Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr1
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: 96304692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2448173 characters in sequence are not A, C, G, or T
File 93 of 313
Found at i:30994291 original size:17 final size:17
Alignment explanation
Indices: 30994269--30994302 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
30994259 CGAGTATTTA
30994269 TGATTTGGCACTTGTAC
1 TGATTTGGCACTTGTAC
*
30994286 TGATTTGGCTCTTGTAC
1 TGATTTGGCACTTGTAC
30994303 AGTAGCTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.15, C:0.18, G:0.24, T:0.44
Consensus pattern (17 bp):
TGATTTGGCACTTGTAC
Found at i:30996427 original size:23 final size:23
Alignment explanation
Indices: 30996401--30996449 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
30996391 GAATGAAAAA
*
30996401 AAAAGAA-AAAAAAAAGGAAAGTT
1 AAAAGAATAAAAAAAA-GAAAATT
*
30996424 AAAAGAATAAAAGAAAGAAAATT
1 AAAAGAATAAAAAAAAGAAAATT
30996447 AAA
1 AAA
30996450 TTGCTCAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (23 bp):
AAAAGAATAAAAAAAAGAAAATT
Found at i:30997169 original size:16 final size:17
Alignment explanation
Indices: 30997133--30997173 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
30997123 ATGGTATGTA
30997133 TAAAAA-ATTTAATGAT
1 TAAAAATATTTAATGAT
*
30997149 T-AAAATATTTAAT-TT
1 TAAAAATATTTAATGAT
30997164 TAAAAATATT
1 TAAAAATATT
30997174 AGTGATTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (17 bp):
TAAAAATATTTAATGAT
Found at i:31004035 original size:36 final size:36
Alignment explanation
Indices: 31003987--31004061 Score: 132
Period size: 36 Copynumber: 2.1 Consensus size: 36
31003977 AAATGGGGTA
31003987 TTACTCGACACTTGTAGGCAAAAGATAAAACAGATG
1 TTACTCGACACTTGTAGGCAAAAGATAAAACAGATG
* *
31004023 TTACTCGTCACTTGTAGGGAAAAGATAAAACAGATG
1 TTACTCGACACTTGTAGGCAAAAGATAAAACAGATG
31004059 TTA
1 TTA
31004062 GACAAGATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (36 bp):
TTACTCGACACTTGTAGGCAAAAGATAAAACAGATG
Found at i:31006283 original size:28 final size:28
Alignment explanation
Indices: 31006243--31006300 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
31006233 CATCTTGTCG
31006243 TCTGATTGCTGGTTATGCTAGCTGCGGC
1 TCTGATTGCTGGTTATGCTAGCTGCGGC
31006271 TCTGATTGCTGGTTATGCTAGCTGCGGC
1 TCTGATTGCTGGTTATGCTAGCTGCGGC
31006299 TC
1 TC
31006301 GTATGATGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.10, C:0.22, G:0.31, T:0.36
Consensus pattern (28 bp):
TCTGATTGCTGGTTATGCTAGCTGCGGC
Found at i:31022359 original size:19 final size:19
Alignment explanation
Indices: 31022335--31022371 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
31022325 GCATGACCTC
31022335 TATATGCACCTGAACGATG
1 TATATGCACCTGAACGATG
*
31022354 TATATGTACCTGAACGAT
1 TATATGCACCTGAACGAT
31022372 AATATTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (19 bp):
TATATGCACCTGAACGATG
Found at i:31024542 original size:44 final size:45
Alignment explanation
Indices: 31024477--31024567 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
31024467 ACCTCTATTC
* * *
31024477 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
31024521 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
31024566 CA
1 CA
31024568 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:31026026 original size:18 final size:17
Alignment explanation
Indices: 31026000--31026034 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
31025990 AATATTAAGA
*
31026000 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
31026017 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
31026035 TTAATAGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:31026046 original size:120 final size:120
Alignment explanation
Indices: 31025893--31026176 Score: 446
Period size: 120 Copynumber: 2.4 Consensus size: 120
31025883 TAATTGAAAA
* * *
31025893 TATATATTTT-ATTAAATTATATTTAATAATAATTATGTTAAATTATATTTCATAGTATTATATA
1 TATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTCACAGTATCATATA
* *
31025957 TTATGATTTTAGAAAATTCATATAAGAATATTTAA-TATTAAGAATTTTATTAAAT
66 TTATGATTTCAGAAAATTAATATAAGAATA-TTAATTATTAAGAATTTTATTAAAT
* * *
31026012 TATATATTTTAATTAAAATATATTTAATAGTAATTATGTTAATTTATATTTTACAGTATCATATA
1 TATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTCACAGTATCATATA
*
31026077 TTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAAT
66 TTATGATTTCAGAAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAAT
*
31026132 TATATATTTTAATTAAAATATATTTAATAAAAATTATGTTTAAAT
1 TATATATTTTAATTAAAATATATTTAATAATAATTATG-TTAAAT
31026177 ATGATTAAAT
Statistics
Matches: 150, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
119 14 0.09
120 131 0.87
121 5 0.03
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (120 bp):
TATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTCACAGTATCATATA
TTATGATTTCAGAAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAAT
Found at i:31026148 original size:18 final size:17
Alignment explanation
Indices: 31026120--31026154 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
31026110 ATTATTAAGA
*
31026120 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
31026137 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
31026155 TTAATAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:31026154 original size:16 final size:16
Alignment explanation
Indices: 31026120--31026174 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
31026110 ATTATTAAGA
31026120 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAA--ATAT
31026137 ATTTTAATTAAAATAT
1 ATTTTAATTAAAATAT
*
31026153 A-TTTAATAAAAAT-T
1 ATTTTAATTAAAATAT
31026167 ATGTTTAA
1 AT-TTTAA
31026175 ATATGATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 2 0.06
15 11 0.32
16 10 0.29
17 5 0.15
18 6 0.18
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
ATTTTAATTAAAATAT
Found at i:31026411 original size:16 final size:16
Alignment explanation
Indices: 31026390--31026457 Score: 127
Period size: 16 Copynumber: 4.2 Consensus size: 16
31026380 GATTTGCTAT
31026390 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
31026406 TACACCTTTAATCCAA
1 TACACCTCTAATCCAA
31026422 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
31026438 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
31026454 TACA
1 TACA
31026458 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.38, C:0.35, G:0.00, T:0.26
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:31035079 original size:29 final size:29
Alignment explanation
Indices: 31035046--31035105 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
31035036 TCTTTACTTT
*
31035046 GTCAATTTTATAGTTTATATTTAGAGTTC
1 GTCAATTTTACAGTTTATATTTAGAGTTC
31035075 GTCAATTTTACAGTTTATATTTAGAGTTC
1 GTCAATTTTACAGTTTATATTTAGAGTTC
31035104 GT
1 GT
31035106 GACTTTCTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.27, C:0.08, G:0.15, T:0.50
Consensus pattern (29 bp):
GTCAATTTTACAGTTTATATTTAGAGTTC
Found at i:31046760 original size:30 final size:31
Alignment explanation
Indices: 31046726--31046795 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
31046716 AAACTAATAT
31046726 TTAATATATAAAATTATA-AAAAAATCAAAA
1 TTAATATATAAAATTATACAAAAAATCAAAA
* * **
31046756 TTAATATATAATATTTTACATTAAATCAAAA
1 TTAATATATAAAATTATACAAAAAATCAAAA
*
31046787 ATAATATAT
1 TTAATATAT
31046796 GACATTTTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 16 0.47
31 18 0.53
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (31 bp):
TTAATATATAAAATTATACAAAAAATCAAAA
Found at i:31057923 original size:70 final size:70
Alignment explanation
Indices: 31057802--31057976 Score: 235
Period size: 70 Copynumber: 2.5 Consensus size: 70
31057792 CTTTCCAAGG
* ** *
31057802 AAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTTAT
*
31057867 TTTTT
66 GTTTT
** * *
31057872 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTAT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTTAT
31057937 GTTTT
66 GTTTT
** *
31057942 -AAATTGACTCATATTGCGAGAGGTGAGTTAAGCCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
31057977 TTTAATTTTT
Statistics
Matches: 93, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
69 32 0.34
70 61 0.66
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.34
Consensus pattern (70 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTTAT
GTTTT
Found at i:31058108 original size:75 final size:75
Alignment explanation
Indices: 31057994--31058336 Score: 399
Period size: 72 Copynumber: 4.5 Consensus size: 75
31057984 TTTGTTTTTC
* **
31057994 AAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
31058059 GTTGTT-AAAA
66 GTT-TTAAAAA
*
31058069 AAAATCAACTCATATTGCGAGAAATAAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
*
31058134 GTTTT---CA
66 GTTTTAAAAA
* * * * *
31058141 AAATTCAACTTATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
31058206 GTTTTCAAAAAA
66 GTTTT--AAAAA
* ** * * *
31058218 AAAATCAACTTATATTGCGAGAGGTGAGTTAAGCCTC-GGTTCACATGCTGAGGTATTTTCAATT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGG---ACACGCTGAGGTAATTTCAATT
31058282 TCTGTTTTTAAAAAAA
63 TCTG-TTTT--AAAAA
** *
31058298 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAG
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAG
31058337 ATTATACACT
Statistics
Matches: 235, Mismatches: 23, Indels: 14
0.86 0.08 0.05
Matches are distributed among these distances:
72 65 0.28
74 2 0.01
75 64 0.27
76 1 0.00
77 34 0.14
79 24 0.10
80 44 0.19
81 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (75 bp):
AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
GTTTTAAAAA
Found at i:31058760 original size:88 final size:86
Alignment explanation
Indices: 31058559--31058803 Score: 276
Period size: 88 Copynumber: 2.8 Consensus size: 86
31058549 TGTTTTAATT
* * *
31058559 TCAACTCATATTGCGAGAGATTAGTTGAGCCTCAGGACACACGCCGAGATATTTTCAATTAAGC-
1 TCAACTCATATTGCGAGAGATGAGTTGAGCCTCAGGACACA--CCGAGGTATTTTCAATT--TCT
* * *
31058623 CTTTTGATTTCTGTTTTTCAAAAAA
62 GTTTTCATTTATGTTTTTCAAAAAA
* * * *
31058648 ACAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACCGAGGTATTTTCCATTTCTGTTT
1 TCAACTCATATTGCGAGAGATGAGTTGAGCCTCAGGACACACCGAGGTATTTTCAATTTCTGTTT
* *
31058713 TCATTATTATGTTTTTGAAAGAA
66 TCA-T-TTATGTTTTTCAAAAAA
* * ** *
31058736 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTAATTTCAATTTCTGTTT
1 TCAACTCATATTGCGAGAGATGAGTTGAGCCTCAGGACACACCGAGGTATTTTCAATTTCTGTTT
31058801 TCA
66 TCA
31058804 AAATTCAACT
Statistics
Matches: 132, Mismatches: 21, Indels: 7
0.82 0.13 0.04
Matches are distributed among these distances:
85 1 0.01
86 5 0.04
87 16 0.12
88 73 0.55
89 37 0.28
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (86 bp):
TCAACTCATATTGCGAGAGATGAGTTGAGCCTCAGGACACACCGAGGTATTTTCAATTTCTGTTT
TCATTTATGTTTTTCAAAAAA
Found at i:31058917 original size:73 final size:73
Alignment explanation
Indices: 31058725--31059562 Score: 835
Period size: 73 Copynumber: 11.1 Consensus size: 73
31058715 ATTATTATGT
* ** * * *
31058725 TTTTGAAAGAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTAATTTC
1 TTTTCAAA-AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGTTGAGGTATTTTC
31058790 AATTTCTG-
65 AATTTCTGC
* * ** *
31058798 TTTTCAAAATTCAACTCATATTGTGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCA
1 TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGTTGAGGTATTTTCA
31058863 ATTTCTGC
66 ATTTCTGC
* ** *
31058871 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCA
1 TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGTTGAGGTATTTTCA
31058936 ATTTCTGC
66 ATTTCTGC
* ** *
31058944 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTTC
1 TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGTTGAGGT-ATTTTC
31059009 AATTTCTG-
65 AATTTCTGC
* * *
31059017 TTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACATTGAGGTATTTT
1 TTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGTTGAGGTATTTT
31059082 CAATTTCTGC
64 CAATTTCTGC
*
31059092 TTTTCAAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTT
1 TTTTC-A-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGTTGAGGTATTTT
*
31059157 CAATTCCTGTTC
64 CAATTTCTG--C
* *
31059169 AATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTCAGGACACGCTGAG
1 ---------TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGTTGAG
* *
31059234 GTAATTTCAATTTCTGT
57 GTATTTTCAATTTCTGC
* * ***
31059251 TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACACCGAGGTATTTTCA
1 TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGTTGAGGTATTTTCA
* *
31059316 AATTCTAC
66 ATTTCTGC
* * * *
31059324 -TTTCAAAAAAATCAACTCATATTGTGAAAGGTGAGTTGAGCCT-TGGCTCACGTGTTGA-GTCA
1 TTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-ACAC--GTTGAGGT-A
*
31059386 CTTTCAATTTCTGTTTTTATGTC
60 TTTTCAATTTC--------TG-C
* * *
31059409 TGTTTTC-TAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTT
1 --TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGTTGAGGTATTTT
*
31059473 CAATTACTG-
64 CAATTTCTGC
* * * * * * *
31059482 TTTGGCAAAAACCAACTCATACTGCGAGAGATGAGTTGAGCCTCAGGACATGCTGAAGTATTTTC
1 TTT-TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGTTGAGGTATTTTC
* *
31059547 CATTTCTGT
65 AATTTCTGC
31059556 TTTTCAA
1 TTTTCAA
31059563 TTTATGTTTT
Statistics
Matches: 663, Mismatches: 62, Indels: 80
0.82 0.08 0.10
Matches are distributed among these distances:
71 3 0.00
72 65 0.10
73 265 0.40
74 71 0.11
75 119 0.18
76 12 0.02
77 1 0.00
83 14 0.02
84 64 0.10
85 38 0.06
86 7 0.01
88 4 0.01
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.33
Consensus pattern (73 bp):
TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGTTGAGGTATTTTCA
ATTTCTGC
Found at i:31059196 original size:307 final size:292
Alignment explanation
Indices: 31058734--31059562 Score: 892
Period size: 307 Copynumber: 2.7 Consensus size: 292
31058724 TTTTTGAAAG
**
31058734 AATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTAATTTCAATTTCTGT
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACATTGAGGTAATTTCAATTTCTGT
* *
31058799 TTTCAAAATTCAACTCATATTGTGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAA
66 TTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAA
* * *
31058864 TTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGT
131 TTCCTGCTTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGT
* *
31058929 ATTTTCAATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACAC
196 AATTTCAATTTCTGCTTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACAC
* * * *
31058994 GCTGAGGTAATTTTCAATTTCT-GTTGTCAAAAA
261 ACCGAGGT-ATTTTCAAATTCTACTT-TCAAAAA
*
31059027 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACATTGAGGTATTTTCAATTTCTGC
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACATTGAGGTAATTTCAATTTCTG-
**
31059092 TTTTCAAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTT
65 TTTTC-A-AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTT
** *
31059157 CAATTCCTGTTCAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTCA
128 CAATTCCTG--C---------TTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCA
* * **
31059222 GGACACGCTGAGGTAATTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTT
182 AGACACGCTGAGGTAATTTCAATTTCTGCTTTTCAAAAATCAACTCATATTGCGAGAAATGAGTT
* *
31059287 GAGCCTCGGGGCACACCGAGGTATTTTCAAATTCTACTTTCAAAAA
247 GAGCCTCAGGACACACCGAGGTATTTTCAAATTCTACTTTCAAAAA
* * ** * * *
31059333 AATCAACTCATATTGTGAAAGGTGAGTTGAGCCT-TGGCTCACGTGTTGA-GTCACTTTCAATTT
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG-ACAC--ATTGAGGT-AATTTCAATTT
** ** **
31059396 CTGTTTTTATGTCTGTTTTCTAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACG
62 CTG---TT-T-TC------AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACG
* * * * * *
31059461 CTGAGGTATTTTCAATTACTG-TTTGGCAAAAACCAACTCATACTGCGAGAGATGAGTTGAGCCT
116 TTGAGGTATTTTCAATTCCTGCTTT-TCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCT
* * * * * *
31059525 CAGGACATGCTGAAGTATTTTCCATTTCTGTTTTTCAA
180 CAAGACACGCTGAGGTAATTTCAATTTCTGCTTTTCAA
31059563 TTTATGTTTT
Statistics
Matches: 458, Mismatches: 49, Indels: 46
0.83 0.09 0.08
Matches are distributed among these distances:
293 61 0.13
294 5 0.01
295 1 0.00
296 61 0.13
298 1 0.00
304 3 0.01
305 69 0.15
306 54 0.12
307 120 0.26
308 17 0.04
310 2 0.00
311 1 0.00
312 2 0.00
316 61 0.13
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (292 bp):
AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACATTGAGGTAATTTCAATTTCTGT
TTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAA
TTCCTGCTTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGT
AATTTCAATTTCTGCTTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACAC
ACCGAGGTATTTTCAAATTCTACTTTCAAAAA
Found at i:31059329 original size:159 final size:159
Alignment explanation
Indices: 31059024--31059316 Score: 464
Period size: 159 Copynumber: 1.9 Consensus size: 159
31059014 CTGTTGTCAA
* *
31059024 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACATTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACACTGAGGTAATTTCAATTTC
***
31059089 TGCTTTTCAAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAT
66 TGCTTTTCAAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACACCGAGGTAT
31059154 TTTCAATTCCTGTTCAATTTATATTTTTC
131 TTTCAATTCCTGTTCAATTTATATTTTTC
* * *
31059183 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTCAGGACACGCTGAGGTAATTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACACTGAGGTAATTTCAATTTC
* ** *
31059248 TGTTTTTC-A-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACACCGAGGTAT
66 TGCTTTTCAAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACACCGAGGTAT
31059311 TTTCAA
131 TTTCAA
31059317 ATTCTACTTT
Statistics
Matches: 122, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
157 54 0.44
158 1 0.01
159 67 0.55
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.31
Consensus pattern (159 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACACTGAGGTAATTTCAATTTC
TGCTTTTCAAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACACCGAGGTAT
TTTCAATTCCTGTTCAATTTATATTTTTC
Found at i:31059450 original size:159 final size:159
Alignment explanation
Indices: 31059251--31059636 Score: 442
Period size: 159 Copynumber: 2.4 Consensus size: 159
31059241 CAATTTCTGT
* *
31059251 TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACACCGAGGTATTTTCA
1 TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCA
* * * * * * *
31059316 AATT-CTACTTTCAAAAAAATCAACTCATATTGTGAAAGGTGAGTTGAGCCT-TGGCTCACGTGT
66 AATTACT-CTTTCAAAAAAACCAACTCATACTGCGAAAGATGAGTTGAGCCTCAGG---ACATGC
*
31059379 TG-AGTCACTTTCAATTTCTGTTTTT-ATGTCTG
127 TGAAGT-ACTTTCAATTTCTGTTTTTAATGTATG
* *
31059411 TTTTC-TAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTC-
1 TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCA
* *** *
31059474 AATTACTGTTTGGCAAAAACCAACTCATACTGCGAGAGATGAGTTGAGCCTCAGGACATGCTGAA
66 AATTACTCTTTCAAAAAAACCAACTCATACTGCGAAAGATGAGTTGAGCCTCAGGACATGCTGAA
* * *
31059539 GTATTTTCCATTTCTGTTTTTCAATTTATG
131 GTACTTTCAATTTCTGTTTTT-AATGTATG
* * * *
31059569 TTTTCAAAAATCAATTCATATTGCTAAAGGTGAGTTGAGCCTCGGCTCGCACGCTGAGGTATTTT
1 TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG--GGCACGCTGAGGTATTTT
31059634 CAA
64 CAA
31059637 TTTTTCGTTT
Statistics
Matches: 191, Mismatches: 26, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
156 23 0.12
157 3 0.02
158 49 0.26
159 93 0.49
160 5 0.03
161 17 0.09
162 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (159 bp):
TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCA
AATTACTCTTTCAAAAAAACCAACTCATACTGCGAAAGATGAGTTGAGCCTCAGGACATGCTGAA
GTACTTTCAATTTCTGTTTTTAATGTATG
Found at i:31059545 original size:232 final size:230
Alignment explanation
Indices: 31058637--31059546 Score: 935
Period size: 232 Copynumber: 4.0 Consensus size: 230
31058627 TGATTTCTGT
* * * *** *
31058637 TTTTCAAAAAAA-CAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACCGAGGTATTTT
1 TTTTCAAAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCAAGACACGTTGAGGTACTTT
* * * * * **
31058701 CCATTTCTGTTTTCATTATTATGTTTTTGAAAGAATCAACTCATATTGCGAGAAATGAGTTGAGC
66 CAATTCCTGTTAT--TTA-TCTG-TTTT-CAA-AATCAACTCATATTGCGAGAGGTGAGTTGAGC
* ** * * * **
31058766 CTCAAGACACATTGAGGTAATTTCAATTTCTGTTT-TCAAAATTCAACTCATATTGTGAGAAATG
125 CTCAGGACACGCTGAGGTATTTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTG
* ** * *
31058830 AGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGC
190 AGTTGAGCCTCAGGACACACTGAGGTATTTTCAAATTCTAC
* * *
31058871 TTTTC--AAAATTCAACTCATATTGCGAGAA-ATGAGTTGAGCCTCAAGACACGTTGAGGTATTT
1 TTTTCAAAAAAATCAACTCATATTGCGA-AAGGTGAGTTGAGCCTCAAGACACGTTGAGGTACTT
* **
31058933 TCAATTTCTG--------C--TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCA
65 TCAATTCCTGTTATTTATCTGTTTTCAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA
31058988 GGACACGCTGAGGTAATTTTCAATTTCTG-TTGTCAAAAAAATCAACTCATATTGCGAGAGGTGA
129 GGACACGCTGAGGT-ATTTTCAATTTCTGTTTGTC--AAAAATCAACTCATATTGCGAGAGGTGA
* * * *
31059052 GTTGAGCCTCAAGACACATTGAGGTATTTTCAATTTCTGC
191 GTTGAGCCTCAGGACACACTGAGGTATTTTCAAATTCTAC
* * *
31059092 TTTTCAAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTT
1 TTTTCAAAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCAAGACACGTTGAGGTACTTT
* *
31059157 CAATTCCTGTTCAATTTATAT-TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTC
66 CAATTCCTGTT--ATTTATCTGTTTTC-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
* *
31059221 AGGACACGCTGAGGTAATTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGT
128 AGGACACGCTGAGGTATTTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGT
* * *
31059286 TGAGCCTCGGGGCACACCGAGGTATTTTCAAATTCTAC
193 TGAGCCTCAGGACACACTGAGGTATTTTCAAATTCTAC
* ** *
31059324 -TTTCAAAAAAATCAACTCATATTGTGAAAGGTGAGTTGAGCCT-TGGCTCACGTGTTGA-GTCA
1 TTTTCAAAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCAAG-ACAC--GTTGAGGT-A
* *
31059386 CTTTCAATTTCTGTT-TTTATGTCTGTTTTCTAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
62 CTTTCAATTCCTGTTATTTA--TCTGTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
* * * * * *
31059450 CTCGGGACACGCTGAGGTATTTTCAATTACTGTTTGGCAAAAACCAACTCATACTGCGAGAGATG
125 CTCAGGACACGCTGAGGTATTTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTG
** *
31059515 AGTTGAGCCTCAGGACATGCTGAAGTATTTTC
190 AGTTGAGCCTCAGGACACACTGAGGTATTTTC
31059547 CATTTCTGTT
Statistics
Matches: 583, Mismatches: 63, Indels: 62
0.82 0.09 0.09
Matches are distributed among these distances:
217 2 0.00
218 49 0.08
219 19 0.03
221 68 0.12
222 1 0.00
223 60 0.10
230 5 0.01
231 43 0.07
232 184 0.32
233 88 0.15
234 60 0.10
235 4 0.01
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.33
Consensus pattern (230 bp):
TTTTCAAAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCAAGACACGTTGAGGTACTTT
CAATTCCTGTTATTTATCTGTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG
ACACGCTGAGGTATTTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
GCCTCAGGACACACTGAGGTATTTTCAAATTCTAC
Found at i:31059779 original size:89 final size:89
Alignment explanation
Indices: 31059488--31059813 Score: 342
Period size: 92 Copynumber: 3.7 Consensus size: 89
31059478 ACTGTTTGGC
* * * * *
31059488 AAAAACCAACTCATACTGCGAGAGATGAGTTGAGCCTC-AG-GACATGCTGAAGTATTTTCCATT
1 AAAAACCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGTCACATGCTGAGGTATTTTCAATT
*
31059551 TCTGTTTTTCAATTTATGTTTTC-
66 TCTGTTTTTCAATTTATGCTTTCA
* * * * * *
31059574 AAAAATCAATTCATATTGCTAAAGGTGAGTTGAGCCTCG-GCTCGCACGCTGAGGTATTTTCAAT
1 AAAAACCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAG-TCACATGCTGAGGTATTTTCAAT
*
31059638 TTTTCGTTTTTTCAATTTATGCTTTCCA
65 TTCT-G-TTTTTCAATTTATGCTTT-CA
* * *
31059666 AAAAATCAACTCATATTGCGAGAGGTAAGTTGAGCCTCGAGTCACATG-TCGAGGTATTTTCAAA
1 AAAAACCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGTCACATGCT-GAGGTATTTTCAAT
* * *
31059730 ATCTGTTTTTCAAATTAAG-TTTCAA
65 TTCTGTTTTTCAATTTATGCTTTC-A
* * *
31059755 AAAAACCAACTCATATTGCGAGAGGTGAGTTGAGCCT-TAGCTCACGTGCTGAGCTATTT
1 AAAAACCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAG-TCACATGCTGAGGTATTT
31059814 CTGTTTTAAT
Statistics
Matches: 199, Mismatches: 29, Indels: 21
0.80 0.12 0.08
Matches are distributed among these distances:
86 33 0.17
88 23 0.12
89 54 0.27
90 30 0.15
91 3 0.02
92 55 0.28
93 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (89 bp):
AAAAACCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGTCACATGCTGAGGTATTTTCAATT
TCTGTTTTTCAATTTATGCTTTCA
Found at i:31060523 original size:22 final size:22
Alignment explanation
Indices: 31060494--31060556 Score: 99
Period size: 22 Copynumber: 2.9 Consensus size: 22
31060484 GCAACCATGA
31060494 AGCAGCCCCATACCTCCACTAC
1 AGCAGCCCCATACCTCCACTAC
* *
31060516 AGCGGCCCCATACCCCCACTAC
1 AGCAGCCCCATACCTCCACTAC
*
31060538 AGCAGTCCCATACCTCCAC
1 AGCAGCCCCATACCTCCAC
31060557 AGCCCTCGTA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.25, C:0.51, G:0.11, T:0.13
Consensus pattern (22 bp):
AGCAGCCCCATACCTCCACTAC
Found at i:31064618 original size:38 final size:38
Alignment explanation
Indices: 31064559--31064664 Score: 105
Period size: 37 Copynumber: 2.8 Consensus size: 38
31064549 CATTTTTAAG
*
31064559 AATAT-AAAGAATATATATAAGTATGTATATG-ATGTA-A
1 AATATGAAA-AATATATATAAGTATGTATAAGAAT-TAGA
* *
31064596 AATATGCATAAATATATGTAAGTA--TATAAGAATTATGA
1 AATATG-AAAAATATATATAAGTATGTATAAGAATTA-GA
*
31064634 AATATGAAAAATATATTTAAGTATGTATAAG
1 AATATGAAAAATATATATAAGTATGTATAAG
31064665 TACGTATATA
Statistics
Matches: 57, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
36 7 0.12
37 22 0.39
38 20 0.35
39 8 0.14
ACGTcount: A:0.51, C:0.01, G:0.13, T:0.35
Consensus pattern (38 bp):
AATATGAAAAATATATATAAGTATGTATAAGAATTAGA
Found at i:31065493 original size:11 final size:11
Alignment explanation
Indices: 31065477--31065512 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
31065467 AAAAAAAAAA
31065477 GAAGAGAGAGG
1 GAAGAGAGAGG
*
31065488 GAAGAGAGAAG
1 GAAGAGAGAGG
31065499 GAAGAGAGAAGG
1 GAAGAGAG-AGG
31065511 GA
1 GA
31065513 GGGGGAAGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 18 0.82
12 4 0.18
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (11 bp):
GAAGAGAGAGG
Found at i:31065639 original size:16 final size:17
Alignment explanation
Indices: 31065618--31065655 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
31065608 AGGTAAAAAA
* *
31065618 TTTATTTTTTGT-TTTT
1 TTTATTTGTTGTATATT
31065634 TTTATTTGTTGTATATT
1 TTTATTTGTTGTATATT
31065651 TTTAT
1 TTTAT
31065656 GTTAAATAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.13, C:0.00, G:0.08, T:0.79
Consensus pattern (17 bp):
TTTATTTGTTGTATATT
Found at i:31067968 original size:20 final size:19
Alignment explanation
Indices: 31067939--31067992 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
31067929 AGAAGTACTG
*
31067939 AAAATTTTGAGGGAATATC
1 AAAATTTTGAGGGAATACC
*
31067958 AAAACTTTTGAGGAAATACC
1 AAAA-TTTTGAGGGAATACC
31067978 AAAAATTTATGAGGG
1 -AAAATTT-TGAGGG
31067993 TGTGCCAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 4 0.14
20 16 0.55
21 9 0.31
ACGTcount: A:0.44, C:0.07, G:0.20, T:0.28
Consensus pattern (19 bp):
AAAATTTTGAGGGAATACC
Found at i:31068592 original size:9 final size:9
Alignment explanation
Indices: 31068575--31068608 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
31068565 TTTTTTTAAA
*
31068575 TTTATATAT
1 TTTAAATAT
31068584 TTTAAATAT
1 TTTAAATAT
*
31068593 TTTACATAT
1 TTTAAATAT
31068602 TTTAAAT
1 TTTAAAT
31068609 TTCAAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (9 bp):
TTTAAATAT
Found at i:31068638 original size:21 final size:21
Alignment explanation
Indices: 31068598--31068653 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
31068588 AATATTTTAC
31068598 ATATTTTAAATTTC-AAAAAA
1 ATATTTTAAATTTCAAAAAAA
31068618 ATATTTTAAATTTCAAAAAAA
1 ATATTTTAAATTTCAAAAAAA
* *
31068639 AAATTTTAAAATTCA
1 ATATTTTAAATTTCA
31068654 TATGTAACAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
20 14 0.42
21 19 0.58
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (21 bp):
ATATTTTAAATTTCAAAAAAA
Found at i:31069494 original size:16 final size:16
Alignment explanation
Indices: 31069475--31069508 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
31069465 AAGATTACCA
31069475 TAATTCATGTAAAAGG
1 TAATTCATGTAAAAGG
31069491 TAATTCATGTAAAAGG
1 TAATTCATGTAAAAGG
31069507 TA
1 TA
31069509 TCATAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.06, G:0.18, T:0.32
Consensus pattern (16 bp):
TAATTCATGTAAAAGG
Found at i:31070910 original size:28 final size:28
Alignment explanation
Indices: 31070877--31071014 Score: 276
Period size: 28 Copynumber: 4.9 Consensus size: 28
31070867 CTCCACAAAG
31070877 TTTTGTGTCTTTATCATAAAAACAATAA
1 TTTTGTGTCTTTATCATAAAAACAATAA
31070905 TTTTGTGTCTTTATCATAAAAACAATAA
1 TTTTGTGTCTTTATCATAAAAACAATAA
31070933 TTTTGTGTCTTTATCATAAAAACAATAA
1 TTTTGTGTCTTTATCATAAAAACAATAA
31070961 TTTTGTGTCTTTATCATAAAAACAATAA
1 TTTTGTGTCTTTATCATAAAAACAATAA
31070989 TTTTGTGTCTTTATCATAAAAACAAT
1 TTTTGTGTCTTTATCATAAAAACAAT
31071015 CTAAAGAAAA
Statistics
Matches: 110, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 110 1.00
ACGTcount: A:0.38, C:0.11, G:0.07, T:0.43
Consensus pattern (28 bp):
TTTTGTGTCTTTATCATAAAAACAATAA
Found at i:31078162 original size:8 final size:8
Alignment explanation
Indices: 31078149--31078197 Score: 53
Period size: 8 Copynumber: 5.8 Consensus size: 8
31078139 TTTATAACTA
31078149 AACCCACT
1 AACCCACT
31078157 AACCCACT
1 AACCCACT
*
31078165 AACCCAAATTT
1 AACCC--A-CT
*
31078176 AACCTACT
1 AACCCACT
31078184 AACCCACT
1 AACCCACT
31078192 AACCCA
1 AACCCA
31078198 AATTCAACCA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
8 27 0.79
9 1 0.03
10 1 0.03
11 5 0.15
ACGTcount: A:0.41, C:0.43, G:0.00, T:0.16
Consensus pattern (8 bp):
AACCCACT
Found at i:31078184 original size:27 final size:27
Alignment explanation
Indices: 31078149--31078206 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
31078139 TTTATAACTA
*
31078149 AACCCACTAACCCACTAACCCAAATTT
1 AACCCACTAACCCACTAACCCAAATTC
*
31078176 AACCTACTAACCCACTAACCCAAATTC
1 AACCCACTAACCCACTAACCCAAATTC
31078203 AACC
1 AACC
31078207 AATTACCCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.41, C:0.41, G:0.00, T:0.17
Consensus pattern (27 bp):
AACCCACTAACCCACTAACCCAAATTC
Found at i:31079400 original size:15 final size:15
Alignment explanation
Indices: 31079350--31079406 Score: 62
Period size: 15 Copynumber: 3.8 Consensus size: 15
31079340 TTTTCTTTTT
31079350 TTATATATTATTACTA
1 TTATAT-TTATTACTA
* * *
31079366 TTATTTTTATTTCTC
1 TTATATTTATTACTA
31079381 TTATATTTATTACTA
1 TTATATTTATTACTA
*
31079396 ATATA-TTATTA
1 TTATATTTATTA
31079407 TTATAGTTAC
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
14 6 0.18
15 23 0.68
16 5 0.15
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (15 bp):
TTATATTTATTACTA
Found at i:31080029 original size:26 final size:26
Alignment explanation
Indices: 31080000--31080055 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
31079990 TATGTAAATG
31080000 TTTTG-ATGTTATAT-TATATATGCATT
1 TTTTGTATGTTATATATATATAT--ATT
31080026 TTTTGTATGTTATATATATATATATT
1 TTTTGTATGTTATATATATATATATT
31080052 TTTT
1 TTTT
31080056 TCAATATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
26 12 0.43
27 9 0.32
28 7 0.25
ACGTcount: A:0.27, C:0.02, G:0.09, T:0.62
Consensus pattern (26 bp):
TTTTGTATGTTATATATATATATATT
Found at i:31090190 original size:41 final size:40
Alignment explanation
Indices: 31090092--31090254 Score: 143
Period size: 41 Copynumber: 4.0 Consensus size: 40
31090082 TTAAACAGAT
** * * * *
31090092 TCACCGGCATTTTGCCTGCTAGGCTTAAAGCCTG-ATTCAG
1 TCACCGGCATTAAGCCTGCTAGACATAAAGTCTGAATT-AC
*
31090132 TACACCGGCACTT-AGCCTGCTAGACATATAGTCTGAAATGTA-
1 T-CACCGGCA-TTAAGCCTGCTAGACATAAAGTCTG-AAT-TAC
* *
31090174 TCACTGGCATTAAGCCTGCTAGACTTAAAGTCTGAATTAC
1 TCACCGGCATTAAGCCTGCTAGACATAAAGTCTGAATTAC
* * *
31090214 TTCACCGGCATTAAGCCTGCTAGACGTAACGTCTGTATTAC
1 -TCACCGGCATTAAGCCTGCTAGACATAAAGTCTGAATTAC
31090255 ATTCAATCAC
Statistics
Matches: 103, Mismatches: 12, Indels: 15
0.79 0.09 0.12
Matches are distributed among these distances:
39 2 0.02
40 6 0.06
41 88 0.85
42 3 0.03
43 3 0.03
44 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (40 bp):
TCACCGGCATTAAGCCTGCTAGACATAAAGTCTGAATTAC
Found at i:31093531 original size:62 final size:62
Alignment explanation
Indices: 31093460--31093654 Score: 354
Period size: 62 Copynumber: 3.1 Consensus size: 62
31093450 TTACTATGGC
31093460 TAGGAAAATTATGAGACTCGGTTATTATTGGCTGATGATGGAAAGTGACTGTATTAGTTTTG
1 TAGGAAAATTATGAGACTCGGTTATTATTGGCTGATGATGGAAAGTGACTGTATTAGTTTTG
31093522 TAGGAAAATTATGAGACTCGGTTATTATTGGCTGATGATGGAAAGTGACTGTATTAGTTTTG
1 TAGGAAAATTATGAGACTCGGTTATTATTGGCTGATGATGGAAAGTGACTGTATTAGTTTTG
* *
31093584 TAGGAAAATTATGAGACTCGGTTATTATTGGCTGATAATGGAAAGTGACTGCATTAGTTTTG
1 TAGGAAAATTATGAGACTCGGTTATTATTGGCTGATGATGGAAAGTGACTGTATTAGTTTTG
* *
31093646 CACGAAAAT
1 TAGGAAAAT
31093655 GTCATAAATG
Statistics
Matches: 129, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 129 1.00
ACGTcount: A:0.31, C:0.08, G:0.26, T:0.35
Consensus pattern (62 bp):
TAGGAAAATTATGAGACTCGGTTATTATTGGCTGATGATGGAAAGTGACTGTATTAGTTTTG
Found at i:31095637 original size:75 final size:75
Alignment explanation
Indices: 31095487--31095908 Score: 513
Period size: 74 Copynumber: 5.7 Consensus size: 75
31095477 TGATGTTTTT
* ** * ***
31095487 ATTTCTGT-TTTC--AAAATTCAACTCATATTGCGAGAAAT-AGGTTGAG-CTCAAGAGATGTTG
1 ATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGA-GTTGAGCCTCAAGACACACTG
31095547 AGGTATTTTCA
65 AGGTATTTTCA
* * *
31095558 ATTTCTGTCTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGATCCTCAGGACACACTGA
1 ATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACACTGA
*
31095623 GGTAATTTCA
66 GGTATTTTCA
* * **
31095633 ATTTCAGT-TCGTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTG
1 ATTTCTGTCT-TTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACACTG
*
31095696 AAGTATTTTCA
65 AGGTATTTTCA
* * *
31095707 ATTTCTATCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGATCCT-TAGTACACACTG
1 ATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG-ACACACTG
*
31095771 AGGTAATTTCA
65 AGGTATTTTCA
* **
31095782 ATTTTTGT-TTGTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTG
1 ATTTCTGTCTT-TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACACTG
*
31095845 AAGTATTTTCA
65 AGGTATTTTCA
*
31095856 ATTTCTATCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
1 ATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
31095909 GGGTCACATG
Statistics
Matches: 299, Mismatches: 39, Indels: 22
0.83 0.11 0.06
Matches are distributed among these distances:
71 8 0.03
72 4 0.01
74 154 0.52
75 133 0.44
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (75 bp):
ATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACACTGA
GGTATTTTCA
Found at i:31095731 original size:149 final size:149
Alignment explanation
Indices: 31095499--31095908 Score: 671
Period size: 149 Copynumber: 2.8 Consensus size: 149
31095489 TTCTGTTTTC
* ** * * *
31095499 AAAATTCAACTCATATTGCGAGAAAT-AGGTTGAG-CTCAAGAGATGTTGAGGTATTTTCAATTT
1 AAAAATCAACTCATATTGCGAGAGGTGA-GTTGAGCCTCAAGACACGTTGAAGTATTTTCAATTT
* *
31095562 CTGTCTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGATCCTCAGGACACACTGAGGTA
65 CTATCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGATCCTCAGGACACACTGAGGTA
31095627 ATTTCAATTTCAGTTCGTCA
130 ATTTCAATTTCAGTTCGTCA
31095647 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAAGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAAGTATTTTCAATTTC
* *
31095712 TATCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGATCCTTAGTACACACTGAGGTAA
66 TATCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGATCCTCAGGACACACTGAGGTAA
** *
31095777 TTTCAATTTTTGTTTGTCA
131 TTTCAATTTCAGTTCGTCA
31095796 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAAGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAAGTATTTTCAATTTC
*
31095861 TATCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
66 TATCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGATCCTC
31095909 GGGTCACATG
Statistics
Matches: 245, Mismatches: 15, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
148 29 0.12
149 216 0.88
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.32
Consensus pattern (149 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAAGTATTTTCAATTTC
TATCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGATCCTCAGGACACACTGAGGTAA
TTTCAATTTCAGTTCGTCA
Found at i:31096722 original size:8 final size:8
Alignment explanation
Indices: 31096709--31096738 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
31096699 TTTATAACTA
31096709 AACCCACT
1 AACCCACT
31096717 AACCCACT
1 AACCCACT
31096725 AACCCACT
1 AACCCACT
31096733 AACCCA
1 AACCCA
31096739 AATTCAACCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.40, C:0.50, G:0.00, T:0.10
Consensus pattern (8 bp):
AACCCACT
Found at i:31098141 original size:22 final size:23
Alignment explanation
Indices: 31098104--31098149 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
31098094 TACACATGCA
*
31098104 TTTTTCATATTAATA-TATATATG
1 TTTTTAATATTAATATTAT-TATG
31098127 TTTTTAATATT-ATATTATTATG
1 TTTTTAATATTAATATTATTATG
31098149 T
1 T
31098150 ATATGTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (23 bp):
TTTTTAATATTAATATTATTATG
Found at i:31098168 original size:30 final size:28
Alignment explanation
Indices: 31098110--31098162 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
31098100 TGCATTTTTC
31098110 ATATTAATATATATATGTTTTTAATATT
1 ATATTAATATATATATGTTTTTAATATT
* *
31098138 ATATTATTATGTATATG-TTTTAATA
1 ATATTAATATATATATGTTTTTAATA
31098163 CTATTAGCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.57
Consensus pattern (28 bp):
ATATTAATATATATATGTTTTTAATATT
Found at i:31098348 original size:21 final size:21
Alignment explanation
Indices: 31098307--31098348 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
31098297 TCTAATATAA
* *
31098307 ATATATATATCATATAGGTTT
1 ATATACATATCATACAGGTTT
*
31098328 ATATACATATCATACATGTTT
1 ATATACATATCATACAGGTTT
31098349 CATTATTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (21 bp):
ATATACATATCATACAGGTTT
Found at i:31098596 original size:23 final size:24
Alignment explanation
Indices: 31098547--31098606 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 24
31098537 TATGTAAATG
*
31098547 TTTTGATGTTATATTATATATGCAT
1 TTTTGATATTATATTATATAT-CAT
31098572 TTTTGTATATTATA-TATATAT-AT
1 TTTTG-ATATTATATTATATATCAT
**
31098595 TTTCAATATTAT
1 TTTTGATATTAT
31098607 TAGTTTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
22 7 0.23
23 5 0.16
25 12 0.39
26 7 0.23
ACGTcount: A:0.32, C:0.03, G:0.07, T:0.58
Consensus pattern (24 bp):
TTTTGATATTATATTATATATCAT
Found at i:31100920 original size:6 final size:6
Alignment explanation
Indices: 31100909--31100937 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
31100899 AAATTAAATA
31100909 TATATT TATATT TATATT TATATT TATAT
1 TATATT TATATT TATATT TATATT TATAT
31100938 ATAACTTGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
TATATT
Found at i:31101104 original size:16 final size:16
Alignment explanation
Indices: 31101085--31101116 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
31101075 CTATGACACA
31101085 ATAATAGTTAACCTCG
1 ATAATAGTTAACCTCG
31101101 ATAATAGTTAACCTCG
1 ATAATAGTTAACCTCG
31101117 TTACATAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (16 bp):
ATAATAGTTAACCTCG
Found at i:31104163 original size:20 final size:21
Alignment explanation
Indices: 31104135--31104191 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 21
31104125 TCTATATATA
*
31104135 TTTATCAAACATATTTATAA-T
1 TTTA-CAAACATATTTAAAAGT
31104156 TTTAC-AA-ATATTTAAAAGT
1 TTTACAAACATATTTAAAAGT
*
31104175 TTTAAAAACAT-TTTAAA
1 TTTACAAACATATTTAAA
31104192 TAAAAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
18 9 0.29
19 7 0.23
20 9 0.29
21 6 0.19
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (21 bp):
TTTACAAACATATTTAAAAGT
Found at i:31106357 original size:22 final size:23
Alignment explanation
Indices: 31106330--31106373 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
31106320 ATATGCACTT
31106330 AATAATTTT-ATATTTTAAAAAA
1 AATAATTTTAATATTTTAAAAAA
*
31106352 AATAATTTTAATATTTTTAAAA
1 AATAATTTTAATATTTTAAAAA
31106374 TTACTTGACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
AATAATTTTAATATTTTAAAAAA
Found at i:31110486 original size:16 final size:16
Alignment explanation
Indices: 31110435--31110487 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
31110425 TCTGAATTAT
*
31110435 AAAAAAATTATAAATC
1 AAAAAAATTATATATC
* * *
31110451 CAAAAAATAAAATTAT-
1 AAAAAAATTATA-TATC
31110467 AAAAAAATTATATATC
1 AAAAAAATTATATATC
31110483 AAAAA
1 AAAAA
31110488 GCTTTCTCGA
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
15 3 0.11
16 23 0.82
17 2 0.07
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.25
Consensus pattern (16 bp):
AAAAAAATTATATATC
Found at i:31110567 original size:19 final size:20
Alignment explanation
Indices: 31110527--31110570 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
31110517 ATTTTCTTTA
*
31110527 TTTTTCTTGGTTTGTCGTTT
1 TTTTTCTTGATTTGTCGTTT
31110547 TTTTTCTTGATTTGGT-GTTT
1 TTTTTCTTGATTT-GTCGTTT
31110567 TTTT
1 TTTT
31110571 AAGGTTGAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.02, C:0.07, G:0.18, T:0.73
Consensus pattern (20 bp):
TTTTTCTTGATTTGTCGTTT
Found at i:31119805 original size:21 final size:21
Alignment explanation
Indices: 31119775--31119830 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
31119765 ATGGGCTATT
31119775 CACACGGGCGTGTGCCCTCTC
1 CACACGGGCGTGTGCCCTCTC
* *
31119796 CACACAGGCGTGTGCCTTCTC
1 CACACGGGCGTGTGCCCTCTC
*
31119817 CATACGGGCGTGTG
1 CACACGGGCGTGTG
31119831 TGACCTTCAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.12, C:0.36, G:0.30, T:0.21
Consensus pattern (21 bp):
CACACGGGCGTGTGCCCTCTC
Found at i:31123064 original size:21 final size:20
Alignment explanation
Indices: 31123036--31123074 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
31123026 CAAAACTTGT
31123036 ATAACTATCATCAAACATTC
1 ATAACTATCATCAAACATTC
*
31123056 ATAATCTATCATTAAACAT
1 ATAA-CTATCATCAAACAT
31123075 AAAAATACTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAACTATCATCAAACATTC
Found at i:31123403 original size:16 final size:16
Alignment explanation
Indices: 31123382--31123433 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
31123372 TTTGGTTCGC
31123382 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
31123398 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* *
31123414 TGTAATGGAATAGAGG
1 TGTATTGGATTAGAGG
31123430 TGTA
1 TGTA
31123434 ATAGCAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.29, C:0.00, G:0.37, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:31123480 original size:45 final size:44
Alignment explanation
Indices: 31123414--31123508 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
31123404 GGATTAGAGG
* *
31123414 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
31123459 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
31123503 TGTAAT
1 TGTAAT
31123509 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:31123691 original size:18 final size:17
Alignment explanation
Indices: 31123670--31123704 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
31123660 TTATTATTTA
*
31123670 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
31123688 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
31123705 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:31123698 original size:28 final size:27
Alignment explanation
Indices: 31123628--31123700 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
31123618 TTTATTATCA
*
31123628 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
31123656 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
31123683 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
31123701 AAATTCTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:31123838 original size:18 final size:17
Alignment explanation
Indices: 31123817--31123851 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
31123807 TTATTATTAA
*
31123817 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
31123835 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
31123852 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:31123863 original size:147 final size:149
Alignment explanation
Indices: 31123589--31123863 Score: 509
Period size: 147 Copynumber: 1.9 Consensus size: 149
31123579 ATGATTATTG
*
31123589 TTATTGTTATTTAAATTTTAATAAGATTATTTATTATCAAAAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
*
31123654 ACATAATTATTATTTAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
66 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
31123719 AGAAATTTGTTTTGGTAAA
131 AGAAATTTGTTTTGGTAAA
*
31123738 TTATT-TTATTTAAATTTTAATAAGATTA-TTAATATCAATAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
31123801 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
66 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
31123864 ATATTCTTAT
Statistics
Matches: 123, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
147 95 0.77
148 23 0.19
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (149 bp):
TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
AGAAATTTGTTTTGGTAAA
Found at i:31130214 original size:4 final size:5
Alignment explanation
Indices: 31130196--31130234 Score: 53
Period size: 5 Copynumber: 7.6 Consensus size: 5
31130186 AAAAAGATCA
31130196 TATTT TATTT T-TATT TATTT TATTT TATTT TGATTT TAT
1 TATTT TATTT TAT-TT TATTT TATTT TATTT T-ATTT TAT
31130235 GTTAAATTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
4 1 0.03
5 24 0.77
6 6 0.19
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.77
Consensus pattern (5 bp):
TATTT
Found at i:31130216 original size:15 final size:14
Alignment explanation
Indices: 31130196--31130225 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
31130186 AAAAAGATCA
31130196 TATTTTATTTTTATT
1 TATTTTA-TTTTATT
31130211 TATTTTATTTTATT
1 TATTTTATTTTATT
31130225 T
1 T
31130226 TGATTTTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (14 bp):
TATTTTATTTTATT
Found at i:31136825 original size:19 final size:19
Alignment explanation
Indices: 31136801--31136838 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
31136791 TGAAAACATG
31136801 TTTGCTTGTACATAAATAA
1 TTTGCTTGTACATAAATAA
31136820 TTTGCTTGTACATAAATAA
1 TTTGCTTGTACATAAATAA
31136839 ATGAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.42
Consensus pattern (19 bp):
TTTGCTTGTACATAAATAA
Found at i:31138840 original size:105 final size:105
Alignment explanation
Indices: 31138655--31138865 Score: 332
Period size: 105 Copynumber: 2.0 Consensus size: 105
31138645 GACGCCCATT
* * *
31138655 AGTGCTCTAGCCTCGGATCTTACTGTAGAATCTCTCATTGAACCGTGATTACCACTCGCATTTCC
1 AGTGCTCTAGCCTCGGATCTTACTATAGAATCTCTCATAGAACCGCGATTACCACTCGCATTTCC
* *
31138720 CACATTTCTTTGTGGCCTCCTTCTAGTGGCTGTGTTACTC
66 CACATTTCTTCGTGGCCTCATTCTAGTGGCTGTGTTACTC
* ** *
31138760 AGTGCTCTAGCCTCGGATCTTACTATAGAATCTCTCATAGTATTGCGATTACCATTCGCATTTCC
1 AGTGCTCTAGCCTCGGATCTTACTATAGAATCTCTCATAGAACCGCGATTACCACTCGCATTTCC
*
31138825 CATATTTCTTCGTGGCCTCATTCTAGTGGCTGTGTTACTC
66 CACATTTCTTCGTGGCCTCATTCTAGTGGCTGTGTTACTC
31138865 A
1 A
31138866 ATCTTGCATT
Statistics
Matches: 96, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
105 96 1.00
ACGTcount: A:0.18, C:0.27, G:0.18, T:0.37
Consensus pattern (105 bp):
AGTGCTCTAGCCTCGGATCTTACTATAGAATCTCTCATAGAACCGCGATTACCACTCGCATTTCC
CACATTTCTTCGTGGCCTCATTCTAGTGGCTGTGTTACTC
Found at i:31140037 original size:11 final size:9
Alignment explanation
Indices: 31139998--31140042 Score: 63
Period size: 9 Copynumber: 4.8 Consensus size: 9
31139988 CGAAAACATA
*
31139998 GTATAACAT
1 GTATAGCAT
31140007 GTATAGCAT
1 GTATAGCAT
31140016 GTATAGCAT
1 GTATAGCAT
31140025 GTATATGGCAT
1 GTATA--GCAT
31140036 GTATAGC
1 GTATAGC
31140043 TAGACCCTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
9 24 0.73
11 9 0.27
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.33
Consensus pattern (9 bp):
GTATAGCAT
Found at i:31142707 original size:52 final size:52
Alignment explanation
Indices: 31142651--31142777 Score: 245
Period size: 52 Copynumber: 2.4 Consensus size: 52
31142641 CTAGACGAAT
*
31142651 GAAGAACATAAAAATGGATTCTTTTAGCCTTAGCAATCAGTTCCAAAATGAA
1 GAAGAACATAAAAATGGATTCTTTTAGCCCTAGCAATCAGTTCCAAAATGAA
31142703 GAAGAACATAAAAATGGATTCTTTTAGCCCTAGCAATCAGTTCCAAAATGAA
1 GAAGAACATAAAAATGGATTCTTTTAGCCCTAGCAATCAGTTCCAAAATGAA
31142755 GAAGAACATAAAAATGGATTCTT
1 GAAGAACATAAAAATGGATTCTT
31142778 ATTTTATTTG
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.43, C:0.15, G:0.16, T:0.26
Consensus pattern (52 bp):
GAAGAACATAAAAATGGATTCTTTTAGCCCTAGCAATCAGTTCCAAAATGAA
Found at i:31145258 original size:3 final size:3
Alignment explanation
Indices: 31145250--31145284 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
31145240 TTTATAATAT
31145250 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
31145285 TTTCCTATCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:31154888 original size:17 final size:18
Alignment explanation
Indices: 31154866--31154900 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
31154856 AGAAATAATT
31154866 TTTGAAAAATA-AAAATA
1 TTTGAAAAATAGAAAATA
*
31154883 TTTGAAAATTAGAAAATA
1 TTTGAAAAATAGAAAATA
31154901 ATGAAAACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.31
Consensus pattern (18 bp):
TTTGAAAAATAGAAAATA
Found at i:31154934 original size:21 final size:22
Alignment explanation
Indices: 31154895--31154936 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
31154885 TGAAAATTAG
31154895 AAAATAATGAAAACAACTTTTT
1 AAAATAATGAAAACAACTTTTT
31154917 AAAATAAT-AAAAGC-ACTTTT
1 AAAATAATGAAAA-CAACTTTT
31154937 AACTTCAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.55, C:0.10, G:0.05, T:0.31
Consensus pattern (22 bp):
AAAATAATGAAAACAACTTTTT
Found at i:31155356 original size:22 final size:22
Alignment explanation
Indices: 31155331--31155413 Score: 76
Period size: 22 Copynumber: 3.8 Consensus size: 22
31155321 AATAACAATA
* *
31155331 AAATAATAGCAATATAATAGTG
1 AAATAATAGCAAAACAATAGTG
**
31155353 AAATGGTAGCAAAACAATAGTG
1 AAATAATAGCAAAACAATAGTG
* * ** *
31155375 AAACAACAATAAAACAATAGCG
1 AAATAATAGCAAAACAATAGTG
*
31155397 AAATAGTAGCAAAACAA
1 AAATAATAGCAAAACAA
31155414 CCAATTTGGG
Statistics
Matches: 45, Mismatches: 16, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.58, C:0.11, G:0.14, T:0.17
Consensus pattern (22 bp):
AAATAATAGCAAAACAATAGTG
Found at i:31157612 original size:14 final size:15
Alignment explanation
Indices: 31157589--31157626 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
31157579 GTAGTCAGTA
*
31157589 GAAATAAAATAAA-T
1 GAAATGAAATAAAGT
31157603 GAAATGAAATAAAGT
1 GAAATGAAATAAAGT
31157618 GAAA-GAAAT
1 GAAATGAAAT
31157627 CGTACGAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 17 0.77
15 5 0.23
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.18
Consensus pattern (15 bp):
GAAATGAAATAAAGT
Found at i:31161689 original size:18 final size:17
Alignment explanation
Indices: 31161640--31161694 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
31161630 ATTTTAAGAT
31161640 ATTTATATTAAATAATAA
1 ATTTATATT-AATAATAA
* *
31161658 A-ATATAATAA-AATAA
1 ATTTATATTAATAATAA
31161673 ATTTATATTAATTAAT-A
1 ATTTATATTAA-TAATAA
31161690 ATTTA
1 ATTTA
31161695 ACGTACTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
15 6 0.20
16 9 0.30
17 11 0.37
18 4 0.13
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTTATATTAATAATAA
Found at i:31167707 original size:16 final size:17
Alignment explanation
Indices: 31167681--31167713 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
31167671 TATGGAGAAC
*
31167681 TTTTAATAAATTTTAAA
1 TTTTAATAAATTATAAA
31167698 TTTT-ATAAATTATAAA
1 TTTTAATAAATTATAAA
31167714 AAAATTCATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTTAATAAATTATAAA
Found at i:31173989 original size:20 final size:20
Alignment explanation
Indices: 31173964--31174002 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
31173954 AAACTGCTAA
31173964 CTCCCT-CATCCCTCAATTTT
1 CTCCCTACATCCCT-AATTTT
*
31173984 CTCCCTATATCCCTAATTT
1 CTCCCTACATCCCTAATTT
31174003 CACTCCTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.18, C:0.41, G:0.00, T:0.41
Consensus pattern (20 bp):
CTCCCTACATCCCTAATTTT
Found at i:31174144 original size:42 final size:42
Alignment explanation
Indices: 31174087--31174171 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
31174077 TCCATTCAAA
31174087 CTCCTTTACGACATAAATAGTAAAAAAACAATCCCTTACATT
1 CTCCTTTACGACATAAATAGTAAAAAAACAATCCCTTACATT
*
31174129 CTCCTTTACGGCATAAATAGTAAAAAAACAATCCCTTACATT
1 CTCCTTTACGACATAAATAGTAAAAAAACAATCCCTTACATT
31174171 C
1 C
31174172 ACAGGGACTC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.41, C:0.25, G:0.06, T:0.28
Consensus pattern (42 bp):
CTCCTTTACGACATAAATAGTAAAAAAACAATCCCTTACATT
Found at i:31176138 original size:45 final size:45
Alignment explanation
Indices: 31176069--31176166 Score: 151
Period size: 45 Copynumber: 2.2 Consensus size: 45
31176059 AACTAAAAAT
*
31176069 ACTGAAAATAACTAGCGTTAGTGTTTTGTGAAAATTACAGATAAG
1 ACTGAAAATAACTAGCGTTAGTGTTTTGTGAAAACTACAGATAAG
* * **
31176114 ACTGAAAATAACTAGTGTTGGTGTTTTGTGAAAACTGTAGATAAG
1 ACTGAAAATAACTAGCGTTAGTGTTTTGTGAAAACTACAGATAAG
31176159 ACTGAAAA
1 ACTGAAAA
31176167 ATGTAAAACC
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.40, C:0.08, G:0.21, T:0.31
Consensus pattern (45 bp):
ACTGAAAATAACTAGCGTTAGTGTTTTGTGAAAACTACAGATAAG
Found at i:31182922 original size:52 final size:51
Alignment explanation
Indices: 31182831--31182985 Score: 127
Period size: 52 Copynumber: 3.0 Consensus size: 51
31182821 AACGAAAAAG
* * * * * *
31182831 ATGTGATATATGCTTTCATATAAGACCATATTCGAGCTATGGAATCGGTACA
1 ATGTGATATGTGATTCCGTATAAGACCATACT-GGGCTATGGAATCGGTACA
* ***
31182883 ATGTGAT-TCGTG-TTCCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGTG
1 ATGTGATAT-GTGATT-CCGTATAAGACCATA-CTGGGCTATGGAATCGGTACA
*
31182935 ATGTGATAATGTGATTCCGTATAAGACCATATCTGGGATAT-GACATCGGTA
1 ATGTGAT-ATGTGATTCCGTATAAGACCATA-CTGGGCTATGGA-ATCGGTA
31182986 TGATATGTGA
Statistics
Matches: 83, Mismatches: 13, Indels: 13
0.76 0.12 0.12
Matches are distributed among these distances:
51 3 0.04
52 44 0.53
53 33 0.40
54 3 0.04
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.32
Consensus pattern (51 bp):
ATGTGATATGTGATTCCGTATAAGACCATACTGGGCTATGGAATCGGTACA
Found at i:31182971 original size:53 final size:49
Alignment explanation
Indices: 31182898--31183043 Score: 156
Period size: 53 Copynumber: 3.0 Consensus size: 49
31182888 ATTCGTGTTC
31182898 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTGTGATGTGATAATGTGATT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTGTGA--TGAT-ATGTGA-T
* * *
31182951 CCGTATAAGACCATATCTGGGATATGACATC-G-GT-ATGATATGTGAT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTGTGATGATATGTGAT
* * * * *
31182997 CCGTGTAAGACCATGGCAGGGCTATGGCTTCGGTGTG-TGATGTGTGA
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTGTGATGATATGTGA
31183044 CAATGTGAAA
Statistics
Matches: 79, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
46 25 0.32
47 7 0.09
48 15 0.19
50 1 0.01
51 2 0.03
52 1 0.01
53 28 0.35
ACGTcount: A:0.24, C:0.16, G:0.31, T:0.29
Consensus pattern (49 bp):
CCGTATAAGACCATAGCTGGGCTATGGCATCGGTGTGATGATATGTGAT
Found at i:31185132 original size:143 final size:144
Alignment explanation
Indices: 31184889--31185323 Score: 408
Period size: 159 Copynumber: 2.9 Consensus size: 144
31184879 AATTTCTTTC
*
31184889 TCTTAAATAAAGAAAAACAAGAGTAATGTGCAAATGACAAAAAATGTAATATTTTTTTCGTTCAT
1 TCTTAAATAAAGAAAAACAAGAGTAATGTGCAAATGACAAAAAATGTAATA-TTTTTTCATTCAT
* * * *
31184954 TTTTCAATTGAATTGATACTCGATTTACTTGTGATGTCAATT-TAATAAGAGTTTTAATTACATT
65 TTTTCAATTGAATTGATACTCGATTGACTTGTGATGCCAATTGAAATAAGAGTTTTAATTACAGT
31185018 ATATATATATATATT
130 ATATATATATATATT
* * * * * *
31185033 TCTTAAATAAGGAAAAACCAGAGTAATGTGCAAATGGCCAATAAGTGTAATA-TTTTTCATTTAT
1 TCTTAAATAAAGAAAAACAAGAGTAATGTGCAAAT-GACAAAAAATGTAATATTTTTTCATTCAT
* * * *
31185097 TTTTCAATTGAATTTATACTCGGTTGACTTGTGATGCCAATTGAAATAAGATTTTTATTTACAGT
65 TTTTCAATTGAATTGATACTCGATTGACTTGTGATGCCAATTGAAATAAGAGTTTTAATTACAGT
* * *
31185162 ATAATTTTTTTAGAGAGAATTTTATCTT
130 AT-A------T----A-TA-TATATATT
* * * *
31185190 TCTTAAATAAAGAAAAATAAGAATAATGTGCAAATGACCAATAAATGTAATATTTTTTTCATTTA
1 TCTTAAATAAAGAAAAACAAGAGTAATGTGCAAATGA-CAAAAAATGTAATA-TTTTTTCATTCA
* * ** * * * * *
31185255 TTTTTCACTTGAATTAATGTTCGATTGACTCGTGA-CCTCAATTTAAATAAAAGTTTTAATTATA
64 TTTTTCAATTGAATTGATACTCGATTGACTTGTGATGC-CAATTGAAATAAGAGTTTTAATTACA
31185319 GTATA
128 GTATA
31185324 ATTTTTTTAG
Statistics
Matches: 236, Mismatches: 36, Indels: 24
0.80 0.12 0.08
Matches are distributed among these distances:
143 48 0.20
144 53 0.22
145 14 0.06
151 1 0.00
155 1 0.00
156 2 0.01
157 50 0.21
158 2 0.01
159 65 0.28
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.41
Consensus pattern (144 bp):
TCTTAAATAAAGAAAAACAAGAGTAATGTGCAAATGACAAAAAATGTAATATTTTTTCATTCATT
TTTCAATTGAATTGATACTCGATTGACTTGTGATGCCAATTGAAATAAGAGTTTTAATTACAGTA
TATATATATATATT
Found at i:31185322 original size:159 final size:155
Alignment explanation
Indices: 31185031--31185397 Score: 466
Period size: 159 Copynumber: 2.3 Consensus size: 155
31185021 TATATATATA
* *
31185031 TTTCTTAAATAAGGAAAAACCAGAGTAATGTGCAAATGGCCAATAAGTGTAATATTTTTCATTTA
1 TTTCTTAAATAAAGAAAAACAAGAGTAATGTGCAAAT-GCCAATAAGTGTAATATTTTTCATTTA
* * * * * * *
31185096 TTTTTCAATTGAATTTATACTCGGTTGACTTGTGATGCCAATTGAAATAAGATTTTTATTTACAG
65 TTTTTCAATTGAATTAATACTCGATTGACTCGTGATCCCAATTGAAATAAAAGTTTTAATTACAG
* *
31185161 TATAATTTTTTTAGAGAGAATTTTAT
130 TATAATTTTTTTAGAGAAAATCTTAT
* * *
31185187 CTTTCTTAAATAAAGAAAAATAAGAATAATGTGCAAATGACCAATAAATGTAATATTTTTTTCAT
1 -TTTCTTAAATAAAGAAAAACAAGAGTAATGTGCAAATG-CCAATAAGTGTAATA--TTTTTCAT
* ** *
31185252 TTATTTTTCACTTGAATTAATGTTCGATTGACTCGTGA-CCTCAATTTAAATAAAAGTTTTAATT
62 TTATTTTTCAATTGAATTAATACTCGATTGACTCGTGATCC-CAATTGAAATAAAAGTTTTAATT
*
31185316 ATAGTATAATTTTTTTAGAGAAAATCTTAT
126 ACAGTATAATTTTTTTAGAGAAAATCTTAT
* * *
31185346 TTTCCTTCAATAAAGAAAAACAAGAGTAATTTGCAAATGCGAATAAGTGTAA
1 TTT-CTTAAATAAAGAAAAACAAGAGTAATGTGCAAATGCCAATAAGTGTAA
31185398 CACATTTAAT
Statistics
Matches: 180, Mismatches: 25, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
156 1 0.01
157 47 0.26
158 15 0.08
159 117 0.65
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.40
Consensus pattern (155 bp):
TTTCTTAAATAAAGAAAAACAAGAGTAATGTGCAAATGCCAATAAGTGTAATATTTTTCATTTAT
TTTTCAATTGAATTAATACTCGATTGACTCGTGATCCCAATTGAAATAAAAGTTTTAATTACAGT
ATAATTTTTTTAGAGAAAATCTTAT
Found at i:31192026 original size:42 final size:42
Alignment explanation
Indices: 31191968--31192088 Score: 136
Period size: 43 Copynumber: 2.8 Consensus size: 42
31191958 GTTGATTTGA
* *
31191968 GATTTACGTGTAAGACCATATCTGGGACATCGGCATC-GTATTT
1 GATTT-CGTGTAAGACCATGTCTGGGACAT-GGCATCAATATTT
* *
31192011 GATTTCGTGTAAGACCCTGCCTGGGACAGTGGCATCAATATTT
1 GATTTCGTGTAAGACCATGTCTGGGACA-TGGCATCAATATTT
* * *
31192054 GATTACATGTAAGACCACGTCTGGGACATTGGCAT
1 GATTTCGTGTAAGACCATGTCTGGGACA-TGGCAT
31192089 TGTACGAGCT
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
42 26 0.39
43 40 0.61
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.30
Consensus pattern (42 bp):
GATTTCGTGTAAGACCATGTCTGGGACATGGCATCAATATTT
Found at i:31199393 original size:35 final size:35
Alignment explanation
Indices: 31199354--31199428 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 35
31199344 ATCTGGGCAC
* *
31199354 GTGGGACACACTGGCGTGTGAGCCCACACAAGCAT
1 GTGGGACACACTGGCATGTGAGCACACACAAGCAT
* * * *
31199389 GTGGGTCATACTGGCATGTGAGCACACATAGGCAT
1 GTGGGACACACTGGCATGTGAGCACACACAAGCAT
31199424 GTGGG
1 GTGGG
31199429 CCCATTAATC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.24, C:0.23, G:0.35, T:0.19
Consensus pattern (35 bp):
GTGGGACACACTGGCATGTGAGCACACACAAGCAT
Found at i:31201872 original size:37 final size:37
Alignment explanation
Indices: 31201809--31201911 Score: 120
Period size: 37 Copynumber: 2.8 Consensus size: 37
31201799 TTTTCGGTTA
31201809 GACTAGCTCTT-TGGAGCCATTT-GTGTGTTATCAGGTG
1 GACTAGCTCTTAT-GAG-CATTTGGTGTGTTATCAGGTG
* * *
31201846 GACTGGCTTTTATGAGCATTTGGTGTGCTATCAGGTG
1 GACTAGCTCTTATGAGCATTTGGTGTGTTATCAGGTG
* * *
31201883 GATTAGCTCTTATGAGAATTTGGGGTGTT
1 GACTAGCTCTTATGAGCATTTGGTGTGTT
31201912 TTGGTTAGAA
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
36 5 0.09
37 49 0.89
38 1 0.02
ACGTcount: A:0.17, C:0.13, G:0.31, T:0.39
Consensus pattern (37 bp):
GACTAGCTCTTATGAGCATTTGGTGTGTTATCAGGTG
Found at i:31205431 original size:13 final size:13
Alignment explanation
Indices: 31205413--31205442 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
31205403 ACTTAACAAA
31205413 ATTTAAATTTAAT
1 ATTTAAATTTAAT
31205426 ATTTAAATTTAAT
1 ATTTAAATTTAAT
31205439 ATTT
1 ATTT
31205443 TCATAACAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
ATTTAAATTTAAT
Found at i:31213971 original size:21 final size:20
Alignment explanation
Indices: 31213917--31213976 Score: 72
Period size: 18 Copynumber: 3.0 Consensus size: 20
31213907 GGCTAAGGAC
*
31213917 TAAATTAGAAATCAAAATTAT
1 TAAA-TAGAAATAAAAATTAT
31213938 TAAA-AG--ATGAAAAATTAT
1 TAAATAGAAAT-AAAAATTAT
31213956 TAAATAGAAATAAAAATTAT
1 TAAATAGAAATAAAAATTAT
31213976 T
1 T
31213977 TTTATCATCT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
17 2 0.06
18 12 0.35
19 4 0.12
20 10 0.29
21 6 0.18
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.32
Consensus pattern (20 bp):
TAAATAGAAATAAAAATTAT
Found at i:31216736 original size:27 final size:27
Alignment explanation
Indices: 31216705--31216761 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
31216695 ATAATTAAGA
31216705 AGAAGTTAGATATTTAACATACAATTC
1 AGAAGTTAGATATTTAACATACAATTC
31216732 AGAAGTTAGATATTTAACATACAATTC
1 AGAAGTTAGATATTTAACATACAATTC
31216759 AGA
1 AGA
31216762 TAATAAAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.46, C:0.11, G:0.12, T:0.32
Consensus pattern (27 bp):
AGAAGTTAGATATTTAACATACAATTC
Found at i:31227270 original size:45 final size:44
Alignment explanation
Indices: 31227172--31227302 Score: 153
Period size: 45 Copynumber: 3.0 Consensus size: 44
31227162 AGACTTTTAT
* * * *
31227172 TCAT-TCACCGGCATT-TTGCCTACTAGGCTCGAGGCTCG-ATA
1 TCATCTCACCGGCATTATAGCCTGCTAGGCTCAAGGCCCGAATA
*
31227213 TCATGTCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATA
1 TCATCTCACCGGCATTATAGCCTGCTAGGCTC-AAGGCCCGAATA
* *
31227258 GT-ATCTCACCGGCATAATAGCCTGCTAGGCTCAAGGCCTGAATA
1 -TCATCTCACCGGCATTATAGCCTGCTAGGCTCAAGGCCCGAATA
31227302 T
1 T
31227303 AATACTAGTA
Statistics
Matches: 78, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
41 4 0.05
42 11 0.14
43 14 0.18
44 17 0.22
45 31 0.40
46 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.25
Consensus pattern (44 bp):
TCATCTCACCGGCATTATAGCCTGCTAGGCTCAAGGCCCGAATA
Found at i:31227342 original size:38 final size:38
Alignment explanation
Indices: 31227299--31227493 Score: 273
Period size: 38 Copynumber: 5.1 Consensus size: 38
31227289 CAAGGCCTGA
* * * *
31227299 ATATAATACTAGTACTAGGCCTGCGGGATTTAACCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
*
31227337 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCAG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
*
31227375 ATATAATACCAGCACGAAGCCTGCGGTATTTAACCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
* * *
31227413 ATATATTACCAGCACGAAGCCTGCAGGATTTACCCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
* *
31227451 ATATAATACCAGCACGAAGCCTGTGGGTCTTTAAGCCCGG
1 ATATAATACCAGCACGAAGCCTGCGGG-ATTTAA-CCCGG
31227491 ATA
1 ATA
31227494 CACATCAAAT
Statistics
Matches: 139, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
38 127 0.91
39 4 0.03
40 8 0.06
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (38 bp):
ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
Found at i:31227830 original size:43 final size:44
Alignment explanation
Indices: 31227769--31227859 Score: 148
Period size: 43 Copynumber: 2.1 Consensus size: 44
31227759 ACATAACATT
* *
31227769 TCATTTCACCGGTATTATAGCCTGCTAGGCTCAAAGCCCG-ATA
1 TCATTTCACCGGCATTATAGCCTGCTAGGCCCAAAGCCCGAATA
*
31227812 TCATTTCACCGGCATTATAGCCTGCTAGGCCCCAAGCCCGAATA
1 TCATTTCACCGGCATTATAGCCTGCTAGGCCCAAAGCCCGAATA
31227856 TCAT
1 TCAT
31227860 ATTTTGATAG
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
43 37 0.84
44 7 0.16
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.26
Consensus pattern (44 bp):
TCATTTCACCGGCATTATAGCCTGCTAGGCCCAAAGCCCGAATA
Found at i:31231574 original size:21 final size:21
Alignment explanation
Indices: 31231526--31231566 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
31231516 AAAATTACCC
31231526 CTCTTTCCACCCATTTTTCTA
1 CTCTTTCCACCCATTTTTCTA
*
31231547 CTCTTTCCATCCATTTTTCT
1 CTCTTTCCACCCATTTTTCT
31231567 TTCTTTTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.12, C:0.37, G:0.00, T:0.51
Consensus pattern (21 bp):
CTCTTTCCACCCATTTTTCTA
Found at i:31232969 original size:25 final size:25
Alignment explanation
Indices: 31232933--31233005 Score: 110
Period size: 25 Copynumber: 2.9 Consensus size: 25
31232923 GGAAGAAGTG
*
31232933 CAAAAAGGGCTTTGCCCCAGTTTAC
1 CAAAAAGGGCTTTGCCCCAGTTAAC
* *
31232958 CGAAAAGGGCTTTGCCCCAGTTAAT
1 CAAAAAGGGCTTTGCCCCAGTTAAC
*
31232983 CAAAAAGGGCTTTGCCCTAGTTA
1 CAAAAAGGGCTTTGCCCCAGTTA
31233006 TTAAAAGAGG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.25
Consensus pattern (25 bp):
CAAAAAGGGCTTTGCCCCAGTTAAC
Found at i:31233017 original size:24 final size:25
Alignment explanation
Indices: 31232935--31233017 Score: 84
Period size: 25 Copynumber: 3.4 Consensus size: 25
31232925 AAGAAGTGCA
* *
31232935 AAAAG-GGCTTTGCCCCAGTTTACC
1 AAAAGAGGCTTTGCCCCAGTTAATC
31232959 GAAAAG-GGCTTTGCCCCAGTTAATC
1 -AAAAGAGGCTTTGCCCCAGTTAATC
* *
31232984 AAAA-AGGGCTTTGCCCTAGTT-ATT
1 AAAAGA-GGCTTTGCCCCAGTTAATC
31233008 AAAAGAGGCT
1 AAAAGAGGCT
31233018 AGGCCTCCAG
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
24 14 0.27
25 37 0.73
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (25 bp):
AAAAGAGGCTTTGCCCCAGTTAATC
Found at i:31233028 original size:50 final size:50
Alignment explanation
Indices: 31232933--31233030 Score: 119
Period size: 50 Copynumber: 2.0 Consensus size: 50
31232923 GGAAGAAGTG
**
31232933 CAAAAAGGGCTTTGCCCCAGTTTACCGAAAAGGGCTTTGCCCCAGTTAAT
1 CAAAAAGGGCTTTGCCCCAGTTTACCGAAAAGGGCTAGGCCCCAGTTAAT
* **
31232983 CAAAAAGGGCTTTGCCCTAG-TTA-TTAAAAGAGGCTAGGCCTCCAGTTA
1 CAAAAAGGGCTTTGCCCCAGTTTACCGAAAAG-GGCTAGGCC-CCAGTTA
31233031 CATGATAAAG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
48 5 0.12
49 10 0.24
50 26 0.63
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.24
Consensus pattern (50 bp):
CAAAAAGGGCTTTGCCCCAGTTTACCGAAAAGGGCTAGGCCCCAGTTAAT
Found at i:31240885 original size:10 final size:11
Alignment explanation
Indices: 31240870--31240920 Score: 70
Period size: 10 Copynumber: 4.8 Consensus size: 11
31240860 ATTTTGATCT
31240870 ACATGATATG-
1 ACATGATATGC
31240880 ACATGATATGC
1 ACATGATATGC
31240891 ACATGATATG-
1 ACATGATATGC
**
31240901 TTATGATATGC
1 ACATGATATGC
31240912 ACATGATAT
1 ACATGATAT
31240921 ACTCATTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
10 18 0.51
11 17 0.49
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (11 bp):
ACATGATATGC
Found at i:31240895 original size:21 final size:21
Alignment explanation
Indices: 31240870--31240920 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
31240860 ATTTTGATCT
31240870 ACATGATATGACATGATATGC
1 ACATGATATGACATGATATGC
**
31240891 ACATGATATGTTATGATATGC
1 ACATGATATGACATGATATGC
31240912 ACATGATAT
1 ACATGATAT
31240921 ACTCATTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (21 bp):
ACATGATATGACATGATATGC
Found at i:31241005 original size:24 final size:25
Alignment explanation
Indices: 31240966--31241037 Score: 101
Period size: 25 Copynumber: 2.9 Consensus size: 25
31240956 GGAAGAAGTG
* *
31240966 CAAAAAGGGCTTTGCCCCAGTTTAC
1 CAAAAAGGGTTTTGCCCCAGTTAAC
* *
31240991 CGAAAA-GGTTTTGCCCCAGTTAAT
1 CAAAAAGGGTTTTGCCCCAGTTAAC
31241015 CAAAAAGGGTTTTGCCCCAGTTA
1 CAAAAAGGGTTTTGCCCCAGTTA
31241038 TCAAAAGAGG
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
24 20 0.49
25 21 0.51
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (25 bp):
CAAAAAGGGTTTTGCCCCAGTTAAC
Found at i:31241040 original size:24 final size:24
Alignment explanation
Indices: 31240966--31241043 Score: 104
Period size: 24 Copynumber: 3.2 Consensus size: 24
31240956 GGAAGAAGTG
* *
31240966 CAAAAAGGGCTTTGCCCCAGTTTAC
1 CAAAAAGGGTTTTGCCCCAG-TTAT
*
31240991 CGAAAA-GGTTTTGCCCCAGTTAAT
1 CAAAAAGGGTTTTGCCCCAGTT-AT
31241015 CAAAAAGGGTTTTGCCCCAGTTAT
1 CAAAAAGGGTTTTGCCCCAGTTAT
31241039 CAAAA
1 CAAAA
31241044 GAGGCTAGGC
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
23 2 0.04
24 25 0.53
25 20 0.43
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (24 bp):
CAAAAAGGGTTTTGCCCCAGTTAT
Found at i:31246044 original size:14 final size:14
Alignment explanation
Indices: 31246025--31246059 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
31246015 TTTGTCTATT
31246025 GTTAATCGTTCTTG
1 GTTAATCGTTCTTG
31246039 GTTAATCGTTCTTG
1 GTTAATCGTTCTTG
31246053 GTTAATC
1 GTTAATC
31246060 TCTAAAAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.17, C:0.14, G:0.20, T:0.49
Consensus pattern (14 bp):
GTTAATCGTTCTTG
Found at i:31255032 original size:23 final size:23
Alignment explanation
Indices: 31255002--31255045 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
31254992 TTACATCTCA
31255002 GAGATAGTAAGACTGTATGGGGT
1 GAGATAGTAAGACTGTATGGGGT
31255025 GAGATAGTAAGACTGTATGGG
1 GAGATAGTAAGACTGTATGGG
31255046 TTTCAGTGTC
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:0.32, C:0.05, G:0.39, T:0.25
Consensus pattern (23 bp):
GAGATAGTAAGACTGTATGGGGT
Found at i:31257030 original size:40 final size:39
Alignment explanation
Indices: 31256958--31257047 Score: 114
Period size: 40 Copynumber: 2.3 Consensus size: 39
31256948 GTATACGGTA
* *
31256958 CCAT-TTGGTGTGTAGGGTTGGATGGGTTGATTTTATCC
1 CCATATTGGTGTGTAGGGTAGGATGGGTCGATTTTATCC
*
31256996 CCATACTTGGTGTGTAGGGCTAGGCT-GGTCGATTTTATCC
1 CCATA-TTGGTGTGTAGGG-TAGGATGGGTCGATTTTATCC
31257036 CCATA-TGGTGTG
1 CCATATTGGTGTG
31257048 CTGGGTGGGA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
38 11 0.24
40 31 0.67
41 4 0.09
ACGTcount: A:0.14, C:0.16, G:0.32, T:0.38
Consensus pattern (39 bp):
CCATATTGGTGTGTAGGGTAGGATGGGTCGATTTTATCC
Found at i:31257902 original size:20 final size:21
Alignment explanation
Indices: 31257877--31257927 Score: 59
Period size: 24 Copynumber: 2.3 Consensus size: 21
31257867 CATCAGATAT
31257877 ATACTTATAC-AACAACTACC
1 ATACTTATACTAACAACTACC
*
31257897 ATACTTAACATACTACCAACTACC
1 ATACTT---ATACTAACAACTACC
31257921 ATACTTA
1 ATACTTA
31257928 ACATACTAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
20 6 0.23
21 1 0.04
23 4 0.15
24 15 0.58
ACGTcount: A:0.43, C:0.29, G:0.00, T:0.27
Consensus pattern (21 bp):
ATACTTATACTAACAACTACC
Found at i:31257916 original size:24 final size:24
Alignment explanation
Indices: 31257889--31257935 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
31257879 ACTTATACAA
31257889 CAACTACCATACTTAACATACTAC
1 CAACTACCATACTTAACATACTAC
31257913 CAACTACCATACTTAACATACTA
1 CAACTACCATACTTAACATACTA
31257936 ACTCTCACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.43, C:0.32, G:0.00, T:0.26
Consensus pattern (24 bp):
CAACTACCATACTTAACATACTAC
Found at i:31260738 original size:56 final size:58
Alignment explanation
Indices: 31260654--31260766 Score: 176
Period size: 57 Copynumber: 2.0 Consensus size: 58
31260644 ATAAATGGTG
* *
31260654 AAAATTGAGAAATGAGAAACTTTTGGAAATAAATGTGATTTT-TCCAAAATGAAAATT
1 AAAATAGAGAAATGAGAAACATTTGGAAATAAATGTGATTTTCTCCAAAATGAAAATT
* *
31260711 AAAATAGAGAAATG-GAAACATTTGGAAATGAATGTGGTTTTCTCCAAAATGAAAAT
1 AAAATAGAGAAATGAGAAACATTTGGAAATAAATGTGATTTTCTCCAAAATGAAAAT
31260767 GACCTGAAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
56 24 0.47
57 27 0.53
ACGTcount: A:0.47, C:0.06, G:0.18, T:0.29
Consensus pattern (58 bp):
AAAATAGAGAAATGAGAAACATTTGGAAATAAATGTGATTTTCTCCAAAATGAAAATT
Found at i:31260880 original size:22 final size:22
Alignment explanation
Indices: 31260852--31260898 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
31260842 TTTAATTAGG
31260852 ATTGGGTTGAGAAGACTATTTA
1 ATTGGGTTGAGAAGACTATTTA
31260874 ATTGGGTTGAGAAGACTATTTA
1 ATTGGGTTGAGAAGACTATTTA
31260896 ATT
1 ATT
31260899 AGGAAATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.32, C:0.04, G:0.26, T:0.38
Consensus pattern (22 bp):
ATTGGGTTGAGAAGACTATTTA
Found at i:31267939 original size:19 final size:20
Alignment explanation
Indices: 31267917--31267955 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
31267907 GGTAGGACTC
31267917 TATATATTCTGATCTGATCTA
1 TATATATTCTGATCTGATC-A
31267938 TATATATTCTGATCTGAT
1 TATATATTCTGATCTGAT
31267956 GATTGTATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.13, G:0.10, T:0.49
Consensus pattern (20 bp):
TATATATTCTGATCTGATCA
Found at i:31270168 original size:48 final size:48
Alignment explanation
Indices: 31270096--31270333 Score: 262
Period size: 48 Copynumber: 5.0 Consensus size: 48
31270086 GACATTTAGG
* *
31270096 TGATATGTGTGCCAGTGTAAGACCATGTTTGGGACATGGCGTCGGCCA
1 TGATATGTGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCCA
* * * * *
31270144 CGATATGAGAGCCAGTGTAAGACCATGTTTGGAACAAGGCATCGGCAA
1 TGATATGTGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCCA
* * * * * * *
31270192 TGTTGTGGGATCCAATGTAAGACCATGTCTAGGACATGGCATCGG-CA
1 TGATATGTGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCCA
* * * * * *
31270239 TTAATATGTGTGCTAGTGTAAGACCATGTCTAGGACATGGCATCGGCCT
1 -TGATATGTGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCCA
* *
31270288 TGACATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGC
1 TGATATGTGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGC
31270334 AATTCACTCT
Statistics
Matches: 154, Mismatches: 34, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
47 1 0.01
48 152 0.99
49 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (48 bp):
TGATATGTGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCCA
Found at i:31271953 original size:18 final size:18
Alignment explanation
Indices: 31271932--31272086 Score: 109
Period size: 18 Copynumber: 8.6 Consensus size: 18
31271922 GAACAATTAT
*
31271932 TTATTCAGTAACAGTCAG
1 TTATTCAGTAACAGTCAA
* *
31271950 TTATTCGGTAACAATCAA
1 TTATTCAGTAACAGTCAA
* * ** *
31271968 ATATTCAAT-ACTAACCAG
1 TTATTCAGTAAC-AGTCAA
*
31271986 TTATTCAGTAA-TGATCAA
1 TTATTCAGTAACAG-TCAA
* * *
31272004 TTATTCAGTAATATTCAG
1 TTATTCAGTAACAGTCAA
31272022 TTATTCAGTAACAGTCTAA
1 TTATTCAGTAACAGTC-AA
* *
31272041 -TATCCAGTAGCAGTCAA
1 TTATTCAGTAACAGTCAA
* * *
31272058 TTATCCGGTAAAAGTCAA
1 TTATTCAGTAACAGTCAA
31272076 TTATTCAGTAA
1 TTATTCAGTAA
31272087 TAATCAGTTA
Statistics
Matches: 104, Mismatches: 27, Indels: 12
0.73 0.19 0.08
Matches are distributed among these distances:
17 4 0.04
18 98 0.94
19 2 0.02
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.34
Consensus pattern (18 bp):
TTATTCAGTAACAGTCAA
Found at i:31271973 original size:36 final size:36
Alignment explanation
Indices: 31271933--31272098 Score: 129
Period size: 36 Copynumber: 4.6 Consensus size: 36
31271923 AACAATTATT
* *
31271933 TATTCAGTAACAGTCAGTTATTCGGTAACAATCAAA
1 TATTCAGTAACAATCAGTTATTCAGTAACAATCAAA
* * ** *
31271969 TATTCAAT-ACTAACCAGTTATTCAGTAATGATCAAT
1 TATTCAGTAAC-AATCAGTTATTCAGTAACAATCAAA
* * * *
31272005 TATTCAGTAATATTCAGTTATTCAGTAACAGTCTAA
1 TATTCAGTAACAATCAGTTATTCAGTAACAATCAAA
* * * * * * *
31272041 TATCCAGTAGCAGTCAATTATCCGGTAA-AAGTCAAT
1 TATTCAGTAACAATCAGTTATTCAGTAACAA-TCAAA
*
31272077 TATTCAGTAATAATCAGTTATT
1 TATTCAGTAACAATCAGTTATT
31272099 TTATACCTTT
Statistics
Matches: 95, Mismatches: 32, Indels: 6
0.71 0.24 0.05
Matches are distributed among these distances:
35 3 0.03
36 91 0.96
37 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (36 bp):
TATTCAGTAACAATCAGTTATTCAGTAACAATCAAA
Found at i:31272331 original size:45 final size:45
Alignment explanation
Indices: 31272282--31272455 Score: 303
Period size: 45 Copynumber: 3.9 Consensus size: 45
31272272 GTAACAGTAC
* *
31272282 AGTAACAATATCCAACACACAAAGTGCCGAATCGGTAACGGTAAT
1 AGTAACAATATTCGACACACAAAGTGCCGAATCGGTAACGGTAAT
31272327 AGTAACAATATTCGACACACAAAGTGCCGAATCGGTAACGGTAAT
1 AGTAACAATATTCGACACACAAAGTGCCGAATCGGTAACGGTAAT
* * *
31272372 AGTAACAATATTTGACACACAAAGTGCCGAATTGGTAACGGTAAC
1 AGTAACAATATTCGACACACAAAGTGCCGAATCGGTAACGGTAAT
31272417 AGTAACAATATTCGACACACAAAGTGCCGAATCGGTAAC
1 AGTAACAATATTCGACACACAAAGTGCCGAATCGGTAAC
31272456 AGTAGAAGTA
Statistics
Matches: 122, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 122 1.00
ACGTcount: A:0.41, C:0.21, G:0.19, T:0.20
Consensus pattern (45 bp):
AGTAACAATATTCGACACACAAAGTGCCGAATCGGTAACGGTAAT
Found at i:31287941 original size:48 final size:48
Alignment explanation
Indices: 31287884--31288101 Score: 249
Period size: 48 Copynumber: 4.5 Consensus size: 48
31287874 TGTGCGCTAG
* *
31287884 TGTAAGACCATGTTTGGGACATAGCGTCGGCCACGATATGAGAGCCAA
1 TGTAAGACCATGTTTGGGACATGGCATCGGCCACGATATGAGAGCCAA
* * * * *
31287932 TGTAAGACCATGTTTGGAACATGGCATCGGCGATGTTGTGAGAGCCAA
1 TGTAAGACCATGTTTGGGACATGGCATCGGCCACGATATGAGAGCCAA
* * * * * * *
31287980 TGTAAGACCATGTCTGAGACATGGCATCGG-CATTGATATGTGTGCTAG
1 TGTAAGACCATGTTTGGGACATGGCATCGGCCA-CGATATGAGAGCCAA
* * * *
31288028 TGTAAGACCATGTTTGGGACATGGCATCGGCCTCGACATGTGAGCCAG
1 TGTAAGACCATGTTTGGGACATGGCATCGGCCACGATATGAGAGCCAA
*
31288076 TGTAAGACCATGTTTGGAACATGGCA
1 TGTAAGACCATGTTTGGGACATGGCA
31288102 ACGGTAATTC
Statistics
Matches: 143, Mismatches: 25, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
47 1 0.01
48 141 0.99
49 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.25
Consensus pattern (48 bp):
TGTAAGACCATGTTTGGGACATGGCATCGGCCACGATATGAGAGCCAA
Found at i:31296804 original size:19 final size:20
Alignment explanation
Indices: 31296772--31296809 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
31296762 ATATTACCAA
*
31296772 TTCAGTTACTTTTGGTTAAT
1 TTCAGTTACATTTGGTTAAT
31296792 TTCAGTTA-ATTTGGTTAA
1 TTCAGTTACATTTGGTTAA
31296810 ATAAACATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.24, C:0.08, G:0.16, T:0.53
Consensus pattern (20 bp):
TTCAGTTACATTTGGTTAAT
Found at i:31307546 original size:3 final size:3
Alignment explanation
Indices: 31307538--31307563 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
31307528 CAACGGATGT
31307538 AGG AGG AGG AGG AGG AGG AGG AGG AG
1 AGG AGG AGG AGG AGG AGG AGG AGG AG
31307564 AAGAAGATGA
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:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:31311155 original size:19 final size:19
Alignment explanation
Indices: 31311128--31311169 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
31311118 GATTTTTAAG
**
31311128 TTAACTTAAAGGAAACATT
1 TTAACTTAAAAAAAACATT
*
31311147 TTAATTTAAAAAAAACATT
1 TTAACTTAAAAAAAACATT
31311166 TTAA
1 TTAA
31311170 AATTATTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.36
Consensus pattern (19 bp):
TTAACTTAAAAAAAACATT
Found at i:31314839 original size:57 final size:58
Alignment explanation
Indices: 31314732--31314854 Score: 151
Period size: 57 Copynumber: 2.1 Consensus size: 58
31314722 ATAGAAATGG
* * *
31314732 TGAAAATGGAGAAATAGGAAACAATTGGAAATGATTATGGTCTTATCCAAAATAAAAA
1 TGAAAATGGAGAAATAGGAAACAATTGGAAATGAATATGATCTTACCCAAAATAAAAA
* * * * *
31314790 TGAAAATGGAGAAAT-GGAATCATTTGGAAATGAATGTGAAT-TTCCCCAAAATGAAAA
1 TGAAAATGGAGAAATAGGAAACAATTGGAAATGAATATG-ATCTTACCCAAAATAAAAA
31314847 TGAAAATG
1 TGAAAATG
31314855 AAAATGAAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
57 40 0.71
58 16 0.29
ACGTcount: A:0.48, C:0.07, G:0.20, T:0.24
Consensus pattern (58 bp):
TGAAAATGGAGAAATAGGAAACAATTGGAAATGAATATGATCTTACCCAAAATAAAAA
Found at i:31314846 original size:6 final size:6
Alignment explanation
Indices: 31314837--31314864 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
31314827 GAATTTCCCC
31314837 AAAATG AAAATG AAAATG AAAATG AAAA
1 AAAATG AAAATG AAAATG AAAATG AAAA
31314865 ATGACCTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (6 bp):
AAAATG
Found at i:31315735 original size:40 final size:40
Alignment explanation
Indices: 31315681--31315761 Score: 135
Period size: 40 Copynumber: 2.0 Consensus size: 40
31315671 TTTCCGTTGT
**
31315681 GCAAGAAAACTATTTTCAAATTGAATTTTTTCCAACATGA
1 GCAAGAAAACTATTTTCAAACCGAATTTTTTCCAACATGA
*
31315721 GCAAGAAAACTATTTTCAAACCGGATTTTTTCCAACATGA
1 GCAAGAAAACTATTTTCAAACCGAATTTTTTCCAACATGA
31315761 G
1 G
31315762 TATATGACCT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.32
Consensus pattern (40 bp):
GCAAGAAAACTATTTTCAAACCGAATTTTTTCCAACATGA
Found at i:31316216 original size:34 final size:34
Alignment explanation
Indices: 31316178--31316243 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
31316168 GTTTTTAAGG
*
31316178 GTTAGGGTTTTGTTTATTTAAATTAAGGTTTAAT
1 GTTAGGGTTTTGTTTATTTAAAGTAAGGTTTAAT
* *
31316212 GTTAGGGTTTTGTTTCTTTAAAGTAGGGTTTA
1 GTTAGGGTTTTGTTTATTTAAAGTAAGGTTTA
31316244 GAGGTCTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.23, C:0.02, G:0.24, T:0.52
Consensus pattern (34 bp):
GTTAGGGTTTTGTTTATTTAAAGTAAGGTTTAAT
Found at i:31318791 original size:5 final size:5
Alignment explanation
Indices: 31318781--31318805 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
31318771 AGGTTTAGTT
31318781 ATTTA ATTTA ATTTA ATTTA ATTTA
1 ATTTA ATTTA ATTTA ATTTA ATTTA
31318806 TTGGTTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTTA
Found at i:31329995 original size:30 final size:29
Alignment explanation
Indices: 31329961--31330025 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
31329951 TTTTAAAAAT
* * *
31329961 ATAATTTTTATATAATTTTTAATTTGTTAA
1 ATAATTTTTATAAAAATTTTAAATT-TTAA
*
31329991 ATAATTTTTTTAAAAATTTTAAATTTTAA
1 ATAATTTTTATAAAAATTTTAAATTTTAA
*
31330020 AAAATT
1 ATAATT
31330026 AATTAATTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 9 0.30
30 21 0.70
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (29 bp):
ATAATTTTTATAAAAATTTTAAATTTTAA
Found at i:31329996 original size:19 final size:18
Alignment explanation
Indices: 31329962--31329999 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
31329952 TTTAAAAATA
*
31329962 TAATTTTTATATAATTTT
1 TAATTTTTAAATAATTTT
31329980 TAATTTGTTAAATAATTTT
1 TAATTT-TTAAATAATTTT
31329999 T
1 T
31330000 TTAAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (18 bp):
TAATTTTTAAATAATTTT
Found at i:31331214 original size:13 final size:13
Alignment explanation
Indices: 31331198--31331258 Score: 77
Period size: 13 Copynumber: 4.7 Consensus size: 13
31331188 ACCAAATTTT
31331198 TCAAAAGCACTTC
1 TCAAAAGCACTTC
*
31331211 TCAAAAGCACTTT
1 TCAAAAGCACTTC
* * *
31331224 TCCACAGCATTTC
1 TCAAAAGCACTTC
*
31331237 TCAAAAGCACTTT
1 TCAAAAGCACTTC
31331250 TCAAAAGCA
1 TCAAAAGCA
31331259 TTGTCAAACT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 39 1.00
ACGTcount: A:0.38, C:0.28, G:0.08, T:0.26
Consensus pattern (13 bp):
TCAAAAGCACTTC
Done.