Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 7 of 167
Found at i:2088494 original size:17 final size:17
Alignment explanation
Indices: 2088472--2088507 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
2088462 CTAATTTATT
*
2088472 TGAGCCTTAATTACTTA
1 TGAGCCCTAATTACTTA
2088489 TGAGCCCTAATTACTTA
1 TGAGCCCTAATTACTTA
2088506 TG
1 TG
2088508 TTCAATCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (17 bp):
TGAGCCCTAATTACTTA
Found at i:2089277 original size:22 final size:22
Alignment explanation
Indices: 2089252--2089297 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
2089242 GATGAAGGAA
2089252 AAAGAATTAAACGCGACCTTTG
1 AAAGAATTAAACGCGACCTTTG
*
2089274 AAAGAATTAAGCGCGACCTTTG
1 AAAGAATTAAACGCGACCTTTG
2089296 AA
1 AA
2089298 GTGATTTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (22 bp):
AAAGAATTAAACGCGACCTTTG
Found at i:2089557 original size:27 final size:26
Alignment explanation
Indices: 2089487--2089707 Score: 211
Period size: 26 Copynumber: 8.6 Consensus size: 26
2089477 AAACGAAACA
* *
2089487 AAATAATATATAAAACAATTTGAAGT
1 AAATAATATATAAAACAATTTAAAAT
* *
2089513 AAAT-A-GTACAAAACAATTTAAAAT
1 AAATAATATATAAAACAATTTAAAAT
* *
2089537 AAATAATATGTAAAACAAATTAAAAT
1 AAATAATATATAAAACAATTTAAAAT
* *
2089563 AAATAATATACAAAGCAATTTAAAAT
1 AAATAATATATAAAACAATTTAAAAT
* *
2089589 AAATAATATATAAGACACTTT---A-
1 AAATAATATATAAAACAATTTAAAAT
* * * *
2089611 CAATAACATATAAAAGAATTTAAGAT
1 AAATAATATATAAAACAATTTAAAAT
*
2089637 AAATAATATATAAAATAAATTTAAAAT
1 AAATAATATATAAAA-CAATTTAAAAT
* *
2089664 AAATAATATACAAAACAGTTTAAAAAT
1 AAATAATATATAAAACAATTT-AAAAT
2089691 AAATGATATATATAAAA
1 AAAT-A-ATATATAAAA
2089708 AAACCAATTC
Statistics
Matches: 156, Mismatches: 29, Indels: 17
0.77 0.14 0.08
Matches are distributed among these distances:
22 16 0.10
23 1 0.01
24 19 0.12
25 3 0.02
26 75 0.48
27 32 0.21
28 1 0.01
29 9 0.06
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.29
Consensus pattern (26 bp):
AAATAATATATAAAACAATTTAAAAT
Found at i:2089631 original size:48 final size:50
Alignment explanation
Indices: 2089487--2089853 Score: 250
Period size: 50 Copynumber: 7.2 Consensus size: 50
2089477 AAACGAAACA
* * * * * *
2089487 AAATAATATATAAAACAATTTGAAGTAAATAGTACAAAACAATTTAAAAT
1 AAATAATATATAAAACAAATTAAAATAAATAATATAAAAGAATTTAAAAT
*
2089537 AAATAATATGTAAAACAAATTAAAATAAATAATATACAAAGCAATTTAAAAT
1 AAATAATATATAAAACAAATTAAAATAAATAATATA-AAAG-AATTTAAAAT
* ** * * *
2089589 AAATAATATATAAGACACTTTACAAT-AA-CATATAAAAGAATTTAAGAT
1 AAATAATATATAAAACAAATTAAAATAAATAATATAAAAGAATTTAAAAT
*
2089637 AAATAATATATAAAATAAATTTAAAATAAATAATATACAAA-ACAGTTTAAAAAT
1 AAATAATATATAAAACAAA-TTAAAATAAATAATATA-AAAGA-A-TTT-AAAAT
** * * *
2089691 AAATGATATATATAAAA-AAA-CCAATTCAA-AATGAATAATAG--TTTAAAAT
1 AAAT-A-ATATATAAAACAAATTAAAATAAATAAT--ATAAAAGAATTTAAAAT
* * * * * *
2089740 AAATTATATATAAAA-AAATTTAAAATGGATAATACTTTGAAATAGTTTAAAAT
1 AAATAATATATAAAACAAA-TTAAAAT--A-AATAATATAAAAGAATTTAAAAT
* * * * *
2089793 ACATAATATGTGAAA-AACTTAAAATAAATAATAATAAAATAATTTAAAAT
1 AAATAATATATAAAACAAATTAAAATAAATAAT-ATAAAAGAATTTAAAAT
2089843 AAATAATATAT
1 AAATAATATAT
2089854 GAGACAAAAG
Statistics
Matches: 247, Mismatches: 47, Indels: 46
0.73 0.14 0.14
Matches are distributed among these distances:
47 13 0.05
48 24 0.10
49 27 0.11
50 64 0.26
51 14 0.06
52 47 0.19
53 33 0.13
54 11 0.04
55 4 0.02
56 10 0.04
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.30
Consensus pattern (50 bp):
AAATAATATATAAAACAAATTAAAATAAATAATATAAAAGAATTTAAAAT
Found at i:2089765 original size:26 final size:26
Alignment explanation
Indices: 2089732--2089853 Score: 104
Period size: 25 Copynumber: 4.7 Consensus size: 26
2089722 TGAATAATAG
* *
2089732 TTTAAAATAAATTATATATAAAAAAA
1 TTTAAAATAAATAATATATAAAACAA
** * * * *
2089758 TTTAAAATGGATAATACTTTGAAATAG
1 TTTAAAATAAATAATA-TATAAAACAA
* * *
2089785 TTTAAAATACATAATATGTGAAA-AA
1 TTTAAAATAAATAATATATAAAACAA
* *
2089810 CTTAAAATAAATAATA-ATAAAATAA
1 TTTAAAATAAATAATATATAAAACAA
2089835 TTTAAAATAAATAATATAT
1 TTTAAAATAAATAATATAT
2089854 GAGACAAAAG
Statistics
Matches: 77, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
24 4 0.05
25 32 0.42
26 21 0.27
27 20 0.26
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.34
Consensus pattern (26 bp):
TTTAAAATAAATAATATATAAAACAA
Found at i:2089783 original size:43 final size:44
Alignment explanation
Indices: 2089699--2089783 Score: 109
Period size: 43 Copynumber: 1.9 Consensus size: 44
2089689 ATAAATGATA
*
2089699 TATATAAAAAAACCAATTCAAAATGAATAATAGTTTAAAATAAAT
1 TATATAAAAAAA-CAATTCAAAATGAATAATACTTTAAAATAAAT
* * * *
2089744 TATATATAAAAA-AATTTAAAATGGATAATACTTTGAAATA
1 TATATAAAAAAACAATTCAAAATGAATAATACTTTAAAATA
2089784 GTTTAAAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
43 24 0.69
45 11 0.31
ACGTcount: A:0.58, C:0.05, G:0.06, T:0.32
Consensus pattern (44 bp):
TATATAAAAAAACAATTCAAAATGAATAATACTTTAAAATAAAT
Found at i:2089843 original size:15 final size:16
Alignment explanation
Indices: 2089812--2089852 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
2089802 GTGAAAAACT
2089812 TAAAATAA-ATAATAA
1 TAAAATAATATAATAA
*
2089827 TAAAATAATTTAA-AA
1 TAAAATAATATAATAA
2089842 T-AAATAATATA
1 TAAAATAATATA
2089853 TGAGACAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 9 0.39
15 11 0.48
16 3 0.13
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
TAAAATAATATAATAA
Found at i:2096143 original size:14 final size:14
Alignment explanation
Indices: 2096124--2096153 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
2096114 GTCATTTAGG
2096124 CCAACCAAACTGGC
1 CCAACCAAACTGGC
2096138 CCAACCAAACTGGC
1 CCAACCAAACTGGC
2096152 CC
1 CC
2096154 GGTGATTTGA
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:0.33, C:0.47, G:0.13, T:0.07
Consensus pattern (14 bp):
CCAACCAAACTGGC
Found at i:2096809 original size:19 final size:21
Alignment explanation
Indices: 2096773--2096811 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
2096763 TGGACTAGGG
*
2096773 TTAGTTTTGGGTTATTGGGTT
1 TTAGTTTTGGGATATTGGGTT
2096794 TTAG-TTTGGGAT-TTGGGT
1 TTAGTTTTGGGATATTGGGT
2096812 CTGGTATGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 7 0.41
21 4 0.24
ACGTcount: A:0.10, C:0.00, G:0.36, T:0.54
Consensus pattern (21 bp):
TTAGTTTTGGGATATTGGGTT
Found at i:2106780 original size:2 final size:2
Alignment explanation
Indices: 2106773--2106802 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2106763 AATCACTTCC
2106773 AT AT AT AT 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
2106803 TTATTGCATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2107382 original size:17 final size:17
Alignment explanation
Indices: 2107360--2107397 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
2107350 TATTTTATAA
*
2107360 TATAATTGTATTGTACT
1 TATAATTATATTGTACT
*
2107377 TATAATTATATTGTATT
1 TATAATTATATTGTACT
2107394 TATA
1 TATA
2107398 CTTGCTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.34, C:0.03, G:0.08, T:0.55
Consensus pattern (17 bp):
TATAATTATATTGTACT
Found at i:2116098 original size:16 final size:16
Alignment explanation
Indices: 2116060--2116102 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
2116050 TAGAGTGCAA
* *
2116060 ATATACATACATATAT
1 ATATAAATATATATAT
2116076 ATATAAATATATATAT
1 ATATAAATATATATAT
*
2116092 ATGTAAATATA
1 ATATAAATATA
2116103 ACAATAGAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (16 bp):
ATATAAATATATATAT
Found at i:2119593 original size:41 final size:41
Alignment explanation
Indices: 2119548--2119652 Score: 194
Period size: 41 Copynumber: 2.6 Consensus size: 41
2119538 TGATTCAGTA
2119548 CACCGGCACTT-AGCCTGCTAGACATATAGTCTGAAATGTAT
1 CACCGGCA-TTAAGCCTGCTAGACATATAGTCTGAAATGTAT
2119589 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
1 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
2119630 CACCGGCATTAAGCCTGCTAGAC
1 CACCGGCATTAAGCCTGCTAGAC
2119653 NNNNNNNNNN
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
40 2 0.03
41 61 0.97
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.25
Consensus pattern (41 bp):
CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
Found at i:2138202 original size:29 final size:32
Alignment explanation
Indices: 2138147--2138215 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 32
2138137 ATAAATAGTT
2138147 TTTTTTATTTTGTAAAAAGAATAAGGCTAATAG
1 TTTTTT-TTTTGTAAAAAGAATAAGGCTAATAG
2138180 TTTTTTTTTTG-AAAAA-AA-AAGGCTAATAG
1 TTTTTTTTTTGTAAAAAGAATAAGGCTAATAG
*
2138209 TTATTTT
1 TTTTTTT
2138216 AGTAGAGAGG
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
29 17 0.49
30 2 0.06
31 5 0.14
32 5 0.14
33 6 0.17
ACGTcount: A:0.38, C:0.03, G:0.13, T:0.46
Consensus pattern (32 bp):
TTTTTTTTTTGTAAAAAGAATAAGGCTAATAG
Found at i:2139989 original size:21 final size:22
Alignment explanation
Indices: 2139963--2140007 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
2139953 TGATATTACA
2139963 TTATTATTATTTT-CTTTCTAT
1 TTATTATTATTTTCCTTTCTAT
* *
2139984 TTATTATTTTTTTCCTTTTTAT
1 TTATTATTATTTTCCTTTCTAT
2140006 TT
1 TT
2140008 TATTTTCGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.76
Consensus pattern (22 bp):
TTATTATTATTTTCCTTTCTAT
Found at i:2140727 original size:15 final size:14
Alignment explanation
Indices: 2140701--2140736 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 14
2140691 TATATTTTTG
2140701 TTATACTTATATATA
1 TTATA-TTATATATA
2140716 TGTATATTATATATA
1 T-TATATTATATATA
2140731 TTATAT
1 TTATAT
2140737 AGTATTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 5 0.25
15 11 0.55
16 4 0.20
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.56
Consensus pattern (14 bp):
TTATATTATATATA
Found at i:2141192 original size:24 final size:24
Alignment explanation
Indices: 2141146--2141192 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
2141136 CTTTAATACT
* *
2141146 ATATCATTTTTATTTTTATTTTTC
1 ATATCATTCTTATGTTTATTTTTC
2141170 ATATCA-TCTTATGTTTATGTTTT
1 ATATCATTCTTATGTTTAT-TTTT
2141193 TCAAACTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.21, C:0.09, G:0.04, T:0.66
Consensus pattern (24 bp):
ATATCATTCTTATGTTTATTTTTC
Found at i:2141387 original size:25 final size:23
Alignment explanation
Indices: 2141338--2141387 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
2141328 CATCACCATT
*
2141338 ATTTTTATTATCATATTATTGTC
1 ATTTTTATTATCATATTATTCTC
2141361 ATTTTT-TTATCATTCATTATTTCTC
1 ATTTTTATTATCA-T-ATTA-TTCTC
2141386 AT
1 AT
2141388 CCTTTATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 6 0.26
23 7 0.30
24 4 0.17
25 6 0.26
ACGTcount: A:0.24, C:0.12, G:0.02, T:0.62
Consensus pattern (23 bp):
ATTTTTATTATCATATTATTCTC
Found at i:2141460 original size:3 final size:3
Alignment explanation
Indices: 2141452--2141503 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
2141442 AATTTTACTT
* * * *
2141452 TTA TTA TTA CTA CTA -TA TTA TTTA TTA TTA TCA TTA TCA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
2141497 TTA TTA T
1 TTA TTA T
2141504 CATATTTATA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
2 2 0.05
3 37 0.88
4 3 0.07
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:2141506 original size:21 final size:21
Alignment explanation
Indices: 2141451--2141506 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
2141441 TAATTTTACT
*
2141451 TTTATTATTA-CTACTATATTA
1 TTTATTATTATC-ATTATATTA
2141472 TTTATTATTATCATTATCATTA
1 TTTATTATTATCATTAT-ATTA
2141494 -TTATTATTATCAT
1 TTTATTATTATCAT
2141507 ATTTATACTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 27 0.84
22 5 0.16
ACGTcount: A:0.32, C:0.09, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTATTATTATCATTATATTA
Found at i:2141512 original size:18 final size:18
Alignment explanation
Indices: 2141419--2141512 Score: 63
Period size: 18 Copynumber: 5.1 Consensus size: 18
2141409 ATTAACGTAC
2141419 ATTATTATTATCA-ATTT
1 ATTATTATTATCATATTT
* *
2141436 ACTATTAATT-TTACT-TTT
1 ATTATT-ATTATCA-TATTT
*
2141454 ATTATTACTA-C-TATATT
1 ATTATTATTATCATAT-TT
2141471 ATTTATTATTATCATTATCATT
1 A-TTATTATTATCA-TAT--TT
2141493 ATTATTATTATCATATTT
1 ATTATTATTATCATATTT
2141511 AT
1 AT
2141513 ACTTATATTT
Statistics
Matches: 60, Mismatches: 6, Indels: 21
0.69 0.07 0.24
Matches are distributed among these distances:
15 1 0.02
16 1 0.02
17 12 0.20
18 23 0.38
19 1 0.02
20 3 0.05
21 15 0.25
22 4 0.07
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.59
Consensus pattern (18 bp):
ATTATTATTATCATATTT
Found at i:2141725 original size:3 final size:3
Alignment explanation
Indices: 2141717--2141767 Score: 54
Period size: 3 Copynumber: 17.3 Consensus size: 3
2141707 TATCTCTAAC
*
2141717 TAT TAT TAT TAT T-T TA- TAT ATAT TAT TAT CTA- TAT TAT TAT TAC
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT -TAT TAT TAT TAT TAT
2141761 TAT TAT T
1 TAT TAT T
2141768 CTTTATTGTC
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
2 6 0.15
3 30 0.73
4 5 0.12
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:2141742 original size:14 final size:15
Alignment explanation
Indices: 2141717--2141763 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
2141707 TATCTCTAAC
*
2141717 TATTATTATTATTTTA
1 TATTATTATTA-TCTA
2141733 TATATATTATTATCTA
1 TAT-TATTATTATCTA
2141749 TATTATTATTA-CTA
1 TATTATTATTATCTA
2141763 T
1 T
2141764 TATTCTTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 4 0.14
15 8 0.28
16 9 0.31
17 8 0.28
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (15 bp):
TATTATTATTATCTA
Found at i:2158213 original size:133 final size:133
Alignment explanation
Indices: 2157970--2158237 Score: 473
Period size: 133 Copynumber: 2.0 Consensus size: 133
2157960 CTGCATATCT
* * *
2157970 CAGCCTAAATATTTCAGGAATGGTAGTTCTGGATTCCCCAGAGTTTGAAAGTGATTGTAAATTAT
1 CAGCCTAAATATCTCAGGAATGGTAGTTATGGATTCCCCAGAGCTTGAAAGTGATTGTAAATTAT
* *
2158035 TTGTGTTAATTGTTTTTCTTTTGGTTTGGATTTGCATACTGGGGCAAGAATGTCTCTTCTTTTAC
66 TTGTGTTAAATGTTTTTCTTTTGGTTTGGATTTGCATACTAGGGCAAGAATGTCTCTTCTTTTAC
2158100 GAG
131 GAG
2158103 CAGCCTAAATATCTCAGGAATGGTAGTTATGGATTCCCCAGAGCTTGAAAGTGATTGTAAATTAT
1 CAGCCTAAATATCTCAGGAATGGTAGTTATGGATTCCCCAGAGCTTGAAAGTGATTGTAAATTAT
* *
2158168 TTGTGTTAAATGTTTTTCTTTTGGTTTGGGTTTGCATACTAGGGCAAGAATGTCTCTTCTTTTAT
66 TTGTGTTAAATGTTTTTCTTTTGGTTTGGATTTGCATACTAGGGCAAGAATGTCTCTTCTTTTAC
2158233 GAG
131 GAG
2158236 CA
1 CA
2158238 CATTGTGCAT
Statistics
Matches: 128, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
133 128 1.00
ACGTcount: A:0.24, C:0.13, G:0.22, T:0.40
Consensus pattern (133 bp):
CAGCCTAAATATCTCAGGAATGGTAGTTATGGATTCCCCAGAGCTTGAAAGTGATTGTAAATTAT
TTGTGTTAAATGTTTTTCTTTTGGTTTGGATTTGCATACTAGGGCAAGAATGTCTCTTCTTTTAC
GAG
Found at i:2159654 original size:50 final size:49
Alignment explanation
Indices: 2159579--2159678 Score: 164
Period size: 50 Copynumber: 2.0 Consensus size: 49
2159569 TGTTAGAAAT
* * *
2159579 CTTTGCAAAAAGATGGCTCCTCCTCTTGTGACCTTACTCTCTGCTGAAC
1 CTTTGCAAAAAGATGGCTCCTCCTCTTGTGACATTACTATCTGCAGAAC
2159628 NCTTTGCAAAAAGATGGCTCCTCCTCTTGTGACATTACTATCTGCAGAAC
1 -CTTTGCAAAAAGATGGCTCCTCCTCTTGTGACATTACTATCTGCAGAAC
2159678 C
1 C
2159679 CGAGATACAA
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
49 1 0.02
50 46 0.98
ACGTcount: A:0.23, C:0.29, G:0.16, T:0.31
Consensus pattern (49 bp):
CTTTGCAAAAAGATGGCTCCTCCTCTTGTGACATTACTATCTGCAGAAC
Found at i:2162759 original size:37 final size:36
Alignment explanation
Indices: 2162717--2162790 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 36
2162707 CATTGGCACC
2162717 GGGAGCATCAGCACGAACAATGCTGCCCATGGTATT
1 GGGAGCATCAGCACGAACAATGCTGCCCATGGTATT
*
2162753 GNGGAGCATCAGCAGGAACAATGCTGCCCATGGTATT
1 G-GGAGCATCAGCACGAACAATGCTGCCCATGGTATT
2162790 G
1 G
2162791 TTCCAGAATA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 1 0.03
37 35 0.97
ACGTcount: A:0.27, C:0.23, G:0.30, T:0.19
Consensus pattern (36 bp):
GGGAGCATCAGCACGAACAATGCTGCCCATGGTATT
Found at i:2164412 original size:6 final size:6
Alignment explanation
Indices: 2164401--2164433 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
2164391 TTCTGAGAAT
*
2164401 GATAGG GATAGG GATAGG GATAGG GACAGG GAT
1 GATAGG GATAGG GATAGG GATAGG GATAGG GAT
2164434 GGAGTAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.48, T:0.15
Consensus pattern (6 bp):
GATAGG
Found at i:2172844 original size:16 final size:18
Alignment explanation
Indices: 2172810--2172850 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
2172800 ATGTTTTTTT
2172810 ATATATATTATTATGTTAA
1 ATATATATTA-TATGTTAA
2172829 ATATATATTA-AT-TTAA
1 ATATATATTATATGTTAA
*
2172845 AAATAT
1 ATATAT
2172851 CAACTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 9 0.43
17 2 0.10
19 10 0.48
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
ATATATATTATATGTTAA
Found at i:2173034 original size:15 final size:15
Alignment explanation
Indices: 2173014--2173074 Score: 54
Period size: 13 Copynumber: 4.1 Consensus size: 15
2173004 GAATATATAA
2173014 AAATAATTATATTTG
1 AAATAATTATATTTG
2173029 AAATAA-T-TATTTG
1 AAATAATTATATTTG
* * **
2173042 AAATATTTCACATATAA
1 AAATAATT-ATAT-TTG
2173059 AAATAATTATATTTG
1 AAATAATTATATTTG
2173074 A
1 A
2173075 GATATTTTAT
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
13 11 0.32
14 2 0.06
15 8 0.24
16 5 0.15
17 8 0.24
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (15 bp):
AAATAATTATATTTG
Found at i:2173063 original size:30 final size:32
Alignment explanation
Indices: 2173029--2173091 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
2173019 ATTATATTTG
2173029 AAATAA-T-TATTTGAAATATTTCACATATAA
1 AAATAATTATATTTGAAATATTTCACATATAA
* * *
2173059 AAATAATTATATTTGAGATATTTTATATATAA
1 AAATAATTATATTTGAAATATTTCACATATAA
2173091 A
1 A
2173092 TTTAAAATAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 6 0.21
31 1 0.04
32 21 0.75
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (32 bp):
AAATAATTATATTTGAAATATTTCACATATAA
Found at i:2174168 original size:22 final size:22
Alignment explanation
Indices: 2174126--2174168 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
2174116 AATAGAATAA
*
2174126 ATTTAATATTAATTGTGAATTT
1 ATTTAATATTAATTGTAAATTT
*
2174148 ATTTAATTTTACATT-TAAATT
1 ATTTAATATTA-ATTGTAAATT
2174169 GTCAAATACA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (22 bp):
ATTTAATATTAATTGTAAATTT
Found at i:2182488 original size:35 final size:35
Alignment explanation
Indices: 2182444--2182518 Score: 132
Period size: 35 Copynumber: 2.1 Consensus size: 35
2182434 TAATCATTTA
2182444 AAAATAAAAAAATATAAATAGACTATTAAAATGAT
1 AAAATAAAAAAATATAAATAGACTATTAAAATGAT
*
2182479 AAAATAAAAAAATATATATAGACTATTAAAATGAT
1 AAAATAAAAAAATATAAATAGACTATTAAAATGAT
*
2182514 GAAAT
1 AAAAT
2182519 TGTATTTTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.64, C:0.03, G:0.07, T:0.27
Consensus pattern (35 bp):
AAAATAAAAAAATATAAATAGACTATTAAAATGAT
Found at i:2184917 original size:16 final size:17
Alignment explanation
Indices: 2184889--2184921 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
2184879 AAATAGATTT
2184889 TTAATTAAAAATTTTAA
1 TTAATTAAAAATTTTAA
2184906 TTAATT-AAAATTTTAA
1 TTAATTAAAAATTTTAA
2184922 ACCTAAACCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTAATTAAAAATTTTAA
Found at i:2185991 original size:34 final size:34
Alignment explanation
Indices: 2185946--2186013 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
2185936 GCCATTACTT
*
2185946 TTTTTTCAAAAAAAAAAAAAAACATAGAAAAAAA
1 TTTTTTAAAAAAAAAAAAAAAACATAGAAAAAAA
2185980 TTTTTTAAAAAAAAAAAAAAAACATAGAAAAAAA
1 TTTTTTAAAAAAAAAAAAAAAACATAGAAAAAAA
2186014 GAAGAGACGG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.72, C:0.04, G:0.03, T:0.21
Consensus pattern (34 bp):
TTTTTTAAAAAAAAAAAAAAAACATAGAAAAAAA
Found at i:2187018 original size:28 final size:28
Alignment explanation
Indices: 2186987--2187043 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
2186977 AAAATTATTG
2186987 ATGAAAATAGAAATGGTTAGCATTAATA
1 ATGAAAATAGAAATGGTTAGCATTAATA
*
2187015 ATGAAAATAGAGATGGTTAGCATTAATA
1 ATGAAAATAGAAATGGTTAGCATTAATA
2187043 A
1 A
2187044 GTTGGAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.49, C:0.04, G:0.19, T:0.28
Consensus pattern (28 bp):
ATGAAAATAGAAATGGTTAGCATTAATA
Found at i:2187867 original size:30 final size:30
Alignment explanation
Indices: 2187801--2187867 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
2187791 AACTTAAATG
* **
2187801 AAAACTTTTTTGTAGTTCAGTAACCAAATT
1 AAAACTTTTTTGTAGTTAAGTAACCAAACA
**
2187831 GTAACTTTTTT-TAGTTAAGTAACCAAAACA
1 AAAACTTTTTTGTAGTTAAGTAACC-AAACA
2187861 AAAACTT
1 AAAACTT
2187868 ATCAATAATT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
29 12 0.41
30 17 0.59
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.37
Consensus pattern (30 bp):
AAAACTTTTTTGTAGTTAAGTAACCAAACA
Found at i:2188251 original size:58 final size:58
Alignment explanation
Indices: 2188173--2188290 Score: 218
Period size: 58 Copynumber: 2.0 Consensus size: 58
2188163 ATTATTAGTT
*
2188173 AAAAATGAAATAAAATAGAGGGTGTGATAATTATGCATTTAAAAATAATTATAATGTA
1 AAAAATAAAATAAAATAGAGGGTGTGATAATTATGCATTTAAAAATAATTATAATGTA
*
2188231 AAAAATAAAATAAAATAGAGGGTGTGATAATTATGCATTTAAAAATAATTATAATTTA
1 AAAAATAAAATAAAATAGAGGGTGTGATAATTATGCATTTAAAAATAATTATAATGTA
2188289 AA
1 AA
2188291 TAGAGTTATT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.53, C:0.02, G:0.14, T:0.31
Consensus pattern (58 bp):
AAAAATAAAATAAAATAGAGGGTGTGATAATTATGCATTTAAAAATAATTATAATGTA
Found at i:2189037 original size:90 final size:90
Alignment explanation
Indices: 2188879--2189058 Score: 306
Period size: 90 Copynumber: 2.0 Consensus size: 90
2188869 AAACTACTAC
*
2188879 TTTCCTCTTTCTGTTGTGATTTGAAGCTTACCAGTACCATCTATTTATAAAGAAGGTTGGTAGAA
1 TTTCATCTTTCTGTTGTGATTTGAAGCTTACCAGTACCATCTATTTATAAAGAAGGTTGGTAGAA
2188944 TCCTAGTTGAAGTGGTAGAATACAA
66 TCCTAGTTGAAGTGGTAGAATACAA
* * * * *
2188969 TTTCATCTTTCTGTTGTGATTTGAAGCTTACCCGTTCCATCTATTTATAAATAAGGTTGTTATAA
1 TTTCATCTTTCTGTTGTGATTTGAAGCTTACCAGTACCATCTATTTATAAAGAAGGTTGGTAGAA
2189034 TCCTAGTTGAAGTGGTAGAATACAA
66 TCCTAGTTGAAGTGGTAGAATACAA
2189059 ATAATATTAT
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
90 84 1.00
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.39
Consensus pattern (90 bp):
TTTCATCTTTCTGTTGTGATTTGAAGCTTACCAGTACCATCTATTTATAAAGAAGGTTGGTAGAA
TCCTAGTTGAAGTGGTAGAATACAA
Found at i:2191080 original size:23 final size:23
Alignment explanation
Indices: 2191054--2191174 Score: 88
Period size: 23 Copynumber: 5.2 Consensus size: 23
2191044 ATTTTAGGTG
2191054 TTTGTCTTCCACAATTTTAAGGA
1 TTTGTCTTCCACAATTTTAAGGA
* * *
2191077 TTTGT-TTAGCTAAAATTTTAGGTGA
1 TTTGTCTT--CCACAATTTTAAG-GA
*
2191102 -TTGTCTTCCATAATTTTAAGGA
1 TTTGTCTTCCACAATTTTAAGGA
** *
2191124 TTTGTTCGGCTA-AATTTT-AGGCA
1 TTTG-TCTTCCACAATTTTAAGG-A
* *
2191147 TTTTTCTTCCACAATTTTAAGGG
1 TTTGTCTTCCACAATTTTAAGGA
2191170 TTTGT
1 TTTGT
2191175 TTCTCTTTTA
Statistics
Matches: 74, Mismatches: 15, Indels: 18
0.69 0.14 0.17
Matches are distributed among these distances:
22 11 0.15
23 38 0.51
24 21 0.28
25 4 0.05
ACGTcount: A:0.24, C:0.12, G:0.17, T:0.47
Consensus pattern (23 bp):
TTTGTCTTCCACAATTTTAAGGA
Found at i:2191107 original size:47 final size:46
Alignment explanation
Indices: 2191039--2191176 Score: 188
Period size: 47 Copynumber: 3.0 Consensus size: 46
2191029 TGCAGGTTAG
*
2191039 GCTAAATTTTAGGTGTTTGTCTTCCACAATTTTAAGGATTTGTTTA
1 GCTAAATTTTAGGTGATTGTCTTCCACAATTTTAAGGATTTGTTTA
* **
2191085 GCTAAAATTTTAGGTGATTGTCTTCCATAATTTTAAGGATTTGTTCG
1 GCT-AAATTTTAGGTGATTGTCTTCCACAATTTTAAGGATTTGTTTA
* * *
2191132 GCTAAATTTTAGG-CATTTTTCTTCCACAATTTTAAGGGTTTGTTT
1 GCTAAATTTTAGGTGA-TTGTCTTCCACAATTTTAAGGATTTGTTT
2191177 CTCTTTTATC
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
45 1 0.01
46 38 0.47
47 42 0.52
ACGTcount: A:0.24, C:0.12, G:0.17, T:0.47
Consensus pattern (46 bp):
GCTAAATTTTAGGTGATTGTCTTCCACAATTTTAAGGATTTGTTTA
Found at i:2192550 original size:9 final size:9
Alignment explanation
Indices: 2192536--2192570 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
2192526 TTATTTATCC
2192536 AATTAATTA
1 AATTAATTA
*
2192545 AATTAATTG
1 AATTAATTA
*
2192554 AATTAACTA
1 AATTAATTA
2192563 AATTAATT
1 AATTAATT
2192571 TCTTAATTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (9 bp):
AATTAATTA
Found at i:2192557 original size:18 final size:18
Alignment explanation
Indices: 2192536--2192570 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2192526 TTATTTATCC
*
2192536 AATTAATTAAATTAATTG
1 AATTAACTAAATTAATTG
2192554 AATTAACTAAATTAATT
1 AATTAACTAAATTAATT
2192571 TCTTAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (18 bp):
AATTAACTAAATTAATTG
Found at i:2193550 original size:17 final size:17
Alignment explanation
Indices: 2193528--2193563 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
2193518 GACTTAAAAG
2193528 TAACAATGTTAACTTTT
1 TAACAATGTTAACTTTT
2193545 TAACAATGTTAACTTTT
1 TAACAATGTTAACTTTT
2193562 TA
1 TA
2193564 GTGTTTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.11, G:0.06, T:0.47
Consensus pattern (17 bp):
TAACAATGTTAACTTTT
Found at i:2204800 original size:13 final size:13
Alignment explanation
Indices: 2204782--2204808 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2204772 ATGAGAGTAC
2204782 TTTTAGGAAACCT
1 TTTTAGGAAACCT
2204795 TTTTAGGAAACCT
1 TTTTAGGAAACCT
2204808 T
1 T
2204809 ATCAAGAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTTTAGGAAACCT
Found at i:2205361 original size:40 final size:40
Alignment explanation
Indices: 2205316--2205391 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
2205306 TTACACCATG
* *
2205316 TGGGGATAGAATCGACCCA-CCTAACCTTACACACCAAGTA
1 TGGGGATAGAATCAACCCATCC-AACCCTACACACCAAGTA
**
2205356 TGGGGATTTAATCAACCCATCCAACCCTACACACCA
1 TGGGGATAGAATCAACCCATCCAACCCTACACACCA
2205392 TAAGGTACCG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 29 0.94
41 2 0.06
ACGTcount: A:0.34, C:0.33, G:0.14, T:0.18
Consensus pattern (40 bp):
TGGGGATAGAATCAACCCATCCAACCCTACACACCAAGTA
Found at i:2206921 original size:6 final size:6
Alignment explanation
Indices: 2206910--2207097 Score: 110
Period size: 6 Copynumber: 31.7 Consensus size: 6
2206900 AAATTATTCT
* * * * * *
2206910 TCTCTC TCTCTC TCTCTC TCTCCC ACTCTC TCCCTC CCTTTC TTTCTC
1 TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC
* * * * * * * * *
2206958 T-TC-C TCCCTC CCCCTC CCTCTC CCTCCC TTTCTC CCCCTC TCTCTC
1 TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC
* * * * * *
2207004 TCCCTC TCCCAC TCTCCC ACTCTC CCTCTC TCTCTC TCTCTC TCTCTC
1 TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC
* * * * * * *
2207052 CCTCTC CCCCTT TCTCCC TCTCTC TCTCTC TCTCCC CCTCTC TCTC
1 TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTC
2207098 CCTCACACAC
Statistics
Matches: 137, Mismatches: 43, Indels: 4
0.74 0.23 0.02
Matches are distributed among these distances:
4 2 0.01
5 3 0.02
6 132 0.96
ACGTcount: A:0.02, C:0.59, G:0.00, T:0.39
Consensus pattern (6 bp):
TCTCTC
Found at i:2206923 original size:8 final size:8
Alignment explanation
Indices: 2206910--2207097 Score: 110
Period size: 8 Copynumber: 23.8 Consensus size: 8
2206900 AAATTATTCT
2206910 TCTCTCTC
1 TCTCTCTC
2206918 TCTCTCTC
1 TCTCTCTC
*
2206926 TCTCTCCC
1 TCTCTCTC
*
2206934 ACTCTCTC
1 TCTCTCTC
* * *
2206942 CCTCCCTT
1 TCTCTCTC
*
2206950 TCTTTCTC
1 TCTCTCTC
2206958 T-TC-CTC
1 TCTCTCTC
* * *
2206964 CCTCCCCC
1 TCTCTCTC
*
2206972 TCCCTCTC
1 TCTCTCTC
* * *
2206980 CCTCCCTT
1 TCTCTCTC
* *
2206988 TCTCCCCC
1 TCTCTCTC
2206996 TCTCTCTC
1 TCTCTCTC
*
2207004 TCCCTCTC
1 TCTCTCTC
* *
2207012 CCACTCTC
1 TCTCTCTC
* *
2207020 CCACTCTC
1 TCTCTCTC
*
2207028 CCTCTCTC
1 TCTCTCTC
2207036 TCTCTCTC
1 TCTCTCTC
2207044 TCTCTCTC
1 TCTCTCTC
* *
2207052 CCTCTCCC
1 TCTCTCTC
* *
2207060 CCTTTCTC
1 TCTCTCTC
*
2207068 CCTCTCTC
1 TCTCTCTC
2207076 TCTCTCTC
1 TCTCTCTC
* *
2207084 TCCCCCTC
1 TCTCTCTC
2207092 TCTCTC
1 TCTCTC
2207098 CCTCACACAC
Statistics
Matches: 137, Mismatches: 41, Indels: 4
0.75 0.23 0.02
Matches are distributed among these distances:
6 3 0.02
7 3 0.02
8 131 0.96
ACGTcount: A:0.02, C:0.59, G:0.00, T:0.39
Consensus pattern (8 bp):
TCTCTCTC
Found at i:2207007 original size:38 final size:40
Alignment explanation
Indices: 2206909--2207101 Score: 177
Period size: 38 Copynumber: 4.9 Consensus size: 40
2206899 CAAATTATTC
* * * *
2206909 TTCTCTCTCTCTCTCTCTCTCTCCCACTCTCTCCCTCCCT
1 TTCTCCCTCTCTCTCTCTCTCCCCCTCCCTCTCCCTCCCT
** *
2206949 TTCTTTCTCT-TC-CTCCCTCCCCCTCCCTCTCCCTCCCT
1 TTCTCCCTCTCTCTCTCTCTCCCCCTCCCTCTCCCTCCCT
* * *
2206987 TTCTCCC-C-CTCTCTCTCTCCCTCTCCCACT--CTCCCA
1 TTCTCCCTCTCTCTCTCTCTCCCCCTCCCTCTCCCTCCCT
* *
2207023 CTCTCCCTCTCTCTCTCTCTCTCTCTCTCCCTCT-CC-CCCT
1 TTCTCCCTCTCTCTCTCTCTC-C-CCCTCCCTCTCCCTCCCT
*
2207063 TTCTCCCTCTCTCTCTCTCTCTCCCCCTCTCTCTCCCTC
1 TTCT-CC-CTCTCTCTCTCTCTCCCCCTCCCTCTCCCTC
2207102 ACACACATAC
Statistics
Matches: 125, Mismatches: 17, Indels: 20
0.77 0.10 0.12
Matches are distributed among these distances:
36 11 0.09
37 4 0.03
38 53 0.42
39 3 0.02
40 32 0.26
41 6 0.05
42 16 0.13
ACGTcount: A:0.02, C:0.59, G:0.00, T:0.39
Consensus pattern (40 bp):
TTCTCCCTCTCTCTCTCTCTCCCCCTCCCTCTCCCTCCCT
Found at i:2207100 original size:10 final size:10
Alignment explanation
Indices: 2206913--2207101 Score: 140
Period size: 10 Copynumber: 19.3 Consensus size: 10
2206903 TTATTCTTCT
*
2206913 CTCTCTCTCT
1 CTCTCTCTCC
2206923 CTCTCTCTCC
1 CTCTCTCTCC
*
2206933 CACTCTCTCC
1 CTCTCTCTCC
* * *
2206943 CTCCCTTTCT
1 CTCTCTCTCC
*
2206953 TTCTCTTCCTCC
1 CTCTC-T-CTCC
* *
2206965 CTCCCCCTCC
1 CTCTCTCTCC
*
2206975 CTCTCCCTCC
1 CTCTCTCTCC
2206985 CT-T-TCTCC
1 CTCTCTCTCC
* *
2206993 CCCTCTCTCT
1 CTCTCTCTCC
*
2207003 CTCCCTCTCC
1 CTCTCTCTCC
*
2207013 CACTCTC-CC
1 CTCTCTCTCC
* *
2207022 ACTCTCCCTCT
1 -CTCTCTCTCC
*
2207033 CTCTCTCTCT
1 CTCTCTCTCC
2207043 CTCTCTCTCC
1 CTCTCTCTCC
2207053 CTCTC-C-CC
1 CTCTCTCTCC
2207061 CT-T-TCTCC
1 CTCTCTCTCC
*
2207069 CTCTCTCTCT
1 CTCTCTCTCC
*
2207079 CTCTCTCCCC
1 CTCTCTCTCC
2207089 CTCTCTCTCC
1 CTCTCTCTCC
2207099 CTC
1 CTC
2207102 ACACACATAC
Statistics
Matches: 138, Mismatches: 31, Indels: 20
0.73 0.16 0.11
Matches are distributed among these distances:
7 2 0.01
8 13 0.09
9 6 0.04
10 110 0.80
11 2 0.01
12 5 0.04
ACGTcount: A:0.02, C:0.60, G:0.00, T:0.39
Consensus pattern (10 bp):
CTCTCTCTCC
Found at i:2208082 original size:38 final size:38
Alignment explanation
Indices: 2208040--2208166 Score: 96
Period size: 38 Copynumber: 3.1 Consensus size: 38
2208030 AATTAATTAA
2208040 CATAATTAGCAAAAATAAACCTTTGCACAAATACATAT
1 CATAATTAGCAAAAATAAACCTTTGCACAAATACATAT
* * *** *
2208078 CATAACTTCAACAACCAAATAATTCAACAAAG-AGCAAATTA-ATTAA
1 CATAA-TT-AGCAA--AAATAA---ACCTTTGCA-CAAA-TACA-TAT
2208124 CATAATTAGCAAAAATAAACCTTTGCACAAATACATAT
1 CATAATTAGCAAAAATAAACCTTTGCACAAATACATAT
2208162 CATAA
1 CATAA
2208167 CTTCAACAAC
Statistics
Matches: 65, Mismatches: 12, Indels: 24
0.64 0.12 0.24
Matches are distributed among these distances:
38 14 0.22
39 10 0.15
40 5 0.08
42 12 0.18
44 5 0.08
45 10 0.15
46 9 0.14
ACGTcount: A:0.52, C:0.19, G:0.05, T:0.24
Consensus pattern (38 bp):
CATAATTAGCAAAAATAAACCTTTGCACAAATACATAT
Found at i:2208154 original size:46 final size:46
Alignment explanation
Indices: 2208104--2208237 Score: 119
Period size: 46 Copynumber: 3.1 Consensus size: 46
2208094 AAATAATTCA
2208104 ACAAAGAGCAAATTAATTAACATAATTAGCAAAAATAAACCTTTGC
1 ACAAAGAGCAAATTAATTAACATAATTAGCAAAAATAAACCTTTGC
* * * * *
2208150 ACAAATA-CATA-TCA-TAAC-T--TCAACAACCAAAT-AA---TT-C
1 ACAAAGAGCAAATTAATTAACATAATTAGCAA--AAATAAACCTTTGC
2208187 AACAAAGAGCAAATTAATTAACATAATTAGCAAAAATAAACCTTTGC
1 -ACAAAGAGCAAATTAATTAACATAATTAGCAAAAATAAACCTTTGC
2208234 ACAA
1 ACAA
2208238 TTAATTTAGG
Statistics
Matches: 64, Mismatches: 10, Indels: 28
0.63 0.10 0.27
Matches are distributed among these distances:
37 1 0.02
38 8 0.12
39 3 0.05
40 7 0.11
41 6 0.09
42 10 0.16
43 6 0.09
44 7 0.11
45 3 0.05
46 12 0.19
47 1 0.02
ACGTcount: A:0.53, C:0.18, G:0.06, T:0.23
Consensus pattern (46 bp):
ACAAAGAGCAAATTAATTAACATAATTAGCAAAAATAAACCTTTGC
Found at i:2208154 original size:84 final size:84
Alignment explanation
Indices: 2208013--2208237 Score: 450
Period size: 84 Copynumber: 2.7 Consensus size: 84
2208003 AGCCAGTTGC
2208013 TAATTCAACAAAGAGCAAATTAATTAACATAATTAGCAAAAATAAACCTTTGCACAAATACATAT
1 TAATTCAACAAAGAGCAAATTAATTAACATAATTAGCAAAAATAAACCTTTGCACAAATACATAT
2208078 CATAACTTCAACAACCAAA
66 CATAACTTCAACAACCAAA
2208097 TAATTCAACAAAGAGCAAATTAATTAACATAATTAGCAAAAATAAACCTTTGCACAAATACATAT
1 TAATTCAACAAAGAGCAAATTAATTAACATAATTAGCAAAAATAAACCTTTGCACAAATACATAT
2208162 CATAACTTCAACAACCAAA
66 CATAACTTCAACAACCAAA
2208181 TAATTCAACAAAGAGCAAATTAATTAACATAATTAGCAAAAATAAACCTTTGCACAA
1 TAATTCAACAAAGAGCAAATTAATTAACATAATTAGCAAAAATAAACCTTTGCACAA
2208238 TTAATTTAGG
Statistics
Matches: 141, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 141 1.00
ACGTcount: A:0.52, C:0.18, G:0.05, T:0.24
Consensus pattern (84 bp):
TAATTCAACAAAGAGCAAATTAATTAACATAATTAGCAAAAATAAACCTTTGCACAAATACATAT
CATAACTTCAACAACCAAA
Found at i:2208892 original size:31 final size:31
Alignment explanation
Indices: 2208855--2208916 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
2208845 CACCAAAAGT
2208855 TTATTTTAAAAATA-ATAAATAAATAAAAAAA
1 TTATTTTAAAAATATATAAA-AAATAAAAAAA
* *
2208886 TTATTTTAAAAATATTTTAAAAATAAAAAAA
1 TTATTTTAAAAATATATAAAAAATAAAAAAA
2208917 ATAAAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 25 0.89
32 3 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (31 bp):
TTATTTTAAAAATATATAAAAAATAAAAAAA
Found at i:2208896 original size:12 final size:12
Alignment explanation
Indices: 2208881--2208909 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
2208871 AAATAAATAA
2208881 AAAAATTATTTT
1 AAAAATTATTTT
2208893 AAAAA-TATTTT
1 AAAAATTATTTT
2208904 AAAAAT
1 AAAAAT
2208910 AAAAAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
AAAAATTATTTT
Found at i:2214113 original size:52 final size:54
Alignment explanation
Indices: 2214056--2214159 Score: 149
Period size: 56 Copynumber: 1.9 Consensus size: 54
2214046 AACTCCTAAG
**
2214056 GAACCCTAGGTGTGA-C-AGTATTCTTTCTTCTTGGTTGTTTGATACATGTAAA
1 GAACCCTAGGTGTGACCTAGTATTCTTTCTTCTTGGTTCATTGATACATGTAAA
*
2214108 GAACCCTAGGTGTGACCCTTGGTATTCTTTCTTCTTGGTTCATTGATACATG
1 GAACCCTAGGTGTGA-CC-TAGTATTCTTTCTTCTTGGTTCATTGATACATG
2214160 GAAGAAACCT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
52 15 0.33
54 1 0.02
56 29 0.64
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.40
Consensus pattern (54 bp):
GAACCCTAGGTGTGACCTAGTATTCTTTCTTCTTGGTTCATTGATACATGTAAA
Found at i:2214891 original size:3 final size:3
Alignment explanation
Indices: 2214883--2214908 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2214873 AGACAAGGTG
2214883 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
2214909 GAAAACAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:2223461 original size:35 final size:35
Alignment explanation
Indices: 2223415--2223486 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
2223405 CTCTGGCAAA
*
2223415 GCTAAAGATCCATTCATTTGTTACTTTGGGTACTT
1 GCTAAAGATCCATTCATTTGTTACTTTGGGGACTT
2223450 GCTAAAGATCCATTCATTTGTTACTTTGGGGACTT
1 GCTAAAGATCCATTCATTTGTTACTTTGGGGACTT
2223485 GC
1 GC
2223487 CTTTTTCCCT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.40
Consensus pattern (35 bp):
GCTAAAGATCCATTCATTTGTTACTTTGGGGACTT
Found at i:2232026 original size:18 final size:18
Alignment explanation
Indices: 2232005--2232040 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2231995 GTACCAAAAA
2232005 ATATTAATAATTTAAGTT
1 ATATTAATAATTTAAGTT
2232023 ATATTAATAATTTAAGTT
1 ATATTAATAATTTAAGTT
2232041 TAATATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (18 bp):
ATATTAATAATTTAAGTT
Found at i:2247514 original size:58 final size:58
Alignment explanation
Indices: 2247444--2247558 Score: 185
Period size: 58 Copynumber: 2.0 Consensus size: 58
2247434 TGGAAAGTTG
* * * *
2247444 ATCCATCAAAACATGAAGAAATGTATTAGTGGCTAGAAAGTGGGAGTGTTCTTTCCCT
1 ATCCATCAAAACATAAAGAAATGTATTAGTGGCCAAAAAGCGGGAGTGTTCTTTCCCT
*
2247502 ATCCATCAAAACATAAAGAGATGTATTAGTGGCCAAAAAGCGGGAGTGTTCTTTCCC
1 ATCCATCAAAACATAAAGAAATGTATTAGTGGCCAAAAAGCGGGAGTGTTCTTTCCC
2247559 CACTTAGTGA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (58 bp):
ATCCATCAAAACATAAAGAAATGTATTAGTGGCCAAAAAGCGGGAGTGTTCTTTCCCT
Found at i:2257980 original size:10 final size:10
Alignment explanation
Indices: 2257956--2257989 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
2257946 GAAACAAAAT
*
2257956 AAAAAATTTA
1 AAAAAATTGA
2257966 GAAAAAATTGA
1 -AAAAAATTGA
2257977 AAAAAATTGA
1 AAAAAATTGA
2257987 AAA
1 AAA
2257990 CAGAAGTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.21
Consensus pattern (10 bp):
AAAAAATTGA
Found at i:2260112 original size:16 final size:16
Alignment explanation
Indices: 2260091--2260123 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2260081 ATTCGAATTC
2260091 AACGAGAAAAGTCGCA
1 AACGAGAAAAGTCGCA
2260107 AACGAGAAAAGTCGCA
1 AACGAGAAAAGTCGCA
2260123 A
1 A
2260124 CCTAGTAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.52, C:0.18, G:0.24, T:0.06
Consensus pattern (16 bp):
AACGAGAAAAGTCGCA
Found at i:2260990 original size:22 final size:21
Alignment explanation
Indices: 2260960--2261025 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 21
2260950 TACAAATTAA
2260960 ATCTCCAAGATTACAAGATCAT
1 ATCTCCAAGATTAC-AGATCAT
* * *
2260982 ATCTTCAAGATTGCATATCAT
1 ATCTCCAAGATTACAGATCAT
* *
2261003 ATCT--AGGATTACATATCAT
1 ATCTCCAAGATTACAGATCAT
2261022 ATCT
1 ATCT
2261026 AAGATTGTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
19 17 0.44
21 10 0.26
22 12 0.31
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.35
Consensus pattern (21 bp):
ATCTCCAAGATTACAGATCAT
Found at i:2261017 original size:19 final size:19
Alignment explanation
Indices: 2260977--2261128 Score: 215
Period size: 19 Copynumber: 8.2 Consensus size: 19
2260967 AGATTACAAG
2260977 ATCATATCTTCAAGATTGCAT
1 ATCATATC-T-AAGATTGCAT
* *
2260998 ATCATATCTAGGATTACAT
1 ATCATATCTAAGATTGCAT
2261017 ATCATATCTAAGATTG--T
1 ATCATATCTAAGATTGCAT
2261034 ATCATATCTAAGATTGCA-
1 ATCATATCTAAGATTGCAT
*
2261052 ATCATATCTAATATTGCAT
1 ATCATATCTAAGATTGCAT
*
2261071 ATCATATCTAATATTG--T
1 ATCATATCTAAGATTGCAT
2261088 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
2261107 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
2261126 ATC
1 ATC
2261129 CTTAAAGATT
Statistics
Matches: 120, Mismatches: 6, Indels: 12
0.87 0.04 0.09
Matches are distributed among these distances:
17 33 0.28
18 17 0.14
19 61 0.51
20 1 0.01
21 8 0.07
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (19 bp):
ATCATATCTAAGATTGCAT
Found at i:2261041 original size:36 final size:37
Alignment explanation
Indices: 2260966--2261128 Score: 181
Period size: 36 Copynumber: 4.4 Consensus size: 37
2260956 TTAAATCTCC
*
2260966 AAGATTACAAGATCATATCTTCAAGATTGCATATCATATCT
1 AAGATTAC-ATATCATATC-T-AAGATTG-ATATCATATCT
*
2261007 AGGATTACATATCATATCTAAGATTG-TATCATATCT
1 AAGATTACATATCATATCTAAGATTGATATCATATCT
* *
2261043 AAGATTGCA-ATCATATCTAATATTGCATATCATATCT
1 AAGATTACATATCATATCTAAGATTG-ATATCATATCT
* *
2261080 AATATT--GTATCATATCTAAGATTGCATATCATATCT
1 AAGATTACATATCATATCTAAGATTG-ATATCATATCT
*
2261116 AAGATTGCATATC
1 AAGATTACATATC
2261129 CTTAAAGATT
Statistics
Matches: 107, Mismatches: 10, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
35 15 0.14
36 49 0.46
37 15 0.14
38 11 0.10
39 1 0.01
40 9 0.08
41 7 0.07
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.37
Consensus pattern (37 bp):
AAGATTACATATCATATCTAAGATTGATATCATATCT
Found at i:2261060 original size:54 final size:55
Alignment explanation
Indices: 2260977--2261128 Score: 243
Period size: 54 Copynumber: 2.7 Consensus size: 55
2260967 AGATTACAAG
* *
2260977 ATCATATCTTCAAGATTGCATATCATATCTAGGATTACATATCATATCTAAGATTGT
1 ATCATATC-T-AAGATTGCATATCATATCTAAGATTGCATATCATATCTAAGATTGT
* *
2261034 ATCATATCTAAGATTGCA-ATCATATCTAATATTGCATATCATATCTAATATTGT
1 ATCATATCTAAGATTGCATATCATATCTAAGATTGCATATCATATCTAAGATTGT
2261088 ATCATATCTAAGATTGCATATCATATCTAAGATTGCATATC
1 ATCATATCTAAGATTGCATATCATATCTAAGATTGCATATC
2261129 CTTAAAGATT
Statistics
Matches: 89, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
54 50 0.56
55 30 0.34
56 1 0.01
57 8 0.09
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (55 bp):
ATCATATCTAAGATTGCATATCATATCTAAGATTGCATATCATATCTAAGATTGT
Found at i:2261074 original size:73 final size:74
Alignment explanation
Indices: 2260977--2261124 Score: 212
Period size: 73 Copynumber: 2.0 Consensus size: 74
2260967 AGATTACAAG
*
2260977 ATCATATCTTCAAGATTGCATATCATATCTAGGATTACATATCATATCTAAGATTG-TATCATAT
1 ATCATATCTTCAAGATTGCATATCATATCTAAGATT--ATATCATATCTAAGATTGATATCATAT
2261041 CTAAGATTGCA
64 CTAAGATTGCA
* * *
2261052 ATCATATC-T-AATATTGCATATCATATCTAATATTGTATCATATCTAAGATTGCATATCATATC
1 ATCATATCTTCAAGATTGCATATCATATCTAAGATTATATCATATCTAAGATTG-ATATCATATC
2261115 TAAGATTGCA
65 TAAGATTGCA
2261125 TATCCTTAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
71 17 0.25
73 41 0.61
74 1 0.01
75 8 0.12
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (74 bp):
ATCATATCTTCAAGATTGCATATCATATCTAAGATTATATCATATCTAAGATTGATATCATATCT
AAGATTGCA
Found at i:2262324 original size:79 final size:79
Alignment explanation
Indices: 2262193--2262349 Score: 233
Period size: 79 Copynumber: 2.0 Consensus size: 79
2262183 ATCAGACGTG
* * * * *
2262193 CCCATATACAGATAAAACATATCAGAACATTCTAGTTGCACATATAATTAATAGATCAAAACATG
1 CCCATATACAAATAAAACAGATCAAAACATACTAATTGCACATATAATTAATAGATCAAAACATG
*
2262258 TTATTGGCATATTA
66 CTATTGGCATATTA
* *
2262272 CCCATATGCAAATAAAACAGATCAAAACATACTAATTGCACATATAGTTAATAGATCAAAACATG
1 CCCATATACAAATAAAACAGATCAAAACATACTAATTGCACATATAATTAATAGATCAAAACATG
*
2262337 CTATTGGTATATT
66 CTATTGGCATATT
2262350 CGACCATTAC
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
79 69 1.00
ACGTcount: A:0.44, C:0.17, G:0.10, T:0.29
Consensus pattern (79 bp):
CCCATATACAAATAAAACAGATCAAAACATACTAATTGCACATATAATTAATAGATCAAAACATG
CTATTGGCATATTA
Found at i:2265633 original size:16 final size:15
Alignment explanation
Indices: 2265612--2265643 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
2265602 TAGGGTGTGA
2265612 AATTATTTAATTGAAT
1 AATTATTTAATT-AAT
2265628 AATTATTTAATTAAT
1 AATTATTTAATTAAT
2265643 A
1 A
2265644 TTCAAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (15 bp):
AATTATTTAATTAAT
Found at i:2272292 original size:22 final size:23
Alignment explanation
Indices: 2272266--2272309 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 23
2272256 CCTGATCAAA
2272266 ATACGACACAT-AAGTGCCTGAC
1 ATACGACACATAAAGTGCCTGAC
2272288 ATACGACACATAAAGTGCCTGA
1 ATACGACACATAAAGTGCCTGA
2272310 TCAGTAAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (23 bp):
ATACGACACATAAAGTGCCTGAC
Found at i:2272551 original size:28 final size:29
Alignment explanation
Indices: 2272500--2272574 Score: 98
Period size: 28 Copynumber: 2.6 Consensus size: 29
2272490 AAATGTCTAA
* * *
2272500 CCAAAACACACCAGTATCAGATAATCC-T
1 CCAAAACACACCAGAATAATATAATCCAT
* *
2272528 CCCAAACACACTAGAATAATATAATCCAT
1 CCAAAACACACCAGAATAATATAATCCAT
2272557 CCAAAACACACCAGAATA
1 CCAAAACACACCAGAATA
2272575 GCACAAAGTG
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
28 22 0.56
29 17 0.44
ACGTcount: A:0.48, C:0.31, G:0.05, T:0.16
Consensus pattern (29 bp):
CCAAAACACACCAGAATAATATAATCCAT
Found at i:2273439 original size:65 final size:65
Alignment explanation
Indices: 2273358--2273486 Score: 249
Period size: 65 Copynumber: 2.0 Consensus size: 65
2273348 TTTCATGTTA
2273358 TAATGCATTCAACTAATGCTCTAAACAAAATTATCATTTTACCCCTAAACTTTAAATTAATGACG
1 TAATGCATTCAACTAATGCTCTAAACAAAATTATCATTTTACCCCTAAACTTTAAATTAATGACG
*
2273423 TAATGCATTCAACTAATGCTCTAAACAAAATTATCATTTTACCCCTAAACTTTTAATTAATGAC
1 TAATGCATTCAACTAATGCTCTAAACAAAATTATCATTTTACCCCTAAACTTTAAATTAATGAC
2273487 AATTTCATCC
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 63 1.00
ACGTcount: A:0.40, C:0.20, G:0.05, T:0.35
Consensus pattern (65 bp):
TAATGCATTCAACTAATGCTCTAAACAAAATTATCATTTTACCCCTAAACTTTAAATTAATGACG
Found at i:2283470 original size:75 final size:73
Alignment explanation
Indices: 2283382--2283553 Score: 199
Period size: 75 Copynumber: 2.4 Consensus size: 73
2283372 GGTTTTCCTC
** * * * ** *
2283382 ATTGAAATACCATACCTACATTTTTCAACTCGGTATGGGA-AATGCTATACCTACATTTCTTAAC
1 ATTGAAATACCATACCTACATTTCACAACTCAGTAT-GGATAATACCATACCTACATTTCACAAA
2283446 TCAGTATGG
65 TCAGTATGG
* *
2283455 ATTTGATAATACCATACCTATATTTCACAGCTCAGTATGGATAATACCATACCTACATTTCACAA
1 A-TTGA-AATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAA
2283520 ATCAGTATGG
64 ATCAGTATGG
2283530 A-TG--ATACCATACCTACATTTCACA
1 ATTGAAATACCATACCTACATTTCACA
2283554 CTTTTCCATG
Statistics
Matches: 85, Mismatches: 11, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
70 20 0.24
73 3 0.04
74 7 0.08
75 55 0.65
ACGTcount: A:0.34, C:0.22, G:0.11, T:0.33
Consensus pattern (73 bp):
ATTGAAATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAAAT
CAGTATGG
Found at i:2283489 original size:40 final size:38
Alignment explanation
Indices: 2283387--2283553 Score: 163
Period size: 35 Copynumber: 4.6 Consensus size: 38
2283377 TCCTCATTGA
** *
2283387 AATACCATACCTACATTTTTCAACTCGGTATGG--GA-
1 AATACCATACCTACATTTCACAACTCAGTATGGATGAT
* * **
2283422 AATGCTATACCTACATTTCTTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGA--TGAT
* *
2283462 AATACCATACCTATATTTCACAGCTCAGTAT-G--GAT
1 AATACCATACCTACATTTCACAACTCAGTATGGATGAT
*
2283497 AATACCATACCTACATTTCACAAATCAGTATGGATG--
1 AATACCATACCTACATTTCACAACTCAGTATGGATGAT
2283533 -ATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
2283554 CTTTTCCATG
Statistics
Matches: 110, Mismatches: 14, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
35 80 0.73
36 1 0.01
38 1 0.01
39 3 0.03
40 25 0.23
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (38 bp):
AATACCATACCTACATTTCACAACTCAGTATGGATGAT
Found at i:2286641 original size:46 final size:46
Alignment explanation
Indices: 2286509--2286643 Score: 164
Period size: 46 Copynumber: 2.9 Consensus size: 46
2286499 TTTGACATGA
* * * ** *
2286509 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGCCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATATCACGT
* **
2286555 TGCCATGATATCTTTCAACCATGGTCTTGTTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
*
2286601 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCA
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCA
2286644 GAGAGCACAC
Statistics
Matches: 75, Mismatches: 13, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
45 4 0.05
46 71 0.95
ACGTcount: A:0.21, C:0.24, G:0.13, T:0.41
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
Found at i:2286744 original size:54 final size:54
Alignment explanation
Indices: 2286678--2286976 Score: 598
Period size: 54 Copynumber: 5.5 Consensus size: 54
2286668 TCCTTACAGT
2286678 GGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTC
1 GGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTC
2286732 GGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTC
1 GGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTC
2286786 GGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTC
1 GGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTC
2286840 GGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTC
1 GGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTC
2286894 GGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTC
1 GGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTC
2286948 GGGATTACCAGTCCAGGCTAAATCCCCTG
1 GGGATTACCAGTCCAGGCTAAATCCCCTG
2286977 CAACAACAAT
Statistics
Matches: 245, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 245 1.00
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (54 bp):
GGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTC
Found at i:2305440 original size:465 final size:467
Alignment explanation
Indices: 2304568--2305496 Score: 1718
Period size: 465 Copynumber: 2.0 Consensus size: 467
2304558 TAGTTTCTTG
2304568 AGGGTTAAGTTGAGGGTTAATAATAAAATTTTATTTGCAAAAGTCCATTTTATATATGTTGTAAC
1 AGGGTTAAGTTGAGGGTTAATAATAAAATTTTATTTGCAAAAGTCCATTTTATATATGTTGTAAC
*
2304633 ATATTTACAACTTTTCTGATTATTATCTTTGAATTAATAAAGAGGTCTGGAGACTTTCTATAACT
66 ATATTTACAACTTTTCTGATTATTATCTTTGAATTAATAAAGAGGCCTGGAGACTTTCTATAACT
* * *
2304698 CTTAATTTTTCTAGAGTTTCAAATTCTTTTCTTATTCGTTTTACAGCCTTAATTATTTCAATTAT
131 CTTAAGTTTTCTAGAGTTTCAAATTCTTTGCTTATTCGTTTTACAGCCATAATTATTTCAATTAT
2304763 GGTTGTTTTCTTCCCTAAACCATATCAATTTTGGCATTAGAACTTAATTAGATCCTACGGTTGCT
196 GGTTGTTTTCTTCCCTAAACCATATCAATTTTGGCATTAGAACTTAATTAGATCCTACGGTTGCT
*
2304828 ATTAAGCCATGGTTGGACATAGTGGATATTAAGGAAGCGGAAGTCAAGGTCAAGAGACAATATTG
261 ATTAAGCCATGGTTGGACATAGTAGATATTAAGGAAGCGGAAGTCAAGGTCAAGAGACAATATTG
*
2304893 ACTGCAATACAAAGTGATATTAAAGAATTGTCGCATGCAATTTATGCTACATTGCGACAAGAGCC
326 ACTGCAATACAAAGTGATATTAAAGAATTGTCGCATGCAATTTATGCTACATTGCGACAAGAACC
*
2304958 AGTGGGAGTCCAGATGGA-ATTCTGGAAGGTGCCCACAATTGTGTATGCCTTAGAATTAAATAGG
391 AGTGGGAGTCCAGATGGAGATTCTGGAAGGTGCCCACAATTGTGTAAGCCTTAGAATTAAATAGG
2305022 GTGGAATTATAT
456 GTGGAATTATAT
2305034 AGGGTTAAGTTGAGGGTTAATAATAAAATTTTATTTGCAAAAGTCCATTTTATATATGTTGTAAC
1 AGGGTTAAGTTGAGGGTTAATAATAAAATTTTATTTGCAAAAGTCCATTTTATATATGTTGTAAC
* *
2305099 ATATTTTCAACTTTTCTGATTATTATCTTTGAATTAATAAAGAGGCCTGGAGAGTTTCTATAACT
66 ATATTTACAACTTTTCTGATTATTATCTTTGAATTAATAAAGAGGCCTGGAGACTTTCTATAACT
*
2305164 C-TAAGTTTTCTAGAGTTTCAAATTCTTTGCTTATTCGTTTTACAGCCATAATTCTTTCAATTAT
131 CTTAAGTTTTCTAGAGTTTCAAATTCTTTGCTTATTCGTTTTACAGCCATAATTATTTCAATTAT
*
2305228 GGTTGTTTTCTTCTCTAAACCATATCAATTTTGGCATTAGAACTTAATTAGATCCTACGGTTGCT
196 GGTTGTTTTCTTCCCTAAACCATATCAATTTTGGCATTAGAACTTAATTAGATCCTACGGTTGCT
*
2305293 ATTAAGCCATGGTTGGACATGGTAGATATTAAGGAAGCGGAAGTCAAGGTCAAGAGACAATATTG
261 ATTAAGCCATGGTTGGACATAGTAGATATTAAGGAAGCGGAAGTCAAGGTCAAGAGACAATATTG
*
2305358 ACTGCAATACGAAGTGATATTAAAGAATTGTCGCATGCAATTTATGCTACATTGCGACAAGAACC
326 ACTGCAATACAAAGTGATATTAAAGAATTGTCGCATGCAATTTATGCTACATTGCGACAAGAACC
*
2305423 AGTGGGAGTCCAGATGGAGATTCTGGAAGGTGCCCACAATTGTGTAAGCCTTTGAATTAAATAGG
391 AGTGGGAGTCCAGATGGAGATTCTGGAAGGTGCCCACAATTGTGTAAGCCTTAGAATTAAATAGG
2305488 GTGGAATTA
456 GTGGAATTA
2305497 AGATCAAAGT
Statistics
Matches: 448, Mismatches: 14, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
465 267 0.60
466 181 0.40
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (467 bp):
AGGGTTAAGTTGAGGGTTAATAATAAAATTTTATTTGCAAAAGTCCATTTTATATATGTTGTAAC
ATATTTACAACTTTTCTGATTATTATCTTTGAATTAATAAAGAGGCCTGGAGACTTTCTATAACT
CTTAAGTTTTCTAGAGTTTCAAATTCTTTGCTTATTCGTTTTACAGCCATAATTATTTCAATTAT
GGTTGTTTTCTTCCCTAAACCATATCAATTTTGGCATTAGAACTTAATTAGATCCTACGGTTGCT
ATTAAGCCATGGTTGGACATAGTAGATATTAAGGAAGCGGAAGTCAAGGTCAAGAGACAATATTG
ACTGCAATACAAAGTGATATTAAAGAATTGTCGCATGCAATTTATGCTACATTGCGACAAGAACC
AGTGGGAGTCCAGATGGAGATTCTGGAAGGTGCCCACAATTGTGTAAGCCTTAGAATTAAATAGG
GTGGAATTATAT
Found at i:2312257 original size:33 final size:31
Alignment explanation
Indices: 2312232--2312290 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
2312222 ATATCATCAT
* *
2312232 ATACAAA-AATGAGAGTACAAACCATATTGA
1 ATACAAATAATGAAAGTACAAACCATATTCA
*
2312262 ATTCAAATAATGAAAGTACAAACCATATT
1 ATACAAATAATGAAAGTACAAACCATATT
2312291 AGCCACTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 6 0.23
31 20 0.77
ACGTcount: A:0.53, C:0.14, G:0.10, T:0.24
Consensus pattern (31 bp):
ATACAAATAATGAAAGTACAAACCATATTCA
Found at i:2315419 original size:43 final size:43
Alignment explanation
Indices: 2315358--2315450 Score: 159
Period size: 43 Copynumber: 2.2 Consensus size: 43
2315348 GCAGATTTTT
*
2315358 CACAGCTCATGTAAGCAGCACCGTGTAGCCTAACATCTTAACC
1 CACAGCTCATATAAGCAGCACCGTGTAGCCTAACATCTTAACC
* *
2315401 CACAGCTCATATGAGCAGCATCGTGTAGCCTAACATCTTAACC
1 CACAGCTCATATAAGCAGCACCGTGTAGCCTAACATCTTAACC
2315444 CACAGCT
1 CACAGCT
2315451 TATGTGAGTA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.30, C:0.32, G:0.16, T:0.22
Consensus pattern (43 bp):
CACAGCTCATATAAGCAGCACCGTGTAGCCTAACATCTTAACC
Found at i:2317351 original size:13 final size:13
Alignment explanation
Indices: 2317333--2317357 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2317323 TGGTGCCCAA
2317333 AAGCAATGTTGGC
1 AAGCAATGTTGGC
2317346 AAGCAATGTTGG
1 AAGCAATGTTGG
2317358 AGGATTCTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.12, G:0.32, T:0.24
Consensus pattern (13 bp):
AAGCAATGTTGGC
Found at i:2322057 original size:94 final size:94
Alignment explanation
Indices: 2321896--2322082 Score: 329
Period size: 94 Copynumber: 2.0 Consensus size: 94
2321886 TTACCTACCT
2321896 TTTTCTTGCTTCTTACAGTTAGTTAGTACAAGGAGATTGTAATCCTGAGAGGACGGCTGCTTTTG
1 TTTTCTTGCTTCTTACAGTTAGTTAGTACAAGGAGATTGTAATCCTGAGAGGACGGCTGCTTTTG
* *
2321961 GCATTATCTAAGCTATTATGCGAAATAAG
66 GCATTACCTAAACTATTATGCGAAATAAG
* *
2321990 TTTTCTTGCTTCTTACAGTTAGTTAGTACAAGGAGATTGTAATCCTGCGAGGATGGCTGCTTTTG
1 TTTTCTTGCTTCTTACAGTTAGTTAGTACAAGGAGATTGTAATCCTGAGAGGACGGCTGCTTTTG
*
2322055 GCATTACCTAAATTATTATGCGAAATAA
66 GCATTACCTAAACTATTATGCGAAATAA
2322083 AATTTTGTAA
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
94 88 1.00
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.37
Consensus pattern (94 bp):
TTTTCTTGCTTCTTACAGTTAGTTAGTACAAGGAGATTGTAATCCTGAGAGGACGGCTGCTTTTG
GCATTACCTAAACTATTATGCGAAATAAG
Found at i:2330814 original size:60 final size:59
Alignment explanation
Indices: 2330740--2330857 Score: 173
Period size: 60 Copynumber: 2.0 Consensus size: 59
2330730 TCGGAGATTA
* *
2330740 ACTTCAGCATTAAAACGAGTTTCAAAAGTCAAATTTTCAATAGATTCTAATATTTCATTC
1 ACTTCAACATTAAAACGAGTTCCAAAAGTCAAA-TTTCAATAGATTCTAATATTTCATTC
* * * *
2330800 ACTTCAACATTAAAACGAGTTCCGAAGGTCAAATTTCGATAGATTCTAATGTTTCATT
1 ACTTCAACATTAAAACGAGTTCCAAAAGTCAAATTTCAATAGATTCTAATATTTCATT
2330858 TAAAGCATTA
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
59 23 0.44
60 29 0.56
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (59 bp):
ACTTCAACATTAAAACGAGTTCCAAAAGTCAAATTTCAATAGATTCTAATATTTCATTC
Found at i:2336822 original size:12 final size:13
Alignment explanation
Indices: 2336805--2336833 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2336795 TATATTTTGT
2336805 ATTTAAATTTAA-
1 ATTTAAATTTAAG
2336817 ATTTAAATTTAAG
1 ATTTAAATTTAAG
2336830 ATTT
1 ATTT
2336834 TATTTTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (13 bp):
ATTTAAATTTAAG
Found at i:2336840 original size:48 final size:49
Alignment explanation
Indices: 2336745--2336840 Score: 108
Period size: 48 Copynumber: 2.0 Consensus size: 49
2336735 ATAAAAAAGA
* * *
2336745 TTATAATTTTGTATTGATATTAATATTTAAATCTTATGTTATGTTTTAT
1 TTATAATTTTGTATTGAAATTAATATTTAAATCTTAAGTTATATTTTAT
* *
2336794 TTAT-ATTTTGTATTTAAATTTAA-ATTTAAAT-TTAAGATTTTATTTTA
1 TTATAATTTTGTATTGAAA-TTAATATTTAAATCTTAAG-TTATATTTTA
2336841 ATATATTGTA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
47 4 0.10
48 28 0.70
49 8 0.20
ACGTcount: A:0.33, C:0.01, G:0.06, T:0.59
Consensus pattern (49 bp):
TTATAATTTTGTATTGAAATTAATATTTAAATCTTAAGTTATATTTTAT
Found at i:2336867 original size:15 final size:15
Alignment explanation
Indices: 2336843--2336890 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
2336833 TTATTTTAAT
*
2336843 ATATTGTAATAAAAA
1 ATATTTTAATAAAAA
* *
2336858 ATATTTTAAT--TAT
1 ATATTTTAATAAAAA
2336871 ATATTTTAATAAAAA
1 ATATTTTAATAAAAA
2336886 ATATT
1 ATATT
2336891 GAATTAAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
13 11 0.42
15 15 0.58
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (15 bp):
ATATTTTAATAAAAA
Found at i:2338283 original size:18 final size:19
Alignment explanation
Indices: 2338262--2338318 Score: 73
Period size: 18 Copynumber: 3.0 Consensus size: 19
2338252 AAATTCAAAA
2338262 AAATATAAAAATATA-TTT
1 AAATATAAAAATATATTTT
*
2338280 AAATATGAAAAT-TATTTT
1 AAATATAAAAATATATTTT
2338298 AAATATATAAAATATAATTTT
1 AAATATA-AAAATAT-ATTTT
2338319 TAAAAATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
17 2 0.06
18 20 0.61
19 5 0.15
20 1 0.03
21 5 0.15
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
AAATATAAAAATATATTTT
Found at i:2352247 original size:6 final size:6
Alignment explanation
Indices: 2352236--2352265 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
2352226 TACAAGCCTG
2352236 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC
1 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC
2352266 ATCACCATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (6 bp):
CTCTCC
Found at i:2352276 original size:18 final size:18
Alignment explanation
Indices: 2352237--2352277 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
2352227 ACAAGCCTGC
* * *
2352237 TCTCCCTCTCCCTCTCCC
1 TCTCCCTCTCCATCACCA
2352255 TCTCCCTCTCCATCACCA
1 TCTCCCTCTCCATCACCA
2352273 TCTCC
1 TCTCC
2352278 TACATTTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.07, C:0.61, G:0.00, T:0.32
Consensus pattern (18 bp):
TCTCCCTCTCCATCACCA
Found at i:2357126 original size:170 final size:171
Alignment explanation
Indices: 2356820--2357163 Score: 654
Period size: 170 Copynumber: 2.0 Consensus size: 171
2356810 TCATGAGCTA
2356820 CTGCTACATATATAATAATAAAGACCTTCATCATCTGAGACTTATTTGAAAAGAAAAGTGATTTT
1 CTGCTACATATATAATAATAAAGACCTTCATCATCTGAGACTTATTTGAAAAGAAAAGTGATTTT
2356885 AAAAATAAGGGATGGGATGATGAGTATAGACTAAGTTGCAGCTTTGATGGAAGCCAACGCTTTGA
66 AAAAATAAGGGATGGGATGATGAGTATAGACTAAGTTGCAGCTTTGATGGAAGCCAACGCTTTGA
2356950 GTAGAAAGGCAAAGAAAAGAGTAGGCATGGAGAAAAATGGG
131 GTAGAAAGGCAAAGAAAAGAGTAGGCATGGAGAAAAATGGG
2356991 CTGCTACATATATAATAATAAAGACCTTCATCATCTGAGACTTATTTGAAAAGAAAAGTGATTTT
1 CTGCTACATATATAATAATAAAGACCTTCATCATCTGAGACTTATTTGAAAAGAAAAGTGATTTT
* *
2357056 -AAAATAAGGGATGGGATGATGAGTATAGATTAAGTTGCAGCTTTGATGGAAGCCACCGCTTTGA
66 AAAAATAAGGGATGGGATGATGAGTATAGACTAAGTTGCAGCTTTGATGGAAGCCAACGCTTTGA
*
2357120 GTAGAAAGGCAAAGAGAAGAGTAGGCATGGAGAAAAATGGG
131 GTAGAAAGGCAAAGAAAAGAGTAGGCATGGAGAAAAATGGG
2357161 CTG
1 CTG
2357164 TGATCACTTT
Statistics
Matches: 170, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
170 105 0.62
171 65 0.38
ACGTcount: A:0.39, C:0.11, G:0.25, T:0.25
Consensus pattern (171 bp):
CTGCTACATATATAATAATAAAGACCTTCATCATCTGAGACTTATTTGAAAAGAAAAGTGATTTT
AAAAATAAGGGATGGGATGATGAGTATAGACTAAGTTGCAGCTTTGATGGAAGCCAACGCTTTGA
GTAGAAAGGCAAAGAAAAGAGTAGGCATGGAGAAAAATGGG
Found at i:2365621 original size:5 final size:5
Alignment explanation
Indices: 2365606--2365638 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
2365596 CGCCGTTACG
*
2365606 CTTCT CATCT CTTCT CTTCT CTTCT CTTCT CTT
1 CTTCT CTTCT CTTCT CTTCT CTTCT CTTCT CTT
2365639 TGTTTTATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.03, C:0.39, G:0.00, T:0.58
Consensus pattern (5 bp):
CTTCT
Found at i:2372642 original size:22 final size:22
Alignment explanation
Indices: 2372614--2372658 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
2372604 GTGAGTGGCA
2372614 TAGGGCTGTAAATGAATTGGGT
1 TAGGGCTGTAAATGAATTGGGT
2372636 TAGGGCTGTAAATGAATTGGGT
1 TAGGGCTGTAAATGAATTGGGT
2372658 T
1 T
2372659 TGAACGCATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.04, G:0.36, T:0.33
Consensus pattern (22 bp):
TAGGGCTGTAAATGAATTGGGT
Found at i:2372887 original size:18 final size:17
Alignment explanation
Indices: 2372866--2372899 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2372856 TATAAATATT
2372866 AATAATTATATTGAACAA
1 AATAATTATATT-AACAA
*
2372884 AATAATTTTATTAACA
1 AATAATTATATTAACA
2372900 TATGTGAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (17 bp):
AATAATTATATTAACAA
Found at i:2378269 original size:12 final size:11
Alignment explanation
Indices: 2378253--2378280 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
2378243 AACAAAATAG
2378253 GAAAAAAAAAA
1 GAAAAAAAAAA
2378264 GAAAAAAAAAA
1 GAAAAAAAAAA
2378275 GAAAAA
1 GAAAAA
2378281 GATAGATGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (11 bp):
GAAAAAAAAAA
Found at i:2382961 original size:75 final size:74
Alignment explanation
Indices: 2382874--2383044 Score: 208
Period size: 75 Copynumber: 2.4 Consensus size: 74
2382864 GTTTTCCTCA
** * * * **
2382874 TTGAAATACCATACCTACATTTTTCAACTCGGTATGGGA-AATGCCATACCTACATTTCTTAACT
1 TTGAAATACCATACCTACATTTCACAACTCAGTAT-GGATAATACCATACATACATTTCACAACT
2382938 CAGTATGGAT
65 CAGTATGGAT
*
2382948 TTGATAATACCATACCTACATTTCACAGCTCAGTATGGATAATACCATACATACATTTCACAACT
1 TTGA-AATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACATACATTTCACAACT
2383013 CAGTATGGA-
65 CAGTATGGAT
*
2383022 -TG--ACACCATACCTACATTTCACA
1 TTGAAATACCATACCTACATTTCACA
2383045 CTTTGCCATG
Statistics
Matches: 86, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
70 20 0.23
73 2 0.02
74 7 0.08
75 57 0.66
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.31
Consensus pattern (74 bp):
TTGAAATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACATACATTTCACAACTC
AGTATGGAT
Found at i:2383042 original size:35 final size:35
Alignment explanation
Indices: 2382879--2383044 Score: 172
Period size: 35 Copynumber: 4.6 Consensus size: 35
2382869 CCTCATTGAA
** * *
2382879 ATACCATACCTACATTTTTCAACTCGGTATGGGA-A
1 ATACCATACCTACATTTCACAACTCAGTAT-GGATG
* **
2382914 ATGCCATACCTACATTTCTTAACTCAGTATGGATTTG
1 ATACCATACCTACATTTCACAACTCAGTATGGA--TG
* *
2382951 ATAATACCATACCTACATTTCACAGCTCAGTATGGATA
1 ---ATACCATACCTACATTTCACAACTCAGTATGGATG
*
2382989 ATACCATACATACATTTCACAACTCAGTATGGATG
1 ATACCATACCTACATTTCACAACTCAGTATGGATG
*
2383024 ACACCATACCTACATTTCACA
1 ATACCATACCTACATTTCACA
2383045 CTTTGCCATG
Statistics
Matches: 110, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
34 3 0.03
35 77 0.70
38 1 0.01
40 29 0.26
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.31
Consensus pattern (35 bp):
ATACCATACCTACATTTCACAACTCAGTATGGATG
Found at i:2390270 original size:6 final size:6
Alignment explanation
Indices: 2390261--2390370 Score: 60
Period size: 6 Copynumber: 17.8 Consensus size: 6
2390251 AGACTGAGCC
* * * ** **
2390261 TGAAGT TGAAGA TGAAGA TGAA-A GTGAAGA TGAGGT TGGGGA TGGGGA
1 TGAAGA TGAAGA TGAAGA TGAAGA -TGAAGA TGAAGA TGAAGA TGAAGA
* * * * *
2390309 TGAAGA TGAGGATGA TGAAGA AGAAGA CGAAGA AGAAGA AGAAGA CGAAGA
1 TGAAGA TGA--A-GA TGAAGA TGAAGA TGAAGA TGAAGA TGAAGA TGAAGA
*
2390360 CGAAGA TGAAG
1 TGAAGA TGAAG
2390371 CCGACGCCGA
Statistics
Matches: 87, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
5 1 0.01
6 78 0.90
7 2 0.02
8 1 0.01
9 5 0.06
ACGTcount: A:0.45, C:0.03, G:0.39, T:0.14
Consensus pattern (6 bp):
TGAAGA
Found at i:2390340 original size:9 final size:9
Alignment explanation
Indices: 2390328--2390359 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
2390318 GGATGATGAA
2390328 GAAGAAGAC
1 GAAGAAGAC
*
2390337 GAAGAAGAA
1 GAAGAAGAC
2390346 GAAGAAGAC
1 GAAGAAGAC
2390355 GAAGA
1 GAAGA
2390360 CGAAGATGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.59, C:0.06, G:0.34, T:0.00
Consensus pattern (9 bp):
GAAGAAGAC
Found at i:2390346 original size:18 final size:18
Alignment explanation
Indices: 2390325--2390370 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
2390315 TGAGGATGAT
2390325 GAAGAAGAAGACGAAGAA
1 GAAGAAGAAGACGAAGAA
*
2390343 GAAGAAGAAGACGAAGAC
1 GAAGAAGAAGACGAAGAA
*
2390361 GAAGATGAAG
1 GAAGAAGAAG
2390371 CCGACGCCGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.57, C:0.07, G:0.35, T:0.02
Consensus pattern (18 bp):
GAAGAAGAAGACGAAGAA
Found at i:2392620 original size:31 final size:31
Alignment explanation
Indices: 2392585--2392664 Score: 117
Period size: 31 Copynumber: 2.6 Consensus size: 31
2392575 TATTTTTCAT
* *
2392585 TTGCTTCAATTTCTATGCTTATTCC-CCGTTA
1 TTGCTTCAATTTCCATGCTTATACCTCC-TTA
*
2392616 TTGCTTCAATTTCCATGATTATACCTCCTTA
1 TTGCTTCAATTTCCATGCTTATACCTCCTTA
2392647 TTGCTTCAATTTCCATGC
1 TTGCTTCAATTTCCATGC
2392665 CTTACAATAA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
31 42 0.95
32 2 0.05
ACGTcount: A:0.19, C:0.26, G:0.09, T:0.46
Consensus pattern (31 bp):
TTGCTTCAATTTCCATGCTTATACCTCCTTA
Found at i:2394174 original size:3 final size:3
Alignment explanation
Indices: 2394168--2394196 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2394158 CGTCATATTA
2394168 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
2394197 ATGAAGTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:2399584 original size:13 final size:13
Alignment explanation
Indices: 2399564--2399602 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
2399554 CTTTTTTGAC
2399564 TTTTTTTTTATGT
1 TTTTTTTTTATGT
2399577 TTTGTTTTTTATGT
1 TTT-TTTTTTATGT
*
2399591 TTATTTATTTAT
1 TT-TTTTTTTAT
2399603 TTATTTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 3 0.13
14 19 0.83
15 1 0.04
ACGTcount: A:0.13, C:0.00, G:0.08, T:0.79
Consensus pattern (13 bp):
TTTTTTTTTATGT
Found at i:2399703 original size:21 final size:19
Alignment explanation
Indices: 2399679--2399740 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 19
2399669 TTAAATATAT
2399679 ATTTTGAAATTACTTTTTTAA
1 ATTTT-AAATTA-TTTTTTAA
2399700 ATTTTAAATATTATTTTTTAA
1 ATTTT-AA-ATTATTTTTTAA
*
2399721 ATATTAAATATATTTTTTAA
1 ATTTTAAAT-TATTTTTTAA
2399741 TAATATAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.05
20 12 0.32
21 19 0.51
22 4 0.11
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (19 bp):
ATTTTAAATTATTTTTTAA
Found at i:2399751 original size:22 final size:20
Alignment explanation
Indices: 2399692--2399753 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 20
2399682 TTGAAATTAC
* *
2399692 TTTTTTAAATTTTAAATATTA
1 TTTTTTAAATATAAAATA-TA
*
2399713 TTTTTTAAATATTAAATATA
1 TTTTTTAAATATAAAATATA
2399733 TTTTTTAATAATATAAAATAT
1 TTTTTT-A-AATATAAAATAT
2399754 TTAAATATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 8 0.22
21 18 0.49
22 11 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTTTTAAATATAAAATATA
Found at i:2399755 original size:20 final size:20
Alignment explanation
Indices: 2399692--2399740 Score: 80
Period size: 21 Copynumber: 2.4 Consensus size: 20
2399682 TTGAAATTAC
*
2399692 TTTTTTAAATTTTAAATATTA
1 TTTTTTAAATATTAAATA-TA
2399713 TTTTTTAAATATTAAATATA
1 TTTTTTAAATATTAAATATA
2399733 TTTTTTAA
1 TTTTTTAA
2399741 TAATATAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTTTTAAATATTAAATATA
Found at i:2399916 original size:46 final size:46
Alignment explanation
Indices: 2399849--2399939 Score: 182
Period size: 46 Copynumber: 2.0 Consensus size: 46
2399839 AAAAAAATAA
2399849 TGATTTAAAAGATTTAGGGACCTATTATGCAATTTTTCCATTTTTT
1 TGATTTAAAAGATTTAGGGACCTATTATGCAATTTTTCCATTTTTT
2399895 TGATTTAAAAGATTTAGGGACCTATTATGCAATTTTTCCATTTTT
1 TGATTTAAAAGATTTAGGGACCTATTATGCAATTTTTCCATTTTT
2399940 GAATGGTTGC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.29, C:0.11, G:0.13, T:0.47
Consensus pattern (46 bp):
TGATTTAAAAGATTTAGGGACCTATTATGCAATTTTTCCATTTTTT
Found at i:2401224 original size:17 final size:18
Alignment explanation
Indices: 2401204--2401237 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2401194 AAAAGATTTA
2401204 TTTATTGAAAAA-ATATG
1 TTTATTGAAAAATATATG
*
2401221 TTTATTTAAAAATATAT
1 TTTATTGAAAAATATAT
2401238 ATATTAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (18 bp):
TTTATTGAAAAATATATG
Found at i:2401283 original size:20 final size:20
Alignment explanation
Indices: 2401229--2401288 Score: 84
Period size: 20 Copynumber: 2.9 Consensus size: 20
2401219 TGTTTATTTA
2401229 AAAATATATATATTAAAAAGT
1 AAAA-ATATATATTAAAAAGT
* *
2401250 AAAAATTTAAATTAAAAAGT
1 AAAAATATATATTAAAAAGT
2401270 AAAAATATATATTATAAAA
1 AAAAATATATATTA-AAAA
2401289 TCACATCATG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 26 0.76
21 8 0.24
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (20 bp):
AAAAATATATATTAAAAAGT
Found at i:2401753 original size:20 final size:20
Alignment explanation
Indices: 2401730--2401794 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
2401720 ATAATTTTTT
2401730 AATTTTAGTACACATTTATA
1 AATTTTAGTACACATTTATA
* * *
2401750 AATTTATA-TATTA-ATTTTTT
1 AATTT-TAGTA-CACATTTATA
*
2401770 AATTTTAGTACACATTCATA
1 AATTTTAGTACACATTTATA
2401790 AATTT
1 AATTT
2401795 ATGTACTTAA
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
19 3 0.09
20 28 0.82
21 3 0.09
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (20 bp):
AATTTTAGTACACATTTATA
Found at i:2401765 original size:40 final size:41
Alignment explanation
Indices: 2401721--2401805 Score: 145
Period size: 40 Copynumber: 2.1 Consensus size: 41
2401711 GTGTTGGTTA
*
2401721 TAATTTTTTAATTTTAGTACACATTTATAAATTTATATA-T
1 TAATTTTTTAATTTTAGTACACATTCATAAATTTATATACT
*
2401761 TAATTTTTTAATTTTAGTACACATTCATAAATTTATGTACT
1 TAATTTTTTAATTTTAGTACACATTCATAAATTTATATACT
2401802 TAAT
1 TAAT
2401806 ATATATTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
40 37 0.88
41 5 0.12
ACGTcount: A:0.36, C:0.07, G:0.04, T:0.53
Consensus pattern (41 bp):
TAATTTTTTAATTTTAGTACACATTCATAAATTTATATACT
Found at i:2401816 original size:40 final size:40
Alignment explanation
Indices: 2401729--2401816 Score: 115
Period size: 40 Copynumber: 2.2 Consensus size: 40
2401719 TATAATTTTT
* * *
2401729 TAATTTTAGTACACATTTATAAATTTATATATTAATTTTT
1 TAATTTTAGTACACATTCATAAATTTATATATTAATTATA
*
2401769 TAATTTTAGTACACATTCATAAATTTATGTACTTAA-TATA
1 TAATTTTAGTACACATTCATAAATTTATATA-TTAATTATA
*
2401809 TATTTTTA
1 TAATTTTA
2401817 ATAGATAAAG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
40 38 0.90
41 4 0.10
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.52
Consensus pattern (40 bp):
TAATTTTAGTACACATTCATAAATTTATATATTAATTATA
Found at i:2406983 original size:184 final size:184
Alignment explanation
Indices: 2406668--2407024 Score: 466
Period size: 184 Copynumber: 1.9 Consensus size: 184
2406658 ATAGTCAACA
* * *** *
2406668 CCCAGCCCGGTAAAATATTGTCTGCTTTAGGCGCCCATGGCCCTCATGGTTTTGTTTTTGGGAGG
1 CCCAGCCCGGTAAAATATTGTCTGCTTTAGGCACCCATAGCCCTCATAACTTTGTTCTTGGGAGG
** *
2406733 GCTCATACACCCCTAAAAGGTCTCTTTCCACTTAAGTGTTGCTACCCCTTTATATAGGCTAGGTC
66 GCTCATACACCCCTAAAAGACCTCTTTCCACTTAAGTGTTGCTACCCCTTTATATACGCTAGGTC
*** * * * *
2406798 TCTCTTGTGTTTTTCCAATGTGGGATTTGCCTAGGGTGTTACATTGATAAATTT
131 TCTCCCATGCTTTGCCAATATGAGATTTGCCTAGGGTGTTACATTGATAAATTT
* * * * * *
2406852 CCCATCCCGGTAAAATATTGTTTGCTTTGGGTACTCATAGCCGTCATAACTTTGTTCTTGGGAGG
1 CCCAGCCCGGTAAAATATTGTCTGCTTTAGGCACCCATAGCCCTCATAACTTTGTTCTTGGGAGG
* *
2406917 GCTCATACA-CCTTCAAAAGACCTCTTTCCACTTAAGTGTTGCTACCCCTTTATGTAACGC-AGG
66 GCTCATACACCCCT-AAAAGACCTCTTTCCACTTAAGTGTTGCTACCCCTTTATAT-ACGCTAGG
2406980 TCTCTCCCATGCTTTGCCAATATGAGATTTGCCTAGGGTGTTACA
129 TCTCTCCCATGCTTTGCCAATATGAGATTTGCCTAGGGTGTTACA
2407025 AAGTACATAA
Statistics
Matches: 147, Mismatches: 24, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
183 3 0.02
184 141 0.96
185 3 0.02
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.35
Consensus pattern (184 bp):
CCCAGCCCGGTAAAATATTGTCTGCTTTAGGCACCCATAGCCCTCATAACTTTGTTCTTGGGAGG
GCTCATACACCCCTAAAAGACCTCTTTCCACTTAAGTGTTGCTACCCCTTTATATACGCTAGGTC
TCTCCCATGCTTTGCCAATATGAGATTTGCCTAGGGTGTTACATTGATAAATTT
Found at i:2410179 original size:22 final size:26
Alignment explanation
Indices: 2410154--2410205 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 26
2410144 CAAGAATGTC
2410154 TTATAT-TACGATT-A-TTGTTTT-T
1 TTATATCTACGATTAACTTGTTTTAT
*
2410176 TTAT-TCTATGATTAACTTGTTTTAT
1 TTATATCTACGATTAACTTGTTTTAT
2410201 TTATA
1 TTATA
2410206 CATTAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
21 1 0.04
22 10 0.42
23 1 0.04
24 7 0.29
25 5 0.21
ACGTcount: A:0.25, C:0.06, G:0.08, T:0.62
Consensus pattern (26 bp):
TTATATCTACGATTAACTTGTTTTAT
Found at i:2410961 original size:44 final size:44
Alignment explanation
Indices: 2410912--2411032 Score: 147
Period size: 44 Copynumber: 2.8 Consensus size: 44
2410902 ATTAGGTAGT
* * *
2410912 ACAAAATTAGTTGAAAAC-TCTAGAAGAGATAATTATTTGATAGC
1 ACAAAATTAGTTGAAAACTTC-AAAAGAGATAATCATTCGATAGC
* *
2410956 ACAAAATTAGTTGAAAGCTTCAAAAGAGATAATCATTCGTTAGC
1 ACAAAATTAGTTGAAAACTTCAAAAGAGATAATCATTCGATAGC
* *
2411000 ACAAAATTAGTTG-AAATTTCTAAAAGAGGTAAT
1 ACAAAATTAGTTGAAAACTTC-AAAAGAGATAAT
2411033 ATATCAATAC
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
43 5 0.07
44 60 0.90
45 2 0.03
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.29
Consensus pattern (44 bp):
ACAAAATTAGTTGAAAACTTCAAAAGAGATAATCATTCGATAGC
Found at i:2413207 original size:30 final size:30
Alignment explanation
Indices: 2413173--2413230 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
2413163 AATTGTTTTT
* *
2413173 TGATAATATTGATTGTGATGAATGAAATTA
1 TGATAATATTGATTGTGATAAAAGAAATTA
* *
2413203 TGATAATGTTGCTTGTGATAAAAGAAAT
1 TGATAATATTGATTGTGATAAAAGAAAT
2413231 GAGAAACAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.40, C:0.02, G:0.21, T:0.38
Consensus pattern (30 bp):
TGATAATATTGATTGTGATAAAAGAAATTA
Found at i:2420172 original size:5 final size:5
Alignment explanation
Indices: 2420156--2420185 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
2420146 TATTTGTATT
2420156 CTTCC C-TCC CTTCC CTTCC CTTCC CTTCC C
1 CTTCC CTTCC CTTCC CTTCC CTTCC CTTCC C
2420186 GTGAACATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (5 bp):
CTTCC
Found at i:2437700 original size:23 final size:23
Alignment explanation
Indices: 2437674--2437717 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
2437664 TGGAAACTTA
2437674 ATTTGGTATAATAGTTTCATCTC
1 ATTTGGTATAATAGTTTCATCTC
2437697 ATTTGGTATAATAGTTTCATC
1 ATTTGGTATAATAGTTTCATC
2437718 AGGATTTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.27, C:0.11, G:0.14, T:0.48
Consensus pattern (23 bp):
ATTTGGTATAATAGTTTCATCTC
Found at i:2445226 original size:27 final size:24
Alignment explanation
Indices: 2445167--2445230 Score: 119
Period size: 24 Copynumber: 2.7 Consensus size: 24
2445157 CTGTTGCTGA
2445167 TGCAGCTGCTGCTGTTCCTCATAT
1 TGCAGCTGCTGCTGTTCCTCATAT
2445191 TGCAGCTGCTGCTGTTCCTCATAT
1 TGCAGCTGCTGCTGTTCCTCATAT
*
2445215 TGCAGCTCCTGCTGTT
1 TGCAGCTGCTGCTGTT
2445231 GTTGATCACC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.11, C:0.30, G:0.22, T:0.38
Consensus pattern (24 bp):
TGCAGCTGCTGCTGTTCCTCATAT
Found at i:2447842 original size:20 final size:22
Alignment explanation
Indices: 2447812--2447858 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
2447802 CAAAAGTTAC
2447812 AAAATAATTCAAA-ATAATTTT
1 AAAATAATTCAAACATAATTTT
*
2447833 AAAA-AATTCAAACCTAATTTT
1 AAAATAATTCAAACATAATTTT
2447854 AAAAT
1 AAAAT
2447859 TTAAAATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (22 bp):
AAAATAATTCAAACATAATTTT
Found at i:2447886 original size:17 final size:17
Alignment explanation
Indices: 2447848--2447889 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
2447838 ATTCAAACCT
*
2447848 AATTT-TAAAATTTAAA
1 AATTTATAAAATTCAAA
*
2447864 ATATTTATAAAATTCCAA
1 A-ATTTATAAAATTCAAA
2447882 AATTTATA
1 AATTTATA
2447890 TTTTTTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 1 0.05
17 11 0.50
18 10 0.45
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (17 bp):
AATTTATAAAATTCAAA
Found at i:2451102 original size:19 final size:18
Alignment explanation
Indices: 2451074--2451113 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
2451064 ACGAAATTTT
2451074 AATTAGTATTATGAGATAA
1 AATTAGTATTATGAGA-AA
* *
2451093 AATTATTATTATTAGAAA
1 AATTAGTATTATGAGAAA
2451111 AAT
1 AAT
2451114 AATACTGCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (18 bp):
AATTAGTATTATGAGAAA
Found at i:2451230 original size:15 final size:15
Alignment explanation
Indices: 2451212--2451240 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2451202 ATATTTATAA
2451212 AATTATTATTATTAT
1 AATTATTATTATTAT
2451227 AATTATTATTATTA
1 AATTATTATTATTA
2451241 GATAGGGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
AATTATTATTATTAT
Done.