Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006710.1 Hibiscus syriacus cultivar Beakdansim tig00016725_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2941931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 11
Found at i:1020930 original size:68 final size:72
Alignment explanation
Indices: 1020843--1020989 Score: 176
Period size: 68 Copynumber: 2.1 Consensus size: 72
1020833 CATATACAAT
* * * *
1020843 ATATATATGTTTTTCAAAATATATATAATATAGTTTTGAAAAC-ATATATA-ATGTATATATGGT
1 ATATATATGTTTTTCAAAATATATATAATATAATTTTCAAAACTATATATATATATATATATAGT
*
1020906 TTTGAAA
66 TTTAAAA
* * *
1020913 ATATATA-G-TTTTGAAAATATATATAGTATAATTTTCAAAGCTTATATATATATATATATATAG
1 ATATATATGTTTTTCAAAATATATATAATATAATTTTCAAAAC-TATATATATATATATATATAG
1020976 TTTTAAAA
65 TTTTAAAA
*
1020984 AAATAT
1 ATATAT
1020990 TATTATTATT
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
68 28 0.43
69 1 0.02
70 14 0.22
71 22 0.34
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (72 bp):
ATATATATGTTTTTCAAAATATATATAATATAATTTTCAAAACTATATATATATATATATATAGT
TTTAAAA
Found at i:1020932 original size:14 final size:16
Alignment explanation
Indices: 1020897--1020935 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
1020887 TATATAATGT
*
1020897 ATATATGGTTTTGAAA
1 ATATATAGTTTTGAAA
1020913 ATATATAGTTTTGAAA
1 ATATATAGTTTTGAAA
1020929 ATATATA
1 ATATATA
1020936 TAGTATAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.44
Consensus pattern (16 bp):
ATATATAGTTTTGAAA
Found at i:1024926 original size:21 final size:21
Alignment explanation
Indices: 1024900--1024953 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
1024890 TTCGCAAAAA
1024900 GGATCGATCCTTTTTGCAAAG
1 GGATCGATCCTTTTTGCAAAG
*
1024921 GGATCGATCCTTTTTGCGAAG
1 GGATCGATCCTTTTTGCAAAG
1024942 GGATCGATCCTT
1 GGATCGATCCTT
1024954 GATGAGTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.33
Consensus pattern (21 bp):
GGATCGATCCTTTTTGCAAAG
Found at i:1030057 original size:32 final size:32
Alignment explanation
Indices: 1030020--1030096 Score: 100
Period size: 32 Copynumber: 2.4 Consensus size: 32
1030010 CAGATACTAA
* *
1030020 CAGTGTTGCATTTATATAATGCACATCAGAGT
1 CAGTGTTGCATTTAAATAATGCACAACAGAGT
* * * *
1030052 CAGTGTTGCATTCAAATAGTGCACAAGAGTGT
1 CAGTGTTGCATTTAAATAATGCACAACAGAGT
1030084 CAGTGTTGCATTT
1 CAGTGTTGCATTT
1030097 GGATAATGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.34
Consensus pattern (32 bp):
CAGTGTTGCATTTAAATAATGCACAACAGAGT
Found at i:1030651 original size:94 final size:94
Alignment explanation
Indices: 1030548--1030736 Score: 351
Period size: 94 Copynumber: 2.0 Consensus size: 94
1030538 ATTATATGTC
*
1030548 ACAGAGCTTTAATTAATAAATTTTATTTTAATTGTTGAGTATGTTTATTTTGATACCATGTATTA
1 ACAGAGCTTTAATTAATAAATTTTATTATAATTGTTGAGTATGTTTATTTTGATACCATGTATTA
1030613 TGTTTTTGAAATATGAATGATTAGTTTTG
66 TGTTTTTGAAATATGAATGATTAGTTTTG
*
1030642 ACAGAGCTTTAATTTATAAATTTTATTATAATTGTTGAGTATGTTTATTTTGATACCATGTATTA
1 ACAGAGCTTTAATTAATAAATTTTATTATAATTGTTGAGTATGTTTATTTTGATACCATGTATTA
*
1030707 TGTTTTTGAAATATGAATGATTATTTTTG
66 TGTTTTTGAAATATGAATGATTAGTTTTG
1030736 A
1 A
1030737 AAATCAGAGG
Statistics
Matches: 92, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
94 92 1.00
ACGTcount: A:0.31, C:0.04, G:0.14, T:0.50
Consensus pattern (94 bp):
ACAGAGCTTTAATTAATAAATTTTATTATAATTGTTGAGTATGTTTATTTTGATACCATGTATTA
TGTTTTTGAAATATGAATGATTAGTTTTG
Found at i:1033484 original size:3 final size:3
Alignment explanation
Indices: 1033476--1033559 Score: 89
Period size: 3 Copynumber: 27.7 Consensus size: 3
1033466 AAGATGTATA
* * * * * *
1033476 TAT TAT TAT TAT TAT TAT TAT TAT TCT TGT AAT TAT CAT T-T TTT TACC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T
1033524 TAT ATAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1033560 AACAAAGGCC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
2 2 0.03
3 61 0.90
4 5 0.07
ACGTcount: A:0.31, C:0.05, G:0.01, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1033674 original size:44 final size:45
Alignment explanation
Indices: 1033570--1033667 Score: 146
Period size: 44 Copynumber: 2.2 Consensus size: 45
1033560 AACAAAGGCC
*
1033570 CCAACCTAAAACCCAACTAGAACCCAAACAAGCCCCAACCAGAAT
1 CCAACCTAAAACCCAACCAGAACCCAAACAAGCCCCAACCAGAAT
* *
1033615 CCAACCTAAAACCCAACCAG-ACCCAAACAAGTCCCAATCAGAA-
1 CCAACCTAAAACCCAACCAGAACCCAAACAAGCCCCAACCAGAAT
*
1033658 CCAACTTAAA
1 CCAACCTAAA
1033668 TTCCCAAAAC
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
43 9 0.18
44 21 0.43
45 19 0.39
ACGTcount: A:0.47, C:0.39, G:0.06, T:0.08
Consensus pattern (45 bp):
CCAACCTAAAACCCAACCAGAACCCAAACAAGCCCCAACCAGAAT
Found at i:1046986 original size:13 final size:13
Alignment explanation
Indices: 1046968--1047001 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1046958 CACCTAATAA
1046968 AGAAAAAGAAAAG
1 AGAAAAAGAAAAG
*
1046981 AGAAAAAAAAAAG
1 AGAAAAAGAAAAG
*
1046994 AAAAAAAG
1 AGAAAAAG
1047002 GGTTCAAAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (13 bp):
AGAAAAAGAAAAG
Found at i:1048271 original size:135 final size:134
Alignment explanation
Indices: 1048027--1048735 Score: 853
Period size: 135 Copynumber: 5.3 Consensus size: 134
1048017 AGATAAACCA
* * * * *
1048027 ATTAACATTTCCAATGGAGAGTTAATTATGAGAAAAACTCATCCGATA-AAAGGAGAATAAGTTC
1 ATTAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGA-GAGAAAAAGTTC
* * * * *
1048091 GTAATGAGAATAATTTGTTCAACCTTTGCTCGATTCACGACATTTTGAATCAGCGAAGCCTAACT
65 GTAATGAGAAGAACTTGTTCAACCTTTGCTCGATTC-TGACATTTTGAATCAGTGAAGCCTCACT
*
1048156 TGAGAG
129 TGAGGG
* * * *
1048162 ATTAATATTACCAATGGAGAGTTCATAATGAGAATAACTCATCCGATAGAGGGAGAAAAAGTTCG
1 ATTAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGAGAGAAAAAGTTCG
* * *
1048227 TAATGAGAAGAACTTTTTCAACCTTTGCTCGATTCTTGGA-ATTTTGAACCAGTGAAGCATCACT
66 TAATGAGAAGAACTTGTTCAACCTTTGCTCGATTC-T-GACATTTTGAATCAGTGAAGCCTCACT
1048291 TGAGGG
129 TGAGGG
* *
1048297 ATTAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATTCGATAGAGAGAGAAGAAGTTCG
1 ATTAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGAGAGAAAAAGTTCG
*
1048362 TAAT------AACTTGTTCAACCTTTGCTCGATTC--ACAATATTTAGAATTAGTGAAGCCTCAC
66 TAATGAGAAGAACTTGTTCAACCTTTGCTCGATTCTGAC-AT-TTT-GAATCAGTGAAGCCTCAC
1048419 TTGAGGG
128 TTGAGGG
* * * * **
1048426 ATTAACATTTCTAATGGAGAGTTAATAATGAGAAGAACTCATTCGATAGAGAGAGAAGAAGTTTA
1 ATTAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGAGAGAAAAAGTTCG
*
1048491 TAATGAGAAGAACTTGTTCAACCTTTACTCGATTCATGACATTTTGAATCAGTGAAGCCTCACTT
66 TAATGAGAAGAACTTGTTCAACCTTTGCTCGATTC-TGACATTTTGAATCAGTGAAGCCTCACTT
*
1048556 AAGGG
130 GAGGG
* * * * *
1048561 ATTAACATTTCCAATAGAGAGTTCGTAATGAGAAGAACTCATCTGATAGTGAGAGAAAAAGTTTG
1 ATTAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGAGAGAAAAAGTTCG
* * ** * * * *
1048626 TAATGAGAAGAACTTGTTAAACCTTTGCTCGATTCACGACATTTCAAATCAGCGATGTCTCAATT
66 TAATGAGAAGAACTTGTTCAACCTTTGCTCGATTC-TGACATTTTGAATCAGTGAAGCCTCACTT
*
1048691 GAGGA
130 GAGGG
* * *
1048696 ATTAACATTTCCAGTAGAGAGTTCATGATGAGAAGAACTC
1 ATTAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTC
1048736 GTAGTTGAAG
Statistics
Matches: 501, Mismatches: 58, Indels: 30
0.85 0.10 0.05
Matches are distributed among these distances:
125 1 0.00
127 2 0.00
128 3 0.01
129 111 0.22
135 374 0.75
136 6 0.01
137 2 0.00
138 2 0.00
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (134 bp):
ATTAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGAGAGAAAAAGTTCG
TAATGAGAAGAACTTGTTCAACCTTTGCTCGATTCTGACATTTTGAATCAGTGAAGCCTCACTTG
AGGG
Found at i:1048503 original size:264 final size:264
Alignment explanation
Indices: 1048027--1048735 Score: 859
Period size: 264 Copynumber: 2.6 Consensus size: 264
1048017 AGATAAACCA
* * * * * *
1048027 ATTAACATTTCCAATGGAGAGTTAATTATGAGAAAAACTCATCCGATA-AAAGGAGAATAAGTTC
1 ATTAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATTCGATAGAGA-GAGAAAAAGTTC
* * *
1048091 GTAATGAGAATAATTTGTTCAACCTTTGCTCGATTCACGACATTTTGAATCAGCGAAGCCTAACT
65 G---T---AATAACTTGTTCAACCTTTGCTCGATTCACGACATTTAGAATCAGCGAAGCCTCACT
* * * * *
1048156 TGAGAGATTAATATTACCAATGGAGAGTTCATAATGAGAATAACTCATCCGATAGAGGGAGAAAA
124 TGAGGGATTAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGAGAGAAAA
* * * *
1048221 AGTTCGTAATGAGAAGAACTTTTTCAACCTTTGCTCGATTCTTGGA-ATTTTGAACCAGTGAAGC
189 AGTTCATAATGAGAAGAACTTGTTCAACCTTTACTCGATTCAT-GACATTTTGAACCAGTGAAGC
*
1048285 ATCACTTGAGGG
253 ATCACTTAAGGG
*
1048297 ATTAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATTCGATAGAGAGAGAAGAAGTTCG
1 ATTAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATTCGATAGAGAGAGAAAAAGTTCG
* * * *
1048362 TAATAACTTGTTCAACCTTTGCTCGATTCACAATATTTAGAATTAGTGAAGCCTCACTTGAGGGA
66 TAATAACTTGTTCAACCTTTGCTCGATTCACGACATTTAGAATCAGCGAAGCCTCACTTGAGGGA
* * * * *
1048427 TTAACATTTCTAATGGAGAGTTAATAATGAGAAGAACTCATTCGATAGAGAGAGAAGAAGTTTAT
131 TTAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGAGAGAAAAAGTTCAT
* *
1048492 AATGAGAAGAACTTGTTCAACCTTTACTCGATTCATGACATTTTGAATCAGTGAAGCCTCACTTA
196 AATGAGAAGAACTTGTTCAACCTTTACTCGATTCATGACATTTTGAACCAGTGAAGCATCACTTA
1048557 AGGG
261 AGGG
* * * *
1048561 ATTAACATTTCCAATAGAGAGTTCGTAATGAGAAGAACTCA-TCTGATAGTGAGAGAAAAAGTTT
1 ATTAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATTC-GATAGAGAGAGAAAAAGTTC
* * * *
1048625 GTAATGAGAAGAACTTGTTAAACCTTTGCTCGATTCACGACATTTCA-AATCAGCGATGTCTCAA
65 GTAAT------AACTTGTTCAACCTTTGCTCGATTCACGACATTT-AGAATCAGCGAAGCCTCAC
* * * *
1048689 TTGAGGAATTAACATTTCCAGTAGAGAGTTCATGATGAGAAGAACTC
123 TTGAGGGATTAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTC
1048736 GTAGTTGAAG
Statistics
Matches: 380, Mismatches: 49, Indels: 20
0.85 0.11 0.04
Matches are distributed among these distances:
263 4 0.01
264 232 0.61
267 1 0.00
270 140 0.37
271 3 0.01
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (264 bp):
ATTAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATTCGATAGAGAGAGAAAAAGTTCG
TAATAACTTGTTCAACCTTTGCTCGATTCACGACATTTAGAATCAGCGAAGCCTCACTTGAGGGA
TTAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGAGAGAAAAAGTTCAT
AATGAGAAGAACTTGTTCAACCTTTACTCGATTCATGACATTTTGAACCAGTGAAGCATCACTTA
AGGG
Found at i:1048858 original size:3 final size:3
Alignment explanation
Indices: 1048850--1048875 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1048840 TTTCTACATA
1048850 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
1048876 AACTAAGGTC
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:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1048935 original size:34 final size:34
Alignment explanation
Indices: 1048885--1048970 Score: 111
Period size: 34 Copynumber: 2.6 Consensus size: 34
1048875 AAACTAAGGT
* *
1048885 CCCAACCTAAATCCCAACCAGAACCCAAATAAAC
1 CCCAACCTAAAACCCAACCAGAACCCAAACAAAC
* * * *
1048919 CTCAACCTAAAACCCAACCATATCCCAAACAAGC
1 CCCAACCTAAAACCCAACCAGAACCCAAACAAAC
1048953 CCCAACC-AAAACCCAACC
1 CCCAACCTAAAACCCAACC
1048971 TAAATACCCA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
33 11 0.24
34 34 0.76
ACGTcount: A:0.45, C:0.44, G:0.02, T:0.08
Consensus pattern (34 bp):
CCCAACCTAAAACCCAACCAGAACCCAAACAAAC
Found at i:1048981 original size:13 final size:11
Alignment explanation
Indices: 1048885--1048992 Score: 67
Period size: 11 Copynumber: 9.4 Consensus size: 11
1048875 AAACTAAGGT
*
1048885 CCCAACCTAAAT
1 CCCAACC-AAAA
*
1048897 CCCAACCAGAA
1 CCCAACCAAAA
1048908 CCCAA--ATAAA
1 CCCAACCA-AAA
1048918 CCTCAACCTAAAA
1 CC-CAACC-AAAA
* *
1048931 CCCAACCATAT
1 CCCAACCAAAA
* **
1048942 CCCAAACAAGC
1 CCCAACCAAAA
1048953 CCCAACCAAAA
1 CCCAACCAAAA
1048964 CCCAACCTAAATA
1 CCCAACC-AAA-A
*
1048977 CCCAAAACAAAA
1 CCC-AACCAAAA
1048989 CCCA
1 CCCA
1048993 GACCCGGAGC
Statistics
Matches: 75, Mismatches: 13, Indels: 17
0.71 0.12 0.16
Matches are distributed among these distances:
9 1 0.01
10 4 0.05
11 35 0.47
12 19 0.25
13 12 0.16
14 4 0.05
ACGTcount: A:0.48, C:0.42, G:0.02, T:0.08
Consensus pattern (11 bp):
CCCAACCAAAA
Found at i:1049005 original size:25 final size:24
Alignment explanation
Indices: 1048977--1049031 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
1048967 AACCTAAATA
1048977 CCCAAAACAAAACCCAGACCCGGAG
1 CCCAAAACAAAACCCA-ACCCGGAG
* * *
1049002 CCCAAACCAAGACTCAACCCGGAG
1 CCCAAAACAAAACCCAACCCGGAG
1049026 CCCAAA
1 CCCAAA
1049032 CTAAACTCGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 14 0.52
25 13 0.48
ACGTcount: A:0.42, C:0.42, G:0.15, T:0.02
Consensus pattern (24 bp):
CCCAAAACAAAACCCAACCCGGAG
Found at i:1051662 original size:18 final size:19
Alignment explanation
Indices: 1051641--1051684 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
1051631 TATTTTGATA
1051641 AAAAT-AAAATGTTTTATT
1 AAAATCAAAATGTTTTATT
***
1051659 AAAATCACCCTGTTTTATT
1 AAAATCAAAATGTTTTATT
1051678 AAAATCA
1 AAAATCA
1051685 CCCAGTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.45, C:0.11, G:0.05, T:0.39
Consensus pattern (19 bp):
AAAATCAAAATGTTTTATT
Found at i:1051672 original size:19 final size:19
Alignment explanation
Indices: 1051650--1051693 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
1051640 AAAAATAAAA
1051650 TGTTTTATTAAAATCACCC
1 TGTTTTATTAAAATCACCC
1051669 TGTTTTATTAAAATCACCC
1 TGTTTTATTAAAATCACCC
*
1051688 AGTTTT
1 TGTTTT
1051694 TATGGTGTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.30, C:0.18, G:0.07, T:0.45
Consensus pattern (19 bp):
TGTTTTATTAAAATCACCC
Found at i:1054682 original size:25 final size:26
Alignment explanation
Indices: 1054654--1054710 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
1054644 CTTTAAAAAA
* *
1054654 TTAAAA-TTAAAAAGTATTTAATATT
1 TTAAAATTTAAAAAATATTAAATATT
1054679 TTAAAATTTAAAAAATATTAAATATT
1 TTAAAATTTAAAAAATATTAAATATT
*
1054705 TAAAAA
1 TTAAAA
1054711 CAATAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 6 0.21
26 22 0.79
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (26 bp):
TTAAAATTTAAAAAATATTAAATATT
Found at i:1068980 original size:2 final size:2
Alignment explanation
Indices: 1068938--1068963 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1068928 CACTGAGCGC
1068938 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
1068964 CTACATTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1069926 original size:93 final size:93
Alignment explanation
Indices: 1069663--1069948 Score: 299
Period size: 93 Copynumber: 3.0 Consensus size: 93
1069653 AGAAAGAGAA
* * * * * *
1069663 AAAGGCTGGGAAATCCAAGAACAATGAGAAA-CAAAAAGAAGGCGAGCAAGCTGTAGATGATCAT
1 AAAGCCTGGGAGATCGAAGAACAATGAGAAACCAAAAA-AAGGCGAACAAGCTG--GA-CATGAT
* * * * *
1069727 TATCATGAACCAAATAAGGATACGGCAGCCGA
62 TGTCATGAACCAAAAAAGGATAAGGCAGCAGT
* * * *
1069759 AAAGCCTGGGAGATCGAAGAACAATGACAAGCCAAAAGAAA-GCGAACAAGCTGAACATG-CTGA
1 AAAGCCTGGGAGATCGAAGAACAATGAGAAACCAAAA-AAAGGCGAACAAGCTGGACATGATTG-
* * *
1069822 CCATGAACCAAAGAAGGATAAGGCAGCTGT
64 TCATGAACCAAAAAAGGATAAGGCAGCAGT
*
1069852 AAAGCCTGGGAGATTGAAGAACAATGAGAAACCAAAAAAAGGCGAACAAGCTGGACATGATTGTC
1 AAAGCCTGGGAGATCGAAGAACAATGAGAAACCAAAAAAAGGCGAACAAGCTGGACATGATTGTC
* * *
1069917 GTGACCCAAAAAAGGATAAGACAGCAGT
66 ATGAACCAAAAAAGGATAAGGCAGCAGT
1069945 AAAG
1 AAAG
1069949 ACTGAAGTAG
Statistics
Matches: 158, Mismatches: 27, Indels: 13
0.80 0.14 0.07
Matches are distributed among these distances:
92 4 0.03
93 106 0.67
94 3 0.02
96 37 0.23
97 7 0.04
98 1 0.01
ACGTcount: A:0.45, C:0.17, G:0.26, T:0.12
Consensus pattern (93 bp):
AAAGCCTGGGAGATCGAAGAACAATGAGAAACCAAAAAAAGGCGAACAAGCTGGACATGATTGTC
ATGAACCAAAAAAGGATAAGGCAGCAGT
Found at i:1072885 original size:11 final size:11
Alignment explanation
Indices: 1072869--1072917 Score: 71
Period size: 11 Copynumber: 4.5 Consensus size: 11
1072859 AACTGATTCA
1072869 CTAACTAATTG
1 CTAACTAATTG
1072880 CTAACTAATTG
1 CTAACTAATTG
* *
1072891 CTAACTAACTA
1 CTAACTAATTG
1072902 CTAACTAATTG
1 CTAACTAATTG
*
1072913 TTAAC
1 CTAAC
1072918 AACTAACAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 33 1.00
ACGTcount: A:0.39, C:0.20, G:0.06, T:0.35
Consensus pattern (11 bp):
CTAACTAATTG
Found at i:1076260 original size:21 final size:21
Alignment explanation
Indices: 1076227--1076273 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
1076217 AGGAAATAGA
*
1076227 AGAAAAACAAAGAAAACAATAC
1 AGAAAAACAAAGAAAAAAAT-C
1076249 AGAAAAAC-AAGAAAAAAATC
1 AGAAAAACAAAGAAAAAAATC
1076269 AGAAA
1 AGAAA
1076274 GGTTGAGCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 6 0.25
21 10 0.42
22 8 0.33
ACGTcount: A:0.74, C:0.11, G:0.11, T:0.04
Consensus pattern (21 bp):
AGAAAAACAAAGAAAAAAATC
Found at i:1076423 original size:11 final size:11
Alignment explanation
Indices: 1076409--1076446 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
1076399 CAACTATTCA
1076409 CTAACTAATTG
1 CTAACTAATTG
*
1076420 CTAACTAACTG
1 CTAACTAATTG
1076431 CTAACTAATTG
1 CTAACTAATTG
*
1076442 TTAAC
1 CTAAC
1076447 AACTAACAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.37, C:0.21, G:0.08, T:0.34
Consensus pattern (11 bp):
CTAACTAATTG
Found at i:1076434 original size:22 final size:21
Alignment explanation
Indices: 1076409--1076450 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
1076399 CAACTATTCA
1076409 CTAACTAATTGCTAACTAACTG
1 CTAACTAATTGCTAAC-AACTG
*
1076431 CTAACTAATTGTTAACAACT
1 CTAACTAATTGCTAACAACT
1076451 AACAAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.38, C:0.21, G:0.07, T:0.33
Consensus pattern (21 bp):
CTAACTAATTGCTAACAACTG
Found at i:1087399 original size:100 final size:101
Alignment explanation
Indices: 1087214--1087402 Score: 249
Period size: 101 Copynumber: 1.9 Consensus size: 101
1087204 AACTCTAACC
* * * *
1087214 TTTTTACTAATTTGTTTAAATTATTATACAACCTTGTGGTTACCGGATCTGGGGTATGATCCGCA
1 TTTTTACTAATTTGTTTAAATTATTATACAACCTTGCGGTGACCGGATCTGGGGTACGATCCACA
*
1087279 TTATTCTGGTTCGGACTCTATTAAATCCAAACCTTT
66 TTATTCTGGTTCAGACTCTATTAAATCCAAACCTTT
* * * * *
1087315 TTTTTATTAATTTGTTTGATTTATTATACGACCTTGCGGTGACCTGATC-GGGGTACGA-CTCAC
1 TTTTTACTAATTTGTTTAAATTATTATACAACCTTGCGGTGACCGGATCTGGGGTACGATC-CAC
1087378 ATTATTAC-GGTTCAGACTCTATTAA
65 ATTATT-CTGGTTCAGACTCTATTAA
1087403 CAACCAACTT
Statistics
Matches: 76, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
99 1 0.01
100 32 0.42
101 43 0.57
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.41
Consensus pattern (101 bp):
TTTTTACTAATTTGTTTAAATTATTATACAACCTTGCGGTGACCGGATCTGGGGTACGATCCACA
TTATTCTGGTTCAGACTCTATTAAATCCAAACCTTT
Found at i:1089425 original size:29 final size:30
Alignment explanation
Indices: 1089388--1089444 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
1089378 TGACTAATCA
* * *
1089388 TTTCAACTAACTTGA-TTCTTTTTGTCTTG
1 TTTCAACTAAATTAATTTCCTTTTGTCTTG
*
1089417 TTTCTACTAAATTAATTTCCTTTTGTCT
1 TTTCAACTAAATTAATTTCCTTTTGTCT
1089445 GGTCTTGTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 12 0.52
30 11 0.48
ACGTcount: A:0.19, C:0.18, G:0.07, T:0.56
Consensus pattern (30 bp):
TTTCAACTAAATTAATTTCCTTTTGTCTTG
Found at i:1089930 original size:20 final size:21
Alignment explanation
Indices: 1089905--1089952 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
1089895 AATTCCTTTC
*
1089905 TTGCATTTA-CATTTTGTAT-T
1 TTGCATTTATCA-TTTGCATCT
1089925 TTGCA-TTATCATTTGCATCT
1 TTGCATTTATCATTTGCATCT
1089945 TTGCATTT
1 TTGCATTT
1089953 GCATGTACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 9 0.38
20 13 0.54
21 2 0.08
ACGTcount: A:0.19, C:0.15, G:0.10, T:0.56
Consensus pattern (21 bp):
TTGCATTTATCATTTGCATCT
Found at i:1089953 original size:14 final size:13
Alignment explanation
Indices: 1089905--1089956 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
1089895 AATTCCTTTC
*
1089905 TTGCATTTACATT
1 TTGCATTTGCATT
*
1089918 TTGTATTTTGCATT
1 TTGCA-TTTGCATT
*
1089932 AT-CATTTGCATCT
1 TTGCATTTGCAT-T
1089945 TTGCATTTGCAT
1 TTGCATTTGCAT
1089957 GTACATATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
12 7 0.23
13 7 0.23
14 17 0.55
ACGTcount: A:0.19, C:0.15, G:0.12, T:0.54
Consensus pattern (13 bp):
TTGCATTTGCATT
Found at i:1089971 original size:28 final size:28
Alignment explanation
Indices: 1089935--1090012 Score: 138
Period size: 28 Copynumber: 2.8 Consensus size: 28
1089925 TTGCATTATC
*
1089935 ATTTGCATCTTTGCATTTGCATGTACAT
1 ATTTGCATCTTTGCATTAGCATGTACAT
*
1089963 ATTTACATCTTTGCATTAGCATGTACAT
1 ATTTGCATCTTTGCATTAGCATGTACAT
1089991 ATTTGCATCTTTGCATTAGCAT
1 ATTTGCATCTTTGCATTAGCAT
1090013 CTATAAACAT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.24, C:0.18, G:0.13, T:0.45
Consensus pattern (28 bp):
ATTTGCATCTTTGCATTAGCATGTACAT
Found at i:1092612 original size:102 final size:102
Alignment explanation
Indices: 1092354--1092689 Score: 321
Period size: 102 Copynumber: 3.3 Consensus size: 102
1092344 TTGGGACAGT
* * *
1092354 TTTCCCTTGAAACGCAAATTTTGAAATTGTTTCACTTGAAACCAAAACTGATCTCACTTGAGATT
1 TTTCCCTTGAAACACAAATTTTGAAATTGTTTCACCTGAAACC-AAATTGATCTCACTTGAGATT
* *
1092419 -ATTTTTTTCGTAAAATCAATTTCATCTCGCTAGAGACAA
65 GA-TTTTCTCG-AAAACCAATTTCATCTCGCTAGAGACAA
** * *
1092458 TTTCCCTTGAAACACAAATTTTGAAATCATTTCACCCT-AAACAAAATGGATCTCACTTGAGATT
1 TTTCCCTTGAAACACAAATTTTGAAATTGTTTCA-CCTGAAACCAAATTGATCTCACTTGAGATT
* ** *
1092522 GATTTTCTC-AAAAGCCAATTTCGTCTTTCT-GAGGCAA
65 GATTTTCTCGAAAA-CCAATTTCATCTCGCTAGAGACAA
* * *
1092559 TTTCCCTTGAAACAAAAAATTTGGAATTTGTTTCACCTGAAACCAAATTGATCTCACTTGAGATT
1 TTTCCCTTGAAAC-ACAAATTTTGAAATTGTTTCACCTGAAACCAAATTGATCTCACTTGAGATT
* * * * *
1092624 G-TTTT-T-TAAATA--AATTTCGTCTTGCTTGAGACAG
65 GATTTTCTCGAAA-ACCAATTTCATCTCGCTAGAGACAA
** * *
1092658 TTTCCCTCAAAACGCAAATTTTTAAATTGTTT
1 TTTCCCTTGAAACACAAATTTTGAAATTGTTT
1092690 TACTCGAAAA
Statistics
Matches: 194, Mismatches: 30, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
98 27 0.14
99 16 0.08
100 4 0.02
101 31 0.16
102 53 0.27
103 25 0.13
104 36 0.19
105 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.37
Consensus pattern (102 bp):
TTTCCCTTGAAACACAAATTTTGAAATTGTTTCACCTGAAACCAAATTGATCTCACTTGAGATTG
ATTTTCTCGAAAACCAATTTCATCTCGCTAGAGACAA
Found at i:1093423 original size:139 final size:139
Alignment explanation
Indices: 1093155--1093828 Score: 807
Period size: 139 Copynumber: 4.8 Consensus size: 139
1093145 GGATAAACTA
* * * * * *
1093155 ATCAACATTTCCAATGGAAGAGTTCGTAATGAGAAGAACTC-GTCTGACGAGGGATAAGAAGTTT
1 ATCAACATTTTCAGTGG-AGAGTTCATAATGAGAAGAACTCATTC-GACGAGGGAGAAGAAGTTC
* * * *
1093219 ATAATAAAAAGAATTTGTTCAACCCTAGCTCGATTCATCACATATGGAGTTGAATCAGCGACACC
64 ATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCGACACC
1093284 TCACTCGAGGG
129 TCACTCGAGGG
* *
1093295 ATAAACATTTTCAGTGGAGAGTTCATAATGAGAAGAACTCATTCGACGAGGGAGAATAAGTTCAT
1 ATCAACATTTTCAGTGGAGAGTTCATAATGAGAAGAACTCATTCGACGAGGGAGAAGAAGTTCAT
* * * * *
1093360 AATGATAAGAACTTGTTCAACCCTAGCTCAATTCATCGCATATGGAGTTGAATCAGTGACACCTC
66 AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCGACACCTC
1093425 ACTCGAGGG
131 ACTCGAGGG
* * * **
1093434 ATCAATATTTCCAGTGGAGAGTTCATAATGAGAAGAAGTCATGT-GATTAGGGAGAAGAAGTTCA
1 ATCAACATTTTCAGTGGAGAGTTCATAATGAGAAGAACTCAT-TCGACGAGGGAGAAGAAGTTCA
* ** * * *
1093498 TAATGAGAAGTACTTGTTCAACCTTAGCTCGATTCATCGTATATGGAGTTAAATCAGTGACCCCT
65 TAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCGACACCT
1093563 CACTCGAGGG
130 CACTCGAGGG
* * * ** * *
1093573 ATCAACAATTT-AGTGGAGTGTTCATAAAGAGAAGAACTCACCCGACAAGGGAGAAGATGTTCAT
1 ATCAACATTTTCAGTGGAGAGTTCATAATGAGAAGAACTCATTCGACGAGGGAGAAGAAGTTCAT
* * * * *
1093637 AATGAGAAGAATTTGTTCAACCTTAGCTCGATCCATTACATACT-AAATTGAATCAGCGACACCT
66 AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATA-TGGAGTTGAATCAGCGACACCT
1093701 CACTCGAGGG
130 CACTCGAGGG
* * ** * * * * *
1093711 ATCAATATTTTCAATAAAGAGTTCATAATGAGACGAAATTATCCGATGAGGGAGAAGAAGTTCAT
1 ATCAACATTTTCAGTGGAGAGTTCATAATGAGAAGAACTCATTCGACGAGGGAGAAGAAGTTCAT
* * *
1093776 AATGAGAAGAACTTGTTCAACCTTAGCTTGTTTCCATCACATAAGGAGTTGAA
66 AATGAGAAGAACTTGTTCAACCTTAGCTCGATT-CATCACATATGGAGTTGAA
1093829 ACAACACCGA
Statistics
Matches: 455, Mismatches: 72, Indels: 14
0.84 0.13 0.03
Matches are distributed among these distances:
138 114 0.25
139 310 0.68
140 31 0.07
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.26
Consensus pattern (139 bp):
ATCAACATTTTCAGTGGAGAGTTCATAATGAGAAGAACTCATTCGACGAGGGAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCGACACCTC
ACTCGAGGG
Found at i:1093704 original size:277 final size:278
Alignment explanation
Indices: 1093155--1093825 Score: 860
Period size: 277 Copynumber: 2.4 Consensus size: 278
1093145 GGATAAACTA
* * * * * * *
1093155 ATCAACATTTCCAATGGAAGAGTTCGTAATGAGAAGAACTCGTCTGACGAGGGATAAGAAGTTTA
1 ATCAATATTTCCAATGG-AGAGTTCATAATGAGAAGAAATCATCTGATGAGGGAGAAGAAGTTCA
* * * * *
1093220 TAATAAAAAGAATTTGTTCAACCCTAGCTCGATTCATCACATATGGAGTTGAATCAGCGACACCT
65 TAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTAAATCAGCGACACCT
* * ** *
1093285 CACTCGAGGGATAAACATTTTCAGTGGAGAGTTCATAATGAGAAGAACTCATTCGACGAGGGAGA
130 CACTCGAGGGATAAACAATTTCAGTGGAGAGTTCATAAAGAGAAGAACTCACCCGACAAGGGAGA
* * * * * *
1093350 ATAAGTTCATAATGATAAGAACTTGTTCAACCCTAGCTCAATTCATCGCATATGGAGTTGAATCA
195 AGAAGTTCATAATGAGAAGAACTTGTTCAACCCTAGCTCAATCCATCACATATGAAATTGAATCA
*
1093415 GTGACACCTCACTCGAGGG
260 GCGACACCTCACTCGAGGG
* * * *
1093434 ATCAATATTTCCAGTGGAGAGTTCATAATGAGAAGAAGTCATGTGATTAGGGAGAAGAAGTTCAT
1 ATCAATATTTCCAATGGAGAGTTCATAATGAGAAGAAATCATCTGATGAGGGAGAAGAAGTTCAT
* ** * *
1093499 AATGAGAAGTACTTGTTCAACCTTAGCTCGATTCATCGTATATGGAGTTAAATCAGTGACCCCTC
66 AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTAAATCAGCGACACCTC
* *
1093564 ACTCGAGGGATCAACAATTT-AGTGGAGTGTTCATAAAGAGAAGAACTCACCCGACAAGGGAGAA
131 ACTCGAGGGATAAACAATTTCAGTGGAGAGTTCATAAAGAGAAGAACTCACCCGACAAGGGAGAA
* * * * *
1093628 GATGTTCATAATGAGAAGAATTTGTTCAACCTTAGCTCGATCCATTACATACT-AAATTGAATCA
196 GAAGTTCATAATGAGAAGAACTTGTTCAACCCTAGCTCAATCCATCACATA-TGAAATTGAATCA
1093692 GCGACACCTCACTCGAGGG
260 GCGACACCTCACTCGAGGG
* ** * * *
1093711 ATCAATATTTTCAATAAAGAGTTCATAATGAGACGAAATTATCCGATGAGGGAGAAGAAGTTCAT
1 ATCAATATTTCCAATGGAGAGTTCATAATGAGAAGAAATCATCTGATGAGGGAGAAGAAGTTCAT
* * *
1093776 AATGAGAAGAACTTGTTCAACCTTAGCTTGTTTCCATCACATAAGGAGTT
66 AATGAGAAGAACTTGTTCAACCTTAGCTCGATT-CATCACATATGGAGTT
1093826 GAAACAACAC
Statistics
Matches: 335, Mismatches: 55, Indels: 5
0.85 0.14 0.01
Matches are distributed among these distances:
277 193 0.58
278 127 0.38
279 15 0.04
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.26
Consensus pattern (278 bp):
ATCAATATTTCCAATGGAGAGTTCATAATGAGAAGAAATCATCTGATGAGGGAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTAAATCAGCGACACCTC
ACTCGAGGGATAAACAATTTCAGTGGAGAGTTCATAAAGAGAAGAACTCACCCGACAAGGGAGAA
GAAGTTCATAATGAGAAGAACTTGTTCAACCCTAGCTCAATCCATCACATATGAAATTGAATCAG
CGACACCTCACTCGAGGG
Found at i:1104776 original size:90 final size:89
Alignment explanation
Indices: 1104613--1104778 Score: 287
Period size: 90 Copynumber: 1.9 Consensus size: 89
1104603 CCCAACATAC
1104613 CCTTTTATAGCCAAGTTACCCTAACCATATTAGGGTTTTATTATTTCAAATTAATCAAATCTATA
1 CCTTTTATAGCCAAGTTACCCTAACCATATTAGGGTTTTATTATTTCAAATTAATCAAATCTATA
1104678 TTTAATTAATTGGAATTTAATAAT
66 TTTAATTAATTGGAATTTAATAAT
* * * *
1104702 CCTTTTATATCCAAGTTACCCTAATCATATTAGGGATTTTTTTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAACCATATTAGGG-TTTTATTATTTCAAATTAATCAAATCTAT
1104767 ATTTAATTAATT
65 ATTTAATTAATT
1104779 TAAATTAAAT
Statistics
Matches: 72, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
89 33 0.46
90 39 0.54
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.45
Consensus pattern (89 bp):
CCTTTTATAGCCAAGTTACCCTAACCATATTAGGGTTTTATTATTTCAAATTAATCAAATCTATA
TTTAATTAATTGGAATTTAATAAT
Found at i:1113504 original size:36 final size:36
Alignment explanation
Indices: 1113457--1113526 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
1113447 TAAAAAAGAA
* *
1113457 AGGTTGTTGGTTGTTTTCATAATCTTGAGGGCTTGC
1 AGGTTGTTGGTTGTTGTCAGAATCTTGAGGGCTTGC
1113493 AGGTTGTTGGTTGTTGTCAGAATCTTGAGGGCTT
1 AGGTTGTTGGTTGTTGTCAGAATCTTGAGGGCTT
1113527 TCTTGTACGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.14, C:0.10, G:0.33, T:0.43
Consensus pattern (36 bp):
AGGTTGTTGGTTGTTGTCAGAATCTTGAGGGCTTGC
Found at i:1120325 original size:21 final size:21
Alignment explanation
Indices: 1120283--1120321 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1120273 AATCAGGTTC
*
1120283 TTTGTTGAATCCATGAAATCT
1 TTTGTTGAAGCCATGAAATCT
*
1120304 TTTGTTGAGGCCAT-AAAT
1 TTTGTTGAAGCCATGAAAT
1120322 TCTTGCAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.41
Consensus pattern (21 bp):
TTTGTTGAAGCCATGAAATCT
Found at i:1124732 original size:81 final size:81
Alignment explanation
Indices: 1124597--1124759 Score: 236
Period size: 81 Copynumber: 2.0 Consensus size: 81
1124587 CCAAGATTGG
* * * * **
1124597 TCGCCAAAGCTTGATGAGACACTGTGGGCTTACCGAACAACATTCAAAACGCCACTCGGAATGTC
1 TCGCCAAAACTTGATAAGACACTGTAGGCCTACCGAACAACATTCAAAACGCCACTCAAAATGTC
1124662 CCCATTCAAGATAGTC
66 CCCATTCAAGATAGTC
* *
1124678 TCGCCAAAACTTGATAAGACACTGTAGGCCTACTGACCAACATTCAAAACGCCACTCAAAATGTC
1 TCGCCAAAACTTGATAAGACACTGTAGGCCTACCGAACAACATTCAAAACGCCACTCAAAATGTC
* *
1124743 CCTATTCAAGCTAGTC
66 CCCATTCAAGATAGTC
1124759 T
1 T
1124760 ATGGCAAGGC
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 72 1.00
ACGTcount: A:0.33, C:0.29, G:0.17, T:0.22
Consensus pattern (81 bp):
TCGCCAAAACTTGATAAGACACTGTAGGCCTACCGAACAACATTCAAAACGCCACTCAAAATGTC
CCCATTCAAGATAGTC
Found at i:1131778 original size:27 final size:28
Alignment explanation
Indices: 1131711--1131778 Score: 70
Period size: 27 Copynumber: 2.5 Consensus size: 28
1131701 GATTTAATAA
* *
1131711 AATAAAATAGAAAATGATAAATAAATGGG
1 AATAAAATA-AAAATAATAAATAAATAGG
*
1131740 AA-AATAAT-AAAATAATAAAT-AATAGT
1 AATAA-AATAAAAATAATAAATAAATAGG
1131766 AATAAAATAAAAA
1 AATAAAATAAAAA
1131779 AGGGTTTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
26 9 0.27
27 17 0.52
28 2 0.06
29 5 0.15
ACGTcount: A:0.69, C:0.00, G:0.09, T:0.22
Consensus pattern (28 bp):
AATAAAATAAAAATAATAAATAAATAGG
Found at i:1132434 original size:70 final size:73
Alignment explanation
Indices: 1132354--1132557 Score: 233
Period size: 70 Copynumber: 2.8 Consensus size: 73
1132344 TAAAACATCT
* *
1132354 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCAAAAAAAAATATTTAAA-AT
1 TAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCAAAAAAAAATA-TAAAATAT
1132417 AAAA-T-TA-
64 AAAAGTATAC
* * *
1132424 TAAATCCTAATTAAAATACTAAAACCTATATAAACTAAAATACCTAAAACAAATATAAAATATAA
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCAAAAAAAAATATAAAATATAA
1132489 AAGTAATATCC
66 AAGT-ATA--C
* *
1132500 TAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATA--AAAAGATAAAATATAA
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCAAAA-A-AAAATATAA
1132558 TGTTTAAAAT
Statistics
Matches: 114, Mismatches: 10, Indels: 14
0.83 0.07 0.10
Matches are distributed among these distances:
69 9 0.08
70 51 0.45
71 1 0.01
73 2 0.02
74 3 0.03
75 1 0.01
76 47 0.41
ACGTcount: A:0.60, C:0.12, G:0.01, T:0.27
Consensus pattern (73 bp):
TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCAAAAAAAAATATAAAATATAA
AAGTATAC
Found at i:1132479 original size:25 final size:24
Alignment explanation
Indices: 1132435--1132482 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
1132425 AAATCCTAAT
**
1132435 TAAAATACTAAAACCTATATAAAC
1 TAAAATACTAAAACAAATATAAAC
1132459 TAAAATACCTAAAACAAATATAAA
1 TAAAATA-CTAAAACAAATATAAA
1132483 ATATAAAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.23
Consensus pattern (24 bp):
TAAAATACTAAAACAAATATAAAC
Found at i:1132502 original size:32 final size:32
Alignment explanation
Indices: 1132462--1132523 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
1132452 TATAAACTAA
1132462 AATACCTAAAAC-AAATATAAAATA-TAAAAGT
1 AATACCTAAAACTAAAT-TAAAATACTAAAAGT
*
1132493 AATATCCTAAAACTTAATTAAAATACTAAAA
1 AATA-CCTAAAACTAAATTAAAATACTAAAA
1132524 CCTATTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 4 0.15
32 15 0.56
33 8 0.30
ACGTcount: A:0.61, C:0.11, G:0.02, T:0.26
Consensus pattern (32 bp):
AATACCTAAAACTAAATTAAAATACTAAAAGT
Found at i:1132566 original size:76 final size:72
Alignment explanation
Indices: 1132354--1132578 Score: 224
Period size: 76 Copynumber: 3.1 Consensus size: 72
1132344 TAAAACATCT
* * *
1132354 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCAAAAAAAA-AT-ATTTAAAA
1 TAAAACCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACAAAAAAAAATATAATTTAAAA
* **
1132416 TAAAATTA
65 TAATATCC
* * * * *
1132424 TAAATCCTAATTAAAATACTAAAACCTATATAAACTAAAATACCTAAAACAAATATAAAATATAA
1 TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATA-C-AAAA-AAAAATATAATTTAA
1132489 AAGTAATATCC
63 AA-TAATATCC
*
1132500 TAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATA-AAAAGATAAAATATAATGTTTA
1 TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAA-A-AAAATATAA--TTTA
*
1132564 AAATATTATCC
62 AAATAATATCC
1132575 TAAA
1 TAAA
1132579 CTTGAGTTTA
Statistics
Matches: 128, Mismatches: 17, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
69 5 0.04
70 34 0.27
71 1 0.01
72 3 0.02
73 9 0.07
74 8 0.06
75 18 0.14
76 50 0.39
ACGTcount: A:0.58, C:0.12, G:0.01, T:0.29
Consensus pattern (72 bp):
TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAAAAAAATATAATTTAAAAT
AATATCC
Found at i:1133431 original size:25 final size:25
Alignment explanation
Indices: 1133367--1133467 Score: 125
Period size: 25 Copynumber: 4.0 Consensus size: 25
1133357 AATGGTCTGT
* *
1133367 TTTTTTCTGCTGTTTGAAACAATGAACA
1 TTTTTTCTACTGTTCGAAACAATG---A
*
1133395 TTTTTTGT--TGTTCGAAACAATGA
1 TTTTTTCTACTGTTCGAAACAATGA
1133418 TTTTTTCTACTGTTCGAAACAATGA
1 TTTTTTCTACTGTTCGAAACAATGA
*
1133443 TTTTTTCTACTGTTCAAAACAATGA
1 TTTTTTCTACTGTTCGAAACAATGA
1133468 ACAGTTTTTT
Statistics
Matches: 67, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
23 8 0.12
25 39 0.58
26 13 0.19
28 7 0.10
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.45
Consensus pattern (25 bp):
TTTTTTCTACTGTTCGAAACAATGA
Found at i:1137367 original size:17 final size:18
Alignment explanation
Indices: 1137329--1137372 Score: 72
Period size: 17 Copynumber: 2.5 Consensus size: 18
1137319 GTTGTTTTTT
1137329 TTAAATAAAAGATAAGAA
1 TTAAATAAAAGATAAGAA
*
1137347 TTAAATAAAAGA-AATAA
1 TTAAATAAAAGATAAGAA
1137364 TTAAATAAA
1 TTAAATAAA
1137373 TAATTGAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (18 bp):
TTAAATAAAAGATAAGAA
Found at i:1138029 original size:70 final size:74
Alignment explanation
Indices: 1137952--1138141 Score: 246
Period size: 77 Copynumber: 2.6 Consensus size: 74
1137942 TAAAACATCT
* * *
1137952 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCT-A-AAA-ATAATAT-TTAA
1 TAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAACAAAGATAAAATATAAA
*
1138012 AATAATATTA
65 AATAATATCA
1138022 TAAATCCTAATTAAAATACTAAAACCTATTTAAAACTAAAATACCTAAAACAAAGATAAAATATA
1 TAAATCCTAATTAAAATACTAAAACCTATTT-AAACTAAAATACCT--AACAAAGATAAAATATA
*
1138087 AAAATAATATCC
63 AAAATAATATCA
* *
1138099 TAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATAC
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATAC
1138142 AAAGATAAAA
Statistics
Matches: 105, Mismatches: 7, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
69 5 0.05
70 24 0.23
71 14 0.13
74 1 0.01
75 3 0.03
76 18 0.17
77 40 0.38
ACGTcount: A:0.57, C:0.13, G:0.01, T:0.29
Consensus pattern (74 bp):
TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAACAAAGATAAAATATAAAA
ATAATATCA
Found at i:1138629 original size:30 final size:30
Alignment explanation
Indices: 1138595--1138665 Score: 106
Period size: 30 Copynumber: 2.4 Consensus size: 30
1138585 AGCACCAAAC
*
1138595 AGTACAAGGACTTGGCAACCCATGTTAAAT
1 AGTACAAGGACATGGCAACCCATGTTAAAT
**
1138625 AGTACAAGGACATGGCCTCCCATGTTAAAT
1 AGTACAAGGACATGGCAACCCATGTTAAAT
*
1138655 AGTACATGGAC
1 AGTACAAGGAC
1138666 CAAGGTCATC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (30 bp):
AGTACAAGGACATGGCAACCCATGTTAAAT
Found at i:1142506 original size:20 final size:19
Alignment explanation
Indices: 1142478--1142524 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
1142468 TCTAAAACCT
* *
1142478 TTTTCAAATTTCATTTTGA
1 TTTTCAAAATCCATTTTGA
*
1142497 TTTTCAAAATCCATTTTTA
1 TTTTCAAAATCCATTTTGA
*
1142516 CTTTCAAAA
1 TTTTCAAAA
1142525 GAAAATTGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.32, C:0.15, G:0.02, T:0.51
Consensus pattern (19 bp):
TTTTCAAAATCCATTTTGA
Found at i:1145337 original size:2 final size:2
Alignment explanation
Indices: 1145295--1145326 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1145285 ACACACACAC
1145295 AT 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 AT
1145327 GTAAAATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1147679 original size:20 final size:20
Alignment explanation
Indices: 1147654--1147700 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
1147644 ATCAATATTG
1147654 AACCCTTTAATATCGATACC
1 AACCCTTTAATATCGATACC
**
1147674 AACCCTTTTGTATCGATACC
1 AACCCTTTAATATCGATACC
*
1147694 CACCCTT
1 AACCCTT
1147701 GGTGTTGATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.28, C:0.34, G:0.06, T:0.32
Consensus pattern (20 bp):
AACCCTTTAATATCGATACC
Found at i:1148409 original size:21 final size:21
Alignment explanation
Indices: 1148383--1148437 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
1148373 CAAGCCTTTT
** *
1148383 GTATGGATACCAGTTCATCTG
1 GTATGGATACCAACTCATCAG
1148404 GTATGGATACCAACTCATCAG
1 GTATGGATACCAACTCATCAG
1148425 GTATGGATACCAA
1 GTATGGATACCAA
1148438 TCCATATGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (21 bp):
GTATGGATACCAACTCATCAG
Found at i:1148448 original size:21 final size:20
Alignment explanation
Indices: 1148383--1148475 Score: 73
Period size: 21 Copynumber: 4.5 Consensus size: 20
1148373 CAAGCCTTTT
** *
1148383 GTATGGATACCAGTTCATCTG
1 GTATGGATACCA-ACCATATG
1148404 GTATGGATACCAACTCATCA-G
1 GTATGGATACCAAC-CAT-ATG
1148425 GTATGGATACCAATCCATATG
1 GTATGGATACCAA-CCATATG
* *
1148446 GTATCGG-TACCAACCCTTTG
1 GTAT-GGATACCAACCATATG
*
1148466 GTATCGATAC
1 GTATGGATAC
1148476 AAGCCTCTAG
Statistics
Matches: 60, Mismatches: 6, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
19 1 0.02
20 13 0.22
21 43 0.72
22 3 0.05
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (20 bp):
GTATGGATACCAACCATATG
Found at i:1149673 original size:15 final size:15
Alignment explanation
Indices: 1149653--1149686 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
1149643 AATCACTGAA
1149653 ATAACACTAATAATT
1 ATAACACTAATAATT
1149668 ATAACACTAATAATT
1 ATAACACTAATAATT
1149683 ATAA
1 ATAA
1149687 TTTAATATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (15 bp):
ATAACACTAATAATT
Found at i:1151426 original size:18 final size:17
Alignment explanation
Indices: 1151387--1151428 Score: 52
Period size: 15 Copynumber: 2.5 Consensus size: 17
1151377 TTCAAATTAC
*
1151387 ATAATTGAAAAAAAAAT
1 ATAATTAAAAAAAAAAT
1151404 -T-ATTAAAAATAAAAAT
1 ATAATTAAAAA-AAAAAT
1151420 ATAATTAAA
1 ATAATTAAA
1151429 TTTCAAATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
15 7 0.33
16 7 0.33
17 1 0.05
18 6 0.29
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (17 bp):
ATAATTAAAAAAAAAAT
Found at i:1151514 original size:39 final size:39
Alignment explanation
Indices: 1151468--1151578 Score: 120
Period size: 39 Copynumber: 2.8 Consensus size: 39
1151458 TTTTAAAAAT
1151468 AATTTAGAATGTTAATGTAAAATAATTTAAGAAATTAAG
1 AATTTAGAATGTTAATGTAAAATAATTTAAGAAATTAAG
* *
1151507 AATTTAGAATGTT-ATGGTAGTAAA-ATTTTAA-AAATTAGG
1 AATTTAGAATGTTAAT-GTA--AAATAATTTAAGAAATTAAG
* * * *
1151546 AATTTTGAATGTTAAAGTGAAATAATTTGAGAA
1 AATTTAGAATGTTAATGTAAAATAATTTAAGAA
1151579 TTATAAATAA
Statistics
Matches: 59, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
37 3 0.05
38 7 0.12
39 39 0.66
40 7 0.12
41 3 0.05
ACGTcount: A:0.47, C:0.00, G:0.16, T:0.37
Consensus pattern (39 bp):
AATTTAGAATGTTAATGTAAAATAATTTAAGAAATTAAG
Found at i:1151624 original size:2 final size:2
Alignment explanation
Indices: 1151619--1151643 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1151609 ATAAAAAATA
1151619 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1151644 ATAAACCTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1152977 original size:28 final size:28
Alignment explanation
Indices: 1152918--1152978 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 28
1152908 CTTAAAGTTT
** *
1152918 TTTTTAATCAAAATATGTACTTAAAATA
1 TTTTTAATCAAAATAAATACATAAAATA
* * *
1152946 TTTTTACTCAAAATAAATACATACAATG
1 TTTTTAATCAAAATAAATACATAAAATA
1152974 TTTTT
1 TTTTT
1152979 CTCCATCTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.44
Consensus pattern (28 bp):
TTTTTAATCAAAATAAATACATAAAATA
Found at i:1158405 original size:64 final size:62
Alignment explanation
Indices: 1158325--1158487 Score: 204
Period size: 64 Copynumber: 2.5 Consensus size: 62
1158315 CGGTGCACTA
*
1158325 AGAGTGCGTCGATGCATGAAGTGCATTCGATGTTTGAA-AAAT-AGCCTAGTGCATCGATGCATG
1 AGAGTGCATCGATGCATGAA-TGCATTCGATGTTTGAATAAATCAG---AGTGCATCGATGCATG
1158388 G
62 G
** * *
1158389 ATTGTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAAATCAGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCAT-GAATGCATTCGATGTTTGAA-TAAATCAGAGTGCATCGATGCATGG
1158453 AGAGTGCATCGATGCATAGAATGCATTCGATGTTT
1 AGAGTGCATCGATGCAT-GAATGCATTCGATGTTT
1158488 CAATTTATTC
Statistics
Matches: 86, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
64 78 0.91
65 2 0.02
66 4 0.05
67 2 0.02
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (62 bp):
AGAGTGCATCGATGCATGAATGCATTCGATGTTTGAATAAATCAGAGTGCATCGATGCATGG
Found at i:1158522 original size:21 final size:21
Alignment explanation
Indices: 1158498--1158537 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1158488 CAATTTATTC
1158498 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
*
1158519 ATTGATGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
1158538 CCTTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.33
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGGT
Found at i:1161121 original size:21 final size:21
Alignment explanation
Indices: 1161073--1161149 Score: 102
Period size: 21 Copynumber: 3.6 Consensus size: 21
1161063 CATGGTCTTG
*
1161073 TGCATCGATGCA-CATTCAAGGCA
1 TGCATCGATGCATCATGC--GG-A
*
1161096 TGCATCGGTGCATCATGCGGA
1 TGCATCGATGCATCATGCGGA
1161117 TGCATCGATGCATCATGCGGA
1 TGCATCGATGCATCATGCGGA
1161138 TGCATCGATGCA
1 TGCATCGATGCA
1161150 CATTCAAAGG
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
21 33 0.66
22 2 0.04
23 11 0.22
24 4 0.08
ACGTcount: A:0.25, C:0.25, G:0.27, T:0.23
Consensus pattern (21 bp):
TGCATCGATGCATCATGCGGA
Found at i:1167006 original size:64 final size:62
Alignment explanation
Indices: 1166910--1167089 Score: 186
Period size: 64 Copynumber: 2.8 Consensus size: 62
1166900 TTGGACTCCT
* * *
1166910 AGTGCATCGGTGCACT-AAGAGTGCGTCGATGCATGAAGTGCATTCGATGTTTGAA-AAAT-AG
1 AGTGCATCGATGCA-TGGAGAGTGCATCGATGCATGAA-TGCATTCGATGTTTGAATAAATCAG
* ** * *
1166971 CCTGGTGCATCGATGCATGGATTGTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAAATC
1 ---AGTGCATCGATGCATGGAGAGTGCATCGATGCAT-GAATGCATTCGATGTTTGAA-TAAATC
1167036 AG
61 AG
*
1167038 AGTGCATCGATGCATGGAGAGTGCATCGGTGCATAGAATGCATTCGATGTTT
1 AGTGCATCGATGCATGGAGAGTGCATCGATGCAT-GAATGCATTCGATGTTT
1167090 CAATTTATTC
Statistics
Matches: 97, Mismatches: 14, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
63 1 0.01
64 88 0.91
65 2 0.02
66 4 0.04
67 2 0.02
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.29
Consensus pattern (62 bp):
AGTGCATCGATGCATGGAGAGTGCATCGATGCATGAATGCATTCGATGTTTGAATAAATCAG
Found at i:1167124 original size:21 final size:21
Alignment explanation
Indices: 1167100--1167139 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1167090 CAATTTATTC
1167100 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
*
1167121 ATTGATGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
1167140 CCTTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.33
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGGT
Found at i:1173655 original size:11 final size:13
Alignment explanation
Indices: 1173623--1173652 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1173613 TGGCCAAAGA
1173623 TGAAAAGGTATGT
1 TGAAAAGGTATGT
1173636 TGAAAAGGTATG-
1 TGAAAAGGTATGT
1173648 TGAAA
1 TGAAA
1173653 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:1176629 original size:96 final size:95
Alignment explanation
Indices: 1176465--1176683 Score: 366
Period size: 96 Copynumber: 2.3 Consensus size: 95
1176455 GCAAAGTATA
*
1176465 AAACTCCATGGAAGAGTAGTAGAAGCAAATTCAAATTTGAATCTGATATTCACGGAAGAGCAGTG
1 AAACTCCACGGAAGAGTAGT-GAAGCAAATTCAAATTTGAATCTGATATTCACGGAAGAGCAGTG
*
1176530 AAATTAGATTCTTGTCAAGTCAATCATTTTC
65 AAATTAGATTCTTGTCAAATCAATCATTTTC
* *
1176561 AAACTCCACGGAAGAGTAGTGGAAGCAAATTCAACTTTGAATCTGATATTCACGGAAGAGTAGTG
1 AAACTCCACGGAAGAGTAGT-GAAGCAAATTCAAATTTGAATCTGATATTCACGGAAGAGCAGTG
1176626 AAATTAGATTCTTGTCAAATCAATCATTTTC
65 AAATTAGATTCTTGTCAAATCAATCATTTTC
* *
1176657 AAACTTCACGGAATAGTAGTGAAGCAA
1 AAACTCCACGGAAGAGTAGTGAAGCAA
1176684 GAGCAGAAGT
Statistics
Matches: 116, Mismatches: 7, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
95 7 0.06
96 109 0.94
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (95 bp):
AAACTCCACGGAAGAGTAGTGAAGCAAATTCAAATTTGAATCTGATATTCACGGAAGAGCAGTGA
AATTAGATTCTTGTCAAATCAATCATTTTC
Found at i:1177294 original size:21 final size:21
Alignment explanation
Indices: 1177268--1177310 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1177258 TTACAAAGTG
*
1177268 AGGCACATAGGCCCAATTACA
1 AGGCACACAGGCCCAATTACA
* *
1177289 AGGCACACATGCCCGATTACA
1 AGGCACACAGGCCCAATTACA
1177310 A
1 A
1177311 ACCTGAGCCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.30, G:0.19, T:0.14
Consensus pattern (21 bp):
AGGCACACAGGCCCAATTACA
Found at i:1181732 original size:32 final size:32
Alignment explanation
Indices: 1181691--1181754 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
1181681 TCGAGAGAAG
1181691 ATGGTCTTAAAAGGTGAAGGAAAACTAGAGGA
1 ATGGTCTTAAAAGGTGAAGGAAAACTAGAGGA
*
1181723 ATGGTCTTAAAAGGTGAAGGAACACTAGAGGA
1 ATGGTCTTAAAAGGTGAAGGAAAACTAGAGGA
1181755 GGAACCAGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.42, C:0.08, G:0.31, T:0.19
Consensus pattern (32 bp):
ATGGTCTTAAAAGGTGAAGGAAAACTAGAGGA
Found at i:1185349 original size:23 final size:23
Alignment explanation
Indices: 1185323--1185370 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
1185313 ATAAAGTACA
*
1185323 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
** *
1185346 ATAATGTAATAGGTAGTGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
1185369 AT
1 AT
1185371 TTACCTAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:1185826 original size:23 final size:23
Alignment explanation
Indices: 1185800--1185858 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
1185790 AACCACTACC
1185800 TATTACATTATATAAACGATACA
1 TATTACATTATATAAACGATACA
* * *
1185823 TATTACATTATATAAGCGCTACC
1 TATTACATTATATAAACGATACA
*
1185846 TATTACATCATAT
1 TATTACATTATAT
1185859 TTTTACCTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.37
Consensus pattern (23 bp):
TATTACATTATATAAACGATACA
Found at i:1186220 original size:434 final size:434
Alignment explanation
Indices: 1185437--1186504 Score: 2038
Period size: 434 Copynumber: 2.5 Consensus size: 434
1185427 TATTACATTA
*
1185437 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACCTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
*
1185502 TTATGTTTCAA-TTTTTTGAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
66 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
1185566 ATTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
131 ATTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
*
1185631 A-TA-A-T-AATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAA
196 ACAACATTAAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAA
1185692 AATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCAACAGTGAAAAAAGTATGGAC
261 AATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCAACAGTGAAAAAAGTATGGAC
1185757 ACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATAC
326 ACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATAC
1185822 ATATTACATTATATAAGCGCTACCTATTACATCATATTTTTACC
391 ATATTACATTATATAAGCGCTACCTATTACATCATATTTTTACC
1185866 TATTATATTGAAAGTGTCCATACCTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACCTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
*
1185931 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTT
66 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
*
1185996 ATTTGCACAAAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
131 ATTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
1186061 ACAACATTAAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAA
196 ACAACATTAAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAA
*
1186126 AATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGAC
261 AATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCAACAGTGAAAAAAGTATGGAC
1186191 ACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATAC
326 ACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATAC
*
1186256 CTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACC
391 ATATTACATTATATAAGCGCTACCTATTACATCATATTTTTACC
1186300 TATTATATTGAAAGTGTCCATACCTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACCTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1186365 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
66 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
1186430 ATTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
131 ATTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
1186495 ACAACATTAA
196 ACAACATTAA
1186505 CCAAAGATAA
Statistics
Matches: 625, Mismatches: 9, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
429 75 0.12
430 116 0.19
431 1 0.00
432 1 0.00
433 1 0.00
434 431 0.69
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (434 bp):
TATTATATTGAAAGTGTCCATACCTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
ATTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
ACAACATTAAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAA
AATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCAACAGTGAAAAAAGTATGGAC
ACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATAC
ATATTACATTATATAAGCGCTACCTATTACATCATATTTTTACC
Found at i:1186256 original size:23 final size:23
Alignment explanation
Indices: 1186230--1186292 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
1186220 ATATAACCAC
1186230 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
1186253 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
1186276 TACCTATTACATCATAT
1 TACCTATTACATTATAT
1186293 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:1186769 original size:39 final size:39
Alignment explanation
Indices: 1186715--1186800 Score: 145
Period size: 39 Copynumber: 2.2 Consensus size: 39
1186705 CAAGTTGTAG
*
1186715 ATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTGA
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
* *
1186754 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTGG
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
1186793 ATTTTGAT
1 ATTTTGAT
1186801 GAGCATCGGA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.19, C:0.14, G:0.19, T:0.49
Consensus pattern (39 bp):
ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
Found at i:1187080 original size:18 final size:18
Alignment explanation
Indices: 1187057--1187093 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1187047 CGAAATATAT
1187057 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
1187075 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
1187093 A
1 A
1187094 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:1190995 original size:33 final size:33
Alignment explanation
Indices: 1190958--1191023 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1190948 CATCTTAATA
* *
1190958 TCACCCCTTAACACCCCAACTTCTTTCAGCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
1190991 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
1191024 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.23, C:0.47, G:0.02, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:1191097 original size:21 final size:21
Alignment explanation
Indices: 1191057--1191121 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
1191047 CCCCTTATGC
* *
1191057 CTCTCGAGTGTATCTTCGACT
1 CTCTCGAGTTTCTCTTCGACT
*
1191078 CTCTCGAGTTTCTCTACGACT
1 CTCTCGAGTTTCTCTTCGACT
* *
1191099 -TGATCAAGTTTCTCTTCGACT
1 CT-CTCGAGTTTCTCTTCGACT
1191120 CT
1 CT
1191122 TGATTGTCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.15, C:0.29, G:0.15, T:0.40
Consensus pattern (21 bp):
CTCTCGAGTTTCTCTTCGACT
Found at i:1193369 original size:17 final size:18
Alignment explanation
Indices: 1193347--1193389 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
1193337 ATATATCCGG
1193347 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
1193364 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
1193384 TATCAT
1 TATCAT
1193390 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:1193407 original size:20 final size:19
Alignment explanation
Indices: 1193352--1193398 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
1193342 TCCGGTATCA
1193352 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
1193371 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
1193392 TTTTACC
1 TTTTACC
1193399 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:1193546 original size:20 final size:20
Alignment explanation
Indices: 1193520--1193565 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
1193510 CACTTTTAAA
1193520 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
1193539 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
1193560 TTTACC
1 TTTACC
1193566 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:1195266 original size:13 final size:13
Alignment explanation
Indices: 1195243--1195308 Score: 55
Period size: 13 Copynumber: 4.9 Consensus size: 13
1195233 TTTAAAACTC
1195243 TAAAT-AAATAAA
1 TAAATAAAATAAA
1195255 TAAATAAAATAAAA
1 TAAATAAAAT-AAA
* *
1195269 TAATATAATATTATA
1 TAA-ATAA-AATAAA
*
1195284 TAAATAAAATATA
1 TAAATAAAATAAA
1195297 T-AATAAATATAA
1 TAAATAAA-ATAA
1195309 TGATAAAAAC
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
12 11 0.24
13 13 0.29
14 10 0.22
15 9 0.20
16 2 0.04
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TAAATAAAATAAA
Found at i:1195278 original size:18 final size:18
Alignment explanation
Indices: 1195248--1195308 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 18
1195238 AACTCTAAAT
*
1195248 AAAT-AAATAAATAAAATA
1 AAATAAAAT-AATATAATA
* *
1195266 AAATAATATAATATTATA
1 AAATAAAATAATATAATA
1195284 TAAATAAAAT-ATATAATA
1 -AAATAAAATAATATAATA
1195302 AATATAA
1 AA-ATAA
1195309 TGATAAAAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
17 2 0.06
18 22 0.63
19 11 0.31
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AAATAAAATAATATAATA
Found at i:1195302 original size:26 final size:27
Alignment explanation
Indices: 1195261--1195332 Score: 73
Period size: 26 Copynumber: 2.8 Consensus size: 27
1195251 TAAATAAATA
*
1195261 AAATAAAATA-AT-ATAATATTAT-AT
1 AAATAAAATATATAATAATATAATGAT
1195285 AAATAAAATATATAATAAATATAATGAT
1 AAATAAAATATATAAT-AATATAATGAT
* *
1195313 -AA-AAACTATATAATACTATA
1 AAATAAAATATATAATAATATA
1195333 TTTTCAAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
24 10 0.24
25 7 0.17
26 13 0.32
27 9 0.22
28 2 0.05
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.33
Consensus pattern (27 bp):
AAATAAAATATATAATAATATAATGAT
Found at i:1195314 original size:24 final size:23
Alignment explanation
Indices: 1195244--1195327 Score: 75
Period size: 24 Copynumber: 3.5 Consensus size: 23
1195234 TTAAAACTCT
*
1195244 AAATAAATAA-ATAA-ATAAAATA
1 AAATATATAATATAATAT-AAATA
*
1195266 AAATAATATAATATTATATAAATA
1 AAAT-ATATAATATAATATAAATA
1195290 AAATATATAATA-AATATAATGATAA
1 AAATATATAATATAATATAA--AT-A
1195315 AAACTATATAATA
1 AAA-TATATAATA
1195328 CTATATTTTC
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
22 10 0.19
23 13 0.25
24 14 0.27
25 6 0.12
26 9 0.17
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.31
Consensus pattern (23 bp):
AAATATATAATATAATATAAATA
Found at i:1195396 original size:25 final size:22
Alignment explanation
Indices: 1195342--1195402 Score: 77
Period size: 25 Copynumber: 2.6 Consensus size: 22
1195332 ATTTTCAAAA
1195342 ATATGTTTTCAAAACTTATATT
1 ATATGTTTTCAAAACTTATATT
* *
1195364 ATACGTTTTTAAAACTATATATATT
1 ATATGTTTTCAAAAC--T-TATATT
1195389 ATATGTTTTCAAAA
1 ATATGTTTTCAAAA
1195403 ATGTGTTTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 13 0.41
24 1 0.03
25 18 0.56
ACGTcount: A:0.39, C:0.08, G:0.05, T:0.48
Consensus pattern (22 bp):
ATATGTTTTCAAAACTTATATT
Found at i:1195399 original size:61 final size:61
Alignment explanation
Indices: 1195314--1195428 Score: 171
Period size: 61 Copynumber: 1.9 Consensus size: 61
1195304 TATAATGATA
*
1195314 AAAACTATATAATACTATATTTTCAAAAATATGTTTTCAAAACT-TATATTATACGTTTTT
1 AAAACTATATAATACTATATTTTCAAAAATATGTTTTCAAAACTATATAATATACGTTTTT
* *
1195374 AAAACTATATATATTA-TATGTTTTCAAAAATGTGTTTTCAAAACTATATAATATA
1 AAAACTATATA-A-TACTATATTTTCAAAAATATGTTTTCAAAACTATATAATATA
1195429 TATATATATA
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
60 11 0.22
61 28 0.57
62 10 0.20
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.43
Consensus pattern (61 bp):
AAAACTATATAATACTATATTTTCAAAAATATGTTTTCAAAACTATATAATATACGTTTTT
Found at i:1195517 original size:38 final size:37
Alignment explanation
Indices: 1195475--1195559 Score: 118
Period size: 38 Copynumber: 2.2 Consensus size: 37
1195465 TATATGTTTT
*
1195475 TTTCAAAAAGCGATTTT-TAGAAACTATATATTATATGC
1 TTTCAAAAA-CG-TTTTCTACAAACTATATATTATATGC
*
1195513 TTTCAAAGAACGTTTTCTACAAACTATATATTATATGT
1 TTTCAAA-AACGTTTTCTACAAACTATATATTATATGC
1195551 TTTCAAAAA
1 TTTCAAAAA
1195560 AAATATTTTC
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
37 6 0.14
38 35 0.81
39 2 0.05
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (37 bp):
TTTCAAAAACGTTTTCTACAAACTATATATTATATGC
Found at i:1208519 original size:34 final size:32
Alignment explanation
Indices: 1208464--1208527 Score: 92
Period size: 34 Copynumber: 1.9 Consensus size: 32
1208454 CCCCTTTTTC
* *
1208464 TTCTAACTTTATTTTAGTTTATTTTATATCTGA
1 TTCTAACTTTATCTTAATTTATTTTA-ATCTGA
1208497 TTCTCAACTTTATCTTAATTTATTTTAATCT
1 TTCT-AACTTTATCTTAATTTATTTTAATCT
1208528 TTTATTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 8 0.29
34 20 0.71
ACGTcount: A:0.25, C:0.12, G:0.03, T:0.59
Consensus pattern (32 bp):
TTCTAACTTTATCTTAATTTATTTTAATCTGA
Found at i:1208675 original size:19 final size:19
Alignment explanation
Indices: 1208651--1208713 Score: 62
Period size: 19 Copynumber: 3.3 Consensus size: 19
1208641 TAATTGAAAT
1208651 TAAAAACTATTGTCAATAA
1 TAAAAACTATTGTCAATAA
1208670 T-AAAA--ATTGT-AATTGAAA
1 TAAAAACTATTGTCAA-T--AA
1208688 TTAAAAACTATTGTCAATAA
1 -TAAAAACTATTGTCAATAA
1208708 TAAAAA
1 TAAAAA
1208714 TTGTGAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 16
0.69 0.00 0.31
Matches are distributed among these distances:
15 2 0.06
16 6 0.17
18 6 0.17
19 8 0.22
20 6 0.17
22 6 0.17
23 2 0.06
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.32
Consensus pattern (19 bp):
TAAAAACTATTGTCAATAA
Found at i:1208692 original size:38 final size:38
Alignment explanation
Indices: 1208641--1208717 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
1208631 TCTGATCATT
1208641 TAATTGAAATTAAAAACTATTGTCAATAATAAAAATTG
1 TAATTGAAATTAAAAACTATTGTCAATAATAAAAATTG
1208679 TAATTGAAATTAAAAACTATTGTCAATAATAAAAATTG
1 TAATTGAAATTAAAAACTATTGTCAATAATAAAAATTG
1208717 T
1 T
1208718 GAAAATTAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.52, C:0.05, G:0.08, T:0.35
Consensus pattern (38 bp):
TAATTGAAATTAAAAACTATTGTCAATAATAAAAATTG
Found at i:1208712 original size:18 final size:18
Alignment explanation
Indices: 1208653--1208712 Score: 54
Period size: 18 Copynumber: 3.2 Consensus size: 18
1208643 ATTGAAATTA
1208653 AAAACTATTGTCAATAAT
1 AAAACTATTGTCAATAAT
1208671 AAAA--ATTGT-AATTGAAATT
1 AAAACTATTGTCAA-T--AA-T
1208690 AAAAACTATTGTCAATAAT
1 -AAAACTATTGTCAATAAT
1208709 AAAA
1 AAAA
1208713 ATTGTGAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 16
0.68 0.00 0.32
Matches are distributed among these distances:
15 2 0.06
16 6 0.18
18 10 0.29
19 2 0.06
20 6 0.18
22 6 0.18
23 2 0.06
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.32
Consensus pattern (18 bp):
AAAACTATTGTCAATAAT
Found at i:1209695 original size:54 final size:54
Alignment explanation
Indices: 1209613--1209720 Score: 198
Period size: 54 Copynumber: 2.0 Consensus size: 54
1209603 GCCGGGAATG
*
1209613 TCATTCCCAGTAATCTTACATTACCAATAGTGGATTTTTTGGGGTATATTATGA
1 TCATTCCCAGTAATCTTACATTACCAATAGAGGATTTTTTGGGGTATATTATGA
*
1209667 TCATTCCCGGTAATCTTACATTACCAATAGAGGATTTTTTGGGGTATATTATGA
1 TCATTCCCAGTAATCTTACATTACCAATAGAGGATTTTTTGGGGTATATTATGA
1209721 GGAATGTCAT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.40
Consensus pattern (54 bp):
TCATTCCCAGTAATCTTACATTACCAATAGAGGATTTTTTGGGGTATATTATGA
Found at i:1210047 original size:38 final size:37
Alignment explanation
Indices: 1209955--1210047 Score: 98
Period size: 37 Copynumber: 2.4 Consensus size: 37
1209945 ACCCTTTCAT
*
1209955 TAAACTTTTTTATATTTTAAATTTTGTAAAAAAATAATA
1 TAAA-TTTTTT-TAATTTAAATTTTGTAAAAAAATAATA
* * * *
1209994 TAAATTTTATGAATTTAATTTTTTTAAAGAAAAT-ATA
1 TAAATTTTTTTAATTTAAATTTTGTAAA-AAAATAATA
1210031 TAAATATTTTTTAATTT
1 TAAAT-TTTTTTAATTT
1210048 GTTAAAAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
37 22 0.49
38 19 0.42
39 4 0.09
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (37 bp):
TAAATTTTTTTAATTTAAATTTTGTAAAAAAATAATA
Found at i:1211958 original size:17 final size:18
Alignment explanation
Indices: 1211930--1211963 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1211920 ATTTGACGTA
1211930 TTTATAAAAATATAATTT
1 TTTATAAAAATATAATTT
1211948 TTTAT-AAAATATAATT
1 TTTATAAAAATATAATT
1211964 ATATAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTATAAAAATATAATTT
Found at i:1211973 original size:17 final size:17
Alignment explanation
Indices: 1211935--1211977 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
1211925 ACGTATTTAT
* *
1211935 AAAAATATAATTTTTTA
1 AAAAATATAATTATATA
*
1211952 TAAAATATAATTATATA
1 AAAAATATAATTATATA
1211969 AAAAA-ATAA
1 AAAAATATAA
1211978 AATGAACCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
AAAAATATAATTATATA
Found at i:1214074 original size:16 final size:16
Alignment explanation
Indices: 1214053--1214084 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1214043 CGATACGCTA
1214053 GTTGATGTGCTAATGG
1 GTTGATGTGCTAATGG
1214069 GTTGATGTGCTAATGG
1 GTTGATGTGCTAATGG
1214085 TTGTCGGGGA
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:0.19, C:0.06, G:0.38, T:0.38
Consensus pattern (16 bp):
GTTGATGTGCTAATGG
Found at i:1215496 original size:417 final size:412
Alignment explanation
Indices: 1214694--1215517 Score: 1172
Period size: 417 Copynumber: 2.0 Consensus size: 412
1214684 TTATAATGAT
* * * *
1214694 AAAATATATTGTCACAAAGATTTTCCTTCATATTTTTTGCGTAAAAAAAGTTATATGGTGACAAA
1 AAAATATATTGTCACAAAGATTTTCCTTCATATTTTTTGCGCAAAAAAAGTCATATAGTAACAAA
*
1214759 TTTTATAACTATAAGTGTTAATAATTATTACAAAAAACATTGTCACAAAAATAATGATATTCACG
66 TTTTATAACTATAAGTGTTAATAATTATTACAAAAAACATTGTCACAAAAATAATGATATTCACA
* * *
1214824 TTTTTGTGACAAATTATATTTGTTGTTATAAATTTTAACTATAGTGATAGCATATATTGTCATAA
131 TTTTTGTGACAAATTATAGTTGTAGTTATAAATTTTAACTATAGTGATAGCATATATTATCATAA
* * * * * *
1214889 CTATTTTTCTTCATTTTTTTTTCAAAATTTATAATGACAATTTTTATAATTATAATTTATAGTTA
196 ATATTGTTATCCATTTTTTTTTCAAAAGTGATAATGACAATTTTTATAATTATAATTTATAGTTA
* * *
1214954 TTTTTATAGAAAAAATTATCACATCAAATAATAAAATTCAAGTTTTTTGTAATAAATTATTTTTG
261 TTGTTATAGAAAAAATTATCACATCAAATAATAAAATTAAAGTTTTTTGCAATAAATTATTTTTG
1215019 TACTTATATATTTAAATTATTATGAAAAATTATACTATCTAAATCATTTCTCCATATTTTTTAGT
326 TACTTATATATTTAAATTATTATGAAAAATTATACTATCTAAATCATTTCTCCATATTTTTTAGT
*
1215084 GTAAAAAATGTTATATATTAAC
391 GCAAAAAATGTTATATATTAAC
* * * *
1215106 AAAATATATTGTCATAAAGGTTTT-CTGTCATATTTTTTTGTGCCAAAAAAA-TCATATAGTAAT
1 AAAATATATTGTCACAAAGATTTTCCT-TCATA-TTTTTTGCG-CAAAAAAAGTCATATAGTAAC
* * * *
1215169 AATTTTTGTAACTATAAGTGTTTATAATTATTACAAAAAATATTGTCACAAAAAATAATGATATT
63 AAATTTTATAACTATAAGTGTTAATAATTATTACAAAAAACATTGTCAC-AAAAATAATGATATT
* *
1215234 CACATTTTTGTGATAAATTATAGTTGTAGTTATAAATTTTAATTATAGTGAT-GACATATATTAT
127 CACATTTTTGTGACAAATTATAGTTGTAGTTATAAATTTTAACTATAGTGATAG-CATATATTAT
* * *
1215298 GATAAATATTGTTATCCACTTTTTTGTTTCAAAAAGTGATATTGATAAGTTTTT-TAATTATAAT
191 CATAAATATTGTTATCCA-TTTTTT-TTTC-AAAAGTGATAATGACAA-TTTTTATAATTATAAT
* *
1215362 TTATAGTTATTGTTATAGAAAAAATTATCACATCAGATAATAAAATTAAAGTTTTTTGCAATCAA
252 TTATAGTTATTGTTATAGAAAAAATTATCACATCAAATAATAAAATTAAAGTTTTTTGCAATAAA
* * *
1215427 TTATTTTTGTAGTTATATATTTTAATTATTATGAAAAATTATACTATC-AGAATCATTTCTCCCT
317 TTATTTTTGTACTTATATATTTAAATTATTATGAAAAATTATACTATCTA-AATCATTTCTCCAT
* * *
1215491 ATTTTTTGGTGCCAAAGATGTTATATA
381 ATTTTTTAGTGCAAAAAATGTTATATA
1215518 ATAAAAGTTT
Statistics
Matches: 363, Mismatches: 39, Indels: 15
0.87 0.09 0.04
Matches are distributed among these distances:
411 2 0.01
412 27 0.07
413 62 0.17
414 91 0.25
415 6 0.02
416 5 0.01
417 165 0.45
418 5 0.01
ACGTcount: A:0.39, C:0.08, G:0.09, T:0.44
Consensus pattern (412 bp):
AAAATATATTGTCACAAAGATTTTCCTTCATATTTTTTGCGCAAAAAAAGTCATATAGTAACAAA
TTTTATAACTATAAGTGTTAATAATTATTACAAAAAACATTGTCACAAAAATAATGATATTCACA
TTTTTGTGACAAATTATAGTTGTAGTTATAAATTTTAACTATAGTGATAGCATATATTATCATAA
ATATTGTTATCCATTTTTTTTTCAAAAGTGATAATGACAATTTTTATAATTATAATTTATAGTTA
TTGTTATAGAAAAAATTATCACATCAAATAATAAAATTAAAGTTTTTTGCAATAAATTATTTTTG
TACTTATATATTTAAATTATTATGAAAAATTATACTATCTAAATCATTTCTCCATATTTTTTAGT
GCAAAAAATGTTATATATTAAC
Found at i:1215837 original size:17 final size:18
Alignment explanation
Indices: 1215817--1215850 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1215807 TATAATTATG
*
1215817 TAAATAATTT-AATAAAA
1 TAAAGAATTTGAATAAAA
1215834 TAAAGAATTTGAATAAA
1 TAAAGAATTTGAATAAA
1215851 TCAATATGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (18 bp):
TAAAGAATTTGAATAAAA
Found at i:1219159 original size:22 final size:22
Alignment explanation
Indices: 1219134--1219190 Score: 71
Period size: 23 Copynumber: 2.6 Consensus size: 22
1219124 ATAATCAACT
*
1219134 ATAACAAATTTATTTAGTCATA
1 ATAACAAATTTATTTAGTCAAA
* *
1219156 ATAACATATTAAATTTAGTCAAA
1 ATAACAAATT-TATTTAGTCAAA
1219179 ATAA-AAATTTAT
1 ATAACAAATTTAT
1219191 GTTAAATTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 2 0.07
22 13 0.45
23 14 0.48
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.39
Consensus pattern (22 bp):
ATAACAAATTTATTTAGTCAAA
Found at i:1219161 original size:99 final size:98
Alignment explanation
Indices: 1219038--1219352 Score: 246
Period size: 99 Copynumber: 3.2 Consensus size: 98
1219028 ACAAATTATG
** * *
1219038 ACAAATTTAAATAGTTATAGTAACAAATTATAATTAATATTAATTTCTCAATATAAAATGTTATG
1 ACAAATTTATTTAGTCATAATAACAAATTATAATTAATATTAATTTCTCAATATAAAAT-TTATG
1219103 ACAAATAATATTTTTTTCACAATAATCAACTATA
65 ACAAATAATATTTTTTTCACAATAATCAACTATA
* * * * * *
1219137 ACAAATTTATTTAGTCATAATAACATATTA-AATTTAGTCAAAATAAAAATT-T--ATGTTAAAT
1 ACAAATTTATTTAGTCATAATAACAAATTATAA--T--T-AATAT-TAATTTCTCAATATAAAAT
** ** * * * * *
1219198 TTATTTCGTCACAATATTTTCTCCA-AATAA-CAACTTTTG
60 TTATGAC-AAATAATATTTTTTTCACAATAATCAAC-TATA
* * * * * *
1219237 ACAAATTTATTTAATCAAAATAACAATTTATAATAAATATTAATTTCTCATTATAAAAATTTGTG
1 ACAAATTTATTTAGTCATAATAACAAATTATAATTAATATTAATTTCTCAATAT-AAAATTTATG
* *
1219302 ACAAATAATATTTTTTTCACAATAATAAATTATA
65 ACAAATAATATTTTTTTCACAATAATCAACTATA
*
1219336 ACAAAATTATTTAGTCA
1 ACAAATTTATTTAGTCA
1219353 CAGTAAAAAG
Statistics
Matches: 157, Mismatches: 44, Indels: 30
0.68 0.19 0.13
Matches are distributed among these distances:
95 4 0.03
96 5 0.03
98 16 0.10
99 60 0.38
100 41 0.26
101 21 0.13
102 1 0.01
103 5 0.03
104 4 0.03
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.40
Consensus pattern (98 bp):
ACAAATTTATTTAGTCATAATAACAAATTATAATTAATATTAATTTCTCAATATAAAATTTATGA
CAAATAATATTTTTTTCACAATAATCAACTATA
Found at i:1219281 original size:199 final size:198
Alignment explanation
Indices: 1218942--1219352 Score: 556
Period size: 199 Copynumber: 2.1 Consensus size: 198
1218932 AATTTATGAT
* * *
1218942 AATTTATATAGACAAAATAACAAATTAAATTTAGTTAAAATAAAAATTATGTCAAATTTAATTAG
1 AATTTATTTAGTCAAAATAACAAATTAAATTTAGTCAAAATAAAAATTATGTCAAATTTAATTAG
* * * *
1219007 TCAAAATATTTTACCAAAATAACAAATTATGACAAATTTAAATAGTTATAGTAACAAATTATAAT
66 TCAAAATATTTTACCAAAATAACAAATTATGACAAATTTAAATAATCAAAATAACAAATTATAAT
* *
1219072 TAATATTAATTTCTCAATAT-AAAATGTTATGACAAATAATATTTTTTTCACAATAATCAACTAT
131 AAATATTAATTTCTCAATATAAAAAT-TTATGACAAATAATATTTTTTTCACAATAATAAACTAT
1219136 AACA
195 AACA
* * * * *
1219140 AATTTATTTAGTCATAATAACATATTAAATTTAGTCAAAATAAAAATTTATGTTAAATTTATTTC
1 AATTTATTTAGTCAAAATAACAAATTAAATTTAGTCAAAATAAAAA-TTATGTCAAATTTAATTA
* * * * ** *
1219205 GTCACAATATTTT-CTCCAAATAACAACTTTTGACAAATTTATTTAATCAAAATAACAATTTATA
65 GTCAAAATATTTTAC-CAAAATAACAAATTATGACAAATTTAAATAATCAAAATAACAAATTATA
* * *
1219269 ATAAATATTAATTTCTCATTATAAAAATTTGTGACAAATAATATTTTTTTCACAATAATAAATTA
129 ATAAATATTAATTTCTCAATATAAAAATTTATGACAAATAATATTTTTTTCACAATAATAAACTA
1219334 TAACA
194 TAACA
*
1219339 AAATTATTTAGTCA
1 AATTTATTTAGTCA
1219353 CAGTAAAAAG
Statistics
Matches: 185, Mismatches: 25, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
198 42 0.23
199 138 0.75
200 5 0.03
ACGTcount: A:0.48, C:0.09, G:0.04, T:0.39
Consensus pattern (198 bp):
AATTTATTTAGTCAAAATAACAAATTAAATTTAGTCAAAATAAAAATTATGTCAAATTTAATTAG
TCAAAATATTTTACCAAAATAACAAATTATGACAAATTTAAATAATCAAAATAACAAATTATAAT
AAATATTAATTTCTCAATATAAAAATTTATGACAAATAATATTTTTTTCACAATAATAAACTATA
ACA
Found at i:1219354 original size:32 final size:30
Alignment explanation
Indices: 1219318--1219378 Score: 79
Period size: 32 Copynumber: 2.0 Consensus size: 30
1219308 AATATTTTTT
1219318 TCACAATAATAAA-TTATAACAAAATTATTTAG
1 TCACAATAA-AAAGTTATAA-AAAA-TATTTAG
*
1219350 TCACAGTAAAAAGTTATAAAAAATATTTA
1 TCACAATAAAAAGTTATAAAAAATATTTA
1219379 ATGACGAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 6 0.22
31 7 0.26
32 14 0.52
ACGTcount: A:0.54, C:0.08, G:0.05, T:0.33
Consensus pattern (30 bp):
TCACAATAAAAAGTTATAAAAAATATTTAG
Found at i:1222087 original size:20 final size:19
Alignment explanation
Indices: 1222036--1222092 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
1222026 AACCAATAAT
1222036 AATAAACATAAAAT-AATTG
1 AATAAA-ATAAAATAAATTG
* *
1222055 GATGAAAAAAAAATGAAATTG
1 AAT-AAAATAAAAT-AAATTG
1222076 AATAAAATAAAATAAAT
1 AATAAAATAAAATAAAT
1222093 GAAGATAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
19 12 0.39
20 12 0.39
21 7 0.23
ACGTcount: A:0.67, C:0.02, G:0.09, T:0.23
Consensus pattern (19 bp):
AATAAAATAAAATAAATTG
Found at i:1222240 original size:21 final size:22
Alignment explanation
Indices: 1222191--1222267 Score: 75
Period size: 22 Copynumber: 3.3 Consensus size: 22
1222181 ATATAATGAA
*
1222191 AATAAATAAATAGTATAAATAAAAT
1 AATAAA-AAATA-TATATAT-AAAT
1222216 AATAAAAAATATATATATAAA-
1 AATAAAAAATATATATATAAAT
* *
1222237 AATATAAAAATGTATGTATAATAT
1 AATA-AAAAATATATATATAA-AT
1222261 AATAAAA
1 AATAAAA
1222268 TACTAAATAG
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
21 4 0.09
22 17 0.37
23 10 0.22
24 9 0.20
25 6 0.13
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (22 bp):
AATAAAAAATATATATATAAAT
Found at i:1222256 original size:22 final size:21
Alignment explanation
Indices: 1222177--1222267 Score: 69
Period size: 22 Copynumber: 4.1 Consensus size: 21
1222167 CAAAGAAACT
*
1222177 AAAA-ATATA-ATGAAAATAA
1 AAAATATATATATAAAAATAA
*
1222196 ATAAATAGTATAAATAAAATAATAA
1 A-AAATA-TATATAT-AAA-AATAA
1222221 AAAATATATATATAAAAATATA
1 AAAATATATATATAAAAATA-A
* *
1222243 AAAATGTATGTATAATATAATAA
1 AAAATATATATATAA-A-AATAA
1222266 AA
1 AA
1222268 TACTAAATAG
Statistics
Matches: 59, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
19 1 0.02
20 3 0.05
21 5 0.08
22 21 0.36
23 12 0.20
24 11 0.19
25 6 0.10
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (21 bp):
AAAATATATATATAAAAATAA
Found at i:1223017 original size:37 final size:37
Alignment explanation
Indices: 1222976--1223060 Score: 98
Period size: 37 Copynumber: 2.3 Consensus size: 37
1222966 GGATCCTATC
** *
1222976 TTTAGGAGTTTAAATAATAGTAGAACTCTATCATATT
1 TTTAGGAGTTTAAATAATAACAAAACTCTATCATATT
* ** * *
1223013 TTTAGGAGTTTGAATCCTAACAAAATTCTATCCTATT
1 TTTAGGAGTTTAAATAATAACAAAACTCTATCATATT
1223050 TTTAGGAGTTT
1 TTTAGGAGTTT
1223061 GAATCCTAGT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.42
Consensus pattern (37 bp):
TTTAGGAGTTTAAATAATAACAAAACTCTATCATATT
Found at i:1229107 original size:59 final size:59
Alignment explanation
Indices: 1228643--1229099 Score: 729
Period size: 59 Copynumber: 7.7 Consensus size: 59
1228633 AATTCAATAA
* * *
1228643 GAAATTCACACTA-TTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGTCCTATCTG
1 GAAATTCATAC-ACTTAGTATGATTTCCTTACCATTTTAGCACACGAAGTGCCCTATCTG
1228702 GAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACGAAAG-GCCCTATCTG
1 GAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACG-AAGTGCCCTATCTG
1228761 GAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACGAAGTGCCCTATCTG
1 GAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACGAAGTGCCCTATCTG
* *
1228820 GAAATTCATACACTTAGTATAATTTCCTTACCATTTTAGCACACGAAATGCCCTATCTG
1 GAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACGAAGTGCCCTATCTG
*
1228879 GAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACGAAGTGCCTTATCTG
1 GAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACGAAGTGCCCTATCTG
* * * *
1228938 GAAATTCATACACATAGTGTGATTTCCTTACCATTTTAGAACACGAAGTACCCTATCTG
1 GAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACGAAGTGCCCTATCTG
* * *
1228997 GAAATTCATACACTTACTATGATTTCCTTACCATTTTAGCATATGAAGTGCCCTATCTG
1 GAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACGAAGTGCCCTATCTG
* * * *
1229056 AAAATTCATAAACTAAGTACGATTTCCTTACCATTTTAGCACAC
1 GAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACAC
1229100 TTAGTGCCAT
Statistics
Matches: 368, Mismatches: 27, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
58 4 0.01
59 361 0.98
60 3 0.01
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.34
Consensus pattern (59 bp):
GAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACGAAGTGCCCTATCTG
Found at i:1229459 original size:20 final size:21
Alignment explanation
Indices: 1229430--1229481 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 21
1229420 TGGCCCTTCA
*
1229430 GTATCAATACT-CATACCATG
1 GTATCGATACTACATACCATG
* *
1229450 GTATCGATACTACCCTACTATG
1 GTATCGATACTA-CATACCATG
1229472 GTATCGATAC
1 GTATCGATAC
1229482 CTCCTTCTGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 10 0.37
22 17 0.63
ACGTcount: A:0.31, C:0.25, G:0.13, T:0.31
Consensus pattern (21 bp):
GTATCGATACTACATACCATG
Found at i:1229630 original size:34 final size:34
Alignment explanation
Indices: 1229587--1229663 Score: 145
Period size: 34 Copynumber: 2.3 Consensus size: 34
1229577 CCCCTTCCGA
1229587 TATCGATACCAAAATTAGGTTCGATGTTAACTGG
1 TATCGATACCAAAATTAGGTTCGATGTTAACTGG
*
1229621 TATCGATACCAAAATTAGGTTCGATGTTACCTGG
1 TATCGATACCAAAATTAGGTTCGATGTTAACTGG
1229655 TATCGATAC
1 TATCGATAC
1229664 ACTTACTATG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Consensus pattern (34 bp):
TATCGATACCAAAATTAGGTTCGATGTTAACTGG
Found at i:1242746 original size:16 final size:15
Alignment explanation
Indices: 1242711--1242744 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1242701 AAAATACAAG
1242711 TTTTGGAAATTACAC
1 TTTTGGAAATTACAC
1242726 TTTTGGAAAATTAC-C
1 TTTTGG-AAATTACAC
1242741 TTTT
1 TTTT
1242745 TGCTCTTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (15 bp):
TTTTGGAAATTACAC
Found at i:1243482 original size:6 final size:6
Alignment explanation
Indices: 1243458--1243561 Score: 79
Period size: 6 Copynumber: 16.7 Consensus size: 6
1243448 CCCACTTTTA
* * *
1243458 TTCTTT TCCATT TTGTTT TTCTTTT TTCTTTTT TTCTTT TTCTTT TTC-TT
1 TTCTTT TTCTTT TTCTTT TTC-TTT TTC--TTT TTCTTT TTCTTT TTCTTT
* *
1243508 TT-TTT TTCTTTT TTCTTT TTCTCTT TCTCTTT AT-TTT TTCTCTT TTCTTC
1 TTCTTT TTC-TTT TTCTTT TTCT-TT T-TCTTT TTCTTT TTCT-TT TTCTTT
1243558 TTCT
1 TTCT
1243562 AAGAGTAATA
Statistics
Matches: 80, Mismatches: 9, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
5 12 0.15
6 35 0.44
7 23 0.29
8 10 0.12
ACGTcount: A:0.02, C:0.18, G:0.01, T:0.79
Consensus pattern (6 bp):
TTCTTT
Found at i:1243483 original size:7 final size:7
Alignment explanation
Indices: 1243473--1243559 Score: 72
Period size: 7 Copynumber: 12.1 Consensus size: 7
1243463 TTCCATTTTG
1243473 TTTTTCT
1 TTTTTCT
1243480 TTTTTCT
1 TTTTTCT
1243487 TTTTT-T
1 TTTTTCT
1243493 CTTTTTCTT
1 -TTTTTC-T
*
1243502 TTTCTTTT
1 TTT-TTCT
1243510 TTTTTCT
1 TTTTTCT
1243517 TTTTTC-
1 TTTTTCT
1243523 TTTTTCT
1 TTTTTCT
*
1243530 CTTTCTCT
1 -TTTTTCT
*
1243538 TTATT-T
1 TTTTTCT
*
1243544 TTTCTCT
1 TTTTTCT
1243551 TTTCTTCT
1 TTT-TTCT
1243559 T
1 T
1243560 CTAAGAGTAA
Statistics
Matches: 64, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
6 11 0.17
7 33 0.52
8 17 0.27
9 3 0.05
ACGTcount: A:0.01, C:0.17, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTTCT
Found at i:1243522 original size:37 final size:38
Alignment explanation
Indices: 1243458--1243556 Score: 121
Period size: 37 Copynumber: 2.6 Consensus size: 38
1243448 CCCACTTTTA
* * *
1243458 TTCTTTTCCATTTTGTTTTTCTTTTTTCTTTTTTTCTTT
1 TTCTTTTTC-TTTTCTTTTTCTTTTTTCTTTTTCTCTTT
1243497 TTCTTTTTCTTTT-TTTTTCTTTTTTCTTTTTCTCTTT
1 TTCTTTTTCTTTTCTTTTTCTTTTTTCTTTTTCTCTTT
*
1243534 CTCTTTATT-TTTTCTCTTTTCTT
1 TTCTTT-TTCTTTTCT-TTTTCTT
1243557 CTTCTAAGAG
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
37 32 0.59
38 7 0.13
39 15 0.28
ACGTcount: A:0.02, C:0.17, G:0.01, T:0.80
Consensus pattern (38 bp):
TTCTTTTTCTTTTCTTTTTCTTTTTTCTTTTTCTCTTT
Found at i:1247091 original size:23 final size:23
Alignment explanation
Indices: 1247065--1247121 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
1247055 TCTATGTAAA
*
1247065 AAAATATAAAAAATAAAGAATGT
1 AAAATATAAAAAATAAAGAATGG
* * * *
1247088 AAAAAATGAATAATGAAGAATGG
1 AAAATATAAAAAATAAAGAATGG
*
1247111 AAAATGTAAAA
1 AAAATATAAAA
1247122 GTTGATTGAC
Statistics
Matches: 25, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.67, C:0.00, G:0.14, T:0.19
Consensus pattern (23 bp):
AAAATATAAAAAATAAAGAATGG
Found at i:1255867 original size:29 final size:31
Alignment explanation
Indices: 1255835--1255897 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 31
1255825 AAAATTTTGG
*
1255835 TTAGTGACCAAAATATAAAATTT-G-AAAGT
1 TTAGTAACCAAAATATAAAATTTGGAAAAGT
* *
1255864 TTAGTAACCAAAGTATAAAGTTTGGAAAAGT
1 TTAGTAACCAAAATATAAAATTTGGAAAAGT
1255895 TTA
1 TTA
1255898 TGGACTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 20 0.69
30 1 0.03
31 8 0.28
ACGTcount: A:0.46, C:0.06, G:0.16, T:0.32
Consensus pattern (31 bp):
TTAGTAACCAAAATATAAAATTTGGAAAAGT
Found at i:1263707 original size:3 final size:3
Alignment explanation
Indices: 1263688--1263761 Score: 73
Period size: 3 Copynumber: 25.0 Consensus size: 3
1263678 GATCTGTTTG
* * *
1263688 TAA TAA TAT TAA TTAA TAA TAA TAA TAA TAA -AA AAA TAA TAA TAG
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1263733 TGA TAAA TAA -AA TAA TAA TAA T-A TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
1263762 AAACAAATGG
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
2 6 0.10
3 48 0.81
4 5 0.08
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1263748 original size:18 final size:19
Alignment explanation
Indices: 1263688--1263763 Score: 84
Period size: 21 Copynumber: 3.8 Consensus size: 19
1263678 GATCTGTTTG
1263688 TAATAATATTAATTAATAATAA
1 TAATAATA-TAA-TAA-AATAA
1263710 TAATAATA-AA-AAAATAA
1 TAATAATATAATAAAATAA
*
1263727 TAATAGTGATAAATAAAATAA
1 TAATAAT-AT-AATAAAATAA
1263748 TAATAATATAATAAAA
1 TAATAATATAATAAAA
1263764 ACAAATGGAT
Statistics
Matches: 48, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
17 11 0.23
18 3 0.06
19 7 0.15
20 6 0.12
21 13 0.27
22 8 0.17
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (19 bp):
TAATAATATAATAAAATAA
Found at i:1264261 original size:104 final size:105
Alignment explanation
Indices: 1264123--1264317 Score: 338
Period size: 105 Copynumber: 1.9 Consensus size: 105
1264113 CTTCTTCTAT
*
1264123 AAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTTTTCC-TCTTCAGATAAGTTCTTCTCAT
1 AAAAGGTTAAACAAGCTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATAAGTTCTTCTCAT
* *
1264187 TATGAACTTTCTTTGGAAAAGTTGATCCATGAATTCAAAC
66 TATGAACTTTCTCTAGAAAAGTTGATCCATGAATTCAAAC
* *
1264227 AAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTAAACAAGCTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATAAGTTCTTCTCAT
1264292 TATGAACTTTCTCTAGAAAAGTTGAT
66 TATGAACTTTCTCTAGAAAAGTTGAT
1264318 GTTGATCTAT
Statistics
Matches: 85, Mismatches: 5, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
104 40 0.47
105 45 0.53
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.40
Consensus pattern (105 bp):
AAAAGGTTAAACAAGCTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATAAGTTCTTCTCAT
TATGAACTTTCTCTAGAAAAGTTGATCCATGAATTCAAAC
Found at i:1264317 original size:105 final size:107
Alignment explanation
Indices: 1264016--1264317 Score: 373
Period size: 109 Copynumber: 2.8 Consensus size: 107
1264006 AATTAAAATT
* * *
1264016 AAGGTTGAACAAGTTCTTCTCATTATGAACTTC-TTCTCCTTTTTCAAATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATGAGTTCTTCTCATTA
** * ** ** *
1264080 TGAACACT-TCTGGAAATGTTGATGTTGATCTATCTTCTTCTATAA
66 TGAACTTTCTCTGGAAAAGTTGATCATGA--TA-CTTC-TAAACAA
* *
1264125 AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTTTTCC-TCTTCAGATAAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATGAGTTCTTCTCATTA
*
1264189 TGAACTTTCTTTGGAAAAGTTGATCCATGA-A-TTC-AAACAA
66 TGAACTTTCTCTGGAAAAGTTGAT-CATGATACTTCTAAACAA
*
1264229 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATGAGTTCTTCTCATTA
*
1264294 TGAACTTTCTCTAGAAAAGTTGAT
66 TGAACTTTCTCTGGAAAAGTTGAT
1264318 GTTGATCTAT
Statistics
Matches: 170, Mismatches: 19, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
104 41 0.24
105 45 0.26
106 3 0.02
108 1 0.01
109 59 0.35
110 18 0.11
111 3 0.02
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.41
Consensus pattern (107 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATGAGTTCTTCTCATTA
TGAACTTTCTCTGGAAAAGTTGATCATGATACTTCTAAACAA
Found at i:1264529 original size:97 final size:98
Alignment explanation
Indices: 1264416--1264614 Score: 294
Period size: 97 Copynumber: 2.0 Consensus size: 98
1264406 TCTTCTCATT
* * * *
1264416 ATGAACTTTCTCTGGAAAAGTTGATCCATTAAGTAATGAATTCAAACAAAAGGTTAAACAAGTTC
1 ATGAACTCTCTCTGGAAAAGCTAATCCATCAAGTAATGAATTCAAACAAAAGGTTAAACAAGTTC
1264481 TTCT-CATTATGAACTTCTTT-TTCCTTCTTCAG
66 TT-TACATTATGAACTTCTTTCTTCCTTCTTCAG
* * ** *
1264513 ATGAACTCTCTCTGGAAATGCTAATCCATCAAGTGATGAATTTGAGCAAAAGGTTAAACAAGTTC
1 ATGAACTCTCTCTGGAAAAGCTAATCCATCAAGTAATGAATTCAAACAAAAGGTTAAACAAGTTC
1264578 TTTACATTATGAACTTCTTTCTTCCTTCTTCAG
66 TTTACATTATGAACTTCTTTCTTCCTTCTTCAG
1264611 ATGA
1 ATGA
1264615 GTTCTTCTCA
Statistics
Matches: 91, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
96 1 0.01
97 74 0.81
98 16 0.18
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (98 bp):
ATGAACTCTCTCTGGAAAAGCTAATCCATCAAGTAATGAATTCAAACAAAAGGTTAAACAAGTTC
TTTACATTATGAACTTCTTTCTTCCTTCTTCAG
Found at i:1265250 original size:398 final size:399
Alignment explanation
Indices: 1264513--1265277 Score: 1469
Period size: 398 Copynumber: 1.9 Consensus size: 399
1264503 CCTTCTTCAG
*
1264513 ATGAACTCTCTCTGGAAATGCTAATCCATCAAGTGATGAATTTGAGCAAAAGGTTAAACAAGTTC
1 ATGAACTCTCTCTGGAAATGCTAATCCATCAAGTGATGAATTTGAGAAAAAGGTTAAACAAGTTC
*
1264578 TTTACATTATGAACTTCTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCTAGAA
66 TTCACATTATGAACTTCTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCTAGAA
*
1264643 ATGTTGATCCATCGAATGATGGATTCGAATCTTTGCTAAAATCTTTGAATTTCCTGTCAAATATT
131 ATGTTGATCCATCGAATGATGGATTCAAATCTTTGCTAAAATCTTTGAATTTCCTGTCAAATATT
1264708 TAACATGGATAAAATGGATGAAAATGCACCTATTTTGCAAATGTCTAAATATGATGCATGAATGT
196 TAACATGGATAAAATGGATGAAAATGCACCTATTTTGCAAATGTCTAAATATGATGCATGAATGT
1264773 TAATTTCATCTTTATTTAATTTCAAAGAGGTGAACTTAGTCTTTCTTCAATTGTGTAGAAATCCA
261 TAATTTCATCTTTATTTAATTTCAAAGAGGTGAACTTAGTCTTTCTTCAATTGTGTAGAAATCCA
1264838 ATAAATCTTTCCTCTTCGAATGGAGAATCTATCATCTTTGAACTTCTTCCTTCTTCATATGAGTT
326 ATAAATCTTTCCTCTTCGAATGGAGAATCTATCATCTTTGAACTTCTTCCTTCTTCATATGAGTT
1264903 CTTCTCATT
391 CTTCTCATT
*
1264912 ATGAACTCTCTCTGGAAATGCTGATCCATCAAGTGATGAATTTGAGAAAAAGGTTAAACAAGTTC
1 ATGAACTCTCTCTGGAAATGCTAATCCATCAAGTGATGAATTTGAGAAAAAGGTTAAACAAGTTC
*
1264977 TTCACATTATGAACTTC-TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCTGGAA
66 TTCACATTATGAACTTCTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCTAGAA
1265041 ATGTTGATCCATCGAATGATGGATTCAAATCTTTGCTAAAATCTTTGAATTTCCTGTCAAATATT
131 ATGTTGATCCATCGAATGATGGATTCAAATCTTTGCTAAAATCTTTGAATTTCCTGTCAAATATT
1265106 TAACATGGATAAAATGGATGAAAATGCACCTATTTTGCAAATGTCTAAATATGATGCATGAATGT
196 TAACATGGATAAAATGGATGAAAATGCACCTATTTTGCAAATGTCTAAATATGATGCATGAATGT
1265171 TAATTTCATCTTTATTTAATTTCAAAGAGGTGAACTTAGTCTTTCTTCAATTGTGTAGAAATCCA
261 TAATTTCATCTTTATTTAATTTCAAAGAGGTGAACTTAGTCTTTCTTCAATTGTGTAGAAATCCA
*
1265236 ATAAATCTTTCCTCTTTGAATGGAGAATCTATCATCTTTGAA
326 ATAAATCTTTCCTCTTCGAATGGAGAATCTATCATCTTTGAA
1265278 GAGTGTAGAT
Statistics
Matches: 360, Mismatches: 6, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
398 281 0.78
399 79 0.22
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.38
Consensus pattern (399 bp):
ATGAACTCTCTCTGGAAATGCTAATCCATCAAGTGATGAATTTGAGAAAAAGGTTAAACAAGTTC
TTCACATTATGAACTTCTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCTAGAA
ATGTTGATCCATCGAATGATGGATTCAAATCTTTGCTAAAATCTTTGAATTTCCTGTCAAATATT
TAACATGGATAAAATGGATGAAAATGCACCTATTTTGCAAATGTCTAAATATGATGCATGAATGT
TAATTTCATCTTTATTTAATTTCAAAGAGGTGAACTTAGTCTTTCTTCAATTGTGTAGAAATCCA
ATAAATCTTTCCTCTTCGAATGGAGAATCTATCATCTTTGAACTTCTTCCTTCTTCATATGAGTT
CTTCTCATT
Found at i:1266245 original size:18 final size:18
Alignment explanation
Indices: 1266222--1266256 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1266212 TATATGAAAC
1266222 AAATTGAATTTCAAAAAT
1 AAATTGAATTTCAAAAAT
1266240 AAATTGAATTTCAAAAA
1 AAATTGAATTTCAAAAA
1266257 GATAAACTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.31
Consensus pattern (18 bp):
AAATTGAATTTCAAAAAT
Found at i:1266618 original size:10 final size:9
Alignment explanation
Indices: 1266603--1266672 Score: 50
Period size: 10 Copynumber: 6.8 Consensus size: 9
1266593 CTGACCCTCA
1266603 TTTTCTATTT
1 TTTTCT-TTT
1266613 TTTTCTTTT
1 TTTTCTTTT
*
1266622 TTTCAACATTTTT
1 TTT--TC--TTTT
1266635 TCTTTTCTTTT
1 T-TT-TCTTTT
1266646 TTTTCTTTTT
1 TTTTC-TTTT
1266656 TTTTCTTTT
1 TTTTCTTTT
1266665 TTCTTCTT
1 TT-TTCTT
1266673 CAAGCATAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
9 14 0.28
10 22 0.44
11 6 0.12
13 6 0.12
14 2 0.04
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTCTTTT
Found at i:1266640 original size:5 final size:5
Alignment explanation
Indices: 1266632--1266664 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
1266622 TTTCAACATT
*
1266632 TTTTC TTTTC TTTT- TTTTC TTTTT TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
1266665 TTCTTCTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (5 bp):
TTTTC
Found at i:1266654 original size:20 final size:20
Alignment explanation
Indices: 1266631--1266672 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
1266621 TTTTCAACAT
1266631 TTTTTCTTTTCTTTTTT-TTC
1 TTTTT-TTTTCTTTTTTCTTC
1266651 TTTTTTTTTCTTTTTTCTTC
1 TTTTTTTTTCTTTTTTCTTC
1266671 TT
1 TT
1266673 CAAGCATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (20 bp):
TTTTTTTTTCTTTTTTCTTC
Found at i:1277080 original size:26 final size:28
Alignment explanation
Indices: 1277041--1277108 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 28
1277031 AAATAAAATG
1277041 AAATATTAAT-AAAATAAT-A-TACATAT
1 AAATATT-ATGAAAATAATAAGTACATAT
*
1277067 AAATATTATGAAAATAATAAGTATATAT
1 AAATATTATGAAAATAATAAGTACATAT
* *
1277095 AAAAATTTTGAAAA
1 AAATATTATGAAAA
1277109 GAAAGAATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
25 2 0.06
26 15 0.42
27 1 0.03
28 18 0.50
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.34
Consensus pattern (28 bp):
AAATATTATGAAAATAATAAGTACATAT
Done.