Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167993.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_25, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 17943224
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 94000 characters in sequence are not A, C, G, or T
File 18 of 100
Found at i:3440801 original size:46 final size:45
Alignment explanation
Indices: 3440708--3440826 Score: 116
Period size: 47 Copynumber: 2.5 Consensus size: 45
3440698 TCTTTTTAAT
*
3440708 TTTTTTTATATGTTTTTTATTTATCTCATATTTATCTATTATTTTTA
1 TTTTTTT-TAT-TTTTTTATTTATCTCATATATATCTATTATTTTTA
* *
3440755 TTTTTTTCTATTTTTTTATTTATCTTATA-ATAT-TATTGTTGATTTA
1 TTTTTTT-TATTTTTTTATTTATCTCATATATATCTATTATT--TTTA
* *
3440801 TCTTATTATTATTTTTTTAATTATCT
1 T-TT-TTTTTATTTTTTTATTTATCT
3440827 ATTAATTTTT
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
44 6 0.10
45 3 0.05
46 22 0.35
47 28 0.45
48 3 0.05
ACGTcount: A:0.22, C:0.06, G:0.03, T:0.70
Consensus pattern (45 bp):
TTTTTTTTATTTTTTTATTTATCTCATATATATCTATTATTTTTA
Found at i:3440819 original size:19 final size:19
Alignment explanation
Indices: 3440738--3440853 Score: 71
Period size: 19 Copynumber: 6.0 Consensus size: 19
3440728 TTATCTCATA
*
3440738 TTTATC-TATTATTTTTATT
1 TTTATCTTATTATTATT-TT
* *
3440757 TTTTTC-TATT-TT-TTTA
1 TTTATCTTATTATTATTTT
3440773 TTTATCTTATAATATTATTGTT
1 TTTATCTTAT--TATTATT-TT
3440795 GATTTATCTTATTATTATTTT
1 --TTTATCTTATTATTATTTT
* *
3440816 TTTA-ATTATCTATTAATTT
1 TTTATCTTAT-TATTATTTT
* *
3440835 TTTATCTGATTTTTATTTT
1 TTTATCTTATTATTATTTT
3440854 GGAAGGCTAG
Statistics
Matches: 77, Mismatches: 10, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
16 6 0.08
17 5 0.06
18 6 0.08
19 33 0.43
20 5 0.06
21 4 0.05
22 8 0.10
24 10 0.13
ACGTcount: A:0.22, C:0.05, G:0.03, T:0.70
Consensus pattern (19 bp):
TTTATCTTATTATTATTTT
Found at i:3441163 original size:11 final size:11
Alignment explanation
Indices: 3441134--3441178 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 11
3441124 GGAATTAGCA
3441134 GAAATTTTTTT
1 GAAATTTTTTT
3441145 GAAGATTTTTTGT
1 GAA-ATTTTTT-T
*
3441158 GAATTTTTTTT
1 GAAATTTTTTT
3441169 GAGAATTTTT
1 GA-AATTTTT
3441179 AGAAAATTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
11 6 0.21
12 19 0.66
13 4 0.14
ACGTcount: A:0.24, C:0.00, G:0.16, T:0.60
Consensus pattern (11 bp):
GAAATTTTTTT
Found at i:3441790 original size:26 final size:26
Alignment explanation
Indices: 3441757--3441812 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
3441747 TTTATCTTTA
*
3441757 TTTTATTTTTATTTTTGGTTTTACTT
1 TTTTATTTTTATTTTTAGTTTTACTT
* *
3441783 TTTTATTTTTATTTTTATTTTTATTT
1 TTTTATTTTTATTTTTAGTTTTACTT
3441809 TTTT
1 TTTT
3441813 TCTTCTTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.12, C:0.02, G:0.04, T:0.82
Consensus pattern (26 bp):
TTTTATTTTTATTTTTAGTTTTACTT
Found at i:3441793 original size:43 final size:43
Alignment explanation
Indices: 3441746--3441834 Score: 119
Period size: 43 Copynumber: 2.1 Consensus size: 43
3441736 ATTAATGTTC
* *
3441746 TTTTATCTTTA-TTTTATTTTTATTT-TTGGTTTTACTTTTTTAT
1 TTTTATCTTTATTTTTATTTTT-TTTCTT-CTTTTACTTTATTAT
*
3441789 TTTTATTTTTATTTTTATTTTTTTTCTTCTTTTACTTTATTAT
1 TTTTATCTTTATTTTTATTTTTTTTCTTCTTTTACTTTATTAT
3441832 TTT
1 TTT
3441835 ATTTCCTTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
43 29 0.71
44 12 0.29
ACGTcount: A:0.13, C:0.06, G:0.02, T:0.79
Consensus pattern (43 bp):
TTTTATCTTTATTTTTATTTTTTTTCTTCTTTTACTTTATTAT
Found at i:3441821 original size:37 final size:36
Alignment explanation
Indices: 3441746--3441829 Score: 104
Period size: 37 Copynumber: 2.4 Consensus size: 36
3441736 ATTAATGTTC
3441746 TTTTATCTTTATTTTATTTTTATTTTTGGTTTTACTT
1 TTTTATCTTTATTTTATTTTTATTTTT-GTTTTACTT
*
3441783 TTTTATTTTTATTTTTATTTTTA-TTTT-TTTT-CTT
1 TTTTATCTTTA-TTTTATTTTTATTTTTGTTTTACTT
3441817 CTTTTA-CTTTATT
1 -TTTTATCTTTATT
3441830 ATTTTATTTC
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
33 2 0.05
34 7 0.16
35 9 0.21
37 14 0.33
38 11 0.26
ACGTcount: A:0.13, C:0.06, G:0.02, T:0.79
Consensus pattern (36 bp):
TTTTATCTTTATTTTATTTTTATTTTTGTTTTACTT
Found at i:3441826 original size:6 final size:6
Alignment explanation
Indices: 3441746--3441810 Score: 78
Period size: 6 Copynumber: 10.7 Consensus size: 6
3441736 ATTAATGTTC
* **
3441746 TTTTAT CTTTA- TTTTAT TTTTAT TTTTGG TTTTACTT TTTTAT TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTA--T TTTTAT TTTTAT
3441795 TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TTTT
3441811 TTTCTTCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
5 4 0.08
6 41 0.82
8 5 0.10
ACGTcount: A:0.14, C:0.03, G:0.03, T:0.80
Consensus pattern (6 bp):
TTTTAT
Found at i:3441992 original size:118 final size:116
Alignment explanation
Indices: 3441860--3442264 Score: 634
Period size: 118 Copynumber: 3.5 Consensus size: 116
3441850 AAATCTAAAA
* * *
3441860 AAAAATAAATTTTCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATA
1 AAAAATAAAATTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATA
3441925 AATCTTCAAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTT
66 AATCTTC-AAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTT
*
3441977 AAAAAATAAAATTTCAAAAAAAGTATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAG
1 -AAAAATAAAATTTCAAAAAAA-TATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAA
* * *
3442042 TAAATTTTCAAAAATAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTT
64 TAAATCTTCAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAA-TTTTCTT
* *
3442096 AAAAATAAAATTTCAAAAAAGTATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATA
1 AAAAATAAAATTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATA
*
3442161 AATCTTC-AAAAAAATATTTTTGAGGAAAAGTTGAAAATATCAATTTTCCTT
66 AATCTTCAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTT-CTT
* * *
3442212 AAAAATAAATTTTC-AAAAGATATTTTTGAGGAAAAATTGAAAGTATCAATTTT
1 AAAAATAAAATTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTT
3442265 TCCTACACAA
Statistics
Matches: 265, Mismatches: 19, Indels: 9
0.90 0.06 0.03
Matches are distributed among these distances:
115 39 0.15
116 49 0.18
117 48 0.18
118 75 0.28
119 54 0.20
ACGTcount: A:0.48, C:0.06, G:0.11, T:0.36
Consensus pattern (116 bp):
AAAAATAAAATTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATA
AATCTTCAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTT
Found at i:3442268 original size:58 final size:58
Alignment explanation
Indices: 3441860--3442264 Score: 625
Period size: 58 Copynumber: 6.9 Consensus size: 58
3441850 AAATCTAAAA
* *
3441860 AAAAATAAATTTTCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTT
1 AAAAATAAATTTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT
*
3441918 AAAAATAAATCTTCAAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTT-CTT
1 AAAAATAAATTTTC--AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT
*
3441977 AAAAAATAAAATTTCAAAAAAAGTATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT
1 -AAAAATAAATTTTCAAAAAAA-TATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT
* * *
3442037 AAAAGTAAATTTTCAAAAATAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTT
1 AAAAATAAATTTTCAAAAA-AATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT
* * *
3442096 AAAAATAAAATTTCAAAAAAGTATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTT
1 AAAAATAAATTTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT
* *
3442154 AAAAATAAATCTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAATATCAATTTTCCTT
1 AAAAATAAATTTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT
* *
3442212 AAAAATAAATTTTC-AAAAGATATTTTTGAGGAAAAATTGAAAGTATCAATTTT
1 AAAAATAAATTTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTT
3442265 TCCTACACAA
Statistics
Matches: 320, Mismatches: 21, Indels: 13
0.90 0.06 0.04
Matches are distributed among these distances:
57 36 0.11
58 123 0.38
59 105 0.33
60 56 0.17
ACGTcount: A:0.48, C:0.06, G:0.11, T:0.36
Consensus pattern (58 bp):
AAAAATAAATTTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT
Found at i:3445229 original size:21 final size:24
Alignment explanation
Indices: 3445189--3445233 Score: 69
Period size: 21 Copynumber: 2.0 Consensus size: 24
3445179 ATGGGGACAT
3445189 TTTTCTCTCTAGCAAACTCAAGGC
1 TTTTCTCTCTAGCAAACTCAAGGC
3445213 TTTTCT-TC-AGC-AACTCAAGGC
1 TTTTCTCTCTAGCAAACTCAAGGC
3445234 CCTTTGACCT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 10 0.48
22 3 0.14
23 2 0.10
24 6 0.29
ACGTcount: A:0.24, C:0.29, G:0.13, T:0.33
Consensus pattern (24 bp):
TTTTCTCTCTAGCAAACTCAAGGC
Found at i:3447042 original size:33 final size:33
Alignment explanation
Indices: 3447005--3447086 Score: 96
Period size: 32 Copynumber: 2.5 Consensus size: 33
3446995 AATATTTTTA
* *
3447005 TTATAATTAGATAAAATTCGTTTGTTTTAATT-T
1 TTATAATTAGATAAAATTCATTTGCTTT-ATTAT
*
3447038 TTATAA-TAGATAAAATTTATTTGCTTTATTAT
1 TTATAATTAGATAAAATTCATTTGCTTTATTAT
* *
3447070 TAATAATAAGATAAAAT
1 TTATAATTAGATAAAAT
3447087 CTATTTTTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
31 3 0.07
32 24 0.57
33 15 0.36
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.49
Consensus pattern (33 bp):
TTATAATTAGATAAAATTCATTTGCTTTATTAT
Found at i:3447092 original size:33 final size:31
Alignment explanation
Indices: 3447002--3447092 Score: 94
Period size: 33 Copynumber: 2.8 Consensus size: 31
3446992 AAAAATATTT
* *
3447002 TTATTATAATTAGATAAAATTCGTTTGTTTTAA
1 TTATTATAA-TAGATAAAATT-ATTTGCTTTAA
*
3447035 TTTTTATAATAGATAAAATTTATTTGCTTT-A
1 TTATTATAATAGATAAAA-TTATTTGCTTTAA
3447066 TTATTAATAATAAGATAAAATCTATTT
1 TTATT-ATAAT-AGATAAAAT-TATTT
3447093 TTTTATACAA
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
31 5 0.10
32 22 0.44
33 23 0.46
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.51
Consensus pattern (31 bp):
TTATTATAATAGATAAAATTATTTGCTTTAA
Found at i:3447176 original size:22 final size:21
Alignment explanation
Indices: 3447151--3447201 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 21
3447141 AATTGAATCA
3447151 AAATTTAAA-TAATTCATAATTT
1 AAATTTAAATTAATT-A-AATTT
3447173 AAATTTAAATTAATTAAATTT
1 AAATTTAAATTAATTAAATTT
3447194 ATAATTTA
1 A-AATTTA
3447202 TAAAAATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 6 0.22
22 16 0.59
23 5 0.19
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (21 bp):
AAATTTAAATTAATTAAATTT
Found at i:3463205 original size:34 final size:34
Alignment explanation
Indices: 3463167--3463240 Score: 78
Period size: 34 Copynumber: 2.2 Consensus size: 34
3463157 ATCCATTCCA
*
3463167 AGAAGCTTT-AAAGCCTCTCAGATATTCATTTTTT
1 AGAAG-TTTCAAAGCCTCTCAGATATCCATTTTTT
** * * *
3463201 AGAAGTTTCAAAGTTTCTCGGATATCCATTTCTA
1 AGAAGTTTCAAAGCCTCTCAGATATCCATTTTTT
3463235 AGAAGT
1 AGAAGT
3463241 CCTTAGTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
33 3 0.09
34 30 0.91
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (34 bp):
AGAAGTTTCAAAGCCTCTCAGATATCCATTTTTT
Found at i:3466509 original size:25 final size:27
Alignment explanation
Indices: 3466481--3466536 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 27
3466471 TTTTTTATTT
3466481 TATTTTTTAA-TTTT-TTTTATTTTCA
1 TATTTTTTAAGTTTTATTTTATTTTCA
*
3466506 TA--TTATAAGTTTTATTTTATTTTCA
1 TATTTTTTAAGTTTTATTTTATTTTCA
3466531 T-TTTTT
1 TATTTTT
3466537 GTTTTATTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
23 5 0.20
24 4 0.16
25 14 0.56
26 2 0.08
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.73
Consensus pattern (27 bp):
TATTTTTTAAGTTTTATTTTATTTTCA
Found at i:3467583 original size:28 final size:25
Alignment explanation
Indices: 3467537--3467597 Score: 63
Period size: 28 Copynumber: 2.4 Consensus size: 25
3467527 TTCCTATTTT
3467537 TTTATTT-TTATTGTTTATAT-TCTA
1 TTTATTTATTATTGTTTATATGTC-A
3467561 TTTATTTATTCATTGTATATATATGTCA
1 TTTATTTATT-ATTGT-T-TATATGTCA
*
3467589 TTCATTTAT
1 TTTATTTAT
3467598 ATGGGTATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
24 7 0.23
25 2 0.06
26 5 0.16
27 1 0.03
28 14 0.45
29 2 0.06
ACGTcount: A:0.25, C:0.07, G:0.05, T:0.64
Consensus pattern (25 bp):
TTTATTTATTATTGTTTATATGTCA
Found at i:3470419 original size:62 final size:62
Alignment explanation
Indices: 3470317--3470435 Score: 175
Period size: 62 Copynumber: 1.9 Consensus size: 62
3470307 AAATAAAAAA
* *
3470317 AAATGAAGGAAAAATTAATGGGGTAAAATACCAATATGCTCCACTAAAAAAAAAAAGAAAGG
1 AAATGAAGGAAAAATTAATGGAGTAAAATACCAATATGCTCCACCAAAAAAAAAAAGAAAGG
* * * * *
3470379 AAATGAAGGAGAAATTGATTGAGTAAAATGCCAATGTGCTCCACCAAAAAAAAAAAG
1 AAATGAAGGAAAAATTAATGGAGTAAAATACCAATATGCTCCACCAAAAAAAAAAAG
3470436 TTAAAAATAA
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
62 50 1.00
ACGTcount: A:0.54, C:0.11, G:0.18, T:0.17
Consensus pattern (62 bp):
AAATGAAGGAAAAATTAATGGAGTAAAATACCAATATGCTCCACCAAAAAAAAAAAGAAAGG
Found at i:3470471 original size:65 final size:62
Alignment explanation
Indices: 3470316--3470482 Score: 156
Period size: 62 Copynumber: 2.6 Consensus size: 62
3470306 CAAATAAAAA
** * * * *
3470316 AAAATGAAGGAAAAATTAATGGGGTAAAATACCAATATGCTCCACTAAAAAAAAAAAGAAAG
1 AAAATGAAAAAAAAATTGATGGGGTAAAATGCCAATGTGCTCCACCAAAAAAAAAAAGAAAG
* ** * * *
3470378 GAAATGAAGGAGAAATTGATTGAGTAAAATGCCAATGTGCTCCACCAAAAAAAAAAAGTTAAAAA
1 AAAATGAAAAAAAAATTGATGGGGTAAAATGCCAATGTGCTCCACCAAAAAAAAAAAG----AAA
*
3470443 T
62 G
**
3470444 AAAAT-AAAAAAAAATTGATGGGGTAAAATGTTAATGTGC
1 AAAATGAAAAAAAAATTGATGGGGTAAAATGCCAATGTGC
3470483 ACTACATAAA
Statistics
Matches: 84, Mismatches: 17, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
62 50 0.60
65 27 0.32
66 7 0.08
ACGTcount: A:0.54, C:0.08, G:0.18, T:0.20
Consensus pattern (62 bp):
AAAATGAAAAAAAAATTGATGGGGTAAAATGCCAATGTGCTCCACCAAAAAAAAAAAGAAAG
Found at i:3470757 original size:27 final size:28
Alignment explanation
Indices: 3470727--3470805 Score: 88
Period size: 27 Copynumber: 2.8 Consensus size: 28
3470717 AAGTGTGCAA
*
3470727 AAAAAAAAGAAAAAAGGGAAGAAAAG-G
1 AAAAAAAAGAAAAAAGGGAAAAAAAGAG
* *
3470754 AAAAAAAATAAAAAAAGGAAAAAAAGAG
1 AAAAAAAAGAAAAAAGGGAAAAAAAGAG
* * *
3470782 ACAAAAGAGACAAAAGAGGAAAAA
1 AAAAAAAAGAAAAAAG-GGAAAAA
3470806 TGAAAACTAA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
27 23 0.55
28 12 0.29
29 7 0.17
ACGTcount: A:0.76, C:0.03, G:0.20, T:0.01
Consensus pattern (28 bp):
AAAAAAAAGAAAAAAGGGAAAAAAAGAG
Found at i:3470787 original size:9 final size:9
Alignment explanation
Indices: 3470775--3470799 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3470765 AAAAAGGAAA
3470775 AAAAGAGAC
1 AAAAGAGAC
3470784 AAAAGAGAC
1 AAAAGAGAC
3470793 AAAAGAG
1 AAAAGAG
3470800 GAAAAATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.68, C:0.08, G:0.24, T:0.00
Consensus pattern (9 bp):
AAAAGAGAC
Found at i:3470805 original size:9 final size:9
Alignment explanation
Indices: 3470727--3470779 Score: 61
Period size: 9 Copynumber: 5.9 Consensus size: 9
3470717 AAGTGTGCAA
*
3470727 AAAAAAAAG
1 AAAAAAAGG
*
3470736 AAAAAAGGG
1 AAAAAAAGG
*
3470745 AAGAAAAGG
1 AAAAAAAGG
**
3470754 AAAAAAAAT
1 AAAAAAAGG
3470763 AAAAAAAGG
1 AAAAAAAGG
3470772 AAAAAAAG
1 AAAAAAAG
3470780 AGACAAAAGA
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (9 bp):
AAAAAAAGG
Found at i:3471962 original size:119 final size:119
Alignment explanation
Indices: 3471750--3471965 Score: 254
Period size: 119 Copynumber: 1.8 Consensus size: 119
3471740 TCTTGATCAT
* * * * * ** *
3471750 TTTATCTTTTTGACCCATGGTTTTGTCTTAGTCATTCGATCTTAGTTTTATCCAGATTATTTTTT
1 TTTATCTTTTCGACCCATGATTTTATCTTAGTCATTCAATCTCAGTTCCATCCAGATCATTTTTT
** * * *
3471815 GACTCGTGGTTCCGTCTCGATCAATCATCTTCGACTGGACTTATTTCTGGTCAC
66 GACTCACGATTCCGTCCCAATCAATCATCTTCGACTGGACTTATTTCTGGTCAC
* *
3471869 TTTATCTTTTCGACTCATGATTTTATCTTGGTCATTCAAAT-TCAGTTCCATCCAGATCATTTTT
1 TTTATCTTTTCGACCCATGATTTTATCTTAGTCATTC-AATCTCAGTTCCATCCAGATCATTTTT
* * *
3471933 TGACTCACGATTCTGTCCCAATTAGTCATCTTC
65 TGACTCACGATTCCGTCCCAATCAATCATCTTC
3471966 AACTTCAACT
Statistics
Matches: 78, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
119 76 0.97
120 2 0.03
ACGTcount: A:0.19, C:0.22, G:0.13, T:0.45
Consensus pattern (119 bp):
TTTATCTTTTCGACCCATGATTTTATCTTAGTCATTCAATCTCAGTTCCATCCAGATCATTTTTT
GACTCACGATTCCGTCCCAATCAATCATCTTCGACTGGACTTATTTCTGGTCAC
Found at i:3472113 original size:120 final size:119
Alignment explanation
Indices: 3471630--3472156 Score: 352
Period size: 120 Copynumber: 4.4 Consensus size: 119
3471620 TCTTTATTGT
* ** **
3471630 TTTATCTTTTTGACTCATGATTTTATCTCGATCATTCGATCTC-GATTTTGTTTAGATCATTTTT
1 TTTATCTTTTTGACTCATG-TTTTATCTCGATCATTCAATCTCAG-TTTCATCCAGATCATTTTT
* * * * * * *
3471694 TGATTCGTGGTT-TCATCTCGATCAGCCATTTTCAACCTTGACTCAG-TCTTGATCAT
64 TGACTCGCGGTTCT-ATCTCGATCAACCATCTTCGACCTTGACTCAGTTC-TGGTCAC
* * * * * * *
3471750 TTTATCTTTTTGACCCATGGTTTTGTCT-TAGTCATTCGATCTTAGTTTTATCCAGATTATTTTT
1 TTTATCTTTTTGACTCAT-GTTTTATCTCGA-TCATTCAATCTCAGTTTCATCCAGATCATTTTT
* ** * * * *
3471814 TGACTCGTGGTTCCGTCTCGATCAATCATCTTCGA-CTGGACTTATTTCTGGTCAC
64 TGACTCGCGGTTCTATCTCGATCAACCATCTTCGACCTTGACTCAGTTCTGGTCAC
* * * *
3471869 TTTATCTTTTCGACTCATGATTTTATCTTGGTCATTCAAAT-TCAGTTCCATCCAGATCATTTTT
1 TTTATCTTTTTGACTCATG-TTTTATCTCGATCATTC-AATCTCAGTTTCATCCAGATCATTTTT
* * * * * * ** * * * * ***
3471933 TGACTCACGATTCTGTCCCAATTAGTCATCTTC-AACTTCAACTCGGTCCTGGTTGT
64 TGACTCGCGGTTCTATCTCGATCAACCATCTTCGACCTT-GACTCAGTTCTGGTCAC
* * ** *
3471989 TTTATCTTTTTGACTCATAGTTTCATCTCGATCATTCTATCTTGGTTTCATCCAAATCATTTTTT
1 TTTATCTTTTTGACTCAT-GTTTTATCTCGATCATTCAATCTCAGTTTCATCCAGATCATTTTTT
* * * *
3472054 AACTCGCGGTTCTATC-CTGATCAACCATCTTCGACCTTGACTTAGTTCTTGTCGC
65 GACTCGCGGTTCTATCTC-GATCAACCATCTTCGACCTTGACTCAGTTCTGGTCAC
* ** *
3472109 TTTAT-TTTTTCAACTTGTGGTTTCATCTCGATCATTCAATCTCAGTTT
1 TTTATCTTTTT-GACTCAT-GTTTTATCTCGATCATTCAATCTCAGTTT
3472157 TGTCTAGATG
Statistics
Matches: 313, Mismatches: 79, Indels: 30
0.74 0.19 0.07
Matches are distributed among these distances:
118 2 0.01
119 96 0.31
120 208 0.66
121 7 0.02
ACGTcount: A:0.19, C:0.22, G:0.13, T:0.46
Consensus pattern (119 bp):
TTTATCTTTTTGACTCATGTTTTATCTCGATCATTCAATCTCAGTTTCATCCAGATCATTTTTTG
ACTCGCGGTTCTATCTCGATCAACCATCTTCGACCTTGACTCAGTTCTGGTCAC
Found at i:3473100 original size:21 final size:21
Alignment explanation
Indices: 3473072--3473117 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
3473062 ATACTGAGGA
**
3473072 TTCT-AGATTTAATTTTGGGT
1 TTCTGAGATTTAATTTTACGT
*
3473092 TTCTGAGATTTAGTTTTACGT
1 TTCTGAGATTTAATTTTACGT
3473113 TTCTG
1 TTCTG
3473118 GAATTAGGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.17, C:0.09, G:0.20, T:0.54
Consensus pattern (21 bp):
TTCTGAGATTTAATTTTACGT
Found at i:3473356 original size:2 final size:2
Alignment explanation
Indices: 3473349--3473375 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3473339 ATTGGGGTAA
3473349 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
3473376 ATGAGGTGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3475550 original size:22 final size:24
Alignment explanation
Indices: 3475515--3475561 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
3475505 TTTTTATAGC
*
3475515 TTTTACATATTATTTTAATAAATT
1 TTTTACATATTATTTAAATAAATT
*
3475539 TTTTA-ATA-TATTTAAATATATT
1 TTTTACATATTATTTAAATAAATT
3475561 T
1 T
3475562 ATATATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 13 0.62
23 3 0.14
24 5 0.24
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (24 bp):
TTTTACATATTATTTAAATAAATT
Found at i:3477022 original size:23 final size:24
Alignment explanation
Indices: 3476980--3477027 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
3476970 CACAACATCA
*
3476980 AATTTACAAATCCAACAATTTCAT
1 AATTTACAAATCCAACAATTCCAT
3477004 AATTTA-AAATCC-ACAAATTCCAT
1 AATTTACAAATCCAAC-AATTCCAT
3477027 A
1 A
3477028 CAAATTTCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 2 0.09
23 14 0.64
24 6 0.27
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.31
Consensus pattern (24 bp):
AATTTACAAATCCAACAATTCCAT
Found at i:3477187 original size:53 final size:53
Alignment explanation
Indices: 3477120--3477295 Score: 196
Period size: 53 Copynumber: 3.3 Consensus size: 53
3477110 ATATACCACC
* * *
3477120 AAATTCAGTATCAATTTCATAATTTTCACAATAAGACTCCATACCAATTTCAA
1 AAATTCAGTATCAATTTCACAATTTTCACAATAAGACTACATACAAATTTCAA
* * * * * * *
3477173 ATAATT-GGTATCAATTATCACAATTTCCACAGT-A-ATTTCATACTAATTTCAC
1 A-AATTCAGTATCAATT-TCACAATTTTCACAATAAGACTACATACAAATTTCAA
** *
3477225 AAATTCAACATCTATTTCACAATTTTCACAATAAGACTACATACAAATTTCAA
1 AAATTCAGTATCAATTTCACAATTTTCACAATAAGACTACATACAAATTTCAA
3477278 AAATTCAGTATCAATTTC
1 AAATTCAGTATCAATTTC
3477296 TCAAAATCAG
Statistics
Matches: 97, Mismatches: 21, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
51 18 0.19
52 22 0.23
53 40 0.41
54 17 0.18
ACGTcount: A:0.41, C:0.20, G:0.04, T:0.35
Consensus pattern (53 bp):
AAATTCAGTATCAATTTCACAATTTTCACAATAAGACTACATACAAATTTCAA
Found at i:3477295 original size:20 final size:19
Alignment explanation
Indices: 3477270--3477320 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
3477260 ACTACATACA
3477270 AATTTCAAAAATTCAGTATC
1 AATTTCAAAAA-TCAGTATC
* *
3477290 AATTTCTCAAAATCAGTATT
1 AATTTC-AAAAATCAGTATC
3477310 AATTTCAAAAA
1 AATTTCAAAAA
3477321 CTTAACAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 4 0.15
20 19 0.70
21 4 0.15
ACGTcount: A:0.47, C:0.14, G:0.04, T:0.35
Consensus pattern (19 bp):
AATTTCAAAAATCAGTATC
Found at i:3478313 original size:19 final size:19
Alignment explanation
Indices: 3478272--3478313 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
3478262 ACACATCAAC
**
3478272 TAAAAAATAAACTAAAATT
1 TAAAAAATAAACTAAAAAA
3478291 TAAAAAATAAA-TAAATAAA
1 TAAAAAATAAACTAAA-AAA
3478310 TAAA
1 TAAA
3478314 TAACCCAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (19 bp):
TAAAAAATAAACTAAAAAA
Found at i:3480356 original size:27 final size:27
Alignment explanation
Indices: 3480318--3480371 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
3480308 TTCACATCAT
*
3480318 TTCTTCTTTTTAATTTTGTTGTTCAAA
1 TTCTTCTTTTTAATTTTGTTATTCAAA
*
3480345 TTCTTCTTTTTAATTTTTTTATTCAAA
1 TTCTTCTTTTTAATTTTGTTATTCAAA
3480372 CTTCAATTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.20, C:0.11, G:0.04, T:0.65
Consensus pattern (27 bp):
TTCTTCTTTTTAATTTTGTTATTCAAA
Found at i:3483619 original size:127 final size:129
Alignment explanation
Indices: 3483369--3483621 Score: 397
Period size: 127 Copynumber: 2.0 Consensus size: 129
3483359 GATACATACA
* *
3483369 ATGAAAGCTACAAGAGTTAGGAGTTAAAAAGTAAAATCCATGACATTTATTGCAGTTACAATTAC
1 ATGAAAGCTACAAGAGCTAGGAGTTAAAAAGTAAAATCCATGACATTTATTACAGTTACAATTAC
*
3483434 GATGTTTCTGCAAGAAAGTTAAGTAATAACAACGGGAAAGAGACAAATAGATTCTCTTATAGAC
66 GATGTTTCTGCAAGAAAGTTAAGTAATAACAACAGGAAAGAGACAAATAGATTCTCTTATAGAC
* *
3483498 ATGAAAGCTACAA-AGCCTA-GAGTTAAAAGGTTAAATCCATGACATTTATTACAGTT-CAATTA
1 ATGAAAGCTACAAGAG-CTAGGAGTTAAAAAGTAAAATCCATGACATTTATTACAGTTACAATTA
* *
3483560 TGA-GATTTCTGCAAGAAAGTTAAGTAATAACAACAGGAAAGAGACAAATAGATTGTCTTATA
65 CGATG-TTTCTGCAAGAAAGTTAAGTAATAACAACAGGAAAGAGACAAATAGATTCTCTTATA
3483622 TACGGTAGAG
Statistics
Matches: 115, Mismatches: 7, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
126 1 0.01
127 63 0.55
128 36 0.31
129 15 0.13
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (129 bp):
ATGAAAGCTACAAGAGCTAGGAGTTAAAAAGTAAAATCCATGACATTTATTACAGTTACAATTAC
GATGTTTCTGCAAGAAAGTTAAGTAATAACAACAGGAAAGAGACAAATAGATTCTCTTATAGAC
Found at i:3484572 original size:33 final size:33
Alignment explanation
Indices: 3484530--3484597 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
3484520 GTAATGAGAT
3484530 ACCTCATTAAAATATAAAACAATCCACAAAAAG
1 ACCTCATTAAAATATAAAACAATCCACAAAAAG
* *
3484563 ACCTCATTAAAATATATAACAATCCATAAAAAG
1 ACCTCATTAAAATATAAAACAATCCACAAAAAG
3484596 AC
1 AC
3484598 AAAGTATTGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.56, C:0.21, G:0.03, T:0.21
Consensus pattern (33 bp):
ACCTCATTAAAATATAAAACAATCCACAAAAAG
Found at i:3487338 original size:32 final size:32
Alignment explanation
Indices: 3487265--3487338 Score: 114
Period size: 32 Copynumber: 2.3 Consensus size: 32
3487255 CTAGCTATTG
* *
3487265 TCTTTGTGTGCTATTTATTATCTATGGTCCCT
1 TCTTTGTGTTCTATTTATAATCTATGGTCCCT
3487297 TCTTTGTGTTCTATTTATAAT-TAATGGTCCCT
1 TCTTTGTGTTCTATTTATAATCT-ATGGTCCCT
3487329 TCTTTGTGTT
1 TCTTTGTGTT
3487339 ATTTTGCCTT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
31 1 0.03
32 38 0.97
ACGTcount: A:0.14, C:0.16, G:0.15, T:0.55
Consensus pattern (32 bp):
TCTTTGTGTTCTATTTATAATCTATGGTCCCT
Found at i:3488676 original size:20 final size:21
Alignment explanation
Indices: 3488637--3488676 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
3488627 ACTTTTTTTT
*
3488637 CATATTTTTATATTATATTAC
1 CATATTTTTATATTAAATTAC
*
3488658 CATA-TTTTATTTTAAATTA
1 CATATTTTTATATTAAATTA
3488677 TCAAATTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.57
Consensus pattern (21 bp):
CATATTTTTATATTAAATTAC
Found at i:3490336 original size:11 final size:11
Alignment explanation
Indices: 3490320--3490345 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3490310 TTATATAAAA
3490320 AATTATTTTTT
1 AATTATTTTTT
3490331 AATTATTTTTT
1 AATTATTTTTT
3490342 AATT
1 AATT
3490346 TTTAATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
AATTATTTTTT
Found at i:3493229 original size:3 final size:3
Alignment explanation
Indices: 3493221--3493293 Score: 76
Period size: 3 Copynumber: 24.7 Consensus size: 3
3493211 ATCGGAGTGT
* * * * * * *
3493221 GAA GAA GAA GAG GAA GAT TAT GAA GAT GAT GAT GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
3493269 G-A GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
3493294 GGAGGAGGAG
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
2 2 0.03
3 59 0.97
ACGTcount: A:0.58, C:0.00, G:0.34, T:0.08
Consensus pattern (3 bp):
GAA
Found at i:3500579 original size:7 final size:7
Alignment explanation
Indices: 3500567--3500597 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
3500557 ATTCGAATTG
3500567 AATTTTA
1 AATTTTA
3500574 AATTTTA
1 AATTTTA
3500581 AATTTTA
1 AATTTTA
3500588 AATTTTA
1 AATTTTA
3500595 AAT
1 AAT
3500598 CGAACTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (7 bp):
AATTTTA
Found at i:3501172 original size:23 final size:25
Alignment explanation
Indices: 3501146--3501232 Score: 78
Period size: 23 Copynumber: 3.6 Consensus size: 25
3501136 GGTTCGATTT
3501146 TATTAAATAAAT-TCATTTA-AAA-A
1 TATTAAATAAATAT-ATTTATAAATA
**
3501169 TATTAAACGAATATATTTATAAATA
1 TATTAAATAAATATATTTATAAATA
*
3501194 TATATAAATAAATATGTTT-TAAATA
1 TAT-TAAATAAATATATTTATAAATA
3501219 -A-TAAATTAAATATA
1 TATTAAA-TAAATATA
3501233 ATTAAATAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
22 4 0.08
23 22 0.42
24 5 0.09
25 10 0.19
26 12 0.23
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (25 bp):
TATTAAATAAATATATTTATAAATA
Found at i:3501289 original size:21 final size:22
Alignment explanation
Indices: 3501265--3501306 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
3501255 AATCCTAGAT
3501265 GAATATAAAAGAACC-TAAAAC
1 GAATATAAAAGAACCATAAAAC
*
3501286 GAATATAAATGAACCATAAAA
1 GAATATAAAAGAACCATAAAA
3501307 TAAAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.17
Consensus pattern (22 bp):
GAATATAAAAGAACCATAAAAC
Found at i:3501346 original size:3 final size:3
Alignment explanation
Indices: 3501338--3501362 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3501328 AAATATAAAT
3501338 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
3501363 AAATGAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3501393 original size:11 final size:11
Alignment explanation
Indices: 3501379--3501410 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
3501369 ATAATAAATT
3501379 AATAAATTTAA
1 AATAAATTTAA
*
3501390 AATATATTTAA
1 AATAAATTTAA
3501401 AATAAATTTA
1 AATAAATTTA
3501411 TCCATAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
AATAAATTTAA
Found at i:3506694 original size:22 final size:23
Alignment explanation
Indices: 3506662--3506712 Score: 79
Period size: 21 Copynumber: 2.3 Consensus size: 23
3506652 TAAAATAAAA
*
3506662 ATATAAATTTTTATTTAAAT-AT
1 ATATAAAATTTTATTTAAATAAT
3506684 AT-TAAAATTTTATTTAAATAAT
1 ATATAAAATTTTATTTAAATAAT
3506706 ATATAAA
1 ATATAAA
3506713 TAGAATAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 16 0.62
22 6 0.23
23 4 0.15
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
ATATAAAATTTTATTTAAATAAT
Found at i:3514768 original size:39 final size:39
Alignment explanation
Indices: 3514714--3514789 Score: 143
Period size: 39 Copynumber: 1.9 Consensus size: 39
3514704 CAGTTAGTTA
*
3514714 ATTGCTATATCTAAAACTAGAACTCTAAGTCAAACTAAC
1 ATTGCTATATCTAAAACTAGAACTCCAAGTCAAACTAAC
3514753 ATTGCTATATCTAAAACTAGAACTCCAAGTCAAACTA
1 ATTGCTATATCTAAAACTAGAACTCCAAGTCAAACTA
3514790 TGGAAACTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.43, C:0.21, G:0.08, T:0.28
Consensus pattern (39 bp):
ATTGCTATATCTAAAACTAGAACTCCAAGTCAAACTAAC
Found at i:3524667 original size:32 final size:32
Alignment explanation
Indices: 3524626--3524691 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
3524616 TTCGTGGAAA
*
3524626 GATAGCCACCATAATTTATGTTGCCTTCATAT
1 GATAGCCACCATAATTCATGTTGCCTTCATAT
3524658 GATAGCCACCATAATTCATGTTGCCTTCATAT
1 GATAGCCACCATAATTCATGTTGCCTTCATAT
3524690 GA
1 GA
3524692 CTCTTGCCTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.35
Consensus pattern (32 bp):
GATAGCCACCATAATTCATGTTGCCTTCATAT
Found at i:3527679 original size:44 final size:44
Alignment explanation
Indices: 3527616--3527707 Score: 157
Period size: 44 Copynumber: 2.1 Consensus size: 44
3527606 TTATTATAAC
*
3527616 CTAATTATTACTTTAATCTTACAGCATAATGGCCCAAAAAATTT
1 CTAATTATTAATTTAATCTTACAGCATAATGGCCCAAAAAATTT
* *
3527660 CTAATTATTAATTTAATCTTATAGCATAATGGCCCAAAGAATTT
1 CTAATTATTAATTTAATCTTACAGCATAATGGCCCAAAAAATTT
3527704 CTAA
1 CTAA
3527708 GGTATAAATT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (44 bp):
CTAATTATTAATTTAATCTTACAGCATAATGGCCCAAAAAATTT
Found at i:3528910 original size:3 final size:3
Alignment explanation
Indices: 3528902--3528937 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
3528892 TATCTAAAAC
3528902 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3528938 TGTTTGTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3530902 original size:20 final size:20
Alignment explanation
Indices: 3530877--3530918 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
3530867 AAAATCAAGT
*
3530877 AGAGAAAGAAGAAAAAGCAG
1 AGAGAAAAAAGAAAAAGCAG
* *
3530897 AGAGAAAAAAGAGAAAGGAG
1 AGAGAAAAAAGAAAAAGCAG
3530917 AG
1 AG
3530919 TTGGTTGAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.64, C:0.02, G:0.33, T:0.00
Consensus pattern (20 bp):
AGAGAAAAAAGAAAAAGCAG
Found at i:3532804 original size:16 final size:17
Alignment explanation
Indices: 3532785--3532817 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3532775 AATAAAATTA
3532785 ATTTTA-TATCAAATAT
1 ATTTTATTATCAAATAT
*
3532801 ATTTTATTATTAAATAT
1 ATTTTATTATCAAATAT
3532818 TTTGAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTTTATTATCAAATAT
Found at i:3533211 original size:13 final size:13
Alignment explanation
Indices: 3533193--3533233 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
3533183 ATTTTTAAAT
3533193 TATATTATTTTTA
1 TATATTATTTTTA
*
3533206 TATATTATTTTTG
1 TATATTATTTTTA
* *
3533219 TATGTTATTTATA
1 TATATTATTTTTA
3533232 TA
1 TA
3533234 AGGTATTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (13 bp):
TATATTATTTTTA
Found at i:3537163 original size:2 final size:2
Alignment explanation
Indices: 3537156--3537191 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3537146 GCAGTGATTG
3537156 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
3537192 TTATGTAAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:3542731 original size:16 final size:16
Alignment explanation
Indices: 3542694--3542784 Score: 60
Period size: 16 Copynumber: 5.4 Consensus size: 16
3542684 AATATAATTG
*
3542694 TTAAAATTATTTATTA
1 TTAAAATTATTTAATA
3542710 TTAAAATTA-TTAATA
1 TTAAAATTATTTAATA
* * *
3542725 TTCAAAAATAATTATATT
1 TT-AAAATTATTTA-ATA
3542743 TTAATAA-TATTTAATA
1 TTAA-AATTATTTAATA
*
3542759 TTTAAATATTATATTTATA
1 -TTAAA-ATTAT-TTAATA
*
3542778 TAAAAAT
1 TTAAAAT
3542785 ACTTAAAATA
Statistics
Matches: 60, Mismatches: 7, Indels: 15
0.73 0.09 0.18
Matches are distributed among these distances:
15 7 0.12
16 18 0.30
17 17 0.28
18 13 0.22
19 5 0.08
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (16 bp):
TTAAAATTATTTAATA
Found at i:3542751 original size:17 final size:18
Alignment explanation
Indices: 3542718--3542766 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
3542708 TATTAAAATT
*
3542718 ATTAATATTCAAA-AATA
1 ATTAATATTTAAATAATA
*
3542735 ATT-ATATTTTAATAATA
1 ATTAATATTTAAATAATA
*
3542752 TTTAATATTTAAATA
1 ATTAATATTTAAATA
3542767 TTATATTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
16 7 0.27
17 9 0.35
18 10 0.38
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTAATATTTAAATAATA
Found at i:3542859 original size:20 final size:20
Alignment explanation
Indices: 3542834--3542872 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3542824 CTTAAAATAT
3542834 TTAAAATAATATTATTATTC
1 TTAAAATAATATTATTATTC
* *
3542854 TTAAAATATTATTTTTATT
1 TTAAAATAATATTATTATT
3542873 AATATGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (20 bp):
TTAAAATAATATTATTATTC
Found at i:3542874 original size:17 final size:17
Alignment explanation
Indices: 3542841--3542874 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3542831 TATTTAAAAT
*
3542841 AATATTATTATTCTTAA
1 AATATTATTATTATTAA
*
3542858 AATATTATTTTTATTAA
1 AATATTATTATTATTAA
3542875 TATGAAAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
AATATTATTATTATTAA
Found at i:3543184 original size:29 final size:27
Alignment explanation
Indices: 3543137--3543225 Score: 74
Period size: 29 Copynumber: 3.3 Consensus size: 27
3543127 TTTTTATTTT
* *
3543137 TATTTTTTATTGTTAAAATAATAATATAA
1 TATTATTTATTATTAAAATAATAA-A-AA
* *
3543166 TATTATTTATTATTGAAATATTAAAAA
1 TATTATTTATTATTAAAATAATAAAAA
* * *
3543193 TATTTATTT-TTAATAATAT-ATAAAAT
1 TA-TTATTTATTATTAAAATAATAAAAA
3543219 TATTATT
1 TATTATT
3543226 GTGAATATTT
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
25 5 0.10
26 7 0.14
27 11 0.22
28 7 0.14
29 20 0.40
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (27 bp):
TATTATTTATTATTAAAATAATAAAAA
Found at i:3543217 original size:25 final size:25
Alignment explanation
Indices: 3543153--3543218 Score: 64
Period size: 25 Copynumber: 2.6 Consensus size: 25
3543143 TTATTGTTAA
*
3543153 AATAATAATATAATATTATTTATTATT
1 AATAAT-ATATAA-AATATTTATTATT
* *
3543180 GA-AATAT-TAAAAATATTTATTTTT
1 AATAATATAT-AAAATATTTATTATT
3543204 AATAATATATAAAAT
1 AATAATATATAAAAT
3543219 TATTATTGTG
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
24 13 0.41
25 14 0.44
26 4 0.12
27 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (25 bp):
AATAATATATAAAATATTTATTATT
Found at i:3543225 original size:25 final size:26
Alignment explanation
Indices: 3543153--3543222 Score: 81
Period size: 24 Copynumber: 2.7 Consensus size: 26
3543143 TTATTGTTAA
*
3543153 AATAATAATATAATATTATTTATTATT
1 AATAAT-ATATAAAATTATTTATTATT
* * *
3543180 GA-AATAT-TAAAAATATTTATTTTT
1 AATAATATATAAAATTATTTATTATT
3543204 AATAATATATAAAATTATT
1 AATAATATATAAAATTATT
3543223 ATTGTGAATA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
24 15 0.43
25 7 0.20
26 12 0.34
27 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (26 bp):
AATAATATATAAAATTATTTATTATT
Found at i:3543232 original size:25 final size:25
Alignment explanation
Indices: 3543182--3543232 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
3543172 TTATTATTGA
* *
3543182 AATATTAAAAATATTTATTTTTAAT
1 AATATTAAAAATATTTATTGTGAAT
*
3543207 AATATATAAAATTA-TTATTGTGAAT
1 AATAT-TAAAAATATTTATTGTGAAT
3543232 A
1 A
3543233 TTTTAATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (25 bp):
AATATTAAAAATATTTATTGTGAAT
Found at i:3543290 original size:19 final size:19
Alignment explanation
Indices: 3543252--3543289 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
3543242 TTTAATTAAA
3543252 ATTAAATAAAAATATTTTT
1 ATTAAATAAAAATATTTTT
*
3543271 ATTAATATAATAATATTTT
1 ATTAA-ATAAAAATATTTT
3543290 AAGACCAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTAAATAAAAATATTTTT
Found at i:3543544 original size:18 final size:19
Alignment explanation
Indices: 3543521--3543562 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
3543511 CATATAATGG
*
3543521 TTTTTTTAA-ATAAAATAA
1 TTTTTTTAATACAAAATAA
3543539 TTTTTTTAATTACAAAATAA
1 TTTTTTTAA-TACAAAATAA
3543559 TTTT
1 TTTT
3543563 AAATTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.43
20 12 0.57
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTTTTTAATACAAAATAA
Found at i:3543870 original size:22 final size:20
Alignment explanation
Indices: 3543840--3543880 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
3543830 ACGTAAGATA
3543840 TTAAAATTTTAAGCAATTTTAT
1 TTAAAATTTTAA--AATTTTAT
*
3543862 TTAAGATTTTAAAATTTTA
1 TTAAAATTTTAAAATTTTA
3543881 AAAAATTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
22 11 0.61
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.51
Consensus pattern (20 bp):
TTAAAATTTTAAAATTTTAT
Found at i:3543888 original size:30 final size:30
Alignment explanation
Indices: 3543818--3543889 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
3543808 AATTTTATTG
3543818 TTTAAAAAA-TTTACGTAAGATATTAAAAT
1 TTTAAAAAATTTTACGTAAGATATTAAAAT
** ** *
3543847 TTTAAGCAATTTTATTTAAGATTTTAAAAT
1 TTTAAAAAATTTTACGTAAGATATTAAAAT
3543877 TTTAAAAAATTTT
1 TTTAAAAAATTTT
3543890 CCTCTTAAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
29 7 0.20
30 28 0.80
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.46
Consensus pattern (30 bp):
TTTAAAAAATTTTACGTAAGATATTAAAAT
Found at i:3546081 original size:5 final size:5
Alignment explanation
Indices: 3546062--3546104 Score: 50
Period size: 6 Copynumber: 7.8 Consensus size: 5
3546052 ATTAATTCGT
3546062 AAAAG AAAAAGG AAAAG AAAAGG AAAAG AAAAAG AAAAG AAAA
1 AAAAG -AAAA-G AAAAG AAAA-G AAAAG -AAAAG AAAAG AAAA
3546105 TCTCTCTCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
5 15 0.44
6 18 0.53
7 1 0.03
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:3546084 original size:11 final size:11
Alignment explanation
Indices: 3546062--3546104 Score: 68
Period size: 11 Copynumber: 3.8 Consensus size: 11
3546052 ATTAATTCGT
3546062 AAAAGAAAAAGG
1 AAAAG-AAAAGG
3546074 AAAAGAAAAGG
1 AAAAGAAAAGG
*
3546085 AAAAGAAAAAG
1 AAAAGAAAAGG
3546096 AAAAGAAAA
1 AAAAGAAAA
3546105 TCTCTCTCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
11 25 0.83
12 5 0.17
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAGG
Found at i:3546652 original size:17 final size:17
Alignment explanation
Indices: 3546603--3546654 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
3546593 AAAACTAAGT
* *
3546603 AAAAAAAAGAAAAAAAGC
1 AAAAAAAAG-AAAAGAGA
* **
3546621 TAAAAAAAGTGAAGAGA
1 AAAAAAAAGAAAAGAGA
3546638 AAAAAAAAGAAAAGAGA
1 AAAAAAAAGAAAAGAGA
3546655 GTTGATTGAA
Statistics
Matches: 26, Mismatches: 8, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
17 18 0.69
18 8 0.31
ACGTcount: A:0.77, C:0.02, G:0.17, T:0.04
Consensus pattern (17 bp):
AAAAAAAAGAAAAGAGA
Found at i:3552198 original size:20 final size:21
Alignment explanation
Indices: 3552173--3552223 Score: 79
Period size: 20 Copynumber: 2.5 Consensus size: 21
3552163 GATTCGAAAT
3552173 TATAAAATATTA-TTTTTAAA
1 TATAAAATATTATTTTTTAAA
3552193 TATAAAATA-TATTTTTTAAA
1 TATAAAATATTATTTTTTAAA
3552213 TATAAATATAT
1 TATAAA-ATAT
3552224 AAATATATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 2 0.07
20 23 0.82
21 3 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TATAAAATATTATTTTTTAAA
Found at i:3553009 original size:22 final size:23
Alignment explanation
Indices: 3552981--3553024 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
3552971 TAAATAACAC
*
3552981 AATAATATTATATTA-TTATTAA
1 AATAATATAATATTAGTTATTAA
3553003 AATAATATAATATTAGTTATTA
1 AATAATATAATATTAGTTATTA
3553025 TTGAAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
AATAATATAATATTAGTTATTAA
Found at i:3553031 original size:26 final size:27
Alignment explanation
Indices: 3552982--3553059 Score: 78
Period size: 26 Copynumber: 3.1 Consensus size: 27
3552972 AAATAACACA
3552982 ATAATATTATATTATTATTAAAATAAT
1 ATAATATTATATTATTATTAAAATAAT
* *
3553009 ATAATATTA-GTTATTATTGAAAT-AT
1 ATAATATTATATTATTATTAAAATAAT
* *
3553034 -TAA-A-AATATT-TTATTTAAATAAT
1 ATAATATTATATTATTATTAAAATAAT
3553057 ATA
1 ATA
3553060 TAAAATTAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
22 10 0.23
23 5 0.12
24 5 0.12
25 2 0.05
26 12 0.28
27 9 0.21
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (27 bp):
ATAATATTATATTATTATTAAAATAAT
Found at i:3553141 original size:15 final size:16
Alignment explanation
Indices: 3553118--3553150 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3553108 ATTAAAACTA
3553118 AATAAAAT-ATATTTT
1 AATAAAATAATATTTT
*
3553133 AATATAATAATATTTT
1 AATAAAATAATATTTT
3553149 AA
1 AA
3553151 ATGAAACAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATAAAATAATATTTT
Found at i:3553223 original size:25 final size:25
Alignment explanation
Indices: 3553195--3553254 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
3553185 TTTAAAGAGT
3553195 AAATTTATAAAAATATTTAAAATTA
1 AAATTTATAAAAATATTTAAAATTA
* * *
3553220 AAATATTA-AAATATTTTTAATATTA
1 AAAT-TTATAAAAATATTTAAAATTA
*
3553245 ATATTT-TAAA
1 AAATTTATAAA
3553255 TTGTTAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
24 5 0.17
25 21 0.72
26 3 0.10
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
AAATTTATAAAAATATTTAAAATTA
Found at i:3554720 original size:11 final size:11
Alignment explanation
Indices: 3554704--3554734 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
3554694 ATTAACTCAT
3554704 AAAAGAAAAAA
1 AAAAGAAAAAA
*
3554715 AAAAGAAAAAG
1 AAAAGAAAAAA
3554726 AAAAGAAAA
1 AAAAGAAAA
3554735 TCTCTTCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAA
Found at i:3555717 original size:52 final size:50
Alignment explanation
Indices: 3555660--3555804 Score: 173
Period size: 52 Copynumber: 2.8 Consensus size: 50
3555650 AAACATACCC
3555660 ATTAAGAATCTTTTTCTTCTTATAATTTTTTTATTGTAAGTCAAACTCACCT
1 ATTAAGAATCTTTTTC-TCTTATAATTTTTTT-TTGTAAGTCAAACTCACCT
* * * * *
3555712 ATTAAGAATTTTTTTCTCTTATAATTCTTTTTTTGCAAGTCAAATTTATCT
1 ATTAAGAATCTTTTTCTCTTATAATT-TTTTTTTGTAAGTCAAACTCACCT
* * *
3555763 ATTAAAAATCTCATTTCTCTTAAAATTTTTTTTTTGTAAGTC
1 ATTAAGAATCT-TTTTCTCTTATAA-TTTTTTTTTGTAAGTC
3555805 TTCTTGTTCA
Statistics
Matches: 80, Mismatches: 10, Indels: 6
0.83 0.10 0.06
Matches are distributed among these distances:
51 34 0.43
52 44 0.55
53 2 0.03
ACGTcount: A:0.29, C:0.13, G:0.06, T:0.52
Consensus pattern (50 bp):
ATTAAGAATCTTTTTCTCTTATAATTTTTTTTTGTAAGTCAAACTCACCT
Found at i:3555843 original size:11 final size:11
Alignment explanation
Indices: 3555827--3555860 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
3555817 AAGTAATATC
3555827 AACAAATCTCA
1 AACAAATCTCA
*
3555838 AACAAATCTCT
1 AACAAATCTCA
*
3555849 AACAAATTTCA
1 AACAAATCTCA
3555860 A
1 A
3555861 TATTCTAAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.53, C:0.24, G:0.00, T:0.24
Consensus pattern (11 bp):
AACAAATCTCA
Found at i:3556279 original size:8 final size:8
Alignment explanation
Indices: 3556266--3556301 Score: 54
Period size: 8 Copynumber: 4.2 Consensus size: 8
3556256 TATTTTTTAA
3556266 ATATAATT
1 ATATAATT
3556274 ATATAATT
1 ATATAATT
3556282 ATATAAATAT
1 ATAT-AAT-T
3556292 ATATAATT
1 ATATAATT
3556300 AT
1 AT
3556302 TAAAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 15 0.58
9 6 0.23
10 5 0.19
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (8 bp):
ATATAATT
Found at i:3556406 original size:12 final size:12
Alignment explanation
Indices: 3556389--3556414 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3556379 AATAATATCT
3556389 AATTTGATTTAA
1 AATTTGATTTAA
3556401 AATTTGATTTAA
1 AATTTGATTTAA
3556413 AA
1 AA
3556415 AAAATTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (12 bp):
AATTTGATTTAA
Found at i:3557056 original size:24 final size:24
Alignment explanation
Indices: 3557029--3557075 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
3557019 TAAATAACAT
*
3557029 AATAAATATTATATTAATTATTAA
1 AATAAATATAATATTAATTATTAA
* *
3557053 AATATATATAATATTAGTTATTA
1 AATAAATATAATATTAATTATTA
3557076 TTGAATATTA
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:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (24 bp):
AATAAATATAATATTAATTATTAA
Found at i:3557568 original size:22 final size:22
Alignment explanation
Indices: 3557523--3557568 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
3557513 ATTATCATAA
*
3557523 TTTTCATTGATGAATAAATCAT
1 TTTTCATTAATGAATAAATCAT
*
3557545 TTTTCATTAATTAATCAAAT-AT
1 TTTTCATTAATGAAT-AAATCAT
3557567 TT
1 TT
3557569 GACAAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.37, C:0.09, G:0.04, T:0.50
Consensus pattern (22 bp):
TTTTCATTAATGAATAAATCAT
Found at i:3560497 original size:3 final size:3
Alignment explanation
Indices: 3560489--3560525 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
3560479 GCCAAGATGA
*
3560489 CTT CTT CTT ATT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
3560526 AGCTGCTGCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:3563392 original size:34 final size:34
Alignment explanation
Indices: 3563344--3563419 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 34
3563334 AGACAAATTC
* * ** *
3563344 AAAATTTTTAAAAATGAATTTCTTAAAAATTTTT
1 AAAACTTTTAAAAATAAATTTCCAAAAAATCTTT
*
3563378 AAAACTTTTGAAAATAAATTTCCAAAAAATCTTT
1 AAAACTTTTAAAAATAAATTTCCAAAAAATCTTT
*
3563412 AAAGCTTT
1 AAAACTTT
3563420 CATAATTGAA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (34 bp):
AAAACTTTTAAAAATAAATTTCCAAAAAATCTTT
Found at i:3563600 original size:24 final size:24
Alignment explanation
Indices: 3563553--3563597 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
3563543 AATTAGAATG
*
3563553 TAAAAAGATAAAATTATTATTTAT
1 TAAAAAGATAAAATTAATATTTAT
3563577 TAAAAA-ATAAAATTAATATTT
1 TAAAAAGATAAAATTAATATTT
3563598 TATATATGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (24 bp):
TAAAAAGATAAAATTAATATTTAT
Found at i:3565443 original size:13 final size:14
Alignment explanation
Indices: 3565425--3565453 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3565415 TCGATTCAAA
3565425 TAAAATA-TATAAT
1 TAAAATATTATAAT
3565438 TAAAATATTATAAT
1 TAAAATATTATAAT
3565452 TA
1 TA
3565454 TATAAATATA
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:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TAAAATATTATAAT
Found at i:3567170 original size:14 final size:14
Alignment explanation
Indices: 3567151--3567181 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3567141 AAAATTAAGT
*
3567151 AAATTATTAATTTA
1 AAATTATGAATTTA
3567165 AAATTATGAATTTA
1 AAATTATGAATTTA
3567179 AAA
1 AAA
3567182 AAATTTAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (14 bp):
AAATTATGAATTTA
Found at i:3567594 original size:84 final size:84
Alignment explanation
Indices: 3567495--3567663 Score: 320
Period size: 84 Copynumber: 2.0 Consensus size: 84
3567485 ATACCAACCT
*
3567495 TTATAAATGCACTTCTTTTCATTGTTTAATTTTCACCTAATTTTATTAATCCGTAATTAATGAAC
1 TTATAAATGCACTTCTTTTCATTGTTTAATTTCCACCTAATTTTATTAATCCGTAATTAATGAAC
3567560 TTCAAAAAAATAGAAATAA
66 TTCAAAAAAATAGAAATAA
*
3567579 TTATAAATGCACTTCTTTTCATTTTTTAATTTCCACCTAATTTTATTAATCCGTAATTAATGAAC
1 TTATAAATGCACTTCTTTTCATTGTTTAATTTCCACCTAATTTTATTAATCCGTAATTAATGAAC
3567644 TTCAAAAAAATAGAAATAA
66 TTCAAAAAAATAGAAATAA
3567663 T
1 T
3567664 ATTAATACGA
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 83 1.00
ACGTcount: A:0.39, C:0.14, G:0.05, T:0.42
Consensus pattern (84 bp):
TTATAAATGCACTTCTTTTCATTGTTTAATTTCCACCTAATTTTATTAATCCGTAATTAATGAAC
TTCAAAAAAATAGAAATAA
Found at i:3571145 original size:22 final size:22
Alignment explanation
Indices: 3571099--3571152 Score: 92
Period size: 21 Copynumber: 2.5 Consensus size: 22
3571089 ATAAAAATTT
3571099 TATATAAAAATTTATTTAAATA
1 TATATAAAAATTTATTTAAATA
3571121 TAT-TAAAAATTTATTTAAATAA
1 TATATAAAAATTTATTTAAAT-A
3571143 TATATAAAAA
1 TATATAAAAA
3571153 AATAAAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
21 17 0.57
22 7 0.23
23 6 0.20
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TATATAAAAATTTATTTAAATA
Found at i:3571536 original size:13 final size:13
Alignment explanation
Indices: 3571518--3571542 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3571508 TTCATTGGTT
3571518 AACCTTTCAAAAA
1 AACCTTTCAAAAA
3571531 AACCTTTCAAAA
1 AACCTTTCAAAA
3571543 CAGATACACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (13 bp):
AACCTTTCAAAAA
Found at i:3579099 original size:39 final size:39
Alignment explanation
Indices: 3579045--3579122 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
3579035 TCAGTTAGTT
*
3579045 ACATTGCTATATCTAAAACTAGAACTCTAAGTCAAACTA
1 ACATTGCTATATCTAAAACTAGAACTCCAAGTCAAACTA
3579084 ACATTGCTATATCTAAAACTAGAACTCCAAGTCAAACTA
1 ACATTGCTATATCTAAAACTAGAACTCCAAGTCAAACTA
3579123 TGGAAACTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.27
Consensus pattern (39 bp):
ACATTGCTATATCTAAAACTAGAACTCCAAGTCAAACTA
Found at i:3583741 original size:17 final size:18
Alignment explanation
Indices: 3583716--3583751 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
3583706 ATTTTATCAC
3583716 TTATGATTTAA-AATTAT
1 TTATGATTTAAGAATTAT
*
3583733 TTATTATTTAAGAATTAT
1 TTATGATTTAAGAATTAT
3583751 T
1 T
3583752 AATTCATATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (18 bp):
TTATGATTTAAGAATTAT
Found at i:3589518 original size:32 final size:32
Alignment explanation
Indices: 3589477--3589542 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
3589467 TTCGTGGAAA
*
3589477 GATAGCCACCATAATTTATGTTGCCTTCATAT
1 GATAGCCACCATAATTCATGTTGCCTTCATAT
3589509 GATAGCCACCATAATTCATGTTGCCTTCATAT
1 GATAGCCACCATAATTCATGTTGCCTTCATAT
3589541 GA
1 GA
3589543 CTCTTGCCTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.35
Consensus pattern (32 bp):
GATAGCCACCATAATTCATGTTGCCTTCATAT
Found at i:3593722 original size:3 final size:3
Alignment explanation
Indices: 3593714--3593761 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
3593704 TATCTAAAAC
3593714 ATA ATA ATA ATA ATA 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
3593762 TGTTTGTATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3598033 original size:13 final size:13
Alignment explanation
Indices: 3598017--3598057 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
3598007 CATTTTAAAT
3598017 TATATTATTTTTA
1 TATATTATTTTTA
*
3598030 TATATTATTTTTG
1 TATATTATTTTTA
* *
3598043 TATGTTATTTATA
1 TATATTATTTTTA
3598056 TA
1 TA
3598058 AGGTATTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (13 bp):
TATATTATTTTTA
Found at i:3607831 original size:20 final size:20
Alignment explanation
Indices: 3607806--3607867 Score: 56
Period size: 20 Copynumber: 3.0 Consensus size: 20
3607796 TTTAATTTAC
3607806 TATTTAATAATATATATTTT
1 TATTTAATAATATATATTTT
* *
3607826 TATTTAAAAAAATATAATTTAT
1 TATTTAATAATATAT-ATTT-T
*
3607848 T-TTTATTTAATATA-ATTTT
1 TATTTA-ATAATATATATTTT
3607867 T
1 T
3607868 CAGGGATATA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
19 2 0.06
20 17 0.50
21 8 0.24
22 7 0.21
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TATTTAATAATATATATTTT
Found at i:3610371 original size:13 final size:14
Alignment explanation
Indices: 3610353--3610381 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3610343 TCGATTCAAA
3610353 TAAAATA-TATAAT
1 TAAAATATTATAAT
3610366 TAAAATATTATAAT
1 TAAAATATTATAAT
3610380 TA
1 TA
3610382 TATAAATATA
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:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TAAAATATTATAAT
Found at i:3610959 original size:22 final size:24
Alignment explanation
Indices: 3610918--3610964 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
3610908 ATTACATGAA
*
3610918 TTAATTAAATTAAATCTTAA-ATT
1 TTAATTAAATTAAATATTAATATT
*
3610941 TTAATT-AATTTAATATTAATATT
1 TTAATTAAATTAAATATTAATATT
3610964 T
1 T
3610965 CTTTTTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (24 bp):
TTAATTAAATTAAATATTAATATT
Found at i:3612475 original size:84 final size:84
Alignment explanation
Indices: 3612376--3612544 Score: 320
Period size: 84 Copynumber: 2.0 Consensus size: 84
3612366 ATACCAACCT
*
3612376 TTATAAATGCACTTCTTTTCATTGTTTAATTTTCACCTAATTTTATTAATCCGTAATTAATGAAC
1 TTATAAATGCACTTCTTTTCATTGTTTAATTTCCACCTAATTTTATTAATCCGTAATTAATGAAC
3612441 TTCAAAAAAATAGAAATAA
66 TTCAAAAAAATAGAAATAA
*
3612460 TTATAAATGCACTTCTTTTCATTTTTTAATTTCCACCTAATTTTATTAATCCGTAATTAATGAAC
1 TTATAAATGCACTTCTTTTCATTGTTTAATTTCCACCTAATTTTATTAATCCGTAATTAATGAAC
3612525 TTCAAAAAAATAGAAATAA
66 TTCAAAAAAATAGAAATAA
3612544 T
1 T
3612545 ATTAATACGA
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 83 1.00
ACGTcount: A:0.39, C:0.14, G:0.05, T:0.42
Consensus pattern (84 bp):
TTATAAATGCACTTCTTTTCATTGTTTAATTTCCACCTAATTTTATTAATCCGTAATTAATGAAC
TTCAAAAAAATAGAAATAA
Found at i:3631375 original size:17 final size:16
Alignment explanation
Indices: 3631338--3631370 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
3631328 TTATTATTTA
3631338 ATTTTAAAATATTAAT
1 ATTTTAAAATATTAAT
3631354 ATTTT-AAATATTAAT
1 ATTTTAAAATATTAAT
3631369 AT
1 AT
3631371 ATTTTTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATTTTAAAATATTAAT
Found at i:3631428 original size:7 final size:7
Alignment explanation
Indices: 3631417--3631450 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
3631407 TGAATAAACT
*
3631417 TTTTGAT
1 TTTTGAA
3631424 TTTTGAA
1 TTTTGAA
3631431 TTTTGAA
1 TTTTGAA
3631438 TTTTGAA
1 TTTTGAA
3631445 TTTTGA
1 TTTTGA
3631451 GTAATTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.24, C:0.00, G:0.15, T:0.62
Consensus pattern (7 bp):
TTTTGAA
Found at i:3634186 original size:19 final size:18
Alignment explanation
Indices: 3634162--3634227 Score: 57
Period size: 19 Copynumber: 3.7 Consensus size: 18
3634152 AATTTTTTAT
3634162 AATTTTATATTTAAATTAA
1 AATTTTAT-TTTAAATTAA
* *
3634181 AA-TTT-TTATAAATTATC
1 AATTTTATTTTAAATTA-A
*
3634198 AA-TTAATTTTAAAATTAA
1 AATTTTATTTT-AAATTAA
3634216 AATTTTATTTTA
1 AATTTTATTTTA
3634228 TTGTTCTTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 9
0.71 0.12 0.17
Matches are distributed among these distances:
16 8 0.22
17 5 0.14
18 9 0.24
19 15 0.41
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
AATTTTATTTTAAATTAA
Found at i:3634203 original size:28 final size:29
Alignment explanation
Indices: 3634145--3634213 Score: 70
Period size: 28 Copynumber: 2.4 Consensus size: 29
3634135 AAGTTTGTTA
* * * *
3634145 AATATTGAATTTTTTATAATTTTATATTT
1 AATATTAAAATTTTTATAATATTATAATT
3634174 AA-ATTAAAATTTTTATAA-ATTATCAATT
1 AATATTAAAATTTTTATAATATTAT-AATT
*
3634202 AATTTTAAAATT
1 AATATTAAAATT
3634214 AAAATTTTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
27 4 0.12
28 19 0.58
29 10 0.30
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (29 bp):
AATATTAAAATTTTTATAATATTATAATT
Found at i:3634404 original size:16 final size:16
Alignment explanation
Indices: 3634383--3634417 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
3634373 ATATGTTGCC
3634383 AATTGATTTTAAATTT
1 AATTGATTTTAAATTT
*
3634399 AATTGATTTTAAGTTT
1 AATTGATTTTAAATTT
3634415 AAT
1 AAT
3634418 GTTTGACTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (16 bp):
AATTGATTTTAAATTT
Found at i:3636245 original size:2 final size:2
Alignment explanation
Indices: 3636238--3636267 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3636228 TATAATTTGC
*
3636238 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3636268 CTATGAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3637057 original size:13 final size:13
Alignment explanation
Indices: 3637039--3637072 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
3637029 ATAATCATAT
3637039 AATTTATTAATAA
1 AATTTATTAATAA
*
3637052 AATTTATTGATAA
1 AATTTATTAATAA
3637065 AATATTAT
1 AAT-TTAT
3637073 ACTTTAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (13 bp):
AATTTATTAATAA
Found at i:3638155 original size:20 final size:20
Alignment explanation
Indices: 3638109--3638160 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
3638099 AGATTTTATA
*
3638109 ATTTTATGAAAATTTATATTT
1 ATTTTAT-AAAATATATATTT
*
3638130 AATTTATAAAATAT-TATTT
1 ATTTTATAAAATATATATTT
3638149 ATTTTTATAAAA
1 A-TTTTATAAAA
3638161 AAAATTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 6 0.22
20 15 0.56
21 6 0.22
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
ATTTTATAAAATATATATTT
Found at i:3639024 original size:20 final size:20
Alignment explanation
Indices: 3638995--3639056 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
3638985 TGATCCGATA
*
3638995 TATATATATAATTTTATAAT
1 TATATATATAATTTTATATT
*
3639015 TATTTATAT-ATTTT-T-TT
1 TATATATATAATTTTATATT
*
3639032 TATATATTTAATTTTATATT
1 TATATATATAATTTTATATT
3639052 TATAT
1 TATAT
3639057 TAAAAATAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
17 8 0.23
18 6 0.17
19 6 0.17
20 15 0.43
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TATATATATAATTTTATATT
Found at i:3639035 original size:13 final size:14
Alignment explanation
Indices: 3638995--3639050 Score: 59
Period size: 13 Copynumber: 4.4 Consensus size: 14
3638985 TGATCCGATA
*
3638995 TATATATATAATTT
1 TATATATTTAATTT
3639009 TATA-A-TT-A-TT
1 TATATATTTAATTT
*
3639019 TATATATTT-TTTT
1 TATATATTTAATTT
3639032 TATATATTTAATTT
1 TATATATTTAATTT
3639046 TATAT
1 TATAT
3639051 TTATATTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 6 0.17
11 2 0.06
12 3 0.09
13 12 0.34
14 12 0.34
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TATATATTTAATTT
Found at i:3639051 original size:12 final size:13
Alignment explanation
Indices: 3638995--3639053 Score: 61
Period size: 12 Copynumber: 4.8 Consensus size: 13
3638985 TGATCCGATA
*
3638995 TATATATATAATT
1 TATATATTTAATT
*
3639008 T-TATAATT-ATT
1 TATATATTTAATT
**
3639019 TATATATTTTTTT
1 TATATATTTAATT
3639032 TATATATTTAATT
1 TATATATTTAATT
3639045 T-TATATTTA
1 TATATATTTA
3639054 TATTAAAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
11 4 0.11
12 19 0.50
13 15 0.39
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TATATATTTAATT
Found at i:3643509 original size:6 final size:6
Alignment explanation
Indices: 3643498--3643531 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
3643488 AGCACAAATA
* *
3643498 CACATG CACATG CACATG CACAAG CACAAG CACA
1 CACATG CACATG CACATG CACATG CACATG CACA
3643532 AGCAAACTGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.41, C:0.35, G:0.15, T:0.09
Consensus pattern (6 bp):
CACATG
Found at i:3643515 original size:12 final size:12
Alignment explanation
Indices: 3643498--3643535 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
3643488 AGCACAAATA
*
3643498 CACATGCACATG
1 CACATGCACAAG
3643510 CACATGCACAAG
1 CACATGCACAAG
*
3643522 CACAAGCACAAG
1 CACATGCACAAG
3643534 CA
1 CA
3643536 AACTGGTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.42, C:0.34, G:0.16, T:0.08
Consensus pattern (12 bp):
CACATGCACAAG
Found at i:3645454 original size:22 final size:23
Alignment explanation
Indices: 3645415--3645458 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3645405 AATGTAAAAA
3645415 AAAAAAAAAAAAGCTTTTTTGAG
1 AAAAAAAAAAAAGCTTTTTTGAG
* *
3645438 AAAAAAGAAAGAG-TTTTTTGA
1 AAAAAAAAAAAAGCTTTTTTGA
3645459 ATTGGAATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.55, C:0.02, G:0.16, T:0.27
Consensus pattern (23 bp):
AAAAAAAAAAAAGCTTTTTTGAG
Found at i:3646168 original size:25 final size:25
Alignment explanation
Indices: 3646136--3646183 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
3646126 TCATATGATA
3646136 AAGAATACACATTATTGTTTGTAAT
1 AAGAATACACATTATTGTTTGTAAT
3646161 AAGAATACACATTATTGTTTGTA
1 AAGAATACACATTATTGTTTGTA
3646184 TTTATATGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (25 bp):
AAGAATACACATTATTGTTTGTAAT
Found at i:3646350 original size:214 final size:215
Alignment explanation
Indices: 3645935--3646355 Score: 790
Period size: 214 Copynumber: 2.0 Consensus size: 215
3645925 GTAAAAATGG
*
3645935 GTTTGTAATAAGAATACACATTATTGTTTGTATTTATATGTAAAATTTTCTTAGTATAAATTAAT
1 GTTTGTAATAAGAATACACATTATTGTTTGTATTTATATGTAAAATTTCCTTAGTATAAATTAAT
*
3646000 TTGTTTTGTACAAAAAAGATGTAATTTAAAAATAAAAAAAAATAATTACAGATGTTAAAATTTTA
66 TTGTTTTGTACAAAAAAGATGTAATTGAAAAAT--AAAAAAATAATTACAGATGTTAAAATTTTA
3646065 TTTTGATCGGTTGTTATTTTTTAAGAATGATAATATAAATAAATTAAATTGATTTTCAAATTCAT
129 TTTTGATCGGTTGTTATTTTTTAAGAATGATAATATAAATAAATTAAATTGATTTTCAAATTCAT
3646130 ATGATAAAGAATACACATTATT
194 ATGATAAAGAATACACATTATT
3646152 GTTTGTAATAAGAATACACATTATTGTTTGTATTTATATGTAAAATTTCCTTAGTATAAATTAAT
1 GTTTGTAATAAGAATACACATTATTGTTTGTATTTATATGTAAAATTTCCTTAGTATAAATTAAT
*
3646217 TTGTTTTGTACAAAAAAGATGTAATTGGAAAAT-AAAAAATAATTACAGATGTTAAAATTTTATT
66 TTGTTTTGTACAAAAAAGATGTAATTGAAAAATAAAAAAATAATTACAGATGTTAAAATTTTATT
3646281 TTGATCGGTTGTTATTTTTTAAGAATGATAATATAAATAAATTAAATTGATTTTCAAATTCATAT
131 TTGATCGGTTGTTATTTTTTAAGAATGATAATATAAATAAATTAAATTGATTTTCAAATTCATAT
3646346 GATAAAGAAT
196 GATAAAGAAT
3646356 TTTATATTTT
Statistics
Matches: 201, Mismatches: 3, Indels: 3
0.97 0.01 0.01
Matches are distributed among these distances:
214 106 0.53
217 95 0.47
ACGTcount: A:0.42, C:0.05, G:0.11, T:0.42
Consensus pattern (215 bp):
GTTTGTAATAAGAATACACATTATTGTTTGTATTTATATGTAAAATTTCCTTAGTATAAATTAAT
TTGTTTTGTACAAAAAAGATGTAATTGAAAAATAAAAAAATAATTACAGATGTTAAAATTTTATT
TTGATCGGTTGTTATTTTTTAAGAATGATAATATAAATAAATTAAATTGATTTTCAAATTCATAT
GATAAAGAATACACATTATT
Found at i:3659104 original size:2 final size:2
Alignment explanation
Indices: 3659091--3659120 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3659081 CCTTTCACGG
*
3659091 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3659121 CAACACTAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3660348 original size:11 final size:11
Alignment explanation
Indices: 3660332--3660365 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
3660322 TTTAAAACAG
3660332 AAAAAAAGGAA
1 AAAAAAAGGAA
*
3660343 AAAAAAAAGAA
1 AAAAAAAGGAA
*
3660354 AGAAAAAGGAA
1 AAAAAAAGGAA
3660365 A
1 A
3660366 CGGTTTGGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
AAAAAAAGGAA
Found at i:3669920 original size:15 final size:15
Alignment explanation
Indices: 3669896--3669925 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3669886 AATGCTAAGA
3669896 TTACCAAAATTATTT
1 TTACCAAAATTATTT
*
3669911 TTACCCAAATTATTT
1 TTACCAAAATTATTT
3669926 GTGGAAGATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.17, G:0.00, T:0.47
Consensus pattern (15 bp):
TTACCAAAATTATTT
Found at i:3674370 original size:4 final size:4
Alignment explanation
Indices: 3674361--3674391 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
3674351 TTTTCTTCAG
3674361 TATT TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TATT TAT
3674392 CCTTAATTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:3680684 original size:25 final size:25
Alignment explanation
Indices: 3680650--3680702 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
3680640 GAAACTAAAT
3680650 AAAAACACAAACTAACCAAAAGAAG
1 AAAAACACAAACTAACCAAAAGAAG
3680675 AAAAACACAAACTAACCAAAAGAAG
1 AAAAACACAAACTAACCAAAAGAAG
3680700 AAA
1 AAA
3680703 GCATTTGATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.70, C:0.19, G:0.08, T:0.04
Consensus pattern (25 bp):
AAAAACACAAACTAACCAAAAGAAG
Found at i:3687443 original size:27 final size:26
Alignment explanation
Indices: 3687399--3687466 Score: 79
Period size: 27 Copynumber: 2.7 Consensus size: 26
3687389 AATAAAAACA
*
3687399 TTTTAAA-AAATAA-TATTTT-TATT
1 TTTTAAATAAAAAATTATTTTATATT
*
3687422 TTATTAATTAACAAAATTATTTTATATT
1 TT-TTAAATAA-AAAATTATTTTATATT
3687450 TTTTAAATAAAAAATTA
1 TTTTAAATAAAAAATTA
3687467 AAATGAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
23 2 0.05
24 4 0.11
25 2 0.05
26 10 0.27
27 13 0.35
28 6 0.16
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (26 bp):
TTTTAAATAAAAAATTATTTTATATT
Found at i:3687446 original size:26 final size:26
Alignment explanation
Indices: 3687415--3687466 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
3687405 AAAATAATAT
*
3687415 TTTTAT-TTTATTAATTAACAAAATTA
1 TTTTATATTTATTAAATAA-AAAATTA
*
3687441 TTTTATATTTTTTAAATAAAAAATTA
1 TTTTATATTTATTAAATAAAAAATTA
3687467 AAATGAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (26 bp):
TTTTATATTTATTAAATAAAAAATTA
Found at i:3687691 original size:19 final size:19
Alignment explanation
Indices: 3687644--3687682 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
3687634 TAATAAAATC
*
3687644 ATTATAATTATGATTAAAA
1 ATTATAAATATGATTAAAA
3687663 ATTATAAATATGATTAAAA
1 ATTATAAATATGATTAAAA
3687682 A
1 A
3687683 ATTTTAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (19 bp):
ATTATAAATATGATTAAAA
Found at i:3687697 original size:14 final size:14
Alignment explanation
Indices: 3687678--3687722 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
3687668 AAATATGATT
*
3687678 AAAAAATTTTAATA
1 AAAAAATTTTATTA
* *
3687692 AAAAAATTATATTT
1 AAAAAATTTTATTA
*
3687706 AATAAATTTTATTA
1 AAAAAATTTTATTA
3687720 AAA
1 AAA
3687723 TTAATATTTA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AAAAAATTTTATTA
Done.