distances:
112 5 0.01
113 57 0.17
114 93 0.27
115 108 0.32
116 24 0.07
117 50 0.15
118 4 0.01
119 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (112 bp):
TTAGTGGCGTTAAGGGAAACGCCGCTAAAGCATACTATTAGCGGCGCTTTTTGAGAAGCGCCGCA
AAATATGCTAACCAAAACGCAGAGTTTTTTCTTGAGGTATACTAGAA
Found at i:1475144 original size:229 final size:230
Alignment explanation
Indices: 1474619--1475156 Score: 575
Period size: 230 Copynumber: 2.3 Consensus size: 230
1474609 CATTTAAGGG
*
1474619 AAAACACCGCTAAAGCATAATATTAGCGGCG-TTTTGTGAGAAGCGCCGCAAAATATCTTAACCA
1 AAAACACCGCTAAAGCATAGTATTAGCGGCGCTTTT-TGAGAAGCGCCGCAAAATATCTTAACCA
* *
1474683 AAACGCAGAGTTTGGTCTTGAGGTATACAAGAATTAGTGGCGCAAAGGGAACACGCCGCTAAGTC
65 AAACGCAGAGTTTTGTCATGAGGTATACAAGAATTAGTGGCGCAAAGGGAACACGCCGCTAAGTC
* * * * * **
1474748 ATACTATTAGCGACGCTTTCGGAGAAGCGCCGCAATATTTGGCAACCAAAATGCAGCGTTTTTTT
130 ATACTATTAGCGACGCTTTCGGAGAAGCGCCGCAAAATATAGCAACAAAAACGCAGCGTTTTAAT
** * **
1474813 GTCTTGATGTATACAGTTATTAGTGGCGTATATTAA
195 GTCTTGATGTATACAGGAATTAGTGGCGTACACGAA
* * * **** * **
1474849 AAAACATCGCTAAATCATAGTATTAGCGGCACTTGGAAAAAAGCGCCGCAAAATATGC-CCACCA
1 AAAACACCGCTAAAGCATAGTATTAGCGGCGCTTTTTGAGAAGCGCCGCAAAATAT-CTTAACCA
* ** * *
1474913 AAACGCAGAGTTTTTTCATGAGGTATATTAGAATTAGTGGCGCTTATGGGAGA-ACGCCGCTAAA
65 AAACGCAGAGTTTTGTCATGAGGTATACAAGAATTAGTGGCGC-AAAGGGA-ACACGCCGCT-AA
* ** * * ** *
1474977 G-CATACTATTAGCGGCGCTTTTTGAGAAGCGCTGTAAAATATATTAACAAAAACGCAGTG-TTT
127 GTCATACTATTAGCGACGCTTTCGGAGAAGCGCCGCAAAATATAGCAACAAAAACGCAGCGTTTT
* * *
1475040 AAT-TCTTGATGTATACTGGAATTAGTGGCGTCCACGAG
192 AATGTCTTGATGTATACAGGAATTAGTGGCGTACACGAA
* * * * *
1475078 AAATCGCCGCTAAAGCATAGTGTTAGCGGCGCTTTTTGAGAAGCGCCGGAAAATATTTTAACCAA
1 AAAACACCGCTAAAGCATAGTATTAGCGGCGCTTTTTGAGAAGCGCCGCAAAATATCTTAACCAA
1475143 AACGCAGAGTTTTG
66 AACGCAGAGTTTTG
1475157 GTCTTAACCG
Statistics
Matches: 245, Mismatches: 57, Indels: 13
0.78 0.18 0.04
Matches are distributed among these distances:
229 89 0.36
230 90 0.37
231 62 0.25
232 4 0.02
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (230 bp):
AAAACACCGCTAAAGCATAGTATTAGCGGCGCTTTTTGAGAAGCGCCGCAAAATATCTTAACCAA
AACGCAGAGTTTTGTCATGAGGTATACAAGAATTAGTGGCGCAAAGGGAACACGCCGCTAAGTCA
TACTATTAGCGACGCTTTCGGAGAAGCGCCGCAAAATATAGCAACAAAAACGCAGCGTTTTAATG
TCTTGATGTATACAGGAATTAGTGGCGTACACGAA
Found at i:1475245 original size:21 final size:20
Alignment explanation
Indices: 1475221--1475259 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1475211 TTTGGTCTAT
*
1475221 GGTTTATGGTTTAAAGGTTGG
1 GGTTTAAGGTTT-AAGGTTGG
1475242 GGTTTAAGGTTTAAGGTT
1 GGTTTAAGGTTTAAGGTT
1475260 ATGTGTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.21, C:0.00, G:0.36, T:0.44
Consensus pattern (20 bp):
GGTTTAAGGTTTAAGGTTGG
Found at i:1475259 original size:14 final size:15
Alignment explanation
Indices: 1475250--1475304 Score: 51
Period size: 14 Copynumber: 3.8 Consensus size: 15
1475240 GGGGTTTAAG
*
1475250 GTTTAAGG-TTATGT
1 GTTTAAGGTTTATGA
*
1475264 GTTAAAGGTTTATGA
1 GTTTAAGGTTTATGA
* *
1475279 TTTTAGGGTTTATG-
1 GTTTAAGGTTTATGA
*
1475293 GTTTAAAGTTTA
1 GTTTAAGGTTTA
1475305 GATTAACTAG
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
14 16 0.50
15 16 0.50
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.49
Consensus pattern (15 bp):
GTTTAAGGTTTATGA
Found at i:1481075 original size:43 final size:43
Alignment explanation
Indices: 1480950--1481340 Score: 218
Period size: 42 Copynumber: 9.2 Consensus size: 43
1480940 AAAAATAGTG
** * *
1480950 GCGTTTTTATACAAAAGCGCCGCTAAAGTCCATGTTCTGTAGCG
1 GCGTTTTTATAC-AAAGCGCCGCTAAAGAACATGTTCTTTAGCA
* * * * ** **
1480994 GCGTTTGTAAAAAAAGTGCCGCTAAAGATTATACTCTTTAGCA
1 GCGTTTTTATACAAAGCGCCGCTAAAGAACATGTTCTTTAGCA
* * *
1481037 GCGTTTTTATACAAAGCGTCGTTAAAGAACATGTTCTTTAGCG
1 GCGTTTTTATACAAAGCGCCGCTAAAGAACATGTTCTTTAGCA
* * * * * * * *
1481080 GCG-CTTAATAAAAAACGCCACTAAAGATCATGTTCTTTCGCG
1 GCGTTTTTATACAAAGCGCCGCTAAAGAACATGTTCTTTAGCA
* * * * *
1481122 GCG--CTTATGAAAAAACGCCGCTAAAGAACATGTTCTTCAGCG
1 GCGTTTTTAT-ACAAAGCGCCGCTAAAGAACATGTTCTTTAGCA
* ** * * * * * * *
1481164 GCGCTTAGAAAAAAAACACCGCTAAAGACCATGTTCTTCAGCG
1 GCGTTTTTATACAAAGCGCCGCTAAAGAACATGTTCTTTAGCA
* ** * * * * **
1481207 GCGCTTAGATA-AAAACACCGCTAAAGACCATGTTCTTCAGTG
1 GCGTTTTTATACAAAGCGCCGCTAAAGAACATGTTCTTTAGCA
* * *
1481249 GCGTTTTTCT-CTAAGCGCCGCTAAAGAACATGTTCTTTAGCG
1 GCGTTTTTATACAAAGCGCCGCTAAAGAACATGTTCTTTAGCA
* * * * * *
1481291 GCGTTTTTCT-CTAAGCGCCACTAAAGAACATGATCTTTAACG
1 GCGTTTTTATACAAAGCGCCGCTAAAGAACATGTTCTTTAGCA
1481333 GCGTTTTT
1 GCGTTTTT
1481341 GGTTGTAAAA
Statistics
Matches: 285, Mismatches: 58, Indels: 10
0.81 0.16 0.03
Matches are distributed among these distances:
41 3 0.01
42 173 0.61
43 99 0.35
44 10 0.04
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (43 bp):
GCGTTTTTATACAAAGCGCCGCTAAAGAACATGTTCTTTAGCA
Found at i:1481112 original size:42 final size:43
Alignment explanation
Indices: 1481059--1481251 Score: 252
Period size: 42 Copynumber: 4.6 Consensus size: 43
1481049 AAAGCGTCGT
* * *
1481059 TAAAGAACATGTTCTTTAGCGGCGCTTA-ATAAAAAACGCCAC
1 TAAAGAACATGTTCTTCAGCGGCGCTTAGATAAAAAACACCGC
* *
1481101 TAAAGATCATGTTCTTTC-GCGGCGCTT--ATGAAAAAACGCCGC
1 TAAAGAACATGTTC-TTCAGCGGCGCTTAGAT-AAAAAACACCGC
*
1481143 TAAAGAACATGTTCTTCAGCGGCGCTTAGAAAAAAAACACCGC
1 TAAAGAACATGTTCTTCAGCGGCGCTTAGATAAAAAACACCGC
*
1481186 TAAAGACCATGTTCTTCAGCGGCGCTTAGAT-AAAAACACCGC
1 TAAAGAACATGTTCTTCAGCGGCGCTTAGATAAAAAACACCGC
* *
1481228 TAAAGACCATGTTCTTCAGTGGCG
1 TAAAGAACATGTTCTTCAGCGGCG
1481252 TTTTTCTCTA
Statistics
Matches: 137, Mismatches: 9, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
41 5 0.04
42 89 0.65
43 42 0.31
44 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (43 bp):
TAAAGAACATGTTCTTCAGCGGCGCTTAGATAAAAAACACCGC
Found at i:1481199 original size:127 final size:127
Alignment explanation
Indices: 1481059--1481293 Score: 312
Period size: 127 Copynumber: 1.9 Consensus size: 127
1481049 AAAGCGTCGT
* * *
1481059 TAAAGAACATGTTCTTTAGCGGCGCTTA-ATAAAAAACGCCACTAAAGATCATGTTCTTTC-GCG
1 TAAAGAACATGTTCTTCAGCGGCGCTTAGAT-AAAAACACCACTAAAGACCATGTTC-TTCAGCG
*
1481122 GCGCTTATGAAAAAACGCCGCTAAAGAACATGTTCTTCAGCGGCGCTTAGAAAAAAAACACCGC
64 GCGCTTATCAAAAAACGCCGCTAAAGAACATGTTCTTCAGCGGCGCTTAGAAAAAAAACACCGC
* * *
1481186 TAAAGACCATGTTCTTCAGCGGCGCTTAGATAAAAACACCGCTAAAGACCATGTTCTTCAGTGGC
1 TAAAGAACATGTTCTTCAGCGGCGCTTAGATAAAAACACCACTAAAGACCATGTTCTTCAGCGGC
* * *** * *
1481251 GTTTTTCTCTAAGCGCCGCTAAAGAACATGTTCTTTAGCGGCG
66 GCTTATCAAAAAACGCCGCTAAAGAACATGTTCTTCAGCGGCG
1481294 TTTTTCTCTA
Statistics
Matches: 92, Mismatches: 14, Indels: 4
0.84 0.13 0.04
Matches are distributed among these distances:
126 3 0.03
127 87 0.95
128 2 0.02
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.25
Consensus pattern (127 bp):
TAAAGAACATGTTCTTCAGCGGCGCTTAGATAAAAACACCACTAAAGACCATGTTCTTCAGCGGC
GCTTATCAAAAAACGCCGCTAAAGAACATGTTCTTCAGCGGCGCTTAGAAAAAAAACACCGC
Found at i:1481213 original size:85 final size:84
Alignment explanation
Indices: 1481059--1481251 Score: 273
Period size: 85 Copynumber: 2.3 Consensus size: 84
1481049 AAAGCGTCGT
* * * *
1481059 TAAAGAACATGTTCTTTAGCGGCGCTTAATAAAAAACGCCACTAAAGATCATGTTCTTTCGCGGC
1 TAAAGAACATGTTCTTCAGCGGCGCTTAAAAAAAAACACCACTAAAGACCATGTTCTTTCGCGGC
*
1481124 GCTTATGA-AAAAACGCCGC
66 GCTTA-GATAAAAACACCGC
*
1481143 TAAAGAACATGTTCTTCAGCGGCGCTTAGAAAAAAAACACCGCTAAAGACCATGTTC-TTCAGCG
1 TAAAGAACATGTTCTTCAGCGGCGCTTA-AAAAAAAACACCACTAAAGACCATGTTCTTTC-GCG
1481207 GCGCTTAGATAAAAACACCGC
64 GCGCTTAGATAAAAACACCGC
* *
1481228 TAAAGACCATGTTCTTCAGTGGCG
1 TAAAGAACATGTTCTTCAGCGGCG
1481252 TTTTTCTCTA
Statistics
Matches: 98, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
84 32 0.33
85 66 0.67
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (84 bp):
TAAAGAACATGTTCTTCAGCGGCGCTTAAAAAAAAACACCACTAAAGACCATGTTCTTTCGCGGC
GCTTAGATAAAAACACCGC
Found at i:1481968 original size:15 final size:14
Alignment explanation
Indices: 1481948--1481977 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
1481938 TCTTTTTTAT
1481948 GGTGAAATTGTAGAA
1 GGTGAAATTGT-GAA
1481963 GGTGAAATTGTGAA
1 GGTGAAATTGTGAA
1481977 G
1 G
1481978 TTGGAAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.37, C:0.00, G:0.37, T:0.27
Consensus pattern (14 bp):
GGTGAAATTGTGAA
Found at i:1485979 original size:22 final size:24
Alignment explanation
Indices: 1485954--1486000 Score: 80
Period size: 22 Copynumber: 2.0 Consensus size: 24
1485944 CATATTTGCG
1485954 TATAATAACTA-TTTAACA-AAAA
1 TATAATAACTATTTTAACATAAAA
1485976 TATAATAACTATTTTAACATAAAA
1 TATAATAACTATTTTAACATAAAA
1486000 T
1 T
1486001 TTTAATGTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 11 0.48
23 7 0.30
24 5 0.22
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (24 bp):
TATAATAACTATTTTAACATAAAA
Found at i:1486392 original size:14 final size:15
Alignment explanation
Indices: 1486373--1486414 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
1486363 ATACAACTCT
*
1486373 TCTTCTTCTT-TTTC
1 TCTTCTTCTTCTTCC
1486387 TCTTC-TCTTCTTCC
1 TCTTCTTCTTCTTCC
*
1486401 TCTTCTTCTACTTC
1 TCTTCTTCTTCTTC
1486415 AAAATTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.17
14 13 0.54
15 7 0.29
ACGTcount: A:0.02, C:0.36, G:0.00, T:0.62
Consensus pattern (15 bp):
TCTTCTTCTTCTTCC
Found at i:1486394 original size:22 final size:23
Alignment explanation
Indices: 1486369--1486414 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
1486359 ATAAATACAA
* *
1486369 CTCTTCTTCTTCTTTTTCT-CTT
1 CTCTTCTTCCTCTTCTTCTACTT
1486391 CTCTTCTTCCTCTTCTTCTACTT
1 CTCTTCTTCCTCTTCTTCTACTT
1486414 C
1 C
1486415 AAAATTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.02, C:0.37, G:0.00, T:0.61
Consensus pattern (23 bp):
CTCTTCTTCCTCTTCTTCTACTT
Found at i:1486920 original size:36 final size:35
Alignment explanation
Indices: 1486848--1486921 Score: 96
Period size: 36 Copynumber: 2.1 Consensus size: 35
1486838 TGATTTAATG
*
1486848 AAAATTTTATTTTACAAAATAAATGTACATAATTCA
1 AAAATTATATTTTACAAAATAAATGTACAT-ATTCA
*
1486884 AAAATTATATTTTACAAAATATAATTTTACAT-TTCA
1 AAAATTATATTTTACAAAATA-AA-TGTACATATTCA
1486920 AA
1 AA
1486922 CATTCTAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 26 0.76
37 2 0.06
38 6 0.18
ACGTcount: A:0.50, C:0.08, G:0.01, T:0.41
Consensus pattern (35 bp):
AAAATTATATTTTACAAAATAAATGTACATATTCA
Found at i:1487366 original size:17 final size:17
Alignment explanation
Indices: 1487344--1487393 Score: 91
Period size: 17 Copynumber: 2.9 Consensus size: 17
1487334 ATAGAAAGTC
1487344 AAAGATATGGGTATCAG
1 AAAGATATGGGTATCAG
*
1487361 AAAGATATAGGTATCAG
1 AAAGATATGGGTATCAG
1487378 AAAGATATGGGTATCA
1 AAAGATATGGGTATCA
1487394 AAATCTGAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.44, C:0.06, G:0.26, T:0.24
Consensus pattern (17 bp):
AAAGATATGGGTATCAG
Found at i:1488614 original size:44 final size:44
Alignment explanation
Indices: 1488551--1488640 Score: 144
Period size: 44 Copynumber: 2.0 Consensus size: 44
1488541 TATAATTTTA
* *
1488551 TAAAAAATGCTACAAATCATCGAACATTGAGCTTCCAACCTATG
1 TAAAAAATGCCACAAATCATCAAACATTGAGCTTCCAACCTATG
* *
1488595 TAAAAAATGCCACACATCATCAAACATTGAGCTTGCAACCTATG
1 TAAAAAATGCCACAAATCATCAAACATTGAGCTTCCAACCTATG
1488639 TA
1 TA
1488641 CCAATCCATT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.41, C:0.23, G:0.11, T:0.24
Consensus pattern (44 bp):
TAAAAAATGCCACAAATCATCAAACATTGAGCTTCCAACCTATG
Found at i:1490270 original size:76 final size:75
Alignment explanation
Indices: 1490129--1490280 Score: 198
Period size: 76 Copynumber: 2.0 Consensus size: 75
1490119 TTCCAAGAAG
** * *
1490129 CATATCCTTGAAAGATCTCGTTGGCTCAATCCCCCGTTCCATGGGATCAGTATTACCATTAGGGG
1 CATATCCTTGAAAGATCTCGTTGGCTCAATCCCCCAATCCATGGGATCAATATTACCATCAGGGG
1490194 GATCCTACTC
66 GATCCTACTC
* * *
1490204 CATATCCTTGAAAGATCTTGGTT-GTTCAATCTCCCAATCCAATGGGATCAATATTACCATCAGG
1 CATATCCTTGAAAGATC-TCGTTGGCTCAATCCCCCAATCC-ATGGGATCAATATTACCATCAGG
* *
1490268 GGGGTCCTCCTC
64 GGGATCCTACTC
1490280 C
1 C
1490281 TTTCGATGAA
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
75 30 0.45
76 36 0.55
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.30
Consensus pattern (75 bp):
CATATCCTTGAAAGATCTCGTTGGCTCAATCCCCCAATCCATGGGATCAATATTACCATCAGGGG
GATCCTACTC
Found at i:1494500 original size:30 final size:29
Alignment explanation
Indices: 1494421--1494500 Score: 90
Period size: 31 Copynumber: 2.7 Consensus size: 29
1494411 AATTTATAGA
*
1494421 TTTAGTCCATATACTTTT-ATTTGATCAT
1 TTTAGTCCATATACTTTTGAATTGATCAT
* * *
1494449 TTTAGTCCTTGTACTTTTTGAATTGTTCAAT
1 TTTAGTCCATATAC-TTTTGAATTGATC-AT
*
1494480 TTTAGTCCCTATACTTTTGAA
1 TTTAGTCCATATACTTTTGAA
1494501 AATTTGAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
28 12 0.28
29 4 0.09
30 13 0.30
31 14 0.33
ACGTcount: A:0.23, C:0.15, G:0.10, T:0.53
Consensus pattern (29 bp):
TTTAGTCCATATACTTTTGAATTGATCAT
Found at i:1495695 original size:18 final size:19
Alignment explanation
Indices: 1495660--1495695 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1495650 CGTATTTTTA
1495660 TGCTTTTTAGCACAGTCTC
1 TGCTTTTTAGCACAGTCTC
*
1495679 TGCTTTTTTGCAC-GTCT
1 TGCTTTTTAGCACAGTCT
1495696 TTGTGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.11, C:0.25, G:0.17, T:0.47
Consensus pattern (19 bp):
TGCTTTTTAGCACAGTCTC
Found at i:1506381 original size:40 final size:40
Alignment explanation
Indices: 1506300--1506491 Score: 221
Period size: 40 Copynumber: 4.8 Consensus size: 40
1506290 GGCCCATTTT
* **
1506300 TATTTTAAAAAT-TTTAAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTTAAAAATATTT-TAAAATTAAAAAAA--ATTAAAAAAA
* *
1506342 TATTTTTAAAATGTTTTAAAATTAAAAAAAATTAAAAAAAA
1 TATTTTAAAAATATTTTAAAATTAAAAAAAATT-AAAAAAA
1506383 GTATTTT-AAAATATTTTAAAATT-AAAAAAATTAAAAAAA
1 -TATTTTAAAAATATTTTAAAATTAAAAAAAATTAAAAAAA
*
1506422 GTATTTTAAAAATATTTTAAAA-TAAAAAAAATTAAAAAAG
1 -TATTTTAAAAATATTTTAAAATTAAAAAAAATTAAAAAAA
* * *
1506462 TATGTAAAAAATATTTTAAAATTTAAAAAA
1 TATTTTAAAAATATTTTAAAATTAAAAAAA
1506492 TAAATATATT
Statistics
Matches: 135, Mismatches: 9, Indels: 14
0.85 0.06 0.09
Matches are distributed among these distances:
39 34 0.25
40 48 0.36
41 20 0.15
42 30 0.22
43 3 0.02
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (40 bp):
TATTTTAAAAATATTTTAAAATTAAAAAAAATTAAAAAAA
Found at i:1506410 original size:39 final size:39
Alignment explanation
Indices: 1506300--1506492 Score: 212
Period size: 39 Copynumber: 4.8 Consensus size: 39
1506290 GGCCCATTTT
**
1506300 TATTTTAAAA-ATTTTAAAAAATTAAAAAAAGTATTTTAAAAA-
1 TATTTTAAAATATTTT--AAAATT-AAAAAA--ATTAAAAAAAG
*
1506342 TATTTTTAAAATGTTTTAAAATTAAAAAAAATTAAAAAAAAG
1 TA-TTTTAAAATATTTTAAAATT-AAAAAAATT-AAAAAAAG
1506384 TATTTTAAAATATTTTAAAATTAAAAAAATTAAAAAAAG
1 TATTTTAAAATATTTTAAAATTAAAAAAATTAAAAAAAG
*
1506423 TATTTTAAAAATATTTTAAAATAAAAAAAATT-AAAAAAG
1 TATTTT-AAAATATTTTAAAATTAAAAAAATTAAAAAAAG
** *
1506462 TATGTAAAAAATATTTTAAAATTTAAAAAAT
1 TAT-TTTAAAATATTTTAAAATTAAAAAAAT
1506493 AAATATATTT
Statistics
Matches: 136, Mismatches: 9, Indels: 15
0.85 0.06 0.09
Matches are distributed among these distances:
39 46 0.34
40 37 0.27
41 24 0.18
42 17 0.12
43 8 0.06
44 4 0.03
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (39 bp):
TATTTTAAAATATTTTAAAATTAAAAAAATTAAAAAAAG
Found at i:1506922 original size:8 final size:8
Alignment explanation
Indices: 1506909--1506935 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
1506899 TTCATTTATT
1506909 TTATAAAA
1 TTATAAAA
1506917 TTATAAAA
1 TTATAAAA
1506925 TTATAAAA
1 TTATAAAA
1506933 TTA
1 TTA
1506936 CACAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
TTATAAAA
Found at i:1507567 original size:16 final size:16
Alignment explanation
Indices: 1507524--1507567 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
1507514 TATTTTTTTT
*
1507524 ATAAATTTAAAAACTA
1 ATAATTTTAAAAACTA
* **
1507540 GTAATTAAAAAAACTA
1 ATAATTTTAAAAACTA
1507556 ATAATTTTAAAA
1 ATAATTTTAAAA
1507568 TTTTGGCCTT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (16 bp):
ATAATTTTAAAAACTA
Found at i:1508044 original size:32 final size:34
Alignment explanation
Indices: 1508003--1508098 Score: 90
Period size: 35 Copynumber: 2.8 Consensus size: 34
1507993 GCTAAAAAAG
1508003 TTACGGTGTATTTGATAAACTGTGAAA-TTCT-T
1 TTACGGTGTATTTGATAAACTGTGAAAGTTCTAT
* * * * *
1508035 TTACGGTGTAAGTGTAAAAAAAT-TGAAAAGTTTTAAT
1 TTACGGTGT-A-TTTGATAAACTGTG-AAAGTTCT-AT
1508072 TTACGGTGTATTTGATAAACTGTGAAA
1 TTACGGTGTATTTGATAAACTGTGAAA
1508099 ATTTTCATTT
Statistics
Matches: 48, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
32 9 0.19
33 3 0.06
34 10 0.21
35 13 0.27
36 3 0.06
37 10 0.21
ACGTcount: A:0.35, C:0.06, G:0.20, T:0.39
Consensus pattern (34 bp):
TTACGGTGTATTTGATAAACTGTGAAAGTTCTAT
Found at i:1510740 original size:26 final size:26
Alignment explanation
Indices: 1510704--1510759 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
1510694 ATGTGGCAAA
1510704 TTTTAAACCTTATAAATATATTCATC
1 TTTTAAACCTTATAAATATATTCATC
1510730 TTTTAAACCTTATAAATATATTCATC
1 TTTTAAACCTTATAAATATATTCATC
1510756 TTTT
1 TTTT
1510760 TTCTTTTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (26 bp):
TTTTAAACCTTATAAATATATTCATC
Found at i:1520352 original size:142 final size:142
Alignment explanation
Indices: 1520195--1520478 Score: 559
Period size: 142 Copynumber: 2.0 Consensus size: 142
1520185 AATCTTATTA
1520195 AAATTTAATAACAATAAGCATCTACCTAAAATTTTTTTTGCTAAGGGTACTCTGGTCATTTTAAT
1 AAATTTAATAACAATAAGCATCTACCTAAAATTTTTTTTGCTAAGGGTACTCTGGTCATTTTAAT
1520260 TTTTTCACTTATGCTATTATAAATCTATTTCATTCAACCAAATACAAGAATATCATTACAGTTTT
66 TTTTTCACTTATGCTATTATAAATCTATTTCATTCAACCAAATACAAGAATATCATTACAGTTTT
1520325 ATTCCAATACAT
131 ATTCCAATACAT
*
1520337 AAATTTAATAACAATAATCATCTACCTAAAATTTTTTTTGCTAAGGGTACTCTGGTCATTTTAAT
1 AAATTTAATAACAATAAGCATCTACCTAAAATTTTTTTTGCTAAGGGTACTCTGGTCATTTTAAT
1520402 TTTTTCACTTATGCTATTATAAATCTATTTCATTCAACCAAATACAAGAATATCATTACAGTTTT
66 TTTTTCACTTATGCTATTATAAATCTATTTCATTCAACCAAATACAAGAATATCATTACAGTTTT
1520467 ATTCCAATACAT
131 ATTCCAATACAT
1520479 TCAACCAAAC
Statistics
Matches: 141, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
142 141 1.00
ACGTcount: A:0.36, C:0.16, G:0.07, T:0.41
Consensus pattern (142 bp):
AAATTTAATAACAATAAGCATCTACCTAAAATTTTTTTTGCTAAGGGTACTCTGGTCATTTTAAT
TTTTTCACTTATGCTATTATAAATCTATTTCATTCAACCAAATACAAGAATATCATTACAGTTTT
ATTCCAATACAT
Found at i:1521089 original size:15 final size:16
Alignment explanation
Indices: 1521069--1521098 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1521059 GGGTATAGTA
1521069 AAATA-TTAAAAAAAT
1 AAATATTTAAAAAAAT
1521084 AAATATTTAAAAAAA
1 AAATATTTAAAAAAA
1521099 ACACATGTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AAATATTTAAAAAAAT
Found at i:1532019 original size:32 final size:32
Alignment explanation
Indices: 1531976--1532188 Score: 144
Period size: 32 Copynumber: 6.7 Consensus size: 32
1531966 TAATGTCATT
* *
1531976 GGCACAAAGCCATCAGTAGCAGTGATACAATC
1 GGCACAAAGCCATCAGTAACAGTGATACGATC
* * ** * * *
1532008 GGCACACAGCCATTAGTAATGGTAACATGATC
1 GGCACAAAGCCATCAGTAACAGTGATACGATC
* * *
1532040 GGTACAAAGCCATCAGTAACAATGATATGATC
1 GGCACAAAGCCATCAGTAACAGTGATACGATC
* * * *
1532072 GGTACACAA-CCACCAGTAACGGTGATATGATC
1 GGCACA-AAGCCATCAGTAACAGTGATACGATC
* * * *
1532104 AGCACACAGCCATC-GATAACGGTAATACGATC
1 GGCACAAAGCCATCAG-TAACAGTGATACGATC
* ** * *
1532136 GGTACAAAGCCATCAGTAGTAGT-ACTATGATT
1 GGCACAAAGCCATCAGTAACAGTGA-TACGATC
*
1532168 GACACAAAGCCATCAGTAACA
1 GGCACAAAGCCATCAGTAACA
1532189 TCACAGCAAA
Statistics
Matches: 138, Mismatches: 38, Indels: 10
0.74 0.20 0.05
Matches are distributed among these distances:
31 3 0.02
32 132 0.96
33 3 0.02
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.19
Consensus pattern (32 bp):
GGCACAAAGCCATCAGTAACAGTGATACGATC
Found at i:1532090 original size:64 final size:63
Alignment explanation
Indices: 1531976--1532188 Score: 196
Period size: 64 Copynumber: 3.3 Consensus size: 63
1531966 TAATGTCATT
* * * * *
1531976 GGCACAAAGCCATCAGTAGCAGTGATACAATCGGCACACAGCCATTAGTAATGGTAACATGATC
1 GGCACAAAGCCATCAGTAACAGTGATACGATCGGTACACAACCATCAGTAATGGT-ACATGATC
* * * * * *
1532040 GGTACAAAGCCATCAGTAACAATGATATGATCGGTACACAACCACCAGTAACGGTGATATGATC
1 GGCACAAAGCCATCAGTAACAGTGATACGATCGGTACACAACCATCAGTAATGGT-ACATGATC
* * * * * *
1532104 AGCACACAGCCATC-GATAACGGTAATACGATCGGTACA-AAGCCATCAGTAGTAGTACTATGAT
1 GGCACAAAGCCATCAG-TAACAGTGATACGATCGGTACACAA-CCATCAGTAATGGTAC-ATGAT
*
1532167 T
63 C
*
1532168 GACACAAAGCCATCAGTAACA
1 GGCACAAAGCCATCAGTAACA
1532189 TCACAGCAAA
Statistics
Matches: 116, Mismatches: 29, Indels: 8
0.76 0.19 0.05
Matches are distributed among these distances:
63 4 0.03
64 111 0.96
65 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.19
Consensus pattern (63 bp):
GGCACAAAGCCATCAGTAACAGTGATACGATCGGTACACAACCATCAGTAATGGTACATGATC
Found at i:1532185 original size:96 final size:96
Alignment explanation
Indices: 1531973--1532188 Score: 233
Period size: 96 Copynumber: 2.2 Consensus size: 96
1531963 CAATAATGTC
* * * * * *
1531973 ATTGGCACAAAGCCATCAGTAGCAGTGATACAATCGGCACACAGCCATTAGTAATGGTAACATGA
1 ATTGACACAAAGCCATCAGTAACAGTGATACAATCAGCACACAGCCATGAGTAACGGTAACACGA
1532038 TCGGTACAAAGCCATCAGTAACAATGATATG
66 TCGGTACAAAGCCATCAGTAACAATGATATG
* * * ** *
1532069 ATCGGTACAC-AA-CCACCAGTAACGGTGATATGATCAGCACACAGCCATCGA-TAACGGTAATA
1 AT-TG-ACACAAAGCCATCAGTAACAGTGATACAATCAGCACACAGCCAT-GAGTAACGGTAACA
** *
1532131 CGATCGGTACAAAGCCATCAGTAGTAGT-ACTATG
63 CGATCGGTACAAAGCCATCAGTAACAATGA-TATG
1532165 ATTGACACAAAGCCATCAGTAACA
1 ATTGACACAAAGCCATCAGTAACA
1532189 TCACAGCAAA
Statistics
Matches: 96, Mismatches: 18, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
94 4 0.04
95 4 0.04
96 81 0.84
97 4 0.04
98 3 0.03
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.20
Consensus pattern (96 bp):
ATTGACACAAAGCCATCAGTAACAGTGATACAATCAGCACACAGCCATGAGTAACGGTAACACGA
TCGGTACAAAGCCATCAGTAACAATGATATG
Found at i:1532390 original size:24 final size:24
Alignment explanation
Indices: 1532357--1532462 Score: 113
Period size: 24 Copynumber: 4.4 Consensus size: 24
1532347 CCATGCTCAG
*
1532357 AATCAGTCATACAAATCACACACA
1 AATCAGTCATACAAATCACAGACA
* *
1532381 AATCAATCATACCAATCACAGACA
1 AATCAGTCATACAAATCACAGACA
** *
1532405 AATCAGTCATTTAAATCACAGATA
1 AATCAGTCATACAAATCACAGACA
* ** *
1532429 AATTAGTCATTTACATCACAGACA
1 AATCAGTCATACAAATCACAGACA
*
1532453 AATCAATCAT
1 AATCAGTCAT
1532463 TTACACTCAA
Statistics
Matches: 69, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 69 1.00
ACGTcount: A:0.47, C:0.24, G:0.06, T:0.24
Consensus pattern (24 bp):
AATCAGTCATACAAATCACAGACA
Found at i:1532638 original size:81 final size:81
Alignment explanation
Indices: 1532500--1532653 Score: 184
Period size: 81 Copynumber: 1.9 Consensus size: 81
1532490 TACCCTCCAG
* * * * **
1532500 GGGCATTATGGTCATTTTACCTCATAAGGGTATTTCGGTCATTTAATCCTATGGGGGTATTACAA
1 GGGCATTACGATCATTTTACCTCATAAGGGTATTTCGGTAATTTAACCCTACAGGGGTATTACAA
1532565 TCATTTTACCCTACTA
66 TCATTTTACCCTACTA
* * * * *
1532581 GGGCATTACGATCATTTTACC-CTATGAGGGTTTTTTGGTAATTTTACCCTACAGGGGTATTACG
1 GGGCATTACGATCATTTTACCTC-ATAAGGGTATTTCGGTAATTTAACCCTACAGGGGTATTACA
*
1532645 GTCATTTTA
65 ATCATTTTA
1532654 TAAATATTAG
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
80 1 0.02
81 59 0.98
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (81 bp):
GGGCATTACGATCATTTTACCTCATAAGGGTATTTCGGTAATTTAACCCTACAGGGGTATTACAA
TCATTTTACCCTACTA
Found at i:1532651 original size:27 final size:27
Alignment explanation
Indices: 1532488--1532653 Score: 115
Period size: 27 Copynumber: 6.1 Consensus size: 27
1532478 AAAATAGTTA
* * *
1532488 TTTACCCTCCAGGGGCATTATGGTCAT
1 TTTACCCTACAGGGGTATTACGGTCAT
*
1532515 TTTACCTCATA-A-GGGTATTTCGGTCAT
1 TTTACC-C-TACAGGGGTATTACGGTCAT
* * ** **
1532542 TTAATCCTATGGGGGTATTACAATCAT
1 TTTACCCTACAGGGGTATTACGGTCAT
* *
1532569 TTTACCCTACTA-GGGCATTACGATCAT
1 TTTACCCTAC-AGGGGTATTACGGTCAT
* * ** *
1532596 TTTACCCTA-TGAGGGTTTTTTGGTAAT
1 TTTACCCTACAG-GGGTATTACGGTCAT
1532623 TTTACCCTACAGGGGTATTACGGTCAT
1 TTTACCCTACAGGGGTATTACGGTCAT
1532650 TTTA
1 TTTA
1532654 TAAATATTAG
Statistics
Matches: 103, Mismatches: 28, Indels: 16
0.70 0.19 0.11
Matches are distributed among these distances:
25 2 0.02
26 1 0.01
27 96 0.93
28 3 0.03
29 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (27 bp):
TTTACCCTACAGGGGTATTACGGTCAT
Found at i:1539262 original size:19 final size:18
Alignment explanation
Indices: 1539240--1539295 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
1539230 AAAAATTAAA
*
1539240 AAAAATCAAAATAATTTTT
1 AAAAATCAAAAT-ATTTAT
*
1539259 AAAATTCAAAATATTTAT
1 AAAAATCAAAATATTTAT
*
1539277 AAAAATTCTAAA-ATTTAT
1 AAAAA-TCAAAATATTTAT
1539295 A
1 A
1539296 TTTTTAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 16 0.50
19 16 0.50
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAAATCAAAATATTTAT
Found at i:1539274 original size:18 final size:20
Alignment explanation
Indices: 1539239--1539326 Score: 65
Period size: 19 Copynumber: 4.3 Consensus size: 20
1539229 CAAAAATTAA
*
1539239 AAAAAATCAAAATAATTT-T
1 AAAAATTCAAAATAATTTAT
*
1539258 TAAAATTCAAAAT-ATTTAT
1 AAAAATTCAAAATAATTTAT
*
1539277 AAAAATTCTAAAATTTATATTTTT
1 AAAAATTC-AAAA--TA-ATTTAT
* *
1539301 AAAGAATT-ATAATAATTTAA
1 AAA-AATTCAAAATAATTTAT
1539321 AAAAAT
1 AAAAAT
1539327 CTAAAGAATA
Statistics
Matches: 55, Mismatches: 7, Indels: 14
0.72 0.09 0.18
Matches are distributed among these distances:
18 4 0.07
19 22 0.40
20 11 0.20
21 2 0.04
22 1 0.02
23 3 0.05
24 8 0.15
25 4 0.07
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (20 bp):
AAAAATTCAAAATAATTTAT
Found at i:1539303 original size:24 final size:26
Alignment explanation
Indices: 1539269--1539319 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 26
1539259 AAAATTCAAA
*
1539269 ATATTTATAAA-AATTCTAA-AATTT
1 ATATTTATAAAGAATTATAATAATTT
*
1539293 ATATTTTTAAAGAATTATAATAATTT
1 ATATTTATAAAGAATTATAATAATTT
1539319 A
1 A
1539320 AAAAAATCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 10 0.43
25 7 0.30
26 6 0.26
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (26 bp):
ATATTTATAAAGAATTATAATAATTT
Found at i:1541785 original size:40 final size:42
Alignment explanation
Indices: 1541731--1541839 Score: 150
Period size: 40 Copynumber: 2.6 Consensus size: 42
1541721 CTTCGATCTG
*
1541731 CTCCACTACTGCTTAGGGAGATAAGATCTGTAAT-TT-CCTA
1 CTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTACCTA
*
1541771 CTCCACTACTGCTTAGGGAGATAAGGTCTATAATCTTCAACCTA
1 CTCCACTACTGCTTAGGGAGATAAGATCTATAATCTT--ACCTA
* *
1541815 CTCCACTGCTGCTCAGGGAGATAAG
1 CTCCACTACTGCTTAGGGAGATAAG
1541840 GCTAGTGGCT
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
40 32 0.52
41 2 0.03
44 27 0.44
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (42 bp):
CTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTACCTA
Found at i:1541833 original size:44 final size:43
Alignment explanation
Indices: 1541767--1542263 Score: 243
Period size: 44 Copynumber: 11.6 Consensus size: 43
1541757 TCTGTAATTT
* *
1541767 CCTACTCCACTACTG-CTTAGGGAGATAAGGTCTATAATCTTCAA
1 CCTACTCCACTGCTGAC-CAGGGAGAT-AGGTCTATAATCTTCAA
** *
1541811 CCTACTCCACTGCTG-CTCAGGGAGATAAGG-CTAGT-GGCTTAAA
1 CCTACTCCACTGCTGAC-CAGGGAGAT-AGGTCTA-TAATCTTCAA
* * * * * ** *
1541854 TCTACTTCC-CTACT-ACCATGGAAAGATAAGATTTACCATCTTCGA
1 CCTAC-TCCACTGCTGACCA-GG-GAGAT-AGGTCTATAATCTTCAA
* * * * * * *
1541899 TCTGCTCCACTACTG-CTTAGGGAGATAAGATCTGTAATTTTCAA
1 CCTACTCCACTGCTGAC-CAGGGAGAT-AGGTCTATAATCTTCAA
* * *
1541943 CATACTCCATTGCTGACCAGGGAGATAGGAT-TCACAATCTTCAA
1 CCTACTCCACTGCTGACCAGGGAGATAGG-TCT-ATAATCTTCAA
* * * *
1541987 CTTATTCCACTACTGACCAGGGAGATAGGAT-TCACAATCTTCAA
1 CCTACTCCACTGCTGACCAGGGAGATAGG-TCT-ATAATCTTCAA
* * *
1542031 CCTATTTCCACTGCT-ACCAGGGAGATAGGAT-TCACAATCTACAA
1 CCTA-CTCCACTGCTGACCAGGGAGATAGG-TCT-ATAATCTTCAA
* *
1542075 -C-ATTCCACTGCTGACCAGGGAG--A----TATGA--TTC-A
1 CCTACTCCACTGCTGACCAGGGAGATAGGTCTATAATCTTCAA
* * *
1542107 CCTATTCCACTGCTGACCAGGGAGATAGGACTTACAATCTTCAA
1 CCTACTCCACTGCTGACCAGGGAGATAGGTC-TATAATCTTCAA
* * *
1542151 CCAATTCCACTGCTGACCAGGGAGATAGGACTCATAATCTTCAA
1 CCTACTCCACTGCTGACCAGGGAGATAGGTCT-ATAATCTTCAA
* * *
1542195 CCTATTCCACTGCTGACCAGGGAGATAGGAT-TCACAATCTACAA
1 CCTACTCCACTGCTGACCAGGGAGATAGG-TCT-ATAATCTTCAA
*
1542239 -C-ATTCCACTGCTGACCAGGGAGATA
1 CCTACTCCACTGCTGACCAGGGAGATA
1542264 TGATTCACCT
Statistics
Matches: 372, Mismatches: 52, Indels: 60
0.77 0.11 0.12
Matches are distributed among these distances:
32 1 0.00
33 3 0.01
34 21 0.06
35 2 0.01
36 2 0.01
40 1 0.00
41 13 0.03
42 36 0.10
43 28 0.08
44 236 0.63
45 28 0.08
46 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (43 bp):
CCTACTCCACTGCTGACCAGGGAGATAGGTCTATAATCTTCAA
Found at i:1541907 original size:88 final size:88
Alignment explanation
Indices: 1541643--1541927 Score: 255
Period size: 88 Copynumber: 3.3 Consensus size: 88
1541633 TAAAAAAATA
** * * * *
1541643 CTCCACTGTTGCTGAGGGAGATAAGGCTAGTGGCTTTAATCTGCTTCCCTATTACCTTAGGAAGA
1 CTCCACTACTGCTTAGGGAGATAAGGCTAGTGGCTTAAATCTACTTCCCTACTACCTTAGGAAGA
** **
1541708 TAAGATTCGCTGTCTTCGATCTG
66 TAAGATTTACAATCTTCGATCTG
* *
1541731 CTCCACTACTGCTTAGGGAGATAA-G--A-T--CTGTAATTTCCTAC-TCCACTACT-GCTTAGG
1 CTCCACTACTGCTTAGGGAGATAAGGCTAGTGGCT-TAA-AT-CTACTTCC-CTACTACCTTAGG
* * * * * * *
1541788 GAGATAAGGTCTATAATCTTCAACCTA
62 AAGATAAGATTTACAATCTTCGATCTG
* * *
1541815 CTCCACTGCTGCTCAGGGAGATAAGGCTAGTGGCTTAAATCTACTTCCCTACTACCAT-GGAAAG
1 CTCCACTACTGCTTAGGGAGATAAGGCTAGTGGCTTAAATCTACTTCCCTACTACCTTAGG-AAG
*
1541879 ATAAGATTTACCATCTTCGATCTG
65 ATAAGATTTACAATCTTCGATCTG
1541903 CTCCACTACTGCTTAGGGAGATAAG
1 CTCCACTACTGCTTAGGGAGATAAG
1541928 ATCTGTAATT
Statistics
Matches: 150, Mismatches: 34, Indels: 26
0.71 0.16 0.12
Matches are distributed among these distances:
82 2 0.01
83 2 0.01
84 49 0.33
85 9 0.06
87 13 0.09
88 70 0.47
89 3 0.02
90 2 0.01
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (88 bp):
CTCCACTACTGCTTAGGGAGATAAGGCTAGTGGCTTAAATCTACTTCCCTACTACCTTAGGAAGA
TAAGATTTACAATCTTCGATCTG
Found at i:1542119 original size:34 final size:34
Alignment explanation
Indices: 1542076--1542297 Score: 156
Period size: 34 Copynumber: 5.7 Consensus size: 34
1542066 AATCTACAAC
1542076 ATTCCACTGCTGACCAGGGAGATATGATTCACCT
1 ATTCCACTGCTGACCAGGGAGATATGATTCACCT
* *
1542110 ATTCCACTGCTGACCAGGGAGATAGGACTTACAATCTTCAACCA
1 ATTCCACTGCTGACCAGGGAGAT---A--T--GA--TTC-ACCT
*
1542154 ATTCCACTGCTGACCAGGGAGATAGGACTCATAATCTTCAACCT
1 ATTCCACTGCTGACCA-GG-G--A-GA-T-ATGA--TTC-ACCT
*
1542198 ATTCCACTGCTGACCAGGGAGATAGGATTCACAATCT
1 ATTCCACTGCTGACCAGGGAGATATGATTCAC---CT
1542235 ACAACATTCCACTGCTGACCAGGGAGATATGATTCACCT
1 -----ATTCCACTGCTGACCAGGGAGATATGATTCACCT
1542274 ATTCCACTGCTGACCAGGGAGATA
1 ATTCCACTGCTGACCAGGGAGATA
1542298 GGACTCACAA
Statistics
Matches: 157, Mismatches: 7, Indels: 48
0.74 0.03 0.23
Matches are distributed among these distances:
34 49 0.31
35 3 0.02
37 5 0.03
38 1 0.01
39 5 0.03
40 1 0.01
41 1 0.01
42 32 0.20
43 5 0.03
44 46 0.29
45 2 0.01
46 2 0.01
48 2 0.01
49 2 0.01
50 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.24
Consensus pattern (34 bp):
ATTCCACTGCTGACCAGGGAGATATGATTCACCT
Found at i:1542224 original size:164 final size:164
Alignment explanation
Indices: 1541948--1542312 Score: 635
Period size: 164 Copynumber: 2.2 Consensus size: 164
1541938 TTCAACATAC
* **
1541948 TCCATTGCTGACCAGGGAGATAGGA-TTCACAATCTTCAACTTATTCCACTACTGACCAGGGAGA
1 TCCACTGCTGACCAGGGAGATAGGACTT-ACAATCTTCAACCAATTCCACTACTGACCAGGGAGA
*
1542012 TAGGATTCACAATCTTCAACCTATTTCCACTGCTACCAGGGAGATAGGATTCACAATCTACAACA
65 TAGGACTCACAATCTTCAACCTATTTCCACTGCTACCAGGGAGATAGGATTCACAATCTACAACA
1542077 TTCCACTGCTGACCAGGGAGATATGATTCACCTAT
130 TTCCACTGCTGACCAGGGAGATATGATTCACCTAT
*
1542112 TCCACTGCTGACCAGGGAGATAGGACTTACAATCTTCAACCAATTCCACTGCTGACCAGGGAGAT
1 TCCACTGCTGACCAGGGAGATAGGACTTACAATCTTCAACCAATTCCACTACTGACCAGGGAGAT
*
1542177 AGGACTCATAATCTTCAACCTA-TTCCACTGCTGACCAGGGAGATAGGATTCACAATCTACAACA
66 AGGACTCACAATCTTCAACCTATTTCCACTGCT-ACCAGGGAGATAGGATTCACAATCTACAACA
1542241 TTCCACTGCTGACCAGGGAGATATGATTCACCTAT
130 TTCCACTGCTGACCAGGGAGATATGATTCACCTAT
*
1542276 TCCACTGCTGACCAGGGAGATAGGACTCACAATCTTC
1 TCCACTGCTGACCAGGGAGATAGGACTTACAATCTTC
1542313 GATTTGCTTC
Statistics
Matches: 192, Mismatches: 7, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
163 10 0.05
164 180 0.94
165 2 0.01
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.25
Consensus pattern (164 bp):
TCCACTGCTGACCAGGGAGATAGGACTTACAATCTTCAACCAATTCCACTACTGACCAGGGAGAT
AGGACTCACAATCTTCAACCTATTTCCACTGCTACCAGGGAGATAGGATTCACAATCTACAACAT
TCCACTGCTGACCAGGGAGATATGATTCACCTAT
Found at i:1549053 original size:12 final size:12
Alignment explanation
Indices: 1549036--1549069 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1549026 ATAAATTAAA
1549036 ATATGTATGTAT
1 ATATGTATGTAT
*
1549048 ATATGTATATAT
1 ATATGTATGTAT
*
1549060 TTATGTATGT
1 ATATGTATGT
1549070 GAAAATTATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (12 bp):
ATATGTATGTAT
Found at i:1549287 original size:22 final size:22
Alignment explanation
Indices: 1549262--1549303 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1549252 AATTTGAAAA
1549262 TATAAAAAATGTACGTATATAT
1 TATAAAAAATGTACGTATATAT
* *
1549284 TATAGAAAATGTATGTATAT
1 TATAAAAAATGTACGTATAT
1549304 TTTGAATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.48, C:0.02, G:0.12, T:0.38
Consensus pattern (22 bp):
TATAAAAAATGTACGTATATAT
Found at i:1549416 original size:3 final size:3
Alignment explanation
Indices: 1549408--1549459 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
1549398 GTACATGGTT
*
1549408 ATA ATA ATA ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1549456 ATA A
1 ATA A
1549460 GAGTATTAAC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:1550613 original size:17 final size:17
Alignment explanation
Indices: 1550593--1550626 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1550583 TTGTAATTAA
1550593 AATCGATATTGGACTAT
1 AATCGATATTGGACTAT
1550610 AATCGATATTGGACTAT
1 AATCGATATTGGACTAT
1550627 GTAAATGGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (17 bp):
AATCGATATTGGACTAT
Found at i:1551103 original size:30 final size:30
Alignment explanation
Indices: 1551054--1551120 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
1551044 CAATTTGAAC
* *
1551054 CTAAATT-TTAAAATCTAAAAA-ATAGAGAAA
1 CTAAATTCTTAAAATATAAAAATATACAG--A
1551084 CTAAATTCTTAAAA-ATAAAAATATACAGA
1 CTAAATTCTTAAAATATAAAAATATACAGA
1551113 CTAAATTC
1 CTAAATTC
1551121 CAAATTCATA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
29 9 0.27
30 13 0.39
31 11 0.33
ACGTcount: A:0.57, C:0.10, G:0.04, T:0.28
Consensus pattern (30 bp):
CTAAATTCTTAAAATATAAAAATATACAGA
Found at i:1558467 original size:7 final size:7
Alignment explanation
Indices: 1558455--1558506 Score: 63
Period size: 7 Copynumber: 7.3 Consensus size: 7
1558445 ACAAAAATTG
1558455 TGAAAAA
1 TGAAAAA
1558462 TGAAAAAA
1 TG-AAAAA
1558470 TG-AAAA
1 TGAAAAA
1558476 TGAAAAA
1 TGAAAAA
1558483 TGAAAAAA
1 TG-AAAAA
1558491 TGAAAAA
1 TGAAAAA
1558498 -GTAAAAA
1 TG-AAAAA
1558505 TG
1 TG
1558507 GAGAGGCTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
6 7 0.17
7 18 0.45
8 15 0.38
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (7 bp):
TGAAAAA
Found at i:1558470 original size:8 final size:8
Alignment explanation
Indices: 1558457--1558497 Score: 61
Period size: 8 Copynumber: 5.5 Consensus size: 8
1558447 AAAAATTGTG
1558457 AAAAATGA
1 AAAAATGA
1558465 AAAAATG-
1 AAAAATGA
1558472 -AAAATG-
1 AAAAATGA
1558478 AAAAATGA
1 AAAAATGA
1558486 AAAAATGA
1 AAAAATGA
1558494 AAAA
1 AAAA
1558498 GTAAAAATGG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 6 0.19
7 6 0.19
8 19 0.61
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (8 bp):
AAAAATGA
Found at i:1558477 original size:14 final size:13
Alignment explanation
Indices: 1558458--1558488 Score: 53
Period size: 13 Copynumber: 2.3 Consensus size: 13
1558448 AAAATTGTGA
1558458 AAAATGAAAAAATG
1 AAAATG-AAAAATG
1558472 AAAATGAAAAATG
1 AAAATGAAAAATG
1558485 AAAA
1 AAAA
1558489 AATGAAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (13 bp):
AAAATGAAAAATG
Found at i:1558481 original size:21 final size:21
Alignment explanation
Indices: 1558455--1558506 Score: 86
Period size: 21 Copynumber: 2.4 Consensus size: 21
1558445 ACAAAAATTG
1558455 TGAAAAATGAAAAAATGAAAA
1 TGAAAAATGAAAAAATGAAAA
1558476 TGAAAAATGAAAAAATGAAAA
1 TGAAAAATGAAAAAATGAAAA
*
1558497 AGTAAAAATG
1 TG-AAAAATG
1558507 GAGAGGCTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 22 0.76
22 7 0.24
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (21 bp):
TGAAAAATGAAAAAATGAAAA
Found at i:1559963 original size:129 final size:129
Alignment explanation
Indices: 1559733--1560553 Score: 1243
Period size: 129 Copynumber: 6.4 Consensus size: 129
1559723 GAACAGATCA
* * * * *
1559733 GGGAAATTACAGATCTTGTCTCCCTAAGCAATAGTGGAGTAGATCGAAGACGGTGAATCTTATCT
1 GGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCAAAGACGGCGAATCTTATCT
* * * * * *
1559798 TCAAGTGTAAGGAAGCAGATTTAAGCCAAAAGTCCTATCTCCTTGGCCAGTAGTGGAATAAGTT
66 TCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTT
* *
1559862 GGGAAATTACAGATCTTGTCTCCCTAAGCACTAGCGGAGTAGATCAAAGACGGCGAATCTTATCT
1 GGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCAAAGACGGCGAATCTTATCT
* * * *
1559927 TCAAGTGTAAGAAAGCAGATTTATGCCACAAGTCCTATCTCCCTGGTCAGTAGTGGAATAGGTT
66 TCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTT
* ** * *
1559991 -GGAAATTACAAATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATTGAAGACGACAAATCTTATCT
1 GGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCAAAGACGGCGAATCTTATCT
* *
1560055 TCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATTCCTGGTCAGCAGTGGAATAGGTT
66 TCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTT
* * * * *
1560119 GGGAAATTACAGATCTTATCTCCATAAGCAGTAGCGGATCAGATCGAAGACGGCAAATCTTATCT
1 GGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCAAAGACGGCGAATCTTATCT
* *
1560184 TCAAGAGTAAGGAAGCAAATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTT
66 TCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTT
* *
1560248 GAGAAATTACAAATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCAAAGACGGCGAATCTTATCT
1 GGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCAAAGACGGCGAATCTTATCT
* *
1560313 TCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTTCTATCTCCTTGGTCAGCAGTGGAATAGGTT
66 TCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTT
*
1560377 -GAAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCAAAGACGGCGAATCTTATCT
1 GGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCAAAGACGGCGAATCTTATCT
1560441 TCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTT
66 TCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTT
* ** * * *
1560505 -GGAAATTTCAGATCTCATCTCCCTACGCAATAGTGGAGCAGATCAAAGA
1 GGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCAAAGA
1560554 TGACATATTT
Statistics
Matches: 637, Mismatches: 54, Indels: 3
0.92 0.08 0.00
Matches are distributed among these distances:
128 280 0.44
129 357 0.56
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (129 bp):
GGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCAAAGACGGCGAATCTTATCT
TCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTT
Found at i:1560214 original size:257 final size:257
Alignment explanation
Indices: 1559734--1560553 Score: 1259
Period size: 257 Copynumber: 3.2 Consensus size: 257
1559724 AACAGATCAG
* * * *
1559734 GGAAATTACAGATCTTGTCTCCCTAAGCAATAGTGGAGTAGATCGAAGACGGTGAATCTTATCTT
1 GGAAATTACAAATCTTGTCTCCCTAAGCAATAGCGGAGCAGATCGAAGACGGCGAATCTTATCTT
* * * * *
1559799 CAAGTGTAAGGAAGCAGATTTAAGCCAAAAGTCCTATCTCCTTGGCCAGTAGTGGAATAAGTTGG
66 CAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATCTCCTTGGTCAGCAGTGGAATAGGTTGG
*
1559864 GAAATTACAGATCTTGTCTCCCTAAGCACTAGCGGAGT-AGATCAAAGACGGCGAATCTTATCTT
131 GAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGA-TCAGATCAAAGACGGCGAATCTTATCTT
* * * *
1559928 CAAGTGTAAGAAAGCAGATTTATGCCACAAGTCCTATCTCCCTGGTCAGTAGTGGAATAGGTT
195 CAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTT
* * * *
1559991 GGAAATTACAAATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATTGAAGACGACAAATCTTATCTT
1 GGAAATTACAAATCTTGTCTCCCTAAGCAATAGCGGAGCAGATCGAAGACGGCGAATCTTATCTT
*
1560056 CAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATTCC-TGGTCAGCAGTGGAATAGGTTG
66 CAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTAT-CTCCTTGGTCAGCAGTGGAATAGGTTG
* * * *
1560120 GGAAATTACAGATCTTATCTCCATAAGCAGTAGCGGATCAGATCGAAGACGGCAAATCTTATCTT
130 GGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGATCAGATCAAAGACGGCGAATCTTATCTT
* *
1560185 CAAGAGTAAGGAAGCAAATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTT
195 CAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTT
* *
1560248 GAGAAATTACAAATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCAAAGACGGCGAATCTTATCT
1 G-GAAATTACAAATCTTGTCTCCCTAAGCAATAGCGGAGCAGATCGAAGACGGCGAATCTTATCT
*
1560313 TCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTTCTATCTCCTTGGTCAGCAGTGGAATAGGTT-
65 TCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATCTCCTTGGTCAGCAGTGGAATAGGTTG
* *
1560377 GAAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCAAAGACGGCGAATCTTATCTT
130 GGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGATCAGATCAAAGACGGCGAATCTTATCTT
1560442 CAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTT
195 CAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTT
* * ** * * *
1560505 GGAAATTTCAGATCTCATCTCCCTACGCAATAGTGGAGCAGATCAAAGA
1 GGAAATTACAAATCTTGTCTCCCTAAGCAATAGCGGAGCAGATCGAAGA
1560554 TGACATATTT
Statistics
Matches: 513, Mismatches: 46, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
256 42 0.08
257 351 0.68
258 120 0.23
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.25
Consensus pattern (257 bp):
GGAAATTACAAATCTTGTCTCCCTAAGCAATAGCGGAGCAGATCGAAGACGGCGAATCTTATCTT
CAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATCTCCTTGGTCAGCAGTGGAATAGGTTGG
GAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGATCAGATCAAAGACGGCGAATCTTATCTTC
AAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTT
Found at i:1560446 original size:386 final size:386
Alignment explanation
Indices: 1559733--1560553 Score: 1286
Period size: 386 Copynumber: 2.1 Consensus size: 386
1559723 GAACAGATCA
* **
1559733 GGGAAATTACAGATCTTGTCTCCCTAAGCAATAGTGGAGT-AGATCGAAGACGGTGAATCTTATC
1 GGGAAATTACAGATCTTATCTCCCTAAGCAATAGTGGA-TCAGATCGAAGACGGCAAATCTTATC
* * * * *
1559797 TTCAAGTGTAAGGAAGCAGATTTAAGCCAAAAGTCCTATCTCCTTGGCCAGTAGTGGAATAAGTT
65 TTCAAGAGTAAGGAAGCAAATTTAAGCCAAAAGTCCTATATCCCTGGCCAGCAGTGGAATAAGTT
* * *
1559862 GGGAAATTACAGATCTTGTCTCCCTAAGCACTAGCGGAGTAGATCAAAGACGGCGAATCTTATCT
130 GAGAAATTACAAATCTTGTCTCCCTAAGCACTAGCGGAGCAGATCAAAGACGGCGAATCTTATCT
* * *
1559927 TCAAGTGTAAGAAAGCAGATTTATGCCACAAGTCCTATCTCCCTGGTCAGTAGTGGAATAGGTTG
195 TCAAGAGTAAGAAAGCAGATTTAAGCCACAAGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTG
* **
1559992 GAAATTACAAATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATTGAAGACGACAAATCTTATCTTC
260 AAAATTACAAATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCAAAGACGACAAATCTTATCTTC
*
1560057 AAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATTCCTGGTCAGCAGTGGAATAGGTT
325 AAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTT
* * *
1560119 GGGAAATTACAGATCTTATCTCCATAAGCAGTAGCGGATCAGATCGAAGACGGCAAATCTTATCT
1 GGGAAATTACAGATCTTATCTCCCTAAGCAATAGTGGATCAGATCGAAGACGGCAAATCTTATCT
* * *
1560184 TCAAGAGTAAGGAAGCAAATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTG
66 TCAAGAGTAAGGAAGCAAATTTAAGCCAAAAGTCCTATATCCCTGGCCAGCAGTGGAATAAGTTG
*
1560249 AGAAATTACAAATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCAAAGACGGCGAATCTTATCTT
131 AGAAATTACAAATCTTGTCTCCCTAAGCACTAGCGGAGCAGATCAAAGACGGCGAATCTTATCTT
* * *
1560314 CAAGAGTAAGGAAGCAGATTTAAGCCACAAGTTCTATCTCCTTGGTCAGCAGTGGAATAGGTTGA
196 CAAGAGTAAGAAAGCAGATTTAAGCCACAAGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGA
* * *
1560379 AAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCAAAGACGGCGAATCTTATCTTCA
261 AAATTACAAATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCAAAGACGACAAATCTTATCTTCA
*
1560444 AGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTT
326 AGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTT
* * * * *
1560505 -GGAAATTTCAGATCTCATCTCCCTACGCAATAGTGGAGCAGATCAAAGA
1 GGGAAATTACAGATCTTATCTCCCTAAGCAATAGTGGATCAGATCGAAGA
1560554 TGACATATTT
Statistics
Matches: 394, Mismatches: 40, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
385 42 0.11
386 352 0.89
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (386 bp):
GGGAAATTACAGATCTTATCTCCCTAAGCAATAGTGGATCAGATCGAAGACGGCAAATCTTATCT
TCAAGAGTAAGGAAGCAAATTTAAGCCAAAAGTCCTATATCCCTGGCCAGCAGTGGAATAAGTTG
AGAAATTACAAATCTTGTCTCCCTAAGCACTAGCGGAGCAGATCAAAGACGGCGAATCTTATCTT
CAAGAGTAAGAAAGCAGATTTAAGCCACAAGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGA
AAATTACAAATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCAAAGACGACAAATCTTATCTTCA
AGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTT
Found at i:1560645 original size:132 final size:132
Alignment explanation
Indices: 1560475--1560747 Score: 388
Period size: 132 Copynumber: 2.1 Consensus size: 132
1560465 GCCACAAGTC
* * * * *
1560475 CTATCTCCCTGGTCAGCAGTGGAATAGGTTGGAAATTTCAGATCTCATCTCCCTACGCAATAGTG
1 CTATCTCCCTGGGCAGCAGCGGAATAGATTGGAAATTTCAGATCTCATCTCCCTAAGCAATAGTC
* *
1560540 GAGCAGATCAAAGAT-GACATATTTTACCTCCTTGTGATTATAGTGGAATACATTGAAGCCAGTA
66 GAGCAGATCAAAGATGGACA-ATTTTACCTCCCTGTGATTACAGTGGAATACATTGAAGCCAGTA
1560604 ATT
130 ATT
*
1560607 CTATCTCCCTGGGCAGCAGCGGAATAGATT-GAAGATTTCAGATCTCATCTCCCTAAGTAATAGT
1 CTATCTCCCTGGGCAGCAGCGGAATAGATTGGAA-ATTTCAGATCTCATCTCCCTAAGCAATAGT
* ** * *
1560671 CGAGTAGATCAAAGATGGTGAATTTTACCTCCCTGTGATTACAGTGGAGTACATTGAAGCCTGTA
65 CGAGCAGATCAAAGATGGACAATTTTACCTCCCTGTGATTACAGTGGAATACATTGAAGCCAGTA
1560736 ATT
130 ATT
*
1560739 TTATCTCCC
1 CTATCTCCC
1560748 CGAGGTTGCA
Statistics
Matches: 125, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
131 3 0.02
132 120 0.96
133 2 0.02
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.30
Consensus pattern (132 bp):
CTATCTCCCTGGGCAGCAGCGGAATAGATTGGAAATTTCAGATCTCATCTCCCTAAGCAATAGTC
GAGCAGATCAAAGATGGACAATTTTACCTCCCTGTGATTACAGTGGAATACATTGAAGCCAGTAA
TT
Found at i:1560781 original size:132 final size:132
Alignment explanation
Indices: 1560513--1560820 Score: 352
Period size: 132 Copynumber: 2.3 Consensus size: 132
1560503 TTGGAAATTT
* * *
1560513 CAGATCTCATCTCCCTACGCAATAGTGGAGCAGATCAAAGATGACATATTTTACCTCCTTGTGAT
1 CAGATCTCATCTCCCTAAGCAATAGTCGAGCAGATCAAAGATGACATATTTTACCTCCCTGTGAT
* * * *
1560578 TATAGTGGAATACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGCGGAATAGATTGAAGAT
66 TACAGTGGAATACATTGAAGCCAGTAATTCTATCTCCCCGGGCAGCAGCGGAACAGACTGAAGAT
**
1560643 TT
131 AA
* * **
1560645 CAGATCTCATCTCCCTAAGTAATAGTCGAGTAGATCAAAGATGGTGA-ATTTTACCTCCCTGTGA
1 CAGATCTCATCTCCCTAAGCAATAGTCGAGCAGATCAAAGAT-GACATATTTTACCTCCCTGTGA
* * * ** *
1560709 TTACAGTGGAGTACATTGAAGCCTGTAATTTTATCTCCCCGAGGTTGCAGCGGAGCAGACTGAAG
65 TTACAGTGGAATACATTGAAGCCAGTAATTCTATCTCCCCG-GGCAGCAGCGGAACAGACTGAAG
1560774 A-AA
129 ATAA
* * * * *
1560777 CAGATCTTATCTCTCTAAGCAGTAGTGGGGCAGATCGAAA-ATGA
1 CAGATCTCATCTCCCTAAGCAATAGTCGAGCAGATC-AAAGATGA
1560821 TAACTCCTAT
Statistics
Matches: 146, Mismatches: 27, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
131 1 0.01
132 121 0.83
133 24 0.16
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (132 bp):
CAGATCTCATCTCCCTAAGCAATAGTCGAGCAGATCAAAGATGACATATTTTACCTCCCTGTGAT
TACAGTGGAATACATTGAAGCCAGTAATTCTATCTCCCCGGGCAGCAGCGGAACAGACTGAAGAT
AA
Found at i:1579486 original size:22 final size:22
Alignment explanation
Indices: 1579434--1579503 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
1579424 AACAAAAAAA
* *
1579434 ATATCAT-ACTATACATACTAAC
1 ATATCATAAC-ATACACACTAAT
1579456 ATATCATAACATACACACTAAT
1 ATATCATAACATACACACTAAT
1579478 ATATCATAACA-A-ACA-TAAT
1 ATATCATAACATACACACTAAT
1579497 ATA-CATA
1 ATATCATA
1579504 CTAATATATC
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
18 4 0.09
19 7 0.16
20 3 0.07
21 1 0.02
22 28 0.62
23 2 0.04
ACGTcount: A:0.51, C:0.20, G:0.00, T:0.29
Consensus pattern (22 bp):
ATATCATAACATACACACTAAT
Found at i:1579501 original size:31 final size:31
Alignment explanation
Indices: 1579460--1579532 Score: 110
Period size: 31 Copynumber: 2.4 Consensus size: 31
1579450 ACTAACATAT
*
1579460 CATAACATACACACTAATATATCATAACAAA
1 CATAATATACACACTAATATATCATAACAAA
* *
1579491 CATAATATACATACTAATATATCATAACATA
1 CATAATATACACACTAATATATCATAACAAA
*
1579522 CAAAATATACA
1 CATAATATACA
1579533 TAAGAATATA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.55, C:0.19, G:0.00, T:0.26
Consensus pattern (31 bp):
CATAATATACACACTAATATATCATAACAAA
Found at i:1579541 original size:31 final size:31
Alignment explanation
Indices: 1579475--1579545 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 31
1579465 CATACACACT
* **
1579475 AATATATCATAACAAACATAATATACATACT
1 AATATATCATAACAAACAAAATATACATAAG
*
1579506 AATATATCATAACATACAAAATATACATAAG
1 AATATATCATAACAAACAAAATATACATAAG
1579537 AATATATCA
1 AATATATCA
1579546 ATTGATTGAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.56, C:0.14, G:0.01, T:0.28
Consensus pattern (31 bp):
AATATATCATAACAAACAAAATATACATAAG
Found at i:1581655 original size:9 final size:9
Alignment explanation
Indices: 1581641--1581671 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1581631 GTTAAACGAA
1581641 TCGAGTTAT
1 TCGAGTTAT
*
1581650 TCGAGTTAA
1 TCGAGTTAT
1581659 TCGAGTTAT
1 TCGAGTTAT
1581668 TCGA
1 TCGA
1581672 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:1581742 original size:9 final size:9
Alignment explanation
Indices: 1581725--1581761 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
1581715 TGAGCTTTCG
1581725 AATTCGAAT
1 AATTCGAAT
*
1581734 AACTCGAAT
1 AATTCGAAT
1581743 AATTCGAAT
1 AATTCGAAT
1581752 AATTCGAAT
1 AATTCGAAT
1581761 A
1 A
1581762 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:1582007 original size:20 final size:20
Alignment explanation
Indices: 1581959--1581998 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1581949 CCCCCAAAAA
1581959 CCCTCAAAACCTTTTATTTT
1 CCCTCAAAACCTTTTATTTT
1581979 CCCTCAAAACCTTTTATTTT
1 CCCTCAAAACCTTTTATTTT
1581999 TCTCCAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.30, G:0.00, T:0.45
Consensus pattern (20 bp):
CCCTCAAAACCTTTTATTTT
Found at i:1582040 original size:30 final size:29
Alignment explanation
Indices: 1581996--1582052 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
1581986 AACCTTTTAT
*
1581996 TTTTCTCCAAAATTTTTACTCCCTTCCAC
1 TTTTCCCCAAAATTTTTACTCCCTTCCAC
* *
1582025 TTTTCCCCTAAAATTTTTATTCTCTTCC
1 TTTTCCCC-AAAATTTTTACTCCCTTCC
1582053 CATCCCACCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 7 0.29
30 17 0.71
ACGTcount: A:0.19, C:0.32, G:0.00, T:0.49
Consensus pattern (29 bp):
TTTTCCCCAAAATTTTTACTCCCTTCCAC
Found at i:1582494 original size:5 final size:5
Alignment explanation
Indices: 1582484--1582510 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
1582474 CTCGAAAATT
1582484 TTCGA TTCGA TTCGA TTCGA TTCGA TT
1 TTCGA TTCGA TTCGA TTCGA TTCGA TT
1582511 GAATGCTCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.44
Consensus pattern (5 bp):
TTCGA
Found at i:1582975 original size:81 final size:81
Alignment explanation
Indices: 1582833--1582996 Score: 260
Period size: 81 Copynumber: 2.0 Consensus size: 81
1582823 TTAAAATGAT
*
1582833 TTTGGTCTGCGAAATTTGAGAAAATGAGTCCGAGAGTCAGTTACGCACGAGGAAGGATTAGCACC
1 TTTGGTCTGCGAAATTTGAGAAAATGAGTCCGAGAGTCAGCTACGCACGAGGAAGGATTAGCACC
*
1582898 CTCGTAACGCCCAAAA
66 CTCGCAACGCCCAAAA
* *
1582914 TTTGGTCTGCGAAATTTGAGAAAAT-AGGTTCGGGAGTCAGCTACGCACGAGGAATGG-TTAGCA
1 TTTGGTCTGCGAAATTTGAGAAAATGA-GTCCGAGAGTCAGCTACGCACGAGGAA-GGATTAGCA
1582977 CCCTCGCAACGCCCAAAA
64 CCCTCGCAACGCCCAAAA
1582995 TT
1 TT
1582997 GGTACCAAAT
Statistics
Matches: 77, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
80 1 0.01
81 74 0.96
82 2 0.03
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.22
Consensus pattern (81 bp):
TTTGGTCTGCGAAATTTGAGAAAATGAGTCCGAGAGTCAGCTACGCACGAGGAAGGATTAGCACC
CTCGCAACGCCCAAAA
Found at i:1583665 original size:2 final size:2
Alignment explanation
Indices: 1583658--1583713 Score: 60
Period size: 2 Copynumber: 28.0 Consensus size: 2
1583648 TTATAAAAGT
* * * *
1583658 TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA AA GA AA TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1583699 TA TA TA TA CTA TA TA
1 TA TA TA TA -TA TA TA
1583714 AGAAATGTGT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
1 1 0.02
2 43 0.93
3 2 0.04
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.45
Consensus pattern (2 bp):
TA
Found at i:1583695 original size:27 final size:26
Alignment explanation
Indices: 1583665--1583719 Score: 83
Period size: 27 Copynumber: 2.1 Consensus size: 26
1583655 AGTTATATAT
*
1583665 ATATATATATATATATTATATAAAGAA
1 ATATATATATATATACTATAT-AAGAA
*
1583692 ATATGTATATATATACTATATAAGAA
1 ATATATATATATATACTATATAAGAA
1583718 AT
1 AT
1583720 GTGTGTATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 7 0.27
27 19 0.73
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (26 bp):
ATATATATATATATACTATATAAGAA
Found at i:1586139 original size:29 final size:27
Alignment explanation
Indices: 1586076--1586141 Score: 69
Period size: 29 Copynumber: 2.4 Consensus size: 27
1586066 TATTTTGTGA
* *
1586076 TTATATTTTTAATTTAAAATTTAATTT
1 TTATATTTTTAATTTAAAATTGAATTG
* * *
1586103 TTAGATTTTTATTTTGAGACATTGAATTG
1 TTATATTTTTAATTT-A-AAATTGAATTG
1586132 TTATATTTTT
1 TTATATTTTT
1586142 CTGATTTAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
27 13 0.42
28 1 0.03
29 17 0.55
ACGTcount: A:0.30, C:0.02, G:0.08, T:0.61
Consensus pattern (27 bp):
TTATATTTTTAATTTAAAATTGAATTG
Found at i:1586338 original size:15 final size:15
Alignment explanation
Indices: 1586320--1586375 Score: 67
Period size: 15 Copynumber: 3.7 Consensus size: 15
1586310 TGAAAAGCAG
*
1586320 AAAAATATAATTTTT
1 AAAAATAAAATTTTT
1586335 AAAAATAAAAATTTTT
1 AAAAAT-AAAATTTTT
**
1586351 AAAAATAAAAACTTT
1 AAAAATAAAATTTTT
*
1586366 AAAATTAAAA
1 AAAAATAAAA
1586376 AAATTAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
15 22 0.61
16 14 0.39
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (15 bp):
AAAAATAAAATTTTT
Found at i:1586347 original size:16 final size:16
Alignment explanation
Indices: 1586328--1586376 Score: 73
Period size: 16 Copynumber: 3.1 Consensus size: 16
1586318 AGAAAAATAT
1586328 AATTTTTAAAAATAAA
1 AATTTTTAAAAATAAA
1586344 AATTTTTAAAAATAAA
1 AATTTTTAAAAATAAA
* *
1586360 AA-CTTTAAAATTAAA
1 AATTTTTAAAAATAAA
1586375 AA
1 AA
1586377 AATTAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
15 13 0.42
16 18 0.58
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (16 bp):
AATTTTTAAAAATAAA
Found at i:1586377 original size:16 final size:16
Alignment explanation
Indices: 1586332--1586387 Score: 62
Period size: 15 Copynumber: 3.6 Consensus size: 16
1586322 AAATATAATT
**
1586332 TTTAAAAATAAAAATT
1 TTTAAAAATAAAAAAC
1586348 TTTAAAAAT-AAAAAC
1 TTTAAAAATAAAAAAC
*
1586363 TTTAAAATTAAAAAA-
1 TTTAAAAATAAAAAAC
*
1586378 ATTAAAAATA
1 TTTAAAAATA
1586388 TCATTTTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
15 20 0.59
16 14 0.41
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (16 bp):
TTTAAAAATAAAAAAC
Found at i:1586937 original size:10 final size:10
Alignment explanation
Indices: 1586882--1586956 Score: 53
Period size: 10 Copynumber: 7.3 Consensus size: 10
1586872 ATGATTAAAA
*
1586882 AATTAATATT
1 AATTTATATT
1586892 AATTGTATATT
1 AATT-TATATT
*
1586903 GATTTATATT
1 AATTTATATT
* *
1586913 AATTGATATAA
1 AATTTATAT-T
*
1586924 AATTTGTATT
1 AATTTATATT
*
1586934 AATTTTTA-T
1 AATTTATATT
*
1586943 AATTAAATATT
1 AATT-TATATT
1586954 AAT
1 AAT
1586957 ATAAGTTTTA
Statistics
Matches: 50, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
9 5 0.10
10 26 0.52
11 19 0.38
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (10 bp):
AATTTATATT
Found at i:1586944 original size:21 final size:21
Alignment explanation
Indices: 1586880--1586937 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
1586870 AGATGATTAA
*
1586880 AAAATTAATATTAATTG-TAT
1 AAAATTTATATTAATTGATAT
**
1586900 ATTGATTTATATTAATTGATAT
1 A-AAATTTATATTAATTGATAT
*
1586922 AAAATTTGTATTAATT
1 AAAATTTATATTAATT
1586938 TTTATAATTA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
20 1 0.03
21 25 0.83
22 4 0.13
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (21 bp):
AAAATTTATATTAATTGATAT
Found at i:1589464 original size:27 final size:27
Alignment explanation
Indices: 1589426--1589524 Score: 148
Period size: 27 Copynumber: 3.7 Consensus size: 27
1589416 ACATCAGGAT
*
1589426 AGAAAAACCTTTGT-GCTGTAATATAAA
1 AGAAACACCTTTGTGGC-GTAATATAAA
1589453 AGAAACACCTTTGTGGCGTAATATAAA
1 AGAAACACCTTTGTGGCGTAATATAAA
*
1589480 AGAAACACCTTTGTGGCGTAATATGAA
1 AGAAACACCTTTGTGGCGTAATATAAA
1589507 AGAATA-ACCTTTGTGGCG
1 AGAA-ACACCTTTGTGGCG
1589525 AACTCTGAAT
Statistics
Matches: 68, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
27 65 0.96
28 3 0.04
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.27
Consensus pattern (27 bp):
AGAAACACCTTTGTGGCGTAATATAAA
Found at i:1601257 original size:27 final size:27
Alignment explanation
Indices: 1601227--1601439 Score: 135
Period size: 27 Copynumber: 7.9 Consensus size: 27
1601217 AAAATGATTA
* *
1601227 TAATAACCCAATAGGGTAAAATGACCG
1 TAATACCCCTATAGGGTAAAATGACCG
* ** * *
1601254 TAATGCCCCCGTAGGATAAAATAACCG
1 TAATACCCCTATAGGGTAAAATGACCG
*
1601281 TAA-AGCCCC-AGTAAGGTAAAATGACCG
1 TAATA-CCCCTA-TAGGGTAAAATGACCG
* * **
1601308 TAATACCCCTCTAAGGTAAAATGATTG
1 TAATACCCCTATAGGGTAAAATGACCG
* * * *
1601335 AAAGACCTCTATAGGGTAAAATGATCG
1 TAATACCCCTATAGGGTAAAATGACCG
* * *
1601362 TAATACCCCTATAGAGTTAAATGACTG
1 TAATACCCCTATAGGGTAAAATGACCG
* *** * *
1601389 AAATACTTTTGTAAGGTAAAATGACCG
1 TAATACCCCTATAGGGTAAAATGACCG
* * *
1601416 TAATGCCCCTAGA-GGTTAAATGAC
1 TAATACCCCTATAGGGTAAAATGAC
1601440 TATAATGCCC
Statistics
Matches: 138, Mismatches: 44, Indels: 9
0.72 0.23 0.05
Matches are distributed among these distances:
26 10 0.07
27 127 0.92
28 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (27 bp):
TAATACCCCTATAGGGTAAAATGACCG
Found at i:1601353 original size:54 final size:54
Alignment explanation
Indices: 1601241--1601440 Score: 167
Period size: 54 Copynumber: 3.7 Consensus size: 54
1601231 AACCCAATAG
* ** * * *
1601241 GGTAAAATGACCGTAATGCCCCCGTAG-GATAAAATAACCGTAAAG-CC-CCAGTAA
1 GGTAAAATGACCGTAATACCCCTATAGAG-TAAAATGACTG-AAAGACCTCTA-TAA
* * *
1601295 GGTAAAATGACCGTAATACCCCTCTA-AGGTAAAATGATTGAAAGACCTCTATAG
1 GGTAAAATGACCGTAATACCCCTATAGA-GTAAAATGACTGAAAGACCTCTATAA
* * * * * *
1601349 GGTAAAATGATCGTAATACCCCTATAGAGTTAAATGACTGAAATACTTTTGTAA
1 GGTAAAATGACCGTAATACCCCTATAGAGTAAAATGACTGAAAGACCTCTATAA
* * *
1601403 GGTAAAATGACCGTAATGCCCCTAGAG-GTTAAATGACT
1 GGTAAAATGACCGTAATACCCCTATAGAGTAAAATGACT
1601441 ATAATGCCCC
Statistics
Matches: 121, Mismatches: 20, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
53 15 0.12
54 102 0.84
55 4 0.03
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (54 bp):
GGTAAAATGACCGTAATACCCCTATAGAGTAAAATGACTGAAAGACCTCTATAA
Found at i:1601462 original size:26 final size:26
Alignment explanation
Indices: 1601402--1601464 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
1601392 TACTTTTGTA
* *
1601402 AGGTAAAATGACCGTAATGCCCCTAG
1 AGGTTAAATGACCATAATGCCCCTAG
* *
1601428 AGGTTAAATGACTATAATGCCCCTCG
1 AGGTTAAATGACCATAATGCCCCTAG
1601454 A-GTGTAAATGA
1 AGGT-TAAATGA
1601465 TTGATATGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 2 0.06
26 30 0.94
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (26 bp):
AGGTTAAATGACCATAATGCCCCTAG
Found at i:1601504 original size:24 final size:24
Alignment explanation
Indices: 1601477--1601566 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
1601467 GATATGTTCG
*
1601477 TGATGTAAATGACTGATTTTTCTA
1 TGATGTAAATGACTGATTTGTCTA
* * *
1601501 TGATTTAAAGGACTGATTTGTCTG
1 TGATGTAAATGACTGATTTGTCTA
1601525 TGATTGGT--ATGACTGATTTGTCTA
1 TGA-T-GTAAATGACTGATTTGTCTA
* **
1601549 TGATTTGTATGACTGATT
1 TGATGTAAATGACTGATT
1601567 CTGAGCATGG
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
22 1 0.02
23 1 0.02
24 50 0.93
25 1 0.02
26 1 0.02
ACGTcount: A:0.24, C:0.08, G:0.22, T:0.46
Consensus pattern (24 bp):
TGATGTAAATGACTGATTTGTCTA
Found at i:1601736 original size:32 final size:32
Alignment explanation
Indices: 1601695--1601851 Score: 156
Period size: 32 Copynumber: 4.9 Consensus size: 32
1601685 GCTGCGATGC
* * *
1601695 TATTGATGGCTTTGTGCCGGTCATATTTCTGT
1 TATTGATGGCTTTGTGCCGATCATATTACCGT
*
1601727 TATTGATGGCTTTGTGCCGATCATATTGCCGT
1 TATTGATGGCTTTGTGCCGATCATATTACCGT
*
1601759 TACTT-ATGGATTTGTGCCGATCATATTACCGT
1 TA-TTGATGGCTTTGTGCCGATCATATTACCGT
** * * * * *
1601791 TAGCGATGGCTGTGTGCCAATCATATCACTGC
1 TATTGATGGCTTTGTGCCGATCATATTACCGT
* *
1601823 TACTT-ATGGCTTTGTGCCAATCAGATTAC
1 TA-TTGATGGCTTTGTGCCGATCATATTAC
1601852 TATACTTATG
Statistics
Matches: 104, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
32 102 0.98
33 2 0.02
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.39
Consensus pattern (32 bp):
TATTGATGGCTTTGTGCCGATCATATTACCGT
Found at i:1601807 original size:64 final size:64
Alignment explanation
Indices: 1601700--1601851 Score: 178
Period size: 64 Copynumber: 2.4 Consensus size: 64
1601690 GATGCTATTG
* * * ** * * ** *
1601700 ATGGCTTTGTGCCGGTCATATTTCTGTTATTGATGGCTTTGTGCCGATCATATTGCCGTTACTT
1 ATGGCTTTGTGCCGATCATATTACCGTTAGCGATGGCTGTGTGCCAATCATATCACCGCTACTT
* *
1601764 ATGGATTTGTGCCGATCATATTACCGTTAGCGATGGCTGTGTGCCAATCATATCACTGCTACTT
1 ATGGCTTTGTGCCGATCATATTACCGTTAGCGATGGCTGTGTGCCAATCATATCACCGCTACTT
* *
1601828 ATGGCTTTGTGCCAATCAGATTAC
1 ATGGCTTTGTGCCGATCATATTAC
1601852 TATACTTATG
Statistics
Matches: 73, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
64 73 1.00
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.38
Consensus pattern (64 bp):
ATGGCTTTGTGCCGATCATATTACCGTTAGCGATGGCTGTGTGCCAATCATATCACCGCTACTT
Found at i:1601861 original size:31 final size:32
Alignment explanation
Indices: 1601796--1601861 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
1601786 ACCGTTAGCG
* *
1601796 ATGGCTGTGTGCCAATCATATCACTGCTACTT
1 ATGGCTGTGTGCCAATCAGATCACTGATACTT
* *
1601828 ATGGCTTTGTGCCAATCAGATTACT-ATACTT
1 ATGGCTGTGTGCCAATCAGATCACTGATACTT
1601859 ATG
1 ATG
1601862 ACTTGTATCC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 8 0.27
32 22 0.73
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.36
Consensus pattern (32 bp):
ATGGCTGTGTGCCAATCAGATCACTGATACTT
Found at i:1604618 original size:27 final size:27
Alignment explanation
Indices: 1604588--1604866 Score: 231
Period size: 27 Copynumber: 10.4 Consensus size: 27
1604578 CCCATTATTT
* * *
1604588 GTAAACTGATCGTAATACCCATATAGG
1 GTAAAATGACCGTAATACCCCTATAGG
* * *
1604615 GTAAAATGATCGAAAAACTCCC-ATAGG
1 GTAAAATGACCGTAATAC-CCCTATAGG
* * **
1604642 CTAAAATGACCGTAATGCCCCCGTAGG
1 GTAAAATGACCGTAATACCCCTATAGG
* * * * *
1604669 GTAAAATGATCGTAATGCCTCTGTAAG
1 GTAAAATGACCGTAATACCCCTATAGG
1604696 GTAAAATGACCGTAATACCCCTATAGG
1 GTAAAATGACCGTAATACCCCTATAGG
* * * *
1604723 GTAAAATGATCGAAAAACCCCCATAGG
1 GTAAAATGACCGTAATACCCCTATAGG
* *
1604750 GTAAAATGACCATAATGCCCCTATAGG
1 GTAAAATGACCGTAATACCCCTATAGG
*
1604777 GTAAAATGACCGTAGTA-CCCTGATAGG
1 GTAAAATGACCGTAATACCCCT-ATAGG
* * * * *
1604804 GTTAAATGACTGAAATACCCCTGTAAG
1 GTAAAATGACCGTAATACCCCTATAGG
* * * * *
1604831 GTCAAATAATCGTAATGCCCCTAGAGG
1 GTAAAATGACCGTAATACCCCTATAGG
1604858 GT-AAATGAC
1 GTAAAATGAC
1604867 AATTTTGCCC
Statistics
Matches: 198, Mismatches: 50, Indels: 9
0.77 0.19 0.04
Matches are distributed among these distances:
26 12 0.06
27 180 0.91
28 6 0.03
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.22
Consensus pattern (27 bp):
GTAAAATGACCGTAATACCCCTATAGG
Found at i:1604728 original size:81 final size:80
Alignment explanation
Indices: 1604588--1604866 Score: 276
Period size: 81 Copynumber: 3.5 Consensus size: 80
1604578 CCCATTATTT
* * * * * *
1604588 GTAAACTGATCGTAATACCCATATAGGGTAAAATGATCGAAAAACTCCC-ATAGGCTAAAATGAC
1 GTAAAATGATCGTAATGCCC-TATAGGGTAAAATGACCGTAATAC-CCCTATAGGGTAAAATGAC
* *
1604652 CGTAATGCCCCCGTAGG
64 CGAAATACCCCCGTAGG
* * *
1604669 GTAAAATGATCGTAATGCCTCTGTAAGGTAAAATGACCGTAATACCCCTATAGGGTAAAATGATC
1 GTAAAATGATCGTAATGCC-CTATAGGGTAAAATGACCGTAATACCCCTATAGGGTAAAATGACC
* *
1604734 GAAAAACCCCCATAGG
65 GAAATACCCCCGTAGG
* * * *
1604750 GTAAAATGACCATAATGCCCCTATAGGGTAAAATGACCGTAGTA-CCCTGATAGGGTTAAATGAC
1 GTAAAATGATCGTAATG-CCCTATAGGGTAAAATGACCGTAATACCCCT-ATAGGGTAAAATGAC
* * *
1604814 TGAAATACCCCTGTAAG
64 CGAAATACCCCCGTAGG
* * *
1604831 GTCAAATAATCGTAATGCCCCTAGAGGGT-AAATGAC
1 GTAAAATGATCGTAATG-CCCTATAGGGTAAAATGAC
1604867 AATTTTGCCC
Statistics
Matches: 164, Mismatches: 30, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
80 14 0.09
81 147 0.90
82 3 0.02
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.22
Consensus pattern (80 bp):
GTAAAATGATCGTAATGCCCTATAGGGTAAAATGACCGTAATACCCCTATAGGGTAAAATGACCG
AAATACCCCCGTAGG
Found at i:1604915 original size:24 final size:24
Alignment explanation
Indices: 1604885--1604931 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1604875 CCCTCGAGTT
*
1604885 TAAATGATTGATATGTCCGTGATG
1 TAAATGACTGATATGTCCGTGATG
* *
1604909 TAAATGACTGATTTGTCTGTGAT
1 TAAATGACTGATATGTCCGTGAT
1604932 TTGTATCACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.28, C:0.09, G:0.23, T:0.40
Consensus pattern (24 bp):
TAAATGACTGATATGTCCGTGATG
Found at i:1604933 original size:11 final size:11
Alignment explanation
Indices: 1604917--1604983 Score: 53
Period size: 11 Copynumber: 5.7 Consensus size: 11
1604907 TGTAAATGAC
1604917 TGATTTGTCTG
1 TGATTTGTCTG
**
1604928 TGATTTGTATCAC
1 TGATTTG--TCTG
1604941 TGATTTGTCTG
1 TGATTTGTCTG
**
1604952 TGATTTGTATCAC
1 TGATTTG--TCTG
*
1604965 TGATTGGTCTG
1 TGATTTGTCTG
1604976 TGATTTGT
1 TGATTTGT
1604984 ATGACTGATT
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
11 25 0.60
13 17 0.40
ACGTcount: A:0.15, C:0.10, G:0.24, T:0.51
Consensus pattern (11 bp):
TGATTTGTCTG
Found at i:1604942 original size:24 final size:24
Alignment explanation
Indices: 1604915--1604993 Score: 140
Period size: 24 Copynumber: 3.3 Consensus size: 24
1604905 GATGTAAATG
1604915 ACTGATTTGTCTGTGATTTGTATC
1 ACTGATTTGTCTGTGATTTGTATC
1604939 ACTGATTTGTCTGTGATTTGTATC
1 ACTGATTTGTCTGTGATTTGTATC
* *
1604963 ACTGATTGGTCTGTGATTTGTATG
1 ACTGATTTGTCTGTGATTTGTATC
1604987 ACTGATT
1 ACTGATT
1604994 CTAAGCATGG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 53 1.00
ACGTcount: A:0.18, C:0.11, G:0.23, T:0.48
Consensus pattern (24 bp):
ACTGATTTGTCTGTGATTTGTATC
Found at i:1604946 original size:13 final size:13
Alignment explanation
Indices: 1604928--1604969 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
1604918 GATTTGTCTG
1604928 TGATTTGTATCAC
1 TGATTTGTATCAC
**
1604941 TGATTTG--TCTG
1 TGATTTGTATCAC
1604952 TGATTTGTATCAC
1 TGATTTGTATCAC
1604965 TGATT
1 TGATT
1604970 GGTCTGTGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
11 9 0.39
13 14 0.61
ACGTcount: A:0.19, C:0.12, G:0.19, T:0.50
Consensus pattern (13 bp):
TGATTTGTATCAC
Found at i:1605217 original size:32 final size:32
Alignment explanation
Indices: 1605165--1605320 Score: 179
Period size: 32 Copynumber: 4.9 Consensus size: 32
1605155 GCTATGATGC
* *
1605165 TACTGATGGCTTTTTACCGATCATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* *
1605197 TACTAATGGCTTTGTGCCGATCATATTACCAT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* *
1605229 TACTGATGGCTTTGTACCGATCATATTATCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* * * * * * *
1605261 TATTGATGGCTGTGTGCTGGTCATATCACTGC
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
*
1605293 TACTGATGGCTTTGTGCCAAT-ATATTAC
1 TACTGATGGCTTTGTGCCGATCATATTAC
1605321 TGTACTTATG
Statistics
Matches: 101, Mismatches: 23, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
31 6 0.06
32 95 0.94
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCGATCATATTACCGT
Found at i:1605361 original size:22 final size:22
Alignment explanation
Indices: 1605336--1605389 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
1605326 TTATGGATTG
1605336 TAGCCATTCTATTTATAGCT-T
1 TAGCCATTCTATTTATAGCTCT
* * * *
1605357 ATAGCTATCCTGTTTATGGCTCT
1 -TAGCCATTCTATTTATAGCTCT
1605380 TAGCCATTCT
1 TAGCCATTCT
1605390 GGTTACTAGA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
22 24 0.96
23 1 0.04
ACGTcount: A:0.20, C:0.22, G:0.13, T:0.44
Consensus pattern (22 bp):
TAGCCATTCTATTTATAGCTCT
Found at i:1606170 original size:17 final size:17
Alignment explanation
Indices: 1606148--1606187 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1606138 GGTTTTGTAC
*
1606148 AAGTTTTAAATGGCAAG
1 AAGTTTGAAATGGCAAG
**
1606165 AAGTTTGAAATTTCAAG
1 AAGTTTGAAATGGCAAG
1606182 AAGTTT
1 AAGTTT
1606188 CAATGAAAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.40, C:0.05, G:0.20, T:0.35
Consensus pattern (17 bp):
AAGTTTGAAATGGCAAG
Found at i:1610076 original size:20 final size:20
Alignment explanation
Indices: 1610051--1610095 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
1610041 GTCCAAACCG
1610051 AATTAATTAG-GTCTTAG-TTT
1 AATTAATT-GTGTCTT-GTTTT
1610071 AATTAATTGTGTCTTGTTTT
1 AATTAATTGTGTCTTGTTTT
1610091 AATTA
1 AATTA
1610096 TGTGAACTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.29, C:0.04, G:0.13, T:0.53
Consensus pattern (20 bp):
AATTAATTGTGTCTTGTTTT
Found at i:1612781 original size:14 final size:14
Alignment explanation
Indices: 1612762--1612791 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1612752 GGAAGGGATG
1612762 AACCAAGTATATAT
1 AACCAAGTATATAT
1612776 AACCAAGTATATAT
1 AACCAAGTATATAT
1612790 AA
1 AA
1612792 ATCTAGCTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.53, C:0.13, G:0.07, T:0.27
Consensus pattern (14 bp):
AACCAAGTATATAT
Found at i:1630807 original size:18 final size:18
Alignment explanation
Indices: 1630773--1630806 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1630763 AACTTTTTAT
1630773 AATTTTTTATTAATTTTG
1 AATTTTTTATTAATTTTG
1630791 AATTTTTTA-TAATTTT
1 AATTTTTTATTAATTTT
1630807 TAAATATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (18 bp):
AATTTTTTATTAATTTTG
Found at i:1640772 original size:16 final size:17
Alignment explanation
Indices: 1640747--1640781 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
1640737 ACTTTTTCAA
1640747 TCATCCCTCATCC-CTC
1 TCATCCCTCATCCTCTC
*
1640763 TCATCTCTCATCCTCTC
1 TCATCCCTCATCCTCTC
1640780 TC
1 TC
1640782 TCAACTCTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.11, C:0.51, G:0.00, T:0.37
Consensus pattern (17 bp):
TCATCCCTCATCCTCTC
Found at i:1647576 original size:20 final size:20
Alignment explanation
Indices: 1647551--1647588 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1647541 GCTTTTCTAG
1647551 TTTAAATTATTT-TGTTAAAT
1 TTTAAATT-TTTATGTTAAAT
1647571 TTTAAATTTTTATGTTAA
1 TTTAAATTTTTATGTTAA
1647589 TAAAGGGGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (20 bp):
TTTAAATTTTTATGTTAAAT
Found at i:1651626 original size:16 final size:17
Alignment explanation
Indices: 1651605--1651640 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1651595 TCAATCATCC
1651605 CTCATCCCTCATCC-CT
1 CTCATCCCTCATCCTCT
*
1651621 CTCATCTCTCATCCTCT
1 CTCATCCCTCATCCTCT
1651638 CTC
1 CTC
1651641 TCAACTCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.11, C:0.53, G:0.00, T:0.36
Consensus pattern (17 bp):
CTCATCCCTCATCCTCT
Found at i:1661230 original size:16 final size:16
Alignment explanation
Indices: 1661209--1661278 Score: 79
Period size: 16 Copynumber: 4.4 Consensus size: 16
1661199 AAAATTACTG
*
1661209 ATTATAGCTCTATTCT
1 ATTATAACTCTATTCT
* *
1661225 ATTATAACTTTAATCT
1 ATTATAACTCTATTCT
1661241 ATTATAACTCTA-TCT
1 ATTATAACTCTATTCT
* *
1661256 AATTACAACACTATTCT
1 -ATTATAACTCTATTCT
1661273 ATTATA
1 ATTATA
1661279 GTAATCAAAC
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
15 3 0.07
16 39 0.87
17 3 0.07
ACGTcount: A:0.36, C:0.17, G:0.01, T:0.46
Consensus pattern (16 bp):
ATTATAACTCTATTCT
Found at i:1662269 original size:15 final size:15
Alignment explanation
Indices: 1662249--1662282 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1662239 AGTGGCCTTG
1662249 TTTCTTTGTTTTTCT
1 TTTCTTTGTTTTTCT
* *
1662264 TTTCTTTTTTTTTGT
1 TTTCTTTGTTTTTCT
1662279 TTTC
1 TTTC
1662283 CATCTGTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.82
Consensus pattern (15 bp):
TTTCTTTGTTTTTCT
Found at i:1677269 original size:20 final size:20
Alignment explanation
Indices: 1677246--1677283 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1677236 TTTTTCCTAA
1677246 AAATAATAAATCAAATGTTT
1 AAATAATAAATCAAATGTTT
* *
1677266 AAATCATAATTCAAATGT
1 AAATAATAAATCAAATGT
1677284 CGTTTTCATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.08, G:0.05, T:0.34
Consensus pattern (20 bp):
AAATAATAAATCAAATGTTT
Found at i:1679414 original size:5 final size:5
Alignment explanation
Indices: 1679404--1679436 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
1679394 TACTATAGAA
*
1679404 TTAAT TTAAT TTAAT TTAAT TT-AT TTCAT TTAA
1 TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAA
1679437 GATTATATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (5 bp):
TTAAT
Found at i:1685226 original size:14 final size:14
Alignment explanation
Indices: 1685167--1685231 Score: 60
Period size: 14 Copynumber: 4.4 Consensus size: 14
1685157 TTTGCACATT
1685167 TTTCTTTTCT-TTC
1 TTTCTTTTCTCTTC
* * *
1685180 TTTATGTTTCTGTTAT
1 TTTCT-TTTCTCTT-C
1685196 TTTCCTTTTCTTCTTC
1 TTT-CTTTTC-TCTTC
1685212 TTTCTTTTCTCTTC
1 TTTCTTTTCTCTTC
1685226 TTTCTT
1 TTTCTT
1685232 GCTTTGCCAA
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
13 4 0.10
14 16 0.38
15 8 0.19
16 10 0.24
17 4 0.10
ACGTcount: A:0.03, C:0.22, G:0.03, T:0.72
Consensus pattern (14 bp):
TTTCTTTTCTCTTC
Found at i:1686340 original size:49 final size:49
Alignment explanation
Indices: 1686270--1686365 Score: 192
Period size: 49 Copynumber: 2.0 Consensus size: 49
1686260 GTATACCACA
1686270 ACATATTGGTGTGATTGAATGGATGGTCTCTAGTAGTCCTATTTGGTCC
1 ACATATTGGTGTGATTGAATGGATGGTCTCTAGTAGTCCTATTTGGTCC
1686319 ACATATTGGTGTGATTGAATGGATGGTCTCTAGTAGTCCTATTTGGT
1 ACATATTGGTGTGATTGAATGGATGGTCTCTAGTAGTCCTATTTGGT
1686366 GTGATAGGTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.21, C:0.12, G:0.27, T:0.40
Consensus pattern (49 bp):
ACATATTGGTGTGATTGAATGGATGGTCTCTAGTAGTCCTATTTGGTCC
Found at i:1688172 original size:18 final size:17
Alignment explanation
Indices: 1688120--1688175 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 17
1688110 AAATTAGTGC
1688120 ATTTTTAAATTAATAATT
1 ATTTTTAAATT-ATAATT
* *
1688138 GTAATTTAAATTATAATT
1 AT-TTTTAAATTATAATT
*
1688156 ATTTTTAAATGTGTAATT
1 ATTTTTAAAT-TATAATT
1688174 AT
1 AT
1688176 CACAACTTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
17 7 0.23
18 16 0.52
19 8 0.26
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (17 bp):
ATTTTTAAATTATAATT
Found at i:1688196 original size:44 final size:44
Alignment explanation
Indices: 1688148--1688231 Score: 159
Period size: 44 Copynumber: 1.9 Consensus size: 44
1688138 GTAATTTAAA
*
1688148 TTATAATTATTTTTAAATGTGTAATTATCACAACTTCTATCAAG
1 TTATAATTATTTTTAAATGTATAATTATCACAACTTCTATCAAG
1688192 TTATAATTATTTTTAAATGTATAATTATCACAACTTCTAT
1 TTATAATTATTTTTAAATGTATAATTATCACAACTTCTAT
1688232 TCCATTTCAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.37, C:0.11, G:0.05, T:0.48
Consensus pattern (44 bp):
TTATAATTATTTTTAAATGTATAATTATCACAACTTCTATCAAG
Found at i:1688595 original size:41 final size:41
Alignment explanation
Indices: 1688538--1688759 Score: 309
Period size: 41 Copynumber: 5.4 Consensus size: 41
1688528 CCTTGTGGGT
* **
1688538 CTTTAGCGGCGTTTTTCAAGAAGCGTCGCTAATGCGTGGAC
1 CTTTAGCGGCGTTTTTCAAGAAGCGCCGCTAATGCGCAGAC
** *
1688579 CTTTAGCGGCCCTTTTCAAGAAGCGCCGCTAATGCGCAAAC
1 CTTTAGCGGCGTTTTTCAAGAAGCGCCGCTAATGCGCAGAC
* * *
1688620 CTTTAGTGGCGTTTTTTAATAAGCGCCGCTAATGCGCAGAC
1 CTTTAGCGGCGTTTTTCAAGAAGCGCCGCTAATGCGCAGAC
* * *
1688661 CTTTAGCGGCGTTTTTCAGGAAGCGCCGCTAATGCACTGAC
1 CTTTAGCGGCGTTTTTCAAGAAGCGCCGCTAATGCGCAGAC
* *
1688702 CTTTAGCGGCATTTTTTCATGAAGCGCCGCTAATGCGCAGAC
1 CTTTAGCGGC-GTTTTTCAAGAAGCGCCGCTAATGCGCAGAC
1688744 CTTTAGCGGCGTTTTT
1 CTTTAGCGGCGTTTTT
1688760 TGTAAAGCGC
Statistics
Matches: 157, Mismatches: 23, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
41 120 0.76
42 37 0.24
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.29
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTCAAGAAGCGCCGCTAATGCGCAGAC
Found at i:1688759 original size:123 final size:123
Alignment explanation
Indices: 1688538--1688760 Score: 349
Period size: 123 Copynumber: 1.8 Consensus size: 123
1688528 CCTTGTGGGT
* *
1688538 CTTTAGCGGCGTTTTTCAAGAAGCGTCGCTAATGCGTGGACCTTTAGCGGCCCTTTTCAAGAAGC
1 CTTTAGCGGCGTTTTTCAAGAAGCGCCGCTAATGCCTGGACCTTTAGCGGCCCTTTTCAAGAAGC
*
1688603 GCCGCTAATGCGCAAACCTTTAGTGGCGTTTTTTAATAAGCGCCGCTAATGCGCAGAC
66 GCCGCTAATGCGCAAACCTTTAGCGGCGTTTTTTAATAAGCGCCGCTAATGCGCAGAC
* ** *
1688661 CTTTAGCGGCGTTTTTCAGGAAGCGCCGCTAATGCACT-GACCTTTAGCGGCATTTTTTCATGAA
1 CTTTAGCGGCGTTTTTCAAGAAGCGCCGCTAATGC-CTGGACCTTTAGCGGC-CCTTTTCAAGAA
*
1688725 GCGCCGCTAATGCGCAGACCTTTAGCGGCGTTTTTT
64 GCGCCGCTAATGCGCAAACCTTTAGCGGCGTTTTTT
1688761 GTAAAGCGCC
Statistics
Matches: 90, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
123 46 0.51
124 44 0.49
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.30
Consensus pattern (123 bp):
CTTTAGCGGCGTTTTTCAAGAAGCGCCGCTAATGCCTGGACCTTTAGCGGCCCTTTTCAAGAAGC
GCCGCTAATGCGCAAACCTTTAGCGGCGTTTTTTAATAAGCGCCGCTAATGCGCAGAC
Done.