Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005349.1 Hibiscus syriacus cultivar Beakdansim tig00012136_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: 1796274
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
File 6 of 8
Found at i:1260706 original size:37 final size:36
Alignment explanation
Indices: 1260645--1260757 Score: 115
Period size: 37 Copynumber: 3.1 Consensus size: 36
1260635 TTGAGATCGC
*
1260645 TTTCTCAAAAACAACCTTTT-TCTCGCTTGAGACAATT
1 TTTCTCAAAAACAA-ATTTTGTCTCGCTTGAGAC-ATT
* *
1260682 TTTCT-AAAAACAAATTTTTGTCTCGCTTTAGAC-GT
1 TTTCTCAAAAACAAA-TTTTGTCTCGCTTGAGACATT
* * *
1260717 TTTCTTGAAAAACAAATTTCGTCTCGCTTGAGATATT
1 TTTC-TCAAAAACAAATTTTGTCTCGCTTGAGACATT
1260754 TTTC
1 TTTC
1260758 CTTCGAGATA
Statistics
Matches: 64, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
35 5 0.08
36 28 0.44
37 31 0.48
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.42
Consensus pattern (36 bp):
TTTCTCAAAAACAAATTTTGTCTCGCTTGAGACATT
Found at i:1260734 original size:175 final size:176
Alignment explanation
Indices: 1260513--1260891 Score: 521
Period size: 175 Copynumber: 2.1 Consensus size: 176
1260503 GTTTCCTTTG
* * * *
1260513 AAACAAAATTTTGTCTCATTTGAGACAGTTTACGTCG-AAAACAAATTGCGTCTCGCTTGAGATA
1 AAAC-AAATGTTGTCTCACTTGAGAC-GTTTTC-TTGAAAAACAAATTGCGTCTCGCTTGAGATA
* * *
1260577 TTTTCCCTTTGAGATACAAATTTTGAATTTGCTTCACATTAAACAAAGTTGATTTCACTTGAGAT
63 TTTTCCCTTCGAGATACAAATTTTGAATTTGCTTCACACTAAACAAAGTTGATCTCACTTGAGAT
* * * *
1260642 CGCTTTC-T-CAAAAACAACCTTTTTCTCGCTTGAGACAATTTTTCTAA
128 CGCTTTCTTAAAAAAACAAACTTTGTCTCGCTTGAGACAATTTCTCTAA
* * * *
1260689 AAACAAATTTTTGTCTCGCTTTAGACGTTTTCTTGAAAAACAAATTTCGTCTCGCTTGAGATATT
1 AAACAAA-TGTTGTCTCACTTGAGACGTTTTCTTGAAAAACAAATTGCGTCTCGCTTGAGATATT
* **
1260754 TTTCCTTCGAGATACAAATTTTGAATTTTTTTCACACTAAACAAAGTTGATCTCACTTGAGATCG
65 TTCCCTTCGAGATACAAATTTTGAATTTGCTTCACACTAAACAAAGTTGATCTCACTTGAGATCG
*
1260819 TTTTCTTAAAAAAAACAAACTTTGTCTCGCTTGAGACAATTTCTCTAA
130 CTTTCTT-AAAAAAACAAACTTTGTCTCGCTTGAGACAATTTCTCTAA
1260867 AAACAAATGTTGTCTCACTTGAGAC
1 AAACAAATGTTGTCTCACTTGAGAC
1260892 AATTTTCCAA
Statistics
Matches: 178, Mismatches: 20, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
174 2 0.01
175 99 0.56
176 20 0.11
177 15 0.08
178 42 0.24
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (176 bp):
AAACAAATGTTGTCTCACTTGAGACGTTTTCTTGAAAAACAAATTGCGTCTCGCTTGAGATATTT
TCCCTTCGAGATACAAATTTTGAATTTGCTTCACACTAAACAAAGTTGATCTCACTTGAGATCGC
TTTCTTAAAAAAACAAACTTTGTCTCGCTTGAGACAATTTCTCTAA
Found at i:1260958 original size:32 final size:32
Alignment explanation
Indices: 1260922--1260993 Score: 87
Period size: 30 Copynumber: 2.3 Consensus size: 32
1260912 TGTTTCACTG
*
1260922 GAAACAAACATCATCTTTGAGTCGT-T-TCTTTT
1 GAAACAAA-AGCATCTTTGAGTC-TATCTCTTTT
*
1260954 GAAAC-AAAGGATCTTTGAGTCTATCTCTTTT
1 GAAACAAAAGCATCTTTGAGTCTATCTCTTTT
1260985 GAAACAAAA
1 GAAACAAAA
1260994 CTTTGTCTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
29 1 0.03
30 13 0.37
31 13 0.37
32 8 0.23
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.35
Consensus pattern (32 bp):
GAAACAAAAGCATCTTTGAGTCTATCTCTTTT
Found at i:1260970 original size:30 final size:31
Alignment explanation
Indices: 1260934--1260992 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
1260924 AACAAACATC
1260934 ATCTTTGAGTCGT-T-TCTTTTGAAACAAAGG
1 ATCTTTGAGTC-TATCTCTTTTGAAACAAAGG
1260964 ATCTTTGAGTCTATCTCTTTTGAAACAAA
1 ATCTTTGAGTCTATCTCTTTTGAAACAAA
1260993 ACTTTGTCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 1 0.04
30 12 0.44
31 14 0.52
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (31 bp):
ATCTTTGAGTCTATCTCTTTTGAAACAAAGG
Found at i:1261229 original size:66 final size:64
Alignment explanation
Indices: 1261058--1261246 Score: 204
Period size: 64 Copynumber: 2.9 Consensus size: 64
1261048 AAAACAAAAT
* * ** * *
1261058 GAAAAATCTTTGAGTATGTTTCTTTGATAACAAAATTCAGTCTCTTTTGTGAAAGTTTCTTTTGA
1 GAAAAATCTTTGAGTTTGTTT-TTTGAAAACAAAATTTTGTCTCTTTTGAGACAGTTTCTTTTGA
* * *
1261123 G-AGAATCTTTGAATTTTTTTCTTTGGAAAA-AAAATTTTGTCTCTTTTGAGACAG-TTCATTTT
1 GAAAAATCTTTGAGTTTGTTT-TTT-GAAAACAAAATTTTGTCTCTTTTGAGACAGTTTC-TTTT
1261185 GAA
63 G-A
* *
1261188 GAAAAATCTTTGAGTTTGTTTTTATGAAAACAAAGTTTTGTCTCTTTTGAGACAATTTC
1 GAAAAATCTTTGAGTTTGTTTTT-TGAAAACAAAATTTTGTCTCTTTTGAGACAGTTTC
1261247 CCTTAAAACA
Statistics
Matches: 103, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
63 3 0.03
64 44 0.43
65 14 0.14
66 39 0.38
67 3 0.03
ACGTcount: A:0.30, C:0.10, G:0.15, T:0.45
Consensus pattern (64 bp):
GAAAAATCTTTGAGTTTGTTTTTTGAAAACAAAATTTTGTCTCTTTTGAGACAGTTTCTTTTGA
Found at i:1261351 original size:29 final size:29
Alignment explanation
Indices: 1261249--1261393 Score: 120
Period size: 29 Copynumber: 4.9 Consensus size: 29
1261239 ACAATTTCCC
* *
1261249 TTAAAACAAACATCTTTGAGATTGTTTCCCT
1 TTAAAACAAAAATCTTTGAG-TTGTTT-CTT
*
1261280 TT-AAACAAAACCTATCTTTGAGTATGTTTCTC
1 TTAAAACAAAA---ATCTTTGAGT-TGTTTCTT
* *
1261312 TTGAAACAAAAGT-TTGTGAGTTGTTTCTT
1 TTAAAACAAAAATCTT-TGAGTTGTTTCTT
*
1261341 TTAAAATAAAAATCTTTGAGTTGTTTCTT
1 TTAAAACAAAAATCTTTGAGTTGTTTCTT
*
1261370 TT--GA-AAAAATCTTTGAGTCTGTTT
1 TTAAAACAAAAATCTTTGAGT-TGTTT
1261394 ATATTGAAAA
Statistics
Matches: 97, Mismatches: 9, Indels: 20
0.77 0.07 0.16
Matches are distributed among these distances:
26 14 0.14
27 6 0.06
29 34 0.35
30 15 0.15
31 2 0.02
32 4 0.04
33 22 0.23
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.43
Consensus pattern (29 bp):
TTAAAACAAAAATCTTTGAGTTGTTTCTT
Found at i:1261384 original size:26 final size:27
Alignment explanation
Indices: 1261293--1261405 Score: 97
Period size: 29 Copynumber: 4.0 Consensus size: 27
1261283 AACAAAACCT
*
1261293 ATCTTTGAGTATGTTTCTCTTGAAACAAA
1 ATCTTTGAGTATGTTTCTTTTG-AA-AAA
*
1261322 AGT-TTGTGAGT-TGTTTCTTTTAAAATAAAA
1 A-TCTT-TGAGTATGTTTCTTTT--GA-AAAA
1261352 ATCTTTGAGT-TGTTTCTTTTGAAAAA
1 ATCTTTGAGTATGTTTCTTTTGAAAAA
* * *
1261378 ATCTTTGAGTCTGTTTATATTGAAAAA
1 ATCTTTGAGTATGTTTCTTTTGAAAAA
1261405 A
1 A
1261406 AAGTTTTGTC
Statistics
Matches: 72, Mismatches: 5, Indels: 16
0.77 0.05 0.17
Matches are distributed among these distances:
26 14 0.19
27 16 0.22
29 28 0.39
30 13 0.18
31 1 0.01
ACGTcount: A:0.32, C:0.08, G:0.15, T:0.45
Consensus pattern (27 bp):
ATCTTTGAGTATGTTTCTTTTGAAAAA
Found at i:1261466 original size:25 final size:25
Alignment explanation
Indices: 1261428--1261495 Score: 64
Period size: 29 Copynumber: 2.5 Consensus size: 25
1261418 GCTTGAGACA
*
1261428 GTTTTTTCATGAAAAATCTTTGAGTC
1 GTTTCTTC-TGAAAAATCTTTGAGTC
* *
1261454 GTTTCTTTTGAAACAAAAATCTTTTAGTC
1 GTTTCTTCTG----AAAAATCTTTGAGTC
1261483 GTTTCTTCTGAAA
1 GTTTCTTCTGAAA
1261496 CACCTATCTT
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
25 5 0.15
26 6 0.18
29 23 0.68
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (25 bp):
GTTTCTTCTGAAAAATCTTTGAGTC
Found at i:1261471 original size:29 final size:29
Alignment explanation
Indices: 1261439--1261532 Score: 116
Period size: 29 Copynumber: 3.2 Consensus size: 29
1261429 TTTTTTCATG
1261439 AAAAATCTTTGAGTCGTTTCTTTTGAAAC
1 AAAAATCTTTGAGTCGTTTCTTTTGAAAC
* *
1261468 AAAAATCTTTTAGTCGTTTCTTCTGAAAC
1 AAAAATCTTTGAGTCGTTTCTTTTGAAAC
*** * *
1261497 ACCTATCTTTGAGTTTGTTTCCTTTGAAAC
1 AAAAATCTTTGAG-TCGTTTCTTTTGAAAC
1261527 AAAAAT
1 AAAAAT
1261533 TTGTCTCTTG
Statistics
Matches: 52, Mismatches: 12, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
29 36 0.69
30 16 0.31
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (29 bp):
AAAAATCTTTGAGTCGTTTCTTTTGAAAC
Found at i:1261951 original size:63 final size:64
Alignment explanation
Indices: 1261856--1261977 Score: 158
Period size: 63 Copynumber: 1.9 Consensus size: 64
1261846 ATTTTCTGAA
* * *
1261856 AAACAAAGTTTTGTCTTTCTTGAGGCAATTTCTTTT-GAAAAATCATTGAATATGTTTCTATGG
1 AAACAAAATTTTGTCTTTCTTAAGACAATTTCTTTTAGAAAAATCATTGAATATGTTTCTATGG
* * *
1261919 AAACAAAATTTTGTCTCTT-TTAAGACAGTTTCTTTTAAGAAAAATCTTTGAGTATGTTT
1 AAACAAAATTTTGTCT-TTCTTAAGACAATTTCTTTT-AGAAAAATCATTGAATATGTTT
1261978 TTCTTGAAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
63 29 0.58
64 2 0.04
65 19 0.38
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (64 bp):
AAACAAAATTTTGTCTTTCTTAAGACAATTTCTTTTAGAAAAATCATTGAATATGTTTCTATGG
Found at i:1262185 original size:29 final size:31
Alignment explanation
Indices: 1262120--1262186 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
1262110 TTTTGTCTCT
* *
1262120 TTTGAGACAGTTGCTTTTGAAACACATTACC
1 TTTGAGTCAGTTGCTTTTGAAACACATCACC
*
1262151 TTTGAGTCAGTTTCTTTTG-AA-ACATCACC
1 TTTGAGTCAGTTGCTTTTGAAACACATCACC
1262180 TTTGAGT
1 TTTGAGT
1262187 TGATTTCTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 14 0.42
30 2 0.06
31 17 0.52
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.40
Consensus pattern (31 bp):
TTTGAGTCAGTTGCTTTTGAAACACATCACC
Found at i:1262199 original size:29 final size:29
Alignment explanation
Indices: 1262120--1262202 Score: 78
Period size: 29 Copynumber: 2.8 Consensus size: 29
1262110 TTTTGTCTCT
* * * *
1262120 TTTGAGACAGTTGCTTTTGAAACACATTACC
1 TTTGAGTCAGTTTCTGTTG-AA-ACATCACC
*
1262151 TTTGAGTCAGTTTCTTTTGAAACATCACC
1 TTTGAGTCAGTTTCTGTTGAAACATCACC
*
1262180 TTTGAGT-TGATTTCTGTTGAAAC
1 TTTGAGTCAG-TTTCTGTTGAAAC
1262203 CATAAAGATG
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
28 1 0.02
29 26 0.57
30 2 0.04
31 17 0.37
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.41
Consensus pattern (29 bp):
TTTGAGTCAGTTTCTGTTGAAACATCACC
Found at i:1262552 original size:134 final size:134
Alignment explanation
Indices: 1262205--1262562 Score: 500
Period size: 134 Copynumber: 2.7 Consensus size: 134
1262195 GTTGAAACCA
* * * *
1262205 TAAAGATGGCAAGAACTCTTCACCACGTATGAGCCGTGTCATCCACCGACCAGACCTCCTCATCA
1 TAAAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCCGACCAGATCTCCTCATCA
* * * * * *
1262270 CGTAGGAGCCGTGTCACTCTTACATAACCAGTCGTCCTTATCACGTAGGAATCGAGTTATCATCA
66 CGTAGGAGCCGTGTCACCCTTAGATAACCAGCCGTCCTCATCACGTAGGAACCGAGTTATCACCA
1262335 TTCC
131 TTCC
* * * *
1262339 TAAAGATGGCCATAACTCTTCATCACGTATGAACCGTGTCATTCCCCGACCAGATCTCCTCATCG
1 TAAAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCCGACCAGATCTCCTCATCA
* * *
1262404 CGTAGGAGCCGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGAGTTATCACCC
66 CGTAGGAGCCGTGTCACCCTTAGATAACCAGCCGTCCTCATCACGTAGGAACCGAGTTATCACCA
1262469 TTCC
131 TTCC
* * * *
1262473 TAAAGATGACCAGAACTCTTCATCACGTATGAGCAGTGTCATCCCCCGACCATATCTCCCCATCA
1 TAAAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCCGACCAGATCTCCTCATCA
** *
1262538 CGTAGGAGTTGTGTCAACCTTAGAT
66 CGTAGGAGCCGTGTCACCCTTAGAT
1262563 GACTAGACCT
Statistics
Matches: 195, Mismatches: 29, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
134 195 1.00
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.24
Consensus pattern (134 bp):
TAAAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCCGACCAGATCTCCTCATCA
CGTAGGAGCCGTGTCACCCTTAGATAACCAGCCGTCCTCATCACGTAGGAACCGAGTTATCACCA
TTCC
Found at i:1262768 original size:3 final size:3
Alignment explanation
Indices: 1262762--1262834 Score: 96
Period size: 3 Copynumber: 24.7 Consensus size: 3
1262752 TTATTAAAAA
**
1262762 TAT TAT TA- TAT TAT TAT TAT CGT TAT T-T TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
1262808 TAC TAT TAT TAT TAT TAT TAAT TAT TA
1 TAT TAT TAT TAT TAT TAT T-AT TAT TA
1262835 CATTTACATT
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
2 4 0.07
3 54 0.89
4 3 0.05
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1264611 original size:16 final size:18
Alignment explanation
Indices: 1264579--1264612 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1264569 TATTAATGTA
1264579 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
1264597 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
1264613 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:1265278 original size:130 final size:130
Alignment explanation
Indices: 1265074--1265321 Score: 406
Period size: 130 Copynumber: 1.9 Consensus size: 130
1265064 AATTTTCTTC
*
1265074 TAATTAGGTGGTAACATGTGTCACCAATAACACATACCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTAACATGTGTCACCAATAACACATACCATGATCATGTGCTAACACATGTCAGAT
** * *
1265139 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACAAAATTGATAGCATATATAAA
* * * **
1265204 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTAACATGTGTCACCAATAACACATACCATGATCATGTGCTAACACATGTCAGAT
1265269 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACAAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACAAAATTGAT
1265322 TATATAAATA
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 108 1.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.35
Consensus pattern (130 bp):
TAATTAGGTGGTAACATGTGTCACCAATAACACATACCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACAAAATTGATAGCATATATAAA
Found at i:1265778 original size:35 final size:35
Alignment explanation
Indices: 1265717--1265792 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
1265707 AATTGAATTT
* * *
1265717 AATTGAATTATTTTGTAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
1265752 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
1265787 AATTGA
1 AATTGA
1265793 GGATTGTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.36, C:0.01, G:0.22, T:0.41
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:1266252 original size:29 final size:30
Alignment explanation
Indices: 1266220--1266289 Score: 106
Period size: 29 Copynumber: 2.4 Consensus size: 30
1266210 ACTATATTTA
* *
1266220 TATTTTGGTCCCTGAAATTTTTA-TTTATT
1 TATTTTAGTCCCTGAAATTTCTATTTTATT
*
1266249 TATTTTAGTCCCTGAAGTTTCTATTTTATT
1 TATTTTAGTCCCTGAAATTTCTATTTTATT
1266279 TATTTTAGTCC
1 TATTTTAGTCC
1266290 TTAACTTTCT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
29 20 0.54
30 17 0.46
ACGTcount: A:0.20, C:0.13, G:0.10, T:0.57
Consensus pattern (30 bp):
TATTTTAGTCCCTGAAATTTCTATTTTATT
Found at i:1266298 original size:29 final size:30
Alignment explanation
Indices: 1266220--1266299 Score: 101
Period size: 29 Copynumber: 2.7 Consensus size: 30
1266210 ACTATATTTA
* * *
1266220 TATTTTGGTCCCTGAAATTTTTA-TTTATT
1 TATTTTAGTCCCTGAACTTTCTATTTTATT
*
1266249 TATTTTAGTCCCTGAAGTTTCTATTTTATT
1 TATTTTAGTCCCTGAACTTTCTATTTTATT
*
1266279 TATTTTAGT-CCTTAACTTTCT
1 TATTTTAGTCCCTGAACTTTCT
1266300 GTTTGTACTA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
29 30 0.67
30 15 0.33
ACGTcount: A:0.20, C:0.14, G:0.09, T:0.57
Consensus pattern (30 bp):
TATTTTAGTCCCTGAACTTTCTATTTTATT
Found at i:1266311 original size:29 final size:30
Alignment explanation
Indices: 1266279--1266377 Score: 84
Period size: 29 Copynumber: 3.4 Consensus size: 30
1266269 CTATTTTATT
*
1266279 TATTTTAGTCC-TTAACTTTCTGTTTGTAC
1 TATTTTAGTCCATTAAATTTCTGTTTGTAC
* * *
1266308 TATTTATA-CCCTTTAAATTTCTGTTT-TGC
1 TATTT-TAGTCCATTAAATTTCTGTTTGTAC
1266337 TATTTTAG-CCATGTAAATTTCTG-TTGTTAAC
1 TATTTTAGTCCAT-TAAATTTCTGTTTG-T-AC
1266368 -ATTTTAGTCC
1 TATTTTAGTCC
1266378 TCTAGGTTTA
Statistics
Matches: 57, Mismatches: 5, Indels: 14
0.75 0.07 0.18
Matches are distributed among these distances:
28 7 0.12
29 24 0.42
30 23 0.40
31 3 0.05
ACGTcount: A:0.21, C:0.16, G:0.10, T:0.53
Consensus pattern (30 bp):
TATTTTAGTCCATTAAATTTCTGTTTGTAC
Found at i:1266421 original size:29 final size:28
Alignment explanation
Indices: 1266369--1266437 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 28
1266359 GTTGTTAACA
* *
1266369 TTTTAGTCCTCTAGGTTTATATTTTTACTG
1 TTTTAGTCC-CTAAGTTTATATTTTTAC-C
* *
1266399 TTTTAGTCCCTAAGTTTTTATTTTTTCC
1 TTTTAGTCCCTAAGTTTATATTTTTACC
1266427 TTTTAGTCCCT
1 TTTTAGTCCCT
1266438 TTAGTTTCTG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 11 0.31
29 15 0.43
30 9 0.26
ACGTcount: A:0.14, C:0.17, G:0.10, T:0.58
Consensus pattern (28 bp):
TTTTAGTCCCTAAGTTTATATTTTTACC
Found at i:1266424 original size:30 final size:27
Alignment explanation
Indices: 1266369--1266437 Score: 75
Period size: 30 Copynumber: 2.4 Consensus size: 27
1266359 GTTGTTAACA
* *
1266369 TTTTAGTCCTCTAGGTTTATATTTTTACTG
1 TTTTAGTCC-CTAAGTTTATATTTTT-C-C
*
1266399 TTTTAGTCCCTAAGTTTTTATTTTTTCC
1 TTTTAGTCCCTAAGTTTATA-TTTTTCC
1266427 TTTTAGTCCCT
1 TTTTAGTCCCT
1266438 TTAGTTTCTG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 11 0.31
29 10 0.29
30 14 0.40
ACGTcount: A:0.14, C:0.17, G:0.10, T:0.58
Consensus pattern (27 bp):
TTTTAGTCCCTAAGTTTATATTTTTCC
Found at i:1266451 original size:29 final size:29
Alignment explanation
Indices: 1266369--1266461 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 29
1266359 GTTGTTAACA
* * *
1266369 TTTTAGTCCTCTAGGTTTATATTTTTA-CTG
1 TTTTAGTCC-CTAAGTTTCTATTTTTATC-C
*
1266399 TTTTAGTCCCTAAGTTTTTATTTTT-TCC
1 TTTTAGTCCCTAAGTTTCTATTTTTATCC
* * *
1266427 TTTTAGTCCCTTTAGTTTCTGTTTTTATTC
1 TTTTAGTCCC-TAAGTTTCTATTTTTATCC
1266457 TTTTA
1 TTTTA
1266462 ATCCTTCAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
28 10 0.19
29 27 0.51
30 16 0.30
ACGTcount: A:0.14, C:0.15, G:0.10, T:0.61
Consensus pattern (29 bp):
TTTTAGTCCCTAAGTTTCTATTTTTATCC
Found at i:1266539 original size:22 final size:24
Alignment explanation
Indices: 1266504--1266552 Score: 59
Period size: 22 Copynumber: 2.1 Consensus size: 24
1266494 CTTGTAAATA
*
1266504 TTTGTATTTTAATGATTT-CTT-TT
1 TTTGTATTGTAATG-TTTACTTATT
1266527 TTTGT-TTGTAATGTTTACTTATT
1 TTTGTATTGTAATGTTTACTTATT
1266550 TTT
1 TTT
1266553 ATGCTAGTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 3 0.13
22 10 0.43
23 10 0.43
ACGTcount: A:0.16, C:0.04, G:0.10, T:0.69
Consensus pattern (24 bp):
TTTGTATTGTAATGTTTACTTATT
Found at i:1272073 original size:79 final size:79
Alignment explanation
Indices: 1271904--1272165 Score: 359
Period size: 79 Copynumber: 3.3 Consensus size: 79
1271894 TTATGGCTTA
* * **
1271904 CCAAGGATATCCTTAGATCCGTAGGGTTACCTTAAGCACACAACAAAAGAAAACCAACCTAAGGA
1 CCAAGGACATCCTTAGATCCGTAGGGTTACCTTAAGCACACAGC-AAAGGGAACCAACCTAAGGA
*
1271969 TATACCTTGGGTCT-C
65 TA-ACCTTGGGCCTAC
1271984 CCAAGGACATCCTTAGATCCGTAGGGTTACCTTAAGCACACAGCAAAGGGAACCAACCTAAGGAT
1 CCAAGGACATCCTTAGATCCGTAGGGTTACCTTAAGCACACAGCAAAGGGAACCAACCTAAGGAT
1272049 AAGCCTT-GGCCTAC
66 AA-CCTTGGGCCTAC
* * *
1272063 CCAAGGACATCCTTAGATCCTTAGGGTTACCTTATGCACACAGCAAAGGGAACTAACCTAAGGAT
1 CCAAGGACATCCTTAGATCCGTAGGGTTACCTTAAGCACACAGCAAAGGGAACCAACCTAAGGAT
*
1272128 ATTCCTTGGGGCCTAC
66 A-ACCTT-GGGCCTAC
* *
1272144 CCAA-GATATCCTTAGGTCCGTA
1 CCAAGGACATCCTTAGATCCGTA
1272166 AGGACTTACA
Statistics
Matches: 165, Mismatches: 12, Indels: 10
0.88 0.06 0.05
Matches are distributed among these distances:
78 5 0.03
79 92 0.56
80 57 0.35
81 11 0.07
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.21
Consensus pattern (79 bp):
CCAAGGACATCCTTAGATCCGTAGGGTTACCTTAAGCACACAGCAAAGGGAACCAACCTAAGGAT
AACCTTGGGCCTAC
Found at i:1275299 original size:79 final size:80
Alignment explanation
Indices: 1275109--1275370 Score: 377
Period size: 79 Copynumber: 3.3 Consensus size: 80
1275099 TTAGGCTTAT
* * * **
1275109 GGCCTA-CCAAGGATATCCTTAGATCCGTAGGCTTACCTTAAGCACACAGCAAAAGAAAACCAAC
1 GGCCTACCCAAGGACATCCTTAGATCCGTAGGGTTACCTTAAGCACACAAC-AAAGGGAACCAAC
* *
1275173 ATAAGGATATACCTTG
65 CTAAGGATATGCCTTG
* * *
1275189 GGTCTACCCAAGGACATCCTTTGATCTGTAGGGTTACCTTAAGCACACAACAAAGGGAACCAACC
1 GGCCTACCCAAGGACATCCTTAGATCCGTAGGGTTACCTTAAGCACACAACAAAGGGAACCAACC
1275254 TAAGGATATGCCTT-
66 TAAGGATATGCCTTG
*
1275268 GGCCTACCCAAGGACATCCTTAGATCCGTAGGGTTACCTTATGCACACAACAAAGGGAACCAACC
1 GGCCTACCCAAGGACATCCTTAGATCCGTAGGGTTACCTTAAGCACACAACAAAGGGAACCAACC
1275333 TAAGGATATGCCTTGG
66 TAAGGATATGCCTT-G
*
1275349 GGCCTACCCAA-GATATCCTTAG
1 GGCCTACCCAAGGACATCCTTAG
1275371 GTTCGTAAGG
Statistics
Matches: 164, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
79 75 0.46
80 39 0.24
81 50 0.30
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (80 bp):
GGCCTACCCAAGGACATCCTTAGATCCGTAGGGTTACCTTAAGCACACAACAAAGGGAACCAACC
TAAGGATATGCCTTG
Found at i:1277747 original size:8 final size:9
Alignment explanation
Indices: 1277731--1277755 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1277721 TACATCCATG
1277731 CATTTTTTT
1 CATTTTTTT
1277740 CATTTTTTT
1 CATTTTTTT
1277749 CATTTTT
1 CATTTTT
1277756 AACATGTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (9 bp):
CATTTTTTT
Found at i:1279541 original size:2 final size:2
Alignment explanation
Indices: 1279534--1279563 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1279524 TAATGATACA
1279534 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
1279564 CGATAATTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1282171 original size:14 final size:14
Alignment explanation
Indices: 1282139--1282181 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
1282129 AACGAACATA
*
1282139 AACGAACAC-AATA
1 AACGAACACAAATG
1282152 AACGAACACAAATG
1 AACGAACACAAATG
*
1282166 AACGAACATAAATG
1 AACGAACACAAATG
1282180 AA
1 AA
1282182 AAAAGATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
13 9 0.33
14 18 0.67
ACGTcount: A:0.60, C:0.19, G:0.12, T:0.09
Consensus pattern (14 bp):
AACGAACACAAATG
Found at i:1282418 original size:24 final size:24
Alignment explanation
Indices: 1282349--1282426 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
1282339 GATTGGGCTA
* * * *
1282349 AACATAAATGAGTGCACACAAATG
1 AACATAAATGACTGAACATAAACG
*
1282373 AACATAAATGAACT-AACGTAAACG
1 AACATAAATG-ACTGAACATAAACG
*
1282397 AACATAAATGTA-TGAACATAAACA
1 AACATAAATG-ACTGAACATAAACG
1282421 AACATA
1 AACATA
1282427 TTTACTAAAC
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
23 1 0.02
24 41 0.93
25 2 0.05
ACGTcount: A:0.55, C:0.15, G:0.12, T:0.18
Consensus pattern (24 bp):
AACATAAATGACTGAACATAAACG
Found at i:1287407 original size:3 final size:3
Alignment explanation
Indices: 1287395--1287436 Score: 68
Period size: 3 Copynumber: 14.0 Consensus size: 3
1287385 AATATGTAAT
1287395 TAA T-A TAA TAA TAA TAA TAAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
1287437 AATTAAAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.05
3 32 0.86
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1287424 original size:22 final size:21
Alignment explanation
Indices: 1287395--1287437 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 21
1287385 AATATGTAAT
1287395 TAATATAATAATAATAATAAA
1 TAATATAATAATAATAATAAA
1287416 TAATAATAATAATAATAATAAA
1 TAAT-ATAATAATAATAATAAA
1287438 ATTAAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
TAATATAATAATAATAATAAA
Found at i:1287754 original size:46 final size:45
Alignment explanation
Indices: 1287694--1287888 Score: 158
Period size: 46 Copynumber: 4.4 Consensus size: 45
1287684 TCGGGGAATG
*
1287694 ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATA
1 ACACGGCTCCTACGTGATGAAGAGTTCTGGCCATCT-AAGGTGATA
* * * ** * *
1287740 ACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGT--TG
1 ACACGGCTCCTACGTGATGAAGA-GTTCTGGCCATCTAAGGTGATA
* * *
1287783 ACACGGCTCCTATGTGAT-AAGGAGATCTGG---TCT--GG-GAATG
1 ACACGGCTCCTACGTGATGAA-GAGTTCTGGCCATCTAAGGTG-ATA
*
1287823 ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTTAAGGTGATA
1 ACACGGCTCCTACGTGATGAAGAGTTCTGGCCATC-TAAGGTGATA
*
1287869 ACACGGTTCCTACGTGATGA
1 ACACGGCTCCTACGTGATGA
1287889 GGACGGCTGG
Statistics
Matches: 117, Mismatches: 18, Indels: 28
0.72 0.11 0.17
Matches are distributed among these distances:
38 2 0.02
40 29 0.25
41 2 0.02
42 2 0.02
43 25 0.21
44 1 0.01
45 4 0.03
46 50 0.43
47 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (45 bp):
ACACGGCTCCTACGTGATGAAGAGTTCTGGCCATCTAAGGTGATA
Found at i:1287800 original size:43 final size:43
Alignment explanation
Indices: 1287740--1287936 Score: 154
Period size: 43 Copynumber: 4.6 Consensus size: 43
1287730 AAAGGTGATA
*
1287740 ACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGTTG
1 ACACGGCTCCTACGTGATGAGGA-GAGCTGGTTATCTATGGTTG
* * * * *
1287783 ACACGGCTCCTATGTGATAAGGAGATCTGG---TCT-GGGAATG
1 ACACGGCTCCTACGTGATGAGGAGAGCTGGTTATCTATGG-TTG
* * ** ** * *
1287823 ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTTAAGGTGATA
1 ACACGGCTCCTACGTGATGAGGAGAGCTGGTTATC-TATGGT--TG
*
1287869 ACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGTTG
1 ACACGGCTCCTACGTGATGAGGA-GAGCTGGTTATCTATGGTTG
*
1287912 ACACGGCTCCTACGTGATAAGGAGA
1 ACACGGCTCCTACGTGATGAGGAGA
1287937 TGGTCTGGGG
Statistics
Matches: 119, Mismatches: 24, Indels: 22
0.72 0.15 0.13
Matches are distributed among these distances:
39 2 0.02
40 30 0.25
42 2 0.02
43 48 0.40
44 1 0.01
45 7 0.06
46 28 0.24
47 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.26
Consensus pattern (43 bp):
ACACGGCTCCTACGTGATGAGGAGAGCTGGTTATCTATGGTTG
Found at i:1287852 original size:40 final size:41
Alignment explanation
Indices: 1287691--1287929 Score: 119
Period size: 46 Copynumber: 5.5 Consensus size: 41
1287681 TGGTCGGGGA
1287691 ATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTG
1 ATGACACGGCTCATACGTGATGAAGAGTTCTGG--ATCT--AGG-G
* * * * * *
1287737 ATAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGG
1 ATGACACGGCTCATACGTGATGAAGA-GTTCTGG--ATCTAGGG
* * * *
1287780 TTGACACGGCTCCTATGTGAT-AAGGAGATCTGG-TCT-GGG
1 ATGACACGGCTCATACGTGATGAA-GAGTTCTGGATCTAGGG
1287819 AATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTTAAGGTG
1 -ATGACACGGCTCATACGTGATGAAGAGTTCTGG--ATC-T-AGG-G
* * * * * *
1287866 ATAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGG
1 ATGACACGGCTCATACGTGATGAAGA-GTTCTGG--ATCTAGGG
* *
1287909 TTGACACGGCTCCTACGTGAT
1 ATGACACGGCTCATACGTGAT
1287930 AAGGAGATGG
Statistics
Matches: 150, Mismatches: 30, Indels: 29
0.72 0.14 0.14
Matches are distributed among these distances:
39 2 0.01
40 29 0.19
41 2 0.01
42 2 0.01
43 45 0.30
44 5 0.03
45 1 0.01
46 61 0.41
47 3 0.02
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (41 bp):
ATGACACGGCTCATACGTGATGAAGAGTTCTGGATCTAGGG
Found at i:1287855 original size:129 final size:129
Alignment explanation
Indices: 1287652--1287969 Score: 514
Period size: 129 Copynumber: 2.5 Consensus size: 129
1287642 CGTCTAAAAG
* * * * * *
1287652 TGACAAGGTTCCTACATGATGAGGACATCTGGTCGGGGAATGACACGGCTCATACGTGATGAAGA
1 TGACACGGCTCCTACGTGATAAGGAGATCTGGTCTGGGAATGACACGGCTCATACGTGATGAAGA
1287717 GTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
66 GTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
*
1287781 TGACACGGCTCCTATGTGATAAGGAGATCTGGTCTGGGAATGACACGGCTCATACGTGATGAAGA
1 TGACACGGCTCCTACGTGATAAGGAGATCTGGTCTGGGAATGACACGGCTCATACGTGATGAAGA
*
1287846 GTTCTGGCCATCTTAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
66 GTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
* * * *
1287910 TGACACGGCTCCTACGTGATAAGGAGA--TGGTCTGGGGATGACACGGTTCCTACATGATGA
1 TGACACGGCTCCTACGTGATAAGGAGATCTGGTCTGGGAATGACACGGCTCATACGTGATGA
1287970 GGACGGCTGG
Statistics
Matches: 176, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
127 29 0.16
129 147 0.84
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.26
Consensus pattern (129 bp):
TGACACGGCTCCTACGTGATAAGGAGATCTGGTCTGGGAATGACACGGCTCATACGTGATGAAGA
GTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
Found at i:1288351 original size:66 final size:65
Alignment explanation
Indices: 1288178--1288343 Score: 167
Period size: 66 Copynumber: 2.6 Consensus size: 65
1288168 TGTCCCGAAA
* * * * * * * *
1288178 GAGACAAGATTCGTTTCAAAGGAAAC-AACCCAAAGAT-GGCATTTAAAGGG-AATTGTCTCAAG
1 GAGACAA-ATTCATTTCAAGGGAAACGATCTCAAAGATCGGTATTTCATGGGAAATTGTCTCAAA
1288240 C
65 C
** * * *
1288241 GAGACAAATTGTTTTTAAGGGAAACGTTCTCAAAGATCGGTATTTCATGGGAAATTGTCTCAAAT
1 GAGACAAATTCATTTCAAGGGAAACGATCTCAAAGATCGGTATTTCATGGGAAATTGTCTCAAAC
*
1288306 GAGACGAAATTCATTTCAAGGTAAACGATCTCAAAGAT
1 GAGAC-AAATTCATTTCAAGGGAAACGATCTCAAAGAT
1288344 GTTTATTTTG
Statistics
Matches: 82, Mismatches: 17, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
62 14 0.17
63 15 0.18
64 10 0.12
65 16 0.20
66 27 0.33
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (65 bp):
GAGACAAATTCATTTCAAGGGAAACGATCTCAAAGATCGGTATTTCATGGGAAATTGTCTCAAAC
Found at i:1288360 original size:35 final size:36
Alignment explanation
Indices: 1288319--1288393 Score: 100
Period size: 35 Copynumber: 2.1 Consensus size: 36
1288309 ACGAAATTCA
* **
1288319 TTTCAAGGTAAAC-GATCTCAAAGAT-GTTTATTTTG
1 TTTCAAGGGAAACAGAT-TCAAAGATGGTAAATTTTG
1288354 TTTCAAGGGAAACAGATTCAAAGATGGTAAATTTTG
1 TTTCAAGGGAAACAGATTCAAAGATGGTAAATTTTG
1288390 TTTC
1 TTTC
1288394 CAAAGAAACA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
35 20 0.57
36 15 0.43
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (36 bp):
TTTCAAGGGAAACAGATTCAAAGATGGTAAATTTTG
Found at i:1288878 original size:65 final size:64
Alignment explanation
Indices: 1288547--1288907 Score: 207
Period size: 65 Copynumber: 5.6 Consensus size: 64
1288537 GTATCTTAGT
* * * * *
1288547 GAGACAAAATTTTGTTTTC-AAAGAAACAGACTC--AGATTTTTCTTCAAAAGAAACTGTTTTAA
1 GAGACAAAATTTTG-TTTCAAAAGAAACAAACTCAAAGATTTTTTTTCAAAAGAAATTGTCTCAA
* * ** * * * * *
1288609 GGGATAAAACCTTGTTTCCAGAGAAACAAACTCAAAGATGATCTTATTTT-AAGAGAAAATGTTT
1 GAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGAT--T-TT-TTTTCAAAAGAAATTGTCT
1288673 CAA
62 CAA
* * ** * * ** * * **
1288676 GAGACAAAA-TTCGTTTGAAGGGAAAC-GACTCAAAGA-TGTCATTGAAAGGAAACGGTCTCATG
1 GAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTTTTTTCAAAAGAAATTGTCTCA--
*
1288738 C
64 A
* * * * * * * * *
1288739 GAGACAAAA-TTAGTTTTAATAGAAACAATCTCAAAGGTGGGTATTTTCAAAAGAAGTTGTCTCG
1 GAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGAT--TTTTTTTCAAAAGAAATTGTCTCA
1288803 A
64 A
* *
1288804 GAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTTTCAAAAGAAATTGTCTTTAA
1 GAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTTTTTTCAAAAGAAATTGTC-TCAA
* **
1288869 GAGATAAAATTTTGTTTCAAAAGAAACTGACTCAAAGAT
1 GAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGAT
1288908 GGATCTCATC
Statistics
Matches: 222, Mismatches: 61, Indels: 29
0.71 0.20 0.09
Matches are distributed among these distances:
60 2 0.01
61 16 0.07
62 23 0.10
63 22 0.10
64 29 0.13
65 55 0.25
66 36 0.16
67 36 0.16
68 3 0.01
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.29
Consensus pattern (64 bp):
GAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTTTTTTCAAAAGAAATTGTCTCAA
Found at i:1289177 original size:66 final size:65
Alignment explanation
Indices: 1289088--1289302 Score: 256
Period size: 67 Copynumber: 3.3 Consensus size: 65
1289078 AAAGATTTAC
** * * * * *
1289088 TTCAAAAGAAACGGTCTCAAGAGATACAAAATTCAT-TTT-AAGAGAAACATATTCAAAGATTTT
1 TTCAAAAGAAACTATCTTAAGAGAGACAAAATT-TTGTTTCAA-AGAAACAAACTCAAAGA-TTT
1289151 TGT
63 TGT
*
1289154 TTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTTT
1 TTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTC-AAAGAAACAAACTCAAAGA-TTTT
1289219 GT
64 GT
* *
1289221 TTCAAAAGAAACTATCATAAGAGAGAAAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTT-
1 TTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTT-CAAAGAAACAAACTCAAAGATTTTG
1289285 T
65 T
*
1289286 TTCAAAAGAAACAATCT
1 TTCAAAAGAAACTATCT
1289303 CAAAGATTTT
Statistics
Matches: 132, Mismatches: 13, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
65 17 0.13
66 35 0.27
67 77 0.58
68 3 0.02
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (65 bp):
TTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCAAAGAAACAAACTCAAAGATTTTGT
Found at i:1289197 original size:37 final size:35
Alignment explanation
Indices: 1289148--1289269 Score: 119
Period size: 37 Copynumber: 3.5 Consensus size: 35
1289138 ATTCAAAGAT
*
1289148 TTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAA
1 TTTTGTTTCAAAAGAAACTATC-TAAGAGAGA-AAAA
* * * *
1289185 TTTTGTTTCAAAAGAAACAAACTCA-A-AG---AT
1 TTTTGTTTCAAAAGAAACTATCTAAGAGAGAAAAA
1289215 TTTTGTTTCAAAAGAAACTATCATAAGAGAGAAAAAA
1 TTTTGTTTCAAAAGAAACTATC-TAAGAGAG-AAAAA
*
1289252 TTTTGTTTCCAAAGAAAC
1 TTTTGTTTCAAAAGAAAC
1289270 AAACTCAAAG
Statistics
Matches: 68, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
30 21 0.31
31 2 0.03
32 1 0.01
33 2 0.03
34 2 0.03
35 1 0.01
36 2 0.03
37 37 0.54
ACGTcount: A:0.46, C:0.11, G:0.12, T:0.31
Consensus pattern (35 bp):
TTTTGTTTCAAAAGAAACTATCTAAGAGAGAAAAA
Found at i:1289224 original size:67 final size:67
Alignment explanation
Indices: 1289130--1289297 Score: 268
Period size: 67 Copynumber: 2.5 Consensus size: 67
1289120 TCATTTTAAG
* * * * *
1289130 AGAAACATATTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCA
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAACTATCATAAGAGAGAAAAAATTTTGTTTCA
1289195 AA
66 AA
*
1289197 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAACTATCATAAGAGAGAAAAAATTTTGTTTCC
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAACTATCATAAGAGAGAAAAAATTTTGTTTCA
1289262 AA
66 AA
1289264 AGAAACAAACTCAAAGA-TTTT-TTTCAAAAGAAAC
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAAC
1289298 AATCTCAAAG
Statistics
Matches: 95, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
65 13 0.14
66 4 0.04
67 78 0.82
ACGTcount: A:0.48, C:0.11, G:0.11, T:0.30
Consensus pattern (67 bp):
AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAACTATCATAAGAGAGAAAAAATTTTGTTTCA
AA
Found at i:1289242 original size:29 final size:30
Alignment explanation
Indices: 1289185--1289313 Score: 127
Period size: 28 Copynumber: 4.1 Consensus size: 30
1289175 AGAGACAAAA
1289185 TTTTGTTTCAAAAGAAACAAACTCAAAGAT
1 TTTTGTTTCAAAAGAAACAAACTCAAAGAT
* * * *
1289215 TTTTGTTTCAAAAGAAACTATCATAAGAGAGAAAAAA
1 TTTTGTTTCAAAAGAAACAAAC-TCA-A-AG----AT
*
1289252 TTTTGTTTCCAAAGAAACAAACTCAAAGA-
1 TTTTGTTTCAAAAGAAACAAACTCAAAGAT
*
1289281 TTTT-TTTCAAAAGAAACAATCTCAAAGAT
1 TTTTGTTTCAAAAGAAACAAACTCAAAGAT
1289310 TTTT
1 TTTT
1289314 TTCACAAAAT
Statistics
Matches: 81, Mismatches: 10, Indels: 17
0.75 0.09 0.16
Matches are distributed among these distances:
28 22 0.27
29 8 0.10
30 21 0.26
31 2 0.02
32 1 0.01
33 2 0.02
34 2 0.02
35 1 0.01
36 2 0.02
37 20 0.25
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.32
Consensus pattern (30 bp):
TTTTGTTTCAAAAGAAACAAACTCAAAGAT
Found at i:1289381 original size:52 final size:53
Alignment explanation
Indices: 1289301--1289404 Score: 183
Period size: 52 Copynumber: 2.0 Consensus size: 53
1289291 AAGAAACAAT
1289301 CTCAAAGATTTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
1 CTCAAAGA-TTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
*
1289355 CTCAAAGA-TTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
1 CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
1289405 AAATAAATAG
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
52 41 0.84
54 8 0.16
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (53 bp):
CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
Found at i:1289527 original size:59 final size:57
Alignment explanation
Indices: 1289415--1289583 Score: 254
Period size: 59 Copynumber: 3.0 Consensus size: 57
1289405 AAATAAATAG
* * *
1289415 ACTCAAAGA--TTTTTCAAAAGAAAC-GACTCAAAGATATTTATTCAAGAGAAACTA
1 ACTCAAAGATTTTTTTCAAAAGAAACAAACTCAAAGATTTTTTTTCAAGAGAAACTA
* *
1289469 ACTCAAAGATTTTTTTCAAGAGGAACAAACTCAAAGATTTTTTTTTTCAAGAGAAACTA
1 ACTCAAAGATTTTTTTCAAAAGAAACAAACTCAAAGA--TTTTTTTTCAAGAGAAACTA
1289528 ACTCAAAGATTTTTTTCAAAAGAAACAAACTCAAAGATTTTTTTTCAAGAGAAACT
1 ACTCAAAGATTTTTTTCAAAAGAAACAAACTCAAAGATTTTTTTTCAAGAGAAACT
1289584 GTCTCAAGAG
Statistics
Matches: 103, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
54 9 0.09
56 13 0.13
57 28 0.27
59 53 0.51
ACGTcount: A:0.44, C:0.14, G:0.11, T:0.31
Consensus pattern (57 bp):
ACTCAAAGATTTTTTTCAAAAGAAACAAACTCAAAGATTTTTTTTCAAGAGAAACTA
Found at i:1289592 original size:28 final size:29
Alignment explanation
Indices: 1289424--1289583 Score: 209
Period size: 28 Copynumber: 5.6 Consensus size: 29
1289414 GACTCAAAGA
* * *
1289424 TTTTTCAAAAGAAAC-GACTCAAAGATAT
1 TTTTTCAAGAGAAACTAACTCAAAGATTT
*
1289452 TTATTCAAGAGAAACTAACTCAAAGA-TT
1 TTTTTCAAGAGAAACTAACTCAAAGATTT
* *
1289480 TTTTTCAAGAGGAACAAACTCAAAGATTTTT
1 TTTTTCAAGAGAAACTAACTCAAAGA--TTT
1289511 TTTTTCAAGAGAAACTAACTCAAAGA-TT
1 TTTTTCAAGAGAAACTAACTCAAAGATTT
* *
1289539 TTTTTCAAAAGAAACAAACTCAAAGATTT
1 TTTTTCAAGAGAAACTAACTCAAAGATTT
1289568 TTTTTCAAGAGAAACT
1 TTTTTCAAGAGAAACT
1289584 GTCTCAAGAG
Statistics
Matches: 114, Mismatches: 13, Indels: 9
0.84 0.10 0.07
Matches are distributed among these distances:
28 63 0.55
29 25 0.22
31 26 0.23
ACGTcount: A:0.44, C:0.14, G:0.11, T:0.32
Consensus pattern (29 bp):
TTTTTCAAGAGAAACTAACTCAAAGATTT
Found at i:1289917 original size:36 final size:36
Alignment explanation
Indices: 1289824--1289927 Score: 124
Period size: 36 Copynumber: 3.0 Consensus size: 36
1289814 GAGAAAATGA
* *
1289824 TGTCTCAAGCGAGACAAAATTTG-CTTTA-AGATAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
* * **
1289858 AGTTTCAAATGAGACAAAATTTGTTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
*
1289894 TGTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAA
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAA
1289928 ACGATCTCAA
Statistics
Matches: 57, Mismatches: 11, Indels: 3
0.80 0.15 0.04
Matches are distributed among these distances:
34 19 0.33
35 10 0.18
36 28 0.49
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.34
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
Found at i:1289955 original size:36 final size:36
Alignment explanation
Indices: 1289862--1289943 Score: 103
Period size: 36 Copynumber: 2.3 Consensus size: 36
1289852 AGATATAGTT
**
1289862 TCAAATGAGACAAAATTTGTTTTTAGAGAAATTGTC
1 TCAAATGAGACAAAATTTGTTTTTAGAGAAAACGTC
** *
1289898 TCAAGCGAGACAAAGTTTGTTTTT-GAGAAAACGATC
1 TCAAATGAGACAAAATTTGTTTTTAGAGAAAACG-TC
1289934 TCAAATGAGA
1 TCAAATGAGA
1289944 TCAACTTTGT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
35 7 0.18
36 31 0.82
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (36 bp):
TCAAATGAGACAAAATTTGTTTTTAGAGAAAACGTC
Found at i:1290074 original size:105 final size:101
Alignment explanation
Indices: 1289895--1290127 Score: 267
Period size: 105 Copynumber: 2.3 Consensus size: 101
1289885 TAGAGAAATT
*
1289895 GTCTCAAGCGAGAC-AAAGTTTGTTTTTGAGAAAACGATCTCAAATGAGATCAACTTTGTTTAAT
1 GTCTCAAGCGAGACGAAA-TTTG-TTTTGAGAAAACAATCTCAAATGAGATCAACTTTGTTTAAT
*
1289959 GTGAAGCAAATTCGAA-ATTTGGATCTCAAAGGGAAAAG
64 GTGAAGCAAATTC-AAGATTTGGATCTCAAAGGAAAAAG
* * *
1289997 GTCTCAAGCGAGACGAAATTTGTTTTGAAAGAAACAACAATCT-AAGGTGAGATTAATTTTGTTT
1 GTCTCAAGCGAGACGAAATTTGTTTTG--AG-AA-AACAATCTCAA-ATGAGATCAACTTTG-TT
* * * *
1290061 TAA-GTGAATCAAATTCAAGGTTTGTATCTCAAAGGAAAAAT
60 TAATGTGAAGCAAATTCAAGATTTGGATCTCAAAGGAAAAAG
*
1290102 GTCTCAAGCGAGACGAAGTTTGTTTT
1 GTCTCAAGCGAGACGAAATTTGTTTT
1290128 AAGAGAATTT
Statistics
Matches: 113, Mismatches: 10, Indels: 13
0.83 0.07 0.10
Matches are distributed among these distances:
101 5 0.04
102 18 0.16
103 5 0.04
104 6 0.05
105 74 0.65
106 5 0.04
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.30
Consensus pattern (101 bp):
GTCTCAAGCGAGACGAAATTTGTTTTGAGAAAACAATCTCAAATGAGATCAACTTTGTTTAATGT
GAAGCAAATTCAAGATTTGGATCTCAAAGGAAAAAG
Found at i:1290190 original size:36 final size:36
Alignment explanation
Indices: 1290101--1290195 Score: 93
Period size: 36 Copynumber: 2.6 Consensus size: 36
1290091 AAAGGAAAAA
* * * *
1290101 TGTCTCAAGCGAGACGAAGTTTGTTTTAAGAGAATT
1 TGTCTCAAGCGAAACAAAATTTGTTTTAAGAGAAAT
* * * *
1290137 TGTCTTAAGTGATACAAACTTTGTTTTTAA-AGAAAT
1 TGTCTCAAGCGAAACAAAATTTG-TTTTAAGAGAAAT
*
1290173 TGTCTCAAGCAAAACAAAATTTG
1 TGTCTCAAGCGAAACAAAATTTG
1290196 AGAAAATGAT
Statistics
Matches: 47, Mismatches: 11, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
36 41 0.87
37 6 0.13
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.35
Consensus pattern (36 bp):
TGTCTCAAGCGAAACAAAATTTGTTTTAAGAGAAAT
Found at i:1290325 original size:36 final size:35
Alignment explanation
Indices: 1290285--1290402 Score: 150
Period size: 36 Copynumber: 3.3 Consensus size: 35
1290275 AGTGAGGCGG
1290285 AATTTGTTTTTCAAGAAATTGTCTCAAGCGAGACAA
1 AATTTGTTTTT-AAGAAATTGTCTCAAGCGAGACAA
* *
1290321 AATTTGTTTTT-AGAAAGCTGTCTCAATCGAGACAA
1 AATTTGTTTTTAAGAAA-TTGTCTCAAGCGAGACAA
*
1290356 AATTT-TCTTTGAAAGAAATTGTCTCAAGCGAGACAAA
1 AATTTGT-TTT-TAAGAAATTGTCTCAAGCGAGAC-AA
1290393 AATTTGTTTT
1 AATTTGTTTT
1290403 AAAATTCTCA
Statistics
Matches: 71, Mismatches: 5, Indels: 11
0.82 0.06 0.13
Matches are distributed among these distances:
34 6 0.08
35 24 0.34
36 25 0.35
37 15 0.21
38 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.36
Consensus pattern (35 bp):
AATTTGTTTTTAAGAAATTGTCTCAAGCGAGACAA
Found at i:1291098 original size:23 final size:24
Alignment explanation
Indices: 1291054--1291098 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1291044 GTCTGAAAAT
*
1291054 ATCAATAGTTTTGAAAAATATTTA
1 ATCAAAAGTTTTGAAAAATATTTA
1291078 ATCAAAAGTTTTG-AAAATATT
1 ATCAAAAGTTTTGAAAAATATT
1291099 GCTCCTTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.47, C:0.04, G:0.09, T:0.40
Consensus pattern (24 bp):
ATCAAAAGTTTTGAAAAATATTTA
Found at i:1297954 original size:3 final size:3
Alignment explanation
Indices: 1297942--1297983 Score: 68
Period size: 3 Copynumber: 14.0 Consensus size: 3
1297932 AATATGTAAT
1297942 TAA T-A TAA TAA TAA TAA TAAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
1297984 AATTAAAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.05
3 32 0.86
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1297971 original size:22 final size:21
Alignment explanation
Indices: 1297942--1297984 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 21
1297932 AATATGTAAT
1297942 TAATATAATAATAATAATAAA
1 TAATATAATAATAATAATAAA
1297963 TAATAATAATAATAATAATAAA
1 TAAT-ATAATAATAATAATAAA
1297985 ATTAAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
TAATATAATAATAATAATAAA
Found at i:1299223 original size:15 final size:15
Alignment explanation
Indices: 1299205--1299235 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1299195 AAATTCTAAA
1299205 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
1299220 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
1299235 T
1 T
1299236 CTATTTGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:1303681 original size:64 final size:63
Alignment explanation
Indices: 1303603--1303789 Score: 191
Period size: 65 Copynumber: 2.9 Consensus size: 63
1303593 GATGCATTAA
* *
1303603 ACCATGCATCGATGCACCAATGAATTAATTGAACATCGAATGCATTTGATGCATCGATCCACAT
1 ACCATGCATCGATGCACCAATGATTTAA-TGAACATCGAATGCATTTGATGCATCGATCCACAG
* * * * * *
1303667 ACCATGCATTGATGCATTCAA-GGTTTTATGAAAACATCGAATGCATTTGATGCATCGATTCATA
1 ACCATGCATCGATGCA-CCAATGATTTAATG--AACATCGAATGCATTTGATGCATCGATCCACA
1303731 G
63 G
* * *
1303732 ACCATGCATCGATGTACTAATGCTATTTCAA--AACATCGAATGCATTTTATGCATCGAT
1 ACCATGCATCGATGCACCAATG--ATTT-AATGAACATCGAATGCATTTGATGCATCGAT
1303790 ACATTCTTCG
Statistics
Matches: 101, Mismatches: 15, Indels: 14
0.78 0.12 0.11
Matches are distributed among these distances:
63 2 0.02
64 47 0.47
65 48 0.48
67 3 0.03
68 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.30
Consensus pattern (63 bp):
ACCATGCATCGATGCACCAATGATTTAATGAACATCGAATGCATTTGATGCATCGATCCACAG
Found at i:1303708 original size:65 final size:64
Alignment explanation
Indices: 1303634--1303789 Score: 197
Period size: 65 Copynumber: 2.4 Consensus size: 64
1303624 GAATTAATTG
* * * * * *
1303634 AACATCGAATGCATTTGATGCATCGATCCACATACCATGCATTGATGCATTCAA-GGTTTTATGA
1 AACATCGAATGCATTTGATGCATCGATCCACAGACCATGCATCGATGCACT-AATGCTATT-TCA
1303698 A
64 A
* * *
1303699 AACATCGAATGCATTTGATGCATCGATTCATAGACCATGCATCGATGTACTAATGCTATTTCAA
1 AACATCGAATGCATTTGATGCATCGATCCACAGACCATGCATCGATGCACTAATGCTATTTCAA
*
1303763 AACATCGAATGCATTTTATGCATCGAT
1 AACATCGAATGCATTTGATGCATCGAT
1303790 ACATTCTTCG
Statistics
Matches: 80, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
64 31 0.39
65 49 0.61
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (64 bp):
AACATCGAATGCATTTGATGCATCGATCCACAGACCATGCATCGATGCACTAATGCTATTTCAA
Found at i:1304669 original size:2 final size:2
Alignment explanation
Indices: 1304662--1304690 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1304652 TCTAAATTTC
1304662 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1304691 TAAAGACTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1313743 original size:17 final size:17
Alignment explanation
Indices: 1313723--1313757 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1313713 TTTCAACCTT
1313723 CCCCATTAGATACATGG
1 CCCCATTAGATACATGG
1313740 CCCCATTAGATACATGG
1 CCCCATTAGATACATGG
1313757 C
1 C
1313758 AACTACCTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (17 bp):
CCCCATTAGATACATGG
Found at i:1317222 original size:24 final size:24
Alignment explanation
Indices: 1317191--1317264 Score: 94
Period size: 24 Copynumber: 3.1 Consensus size: 24
1317181 GATACATGAC
1317191 ATGAATTCTGTTATGATTTCTGAT
1 ATGAATTCTGTTATGATTTCTGAT
* * *
1317215 ATGGATTCTGTTCTGATATCTGAT
1 ATGAATTCTGTTATGATTTCTGAT
* * *
1317239 TTGAATTCTGTTTTGATTTTTGAT
1 ATGAATTCTGTTATGATTTCTGAT
1317263 AT
1 AT
1317265 CTTTGTTTAC
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.22, C:0.08, G:0.18, T:0.53
Consensus pattern (24 bp):
ATGAATTCTGTTATGATTTCTGAT
Found at i:1319285 original size:28 final size:28
Alignment explanation
Indices: 1319254--1319314 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 28
1319244 TTGATATAAC
* *
1319254 AATTTAA-GGCAAAATGTTTTTGGACTT
1 AATTTAATGACAAAATATTTTTGGACTT
*
1319281 GAATTTAATTTACAAAATATTTTTGGACTT
1 -AATTTAA-TGACAAAATATTTTTGGACTT
1319311 AATT
1 AATT
1319315 GAATTTATTC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 7 0.25
29 4 0.14
30 17 0.61
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.44
Consensus pattern (28 bp):
AATTTAATGACAAAATATTTTTGGACTT
Found at i:1319332 original size:29 final size:30
Alignment explanation
Indices: 1319263--1319321 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
1319253 CAATTTAAGG
* *
1319263 CAAAATGTTTTTGGACTTGAATTTAATTTA
1 CAAAATATTTTTGGACTTGAATTGAATTTA
1319293 CAAAATATTTTTGGACTT-AATTGAATTTA
1 CAAAATATTTTTGGACTTGAATTGAATTTA
1319322 TTCAAATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.46
Consensus pattern (30 bp):
CAAAATATTTTTGGACTTGAATTGAATTTA
Found at i:1319427 original size:21 final size:21
Alignment explanation
Indices: 1319401--1319496 Score: 88
Period size: 21 Copynumber: 4.6 Consensus size: 21
1319391 AGGGTGTCAA
1319401 AGTGCATCCATGCATCCATGC
1 AGTGCATCCATGCATCCATGC
* * *
1319422 AGTGCATCTATACATCCCTGC
1 AGTGCATCCATGCATCCATGC
**
1319443 AGTGCATCCATGCA-CCTACAC
1 AGTGCATCCATGCATCC-ATGC
* *
1319464 TAATGCATCGATGCAT-CATGC
1 -AGTGCATCCATGCATCCATGC
*
1319485 AATGCATCCATG
1 AGTGCATCCATG
1319497 TAGTCAAACA
Statistics
Matches: 59, Mismatches: 13, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
20 13 0.22
21 33 0.56
22 13 0.22
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.25
Consensus pattern (21 bp):
AGTGCATCCATGCATCCATGC
Found at i:1319490 original size:20 final size:20
Alignment explanation
Indices: 1319465--1319575 Score: 58
Period size: 20 Copynumber: 5.8 Consensus size: 20
1319455 CACCTACACT
1319465 AATGCATCGATGCATCATGC
1 AATGCATCGATGCATCATGC
*
1319485 AATGCATCCATG--T-A-GTC
1 AATGCATCGATGCATCATG-C
* *
1319502 AA-ACATCGAATGCA-C-T-T
1 AATGCATCG-ATGCATCATGC
* *
1319519 AGTGCATCGATGCATCCTGC
1 AATGCATCGATGCATCATGC
* * *
1319539 CATGCATCGATGCATCCTAC
1 AATGCATCGATGCATCATGC
* *
1319559 GATGCATCCATGCATCA
1 AATGCATCGATGCATCA
1319576 AGGCTGCAAC
Statistics
Matches: 68, Mismatches: 13, Indels: 20
0.67 0.13 0.20
Matches are distributed among these distances:
16 5 0.07
17 13 0.19
18 7 0.10
19 1 0.01
20 42 0.62
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (20 bp):
AATGCATCGATGCATCATGC
Found at i:1319970 original size:34 final size:32
Alignment explanation
Indices: 1319931--1320000 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
1319921 TTTTGTAAAG
*
1319931 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
1319965 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
1319997 GGGA
1 GGGA
1320001 GTTTGTAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:1320882 original size:19 final size:20
Alignment explanation
Indices: 1320858--1320905 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1320848 AACGATTTTC
* *
1320858 TTTTGAAAGCAAAAATG-GA
1 TTTTGAAAACAAAAATGAAA
*
1320877 TTTTGAAAACCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
1320897 TTTTGAAAA
1 TTTTGAAAA
1320906 AGGATTTAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.50, C:0.06, G:0.15, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:1320948 original size:23 final size:22
Alignment explanation
Indices: 1320913--1320956 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
1320903 AAAAGGATTT
1320913 AGAGCTTTCAAAAATGAAAATTG
1 AGAGCTTTCAAAAA-GAAAATTG
* *
1320936 AGAGTTTTGAAAAAGAAAATT
1 AGAGCTTTCAAAAAGAAAATT
1320957 TTGATTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.50, C:0.05, G:0.18, T:0.27
Consensus pattern (22 bp):
AGAGCTTTCAAAAAGAAAATTG
Found at i:1322181 original size:29 final size:30
Alignment explanation
Indices: 1322129--1322187 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
1322119 CAATTTAAGG
*
1322129 CAAAATATTTTTAGACTTGAATTGAATTTA
1 CAAAATATTTTTAGACCTGAATTGAATTTA
*
1322159 CAAAATATTTTTGGACCT-AATTGAATTTA
1 CAAAATATTTTTAGACCTGAATTGAATTTA
1322188 TTCAAAGTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 11 0.41
30 16 0.59
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.42
Consensus pattern (30 bp):
CAAAATATTTTTAGACCTGAATTGAATTTA
Found at i:1322293 original size:21 final size:21
Alignment explanation
Indices: 1322267--1322364 Score: 103
Period size: 21 Copynumber: 4.7 Consensus size: 21
1322257 AAGGTGTCAA
*
1322267 AGTGCATCAATGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
1322288 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
1322309 AGTGCATCCATGCA--CCTGCAC
1 AGTGCATCCATGCATCCCTG--C
* * *
1322330 TAATGCATCGATGCAT-CATGC
1 -AGTGCATCCATGCATCCCTGC
*
1322351 AATGCATCCATGCA
1 AGTGCATCCATGCA
1322365 CTCAAACATC
Statistics
Matches: 68, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
19 4 0.06
20 13 0.19
21 36 0.53
22 12 0.18
23 3 0.04
ACGTcount: A:0.26, C:0.33, G:0.18, T:0.23
Consensus pattern (21 bp):
AGTGCATCCATGCATCCCTGC
Found at i:1322356 original size:20 final size:19
Alignment explanation
Indices: 1322269--1322440 Score: 84
Period size: 20 Copynumber: 8.7 Consensus size: 19
1322259 GGTGTCAAAG
* *
1322269 TGCATCAATGCATCCCTGCAG
1 TGCATCGATGCAT--CTGCAA
* *
1322290 TGCATCCATGCATCCCTGCAG
1 TGCATCGATGCAT--CTGCAA
* *
1322311 TGCATCCATGCACCTGCACTAA
1 TGCATCGATGCATCTG--C-AA
1322333 TGCATCGATGCATCATGCAA
1 TGCATCGATGCATC-TGCAA
*
1322353 TGCATCCATGCA-CT-CAA
1 TGCATCGATGCATCTGCAA
* * *
1322370 -ACATCGAATGCA-CT-TAG
1 TGCATCG-ATGCATCTGCAA
*
1322387 TGCATCGATGCATCCTGCCA
1 TGCATCGATGCAT-CTGCAA
* *
1322407 TGCATTGATGCATCCTGCGA
1 TGCATCGATGCAT-CTGCAA
*
1322427 TGCATCCATGCATC
1 TGCATCGATGCATC
1322441 AAGGCTGCAA
Statistics
Matches: 124, Mismatches: 18, Indels: 20
0.77 0.11 0.12
Matches are distributed among these distances:
16 4 0.03
17 16 0.13
18 6 0.05
19 7 0.06
20 42 0.34
21 34 0.27
22 13 0.10
23 2 0.02
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.25
Consensus pattern (19 bp):
TGCATCGATGCATCTGCAA
Found at i:1325082 original size:121 final size:122
Alignment explanation
Indices: 1324867--1325106 Score: 446
Period size: 121 Copynumber: 2.0 Consensus size: 122
1324857 TTTATTATGG
* *
1324867 TACATTTGGAGATTATGGTACCAAACTACCAATGGCCATACAATGAACGTAGCCCTCCGGCATTC
1 TACATATGGAGATTATGGTACCAAACTACCAATGGCCATACAATGAACGTAGCCCTCCAGCATTC
1324932 TGCTAAATCCAACTCGCGACTTTCACATAGTTCAATCTGAGACTTCCAAGTTGGCCA
66 TGCTAAATCCAACTCGCGACTTTCACATAGTTCAATCTGAGACTTCCAAGTTGGCCA
1324989 TACATATGGAGATTATGGTACCAAACTACCAATGG-CATACAATGAACGTAGCCCTCCAGCATTC
1 TACATATGGAGATTATGGTACCAAACTACCAATGGCCATACAATGAACGTAGCCCTCCAGCATTC
*
1325053 TGCTAAATCCAACTCGCTACTTTCACATAGTTCAATCTGAGACTTCCAAGTTGG
66 TGCTAAATCCAACTCGCGACTTTCACATAGTTCAATCTGAGACTTCCAAGTTGG
1325107 ACTCTTTAAG
Statistics
Matches: 115, Mismatches: 3, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
121 81 0.70
122 34 0.30
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (122 bp):
TACATATGGAGATTATGGTACCAAACTACCAATGGCCATACAATGAACGTAGCCCTCCAGCATTC
TGCTAAATCCAACTCGCGACTTTCACATAGTTCAATCTGAGACTTCCAAGTTGGCCA
Found at i:1326157 original size:12 final size:12
Alignment explanation
Indices: 1326142--1326166 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1326132 TATATATGAA
1326142 TAGATATTTTTT
1 TAGATATTTTTT
1326154 TAGATATTTTTT
1 TAGATATTTTTT
1326166 T
1 T
1326167 TATTTTTAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (12 bp):
TAGATATTTTTT
Found at i:1328158 original size:57 final size:61
Alignment explanation
Indices: 1328088--1328208 Score: 151
Period size: 57 Copynumber: 2.0 Consensus size: 61
1328078 AATGTAGTAA
*
1328088 ATTATTATAAAATAGATTATTTTAATCA-TTTAAAATA-TAATAAATGAT-TATAGAT-AT
1 ATTATTATAAAATAGATTATTTAAATCATTTTAAAATACTAATAAATGATATATAGATAAT
* * * * * *
1328145 ATTATTATTAAATATATTATTTAAATTATTTTGAAATACTAATATATTATATATAGATAAT
1 ATTATTATAAAATAGATTATTTAAATCATTTTAAAATACTAATAAATGATATATAGATAAT
1328206 ATT
1 ATT
1328209 GTACAAACCC
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
57 24 0.45
58 8 0.15
59 9 0.17
60 7 0.13
61 5 0.09
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (61 bp):
ATTATTATAAAATAGATTATTTAAATCATTTTAAAATACTAATAAATGATATATAGATAAT
Found at i:1328582 original size:23 final size:22
Alignment explanation
Indices: 1328548--1328590 Score: 52
Period size: 23 Copynumber: 1.9 Consensus size: 22
1328538 TTCAGGTGCG
*
1328548 TTTGTAAACCCTGATCTTCATCT
1 TTTGTAAACCCTCAT-TTCATCT
1328571 TTTG-AAACCCCTCATTTCAT
1 TTTGTAAA-CCCTCATTTCAT
1328591 TACCAAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.23, C:0.28, G:0.07, T:0.42
Consensus pattern (22 bp):
TTTGTAAACCCTCATTTCATCT
Found at i:1337964 original size:16 final size:16
Alignment explanation
Indices: 1337943--1337973 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1337933 GAGAATTGGG
1337943 TTGGTTTGTTAAAGAA
1 TTGGTTTGTTAAAGAA
1337959 TTGGTTTGTTAAAGA
1 TTGGTTTGTTAAAGA
1337974 GTTGTTTACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.45
Consensus pattern (16 bp):
TTGGTTTGTTAAAGAA
Found at i:1338559 original size:16 final size:16
Alignment explanation
Indices: 1338540--1338573 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1338530 CAATATACGA
1338540 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
1338556 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
1338572 AT
1 AT
1338574 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:1338647 original size:16 final size:18
Alignment explanation
Indices: 1338615--1338648 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1338605 TATTAATGTA
1338615 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
1338633 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
1338649 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:1339319 original size:130 final size:130
Alignment explanation
Indices: 1339115--1339362 Score: 424
Period size: 130 Copynumber: 1.9 Consensus size: 130
1339105 AATTTTCTTC
*
1339115 TAATTAGGTGGTGACATGTGTCACCAATAACACATACCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATACCATGATCATGTGCTAACACATGTCAGAT
** *
1339180 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * **
1339245 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATACCATGATCATGTGCTAACACATGTCAGAT
1339310 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
1339363 TATATAAATA
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 110 1.00
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.35
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATACCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:1339821 original size:35 final size:36
Alignment explanation
Indices: 1339759--1339835 Score: 120
Period size: 35 Copynumber: 2.2 Consensus size: 36
1339749 AATTGAATTT
* *
1339759 AATTGAATTATTTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTATCTTTGGAAATTAGGGTTTAGAATGA
*
1339795 AATTGAATTA-CTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTATCTTTGGAAATTAGGGTTTAGAATGA
1339830 AATTGA
1 AATTGA
1339836 GGATTGTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
35 28 0.74
36 10 0.26
ACGTcount: A:0.35, C:0.01, G:0.23, T:0.40
Consensus pattern (36 bp):
AATTGAATTATCTTTGGAAATTAGGGTTTAGAATGA
Found at i:1355736 original size:65 final size:65
Alignment explanation
Indices: 1355655--1355779 Score: 250
Period size: 65 Copynumber: 1.9 Consensus size: 65
1355645 TAATGGTGGG
1355655 GTTCGAAATAAACAAGCACAAAGCAAGTATCATTCATTCCTTACAACCCAATAACAAAATATGAA
1 GTTCGAAATAAACAAGCACAAAGCAAGTATCATTCATTCCTTACAACCCAATAACAAAATATGAA
1355720 GTTCGAAATAAACAAGCACAAAGCAAGTATCATTCATTCCTTACAACCCAATAACAAAAT
1 GTTCGAAATAAACAAGCACAAAGCAAGTATCATTCATTCCTTACAACCCAATAACAAAAT
1355780 GAAAGGAGAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 60 1.00
ACGTcount: A:0.47, C:0.22, G:0.09, T:0.22
Consensus pattern (65 bp):
GTTCGAAATAAACAAGCACAAAGCAAGTATCATTCATTCCTTACAACCCAATAACAAAATATGAA
Found at i:1356547 original size:24 final size:24
Alignment explanation
Indices: 1356520--1356645 Score: 146
Period size: 24 Copynumber: 5.2 Consensus size: 24
1356510 ATTTTCGATT
1356520 TGAATTCTGATATGATACTTGACA
1 TGAATTCTGATATGATACTTGACA
1356544 TGAATTCTGATATGATA-TCTGACA
1 TGAATTCTGATATGATACT-TGACA
* * *
1356568 TGGATTCTGATCTGATACTTGACT
1 TGAATTCTGATATGATACTTGACA
* * * *
1356592 TGGATTGTGATCTGATACTTGACC
1 TGAATTCTGATATGATACTTGACA
* * *
1356616 TGGATTTTGATATGATACTTAACA
1 TGAATTCTGATATGATACTTGACA
1356640 TGAATT
1 TGAATT
1356646 ATGTTTTGAT
Statistics
Matches: 90, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
23 1 0.01
24 88 0.98
25 1 0.01
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.40
Consensus pattern (24 bp):
TGAATTCTGATATGATACTTGACA
Found at i:1356558 original size:12 final size:11
Alignment explanation
Indices: 1356523--1356583 Score: 50
Period size: 12 Copynumber: 5.2 Consensus size: 11
1356513 TTCGATTTGA
1356523 ATTCTGATATG
1 ATTCTGATATG
* *
1356534 ATACTTGACATG
1 ATTC-TGATATG
1356546 AATTCTGATATG
1 -ATTCTGATATG
*
1356558 ATATCTGACATGG
1 AT-TCTGATAT-G
*
1356571 ATTCTGATCTG
1 ATTCTGATATG
1356582 AT
1 AT
1356584 ACTTGACTTG
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
11 8 0.21
12 25 0.64
13 6 0.15
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.39
Consensus pattern (11 bp):
ATTCTGATATG
Found at i:1356773 original size:35 final size:35
Alignment explanation
Indices: 1356725--1356791 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
1356715 GAATACCTGG
1356725 AGGCTCCCTGGCTTTGTGCTCAGGGCCTTACTTGC
1 AGGCTCCCTGGCTTTGTGCTCAGGGCCTTACTTGC
1356760 AGGCT-CCTCGGCTTTGTGCTCAGGGCCTTACT
1 AGGCTCCCT-GGCTTTGTGCTCAGGGCCTTACT
1356792 ATATGTGACG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
34 3 0.10
35 28 0.90
ACGTcount: A:0.09, C:0.31, G:0.28, T:0.31
Consensus pattern (35 bp):
AGGCTCCCTGGCTTTGTGCTCAGGGCCTTACTTGC
Found at i:1361235 original size:24 final size:24
Alignment explanation
Indices: 1361208--1361322 Score: 151
Period size: 24 Copynumber: 4.8 Consensus size: 24
1361198 ATTTGAATTT
1361208 TGATATGATACTTGACATGGATTC
1 TGATATGATACTTGACATGGATTC
*
1361232 TGATCTGATA-TCTGACATGGATTC
1 TGATATGATACT-TGACATGGATTC
* *
1361256 TGACATGATACTTGACTTGGATTC
1 TGATATGATACTTGACATGGATTC
* * *
1361280 TGATCTGATACTTGACCTGGATTT
1 TGATATGATACTTGACATGGATTC
*
1361304 TGATATGATACTTGGCATG
1 TGATATGATACTTGACATG
1361323 AATTATGGTT
Statistics
Matches: 78, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
23 1 0.01
24 76 0.97
25 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.38
Consensus pattern (24 bp):
TGATATGATACTTGACATGGATTC
Found at i:1361257 original size:12 final size:12
Alignment explanation
Indices: 1361220--1361282 Score: 60
Period size: 12 Copynumber: 5.2 Consensus size: 12
1361210 ATATGATACT
1361220 TGACATGGATTC
1 TGACATGGATTC
1361232 TGATC-T-GATATC
1 TGA-CATGGAT-TC
1361244 TGACATGGATTC
1 TGACATGGATTC
*
1361256 TGACAT-GATAC
1 TGACATGGATTC
*
1361267 TTGACTTGGATTC
1 -TGACATGGATTC
1361280 TGA
1 TGA
1361283 TCTGATACTT
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
11 8 0.19
12 26 0.62
13 8 0.19
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (12 bp):
TGACATGGATTC
Found at i:1361452 original size:35 final size:35
Alignment explanation
Indices: 1361406--1361472 Score: 125
Period size: 35 Copynumber: 1.9 Consensus size: 35
1361396 GAATACCTGG
*
1361406 AGGCTCCTCGGCTTTGTGCTTAGGGCCTTACTTGC
1 AGGCTCCTCGGCTTTGTGCTCAGGGCCTTACTTGC
1361441 AGGCTCCTCGGCTTTGTGCTCAGGGCCTTACT
1 AGGCTCCTCGGCTTTGTGCTCAGGGCCTTACT
1361473 GTACGTGACG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.09, C:0.30, G:0.28, T:0.33
Consensus pattern (35 bp):
AGGCTCCTCGGCTTTGTGCTCAGGGCCTTACTTGC
Found at i:1364823 original size:75 final size:76
Alignment explanation
Indices: 1364756--1364919 Score: 233
Period size: 76 Copynumber: 2.2 Consensus size: 76
1364746 AAAAAATAAT
* *
1364756 ATAATATTCTAAATCCTAATTAAAATACTA-AAACCTATTTAAACTAAAATACAAAGATAAAGAT
1 ATAATATCCTAAAACCTAATTAAAATACTACAAACCTATTTAAACTAAAATACAAAGATAAAGAT
1364820 AAAATATAAAA
66 AAAATATAAAA
* *
1364831 ATAATATCCTAAAACTTAATTAAAATGCTACAAACCTATTTAAACTAAAATACAAAGATAAA-AT
1 ATAATATCCTAAAACCTAATTAAAATACTACAAACCTATTTAAACTAAAATACAAAGATAAAGAT
* * *
1364895 ATAATGTTTAAA
66 AAAAT-ATAAAA
*
1364907 ATATTATCCTAAA
1 ATAATATCCTAAA
1364920 TTTGAGTTTA
Statistics
Matches: 79, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
75 32 0.41
76 47 0.59
ACGTcount: A:0.55, C:0.12, G:0.03, T:0.30
Consensus pattern (76 bp):
ATAATATCCTAAAACCTAATTAAAATACTACAAACCTATTTAAACTAAAATACAAAGATAAAGAT
AAAATATAAAA
Found at i:1366800 original size:19 final size:20
Alignment explanation
Indices: 1366776--1366814 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1366766 AAAGTTCGCT
1366776 AAAAAAT-AAAACAAAAATA
1 AAAAAATAAAAACAAAAATA
1366795 AAAAAATAAAAACAAAAATA
1 AAAAAATAAAAACAAAAATA
1366815 TAACGAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.85, C:0.05, G:0.00, T:0.10
Consensus pattern (20 bp):
AAAAAATAAAAACAAAAATA
Found at i:1373169 original size:13 final size:13
Alignment explanation
Indices: 1373151--1373179 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1373141 TGATTTGGGC
1373151 TTGTAAATGGACT
1 TTGTAAATGGACT
1373164 TTGTAAATGGACT
1 TTGTAAATGGACT
1373177 TTG
1 TTG
1373180 AACACTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.07, G:0.24, T:0.41
Consensus pattern (13 bp):
TTGTAAATGGACT
Found at i:1374096 original size:42 final size:42
Alignment explanation
Indices: 1374048--1374181 Score: 180
Period size: 42 Copynumber: 3.2 Consensus size: 42
1374038 TTACAAATTA
1374048 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
1 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
* * * * * * **
1374090 CCCGAAGGACTT-ATCAACTTGCTCTAAAGGCTTACAGATAA
1 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
*
1374131 CCTGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
1 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
1374173 CCCGAAGGA
1 CCCGAAGGA
1374182 CTTATAAATT
Statistics
Matches: 73, Mismatches: 18, Indels: 2
0.78 0.19 0.02
Matches are distributed among these distances:
41 32 0.44
42 41 0.56
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (42 bp):
CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
Found at i:1374138 original size:41 final size:42
Alignment explanation
Indices: 1374037--1374185 Score: 165
Period size: 42 Copynumber: 3.6 Consensus size: 42
1374027 TTGGTGAAGG
* * *
1374037 CTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGA
1 CTTACAGATGACCCGAAGGACTTAATCATCATGCTCGAAAGA
* * * * * *
1374079 CTTACTGATGGCCCGAAGGACTT-ATCAACTTGCTCTAAAGG
1 CTTACAGATGACCCGAAGGACTTAATCATCATGCTCGAAAGA
* * *
1374120 CTTACAGATAACCTGAAGGATTTAATCATCATGCTCGAAAGA
1 CTTACAGATGACCCGAAGGACTTAATCATCATGCTCGAAAGA
* *
1374162 CTTACTGATGGCCCGAAGGACTTA
1 CTTACAGATGACCCGAAGGACTTA
1374186 TAAATTGTGA
Statistics
Matches: 83, Mismatches: 23, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
41 32 0.39
42 51 0.61
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (42 bp):
CTTACAGATGACCCGAAGGACTTAATCATCATGCTCGAAAGA
Found at i:1374142 original size:83 final size:83
Alignment explanation
Indices: 1374033--1374186 Score: 281
Period size: 83 Copynumber: 1.9 Consensus size: 83
1374023 CTCTTTGGTG
*
1374033 AAGGCTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
1 AAGGCTTACAAATAACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
1374098 ACTTATCAACTTGCTCTA
66 ACTTATCAACTTGCTCTA
* *
1374116 AAGGCTTACAGATAACCTGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
1 AAGGCTTACAAATAACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
1374181 ACTTAT
66 ACTTAT
1374187 AAATTGTGAA
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 68 1.00
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.26
Consensus pattern (83 bp):
AAGGCTTACAAATAACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
ACTTATCAACTTGCTCTA
Found at i:1375259 original size:36 final size:36
Alignment explanation
Indices: 1374390--1375253 Score: 840
Period size: 36 Copynumber: 23.8 Consensus size: 36
1374380 ACTGATGCAG
* * *
1374390 TTGCTTCACTACTCTTTGGTGAAGGCTTCAGATTGA
1 TTGCTTCACTACTCTCTGGTGAAGGCTTAAGATGGA
* * **
1374426 GTTACTTCACTATTCTCTGGTGAAGGCTTAAGACAGA
1 -TTGCTTCACTACTCTCTGGTGAAGGCTTAAGATGGA
* * *
1374463 TTCGTTTCACTCCTCT-TCGGTGAAGGCTTAAGATTGA
1 TT-GCTTCACTACTCTCT-GGTGAAGGCTTAAGATGGA
* *
1374500 TTTGCTTCACTATTCTCAGGTGAAGGCTTAAGATGGA
1 -TTGCTTCACTACTCTCTGGTGAAGGCTTAAGATGGA
* ** *
1374537 TTTGCTTCACTATTCTCAAGTGAAGGCTTAAGATTGA
1 -TTGCTTCACTACTCTCTGGTGAAGGCTTAAGATGGA
* * * * *
1374574 TTTGTTTTACTATTCTCAGGTGAAGGCTTGAGATGGA
1 -TTGCTTCACTACTCTCTGGTGAAGGCTTAAGATGGA
* *
1374611 TTACTTCACTACTCTCTGGTGAAGGCTTAAGATTGA
1 TTGCTTCACTACTCTCTGGTGAAGGCTTAAGATGGA
* * *
1374647 TTTGCTTCACTATTCTCAGGTAAAGGCTTAAGATGGA
1 -TTGCTTCACTACTCTCTGGTGAAGGCTTAAGATGGA
* * * *
1374684 CTGCTTCACTAATCTCTGGTGAAGGCTTAATATTGA
1 TTGCTTCACTACTCTCTGGTGAAGGCTTAAGATGGA
* * *
1374720 TCGCTTCACTCCTCT-TCGGTGAAGGCTTAAAATGGA
1 TTGCTTCACTACTCTCT-GGTGAAGGCTTAAGATGGA
* * *
1374756 TTGCTTCATTAATCTCTGGTGAAGGCTTAAGATTGA
1 TTGCTTCACTACTCTCTGGTGAAGGCTTAAGATGGA
* * * *
1374792 TTTGCTTTATTATTCTCAGGTGAAGGCTTAAGATGGA
1 -TTGCTTCACTACTCTCTGGTGAAGGCTTAAGATGGA
* * *
1374829 TTGCTTCACTAATCTCTGGTGAAGGCTTAAGATAGT
1 TTGCTTCACTACTCTCTGGTGAAGGCTTAAGATGGA
* * ** *
1374865 TTGTTTCACTATTCTCCAGTGAAGGCTTAA-AGTTGA
1 TTGCTTCACTACTCTCTGGTGAAGGCTTAAGA-TGGA
* * *
1374901 TTGCTTCACTAATCTCTGGTGAAGGCTTCAGATGGT
1 TTGCTTCACTACTCTCTGGTGAAGGCTTAAGATGGA
* * *
1374937 TTGCTTCACTACTCTCCGGTGAAGGCTTCAGATGGT
1 TTGCTTCACTACTCTCTGGTGAAGGCTTAAGATGGA
* * *
1374973 TTGCTTCACTACTCTCCGGTGAAGGCTTCAGATGGT
1 TTGCTTCACTACTCTCTGGTGAAGGCTTAAGATGGA
* *
1375009 TTGCTTCACTACTCTCTGGTGAAGGCTTCAGATGGT
1 TTGCTTCACTACTCTCTGGTGAAGGCTTAAGATGGA
* * *
1375045 TTGCTTCACTATTCTCCGGTGAAGGCTT-AGATGGT
1 TTGCTTCACTACTCTCTGGTGAAGGCTTAAGATGGA
* * * * * *
1375080 TTTCTTTACTATTCTCCGGTGAAGGCTTAGGATGGT
1 TTGCTTCACTACTCTCTGGTGAAGGCTTAAGATGGA
* * * * *
1375116 TTACTTCATTACTCTCCGGTGAAGGCTTCAGATGGT
1 TTGCTTCACTACTCTCTGGTGAAGGCTTAAGATGGA
* ** * *
1375152 TTGCTTCACTATTCTCTGGTGAAATCTTAGGATGGT
1 TTGCTTCACTACTCTCTGGTGAAGGCTTAAGATGGA
* * *
1375188 TTTCTTCACTACTCTCCGGTGAAGGCTTCAA-ATTGA
1 TTGCTTCACTACTCTCTGGTGAAGGCTT-AAGATGGA
*
1375224 TTGCTTCACTCCTCT-TCGGTGAAGGCTTAA
1 TTGCTTCACTACTCTCT-GGTGAAGGCTTAA
1375254 AATTGACTTG
Statistics
Matches: 704, Mismatches: 110, Indels: 28
0.84 0.13 0.03
Matches are distributed among these distances:
35 37 0.05
36 448 0.64
37 217 0.31
38 2 0.00
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (36 bp):
TTGCTTCACTACTCTCTGGTGAAGGCTTAAGATGGA
Found at i:1377330 original size:2 final size:2
Alignment explanation
Indices: 1377318--1377355 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1377308 ATTGTATACC
1377318 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1377356 TGTTGGGTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1379475 original size:6 final size:6
Alignment explanation
Indices: 1379464--1379497 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
1379454 ATAACACATG
*
1379464 AAATGC AAATGC AAATGC TAAATGC AAATAC AAA
1 AAATGC AAATGC AAATGC -AAATGC AAATGC AAA
1379498 AGGTGTCATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.56, C:0.15, G:0.12, T:0.18
Consensus pattern (6 bp):
AAATGC
Found at i:1379488 original size:13 final size:12
Alignment explanation
Indices: 1379464--1379497 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
1379454 ATAACACATG
1379464 AAATGCAAATGC
1 AAATGCAAATGC
1379476 AAATGCTAAATGC
1 AAATGC-AAATGC
*
1379489 AAATACAAA
1 AAATGCAAA
1379498 AGGTGTCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.56, C:0.15, G:0.12, T:0.18
Consensus pattern (12 bp):
AAATGCAAATGC
Found at i:1381574 original size:22 final size:22
Alignment explanation
Indices: 1381549--1381600 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
1381539 CCATGCGAAG
*
1381549 TGGTCTTCATGTCTTTATGAAA
1 TGGTCTTCATGTCTTTATAAAA
1381571 TGGTCTTCATGTCTTTATAAAA
1 TGGTCTTCATGTCTTTATAAAA
1381593 TGGTCTTC
1 TGGTCTTC
1381601 TCGTCCTTGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.21, C:0.15, G:0.17, T:0.46
Consensus pattern (22 bp):
TGGTCTTCATGTCTTTATAAAA
Found at i:1381616 original size:19 final size:19
Alignment explanation
Indices: 1381592--1381650 Score: 82
Period size: 19 Copynumber: 3.0 Consensus size: 19
1381582 TCTTTATAAA
1381592 ATGGTCTTCTCGTCCTTGG
1 ATGGTCTTCTCGTCCTTGG
*
1381611 ATGGTCTTCTCGTCCTTATGA
1 ATGGTCTTCTCGTCC-T-TGG
*
1381632 ATGGTCTTCTCATCCTTGG
1 ATGGTCTTCTCGTCCTTGG
1381651 TATGACTATA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 17 0.49
20 2 0.06
21 16 0.46
ACGTcount: A:0.10, C:0.25, G:0.22, T:0.42
Consensus pattern (19 bp):
ATGGTCTTCTCGTCCTTGG
Found at i:1386894 original size:24 final size:23
Alignment explanation
Indices: 1386867--1386941 Score: 73
Period size: 24 Copynumber: 3.1 Consensus size: 23
1386857 TATATCAAAA
1386867 ATCATAAAATAATCCAGGTCAAGT
1 ATCATAAAA-AATCCAGGTCAAGT
* *
1386891 ATCAGATCAAAATCCAGGTCAAGT
1 ATCATA-AAAAATCCAGGTCAAGT
1386915 AT--TAAATCAGAATCCAGGTCAAGT
1 ATCATAAA--A-AATCCAGGTCAAGT
1386939 ATC
1 ATC
1386942 CAATCAGAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
21 1 0.02
22 1 0.02
23 1 0.02
24 37 0.88
25 2 0.05
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.24
Consensus pattern (23 bp):
ATCATAAAAAATCCAGGTCAAGT
Found at i:1386912 original size:12 final size:13
Alignment explanation
Indices: 1386877--1386959 Score: 52
Period size: 12 Copynumber: 6.8 Consensus size: 13
1386867 ATCATAAAAT
1386877 AATCCAGGTCAAG
1 AATCCAGGTCAAG
* *
1386890 TAT-CAGATCAA-
1 AATCCAGGTCAAG
1386901 AATCCAGGTCAAG
1 AATCCAGGTCAAG
* * **
1386914 TAT-TAAATC-AG
1 AATCCAGGTCAAG
1386925 AATCCAGGTCAAG
1 AATCCAGGTCAAG
* *
1386938 TATCCA-ATC-AG
1 AATCCAGGTCAAG
1386949 AATCCAGGTCA
1 AATCCAGGTCA
1386960 GGTATTATAA
Statistics
Matches: 48, Mismatches: 16, Indels: 12
0.63 0.21 0.16
Matches are distributed among these distances:
11 13 0.27
12 24 0.50
13 11 0.23
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.22
Consensus pattern (13 bp):
AATCCAGGTCAAG
Found at i:1386941 original size:48 final size:48
Alignment explanation
Indices: 1386877--1386974 Score: 146
Period size: 48 Copynumber: 2.0 Consensus size: 48
1386867 ATCATAAAAT
1386877 AATCCAGGTCAAGTAT-CAGATCAAAATCCAGGTCAAGTATTA-AATCAG
1 AATCCAGGTCAAGTATCCA-ATCAAAATCCAGGTCAAGTATTATAAT-AG
* *
1386925 AATCCAGGTCAAGTATCCAATCAGAATCCAGGTCAGGTATTATAATAG
1 AATCCAGGTCAAGTATCCAATCAAAATCCAGGTCAAGTATTATAATAG
1386973 AA
1 AA
1386975 ATCAAATCGG
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
48 41 0.89
49 5 0.11
ACGTcount: A:0.41, C:0.18, G:0.17, T:0.23
Consensus pattern (48 bp):
AATCCAGGTCAAGTATCCAATCAAAATCCAGGTCAAGTATTATAATAG
Found at i:1386974 original size:24 final size:24
Alignment explanation
Indices: 1386877--1386974 Score: 126
Period size: 24 Copynumber: 4.1 Consensus size: 24
1386867 ATCATAAAAT
* * *
1386877 AATCCAGGTCAAGTATCAGATCAA
1 AATCCAGGTCAAGTATTAAATCAG
1386901 AATCCAGGTCAAGTATTAAATCAG
1 AATCCAGGTCAAGTATTAAATCAG
**
1386925 AATCCAGGTCAAGTATCCAATCAG
1 AATCCAGGTCAAGTATTAAATCAG
*
1386949 AATCCAGGTCAGGTATTATAAT-AG
1 AATCCAGGTCAAGTATTA-AATCAG
1386973 AA
1 AA
1386975 ATCAAATCGG
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
24 62 0.95
25 3 0.05
ACGTcount: A:0.41, C:0.18, G:0.17, T:0.23
Consensus pattern (24 bp):
AATCCAGGTCAAGTATTAAATCAG
Found at i:1392226 original size:21 final size:20
Alignment explanation
Indices: 1392202--1392256 Score: 51
Period size: 21 Copynumber: 2.8 Consensus size: 20
1392192 TTCAAAATTC
1392202 TAAAAAC-AATCTAAAACATCT
1 TAAAAACTAAT-TAAAACA-CT
**
1392223 TAAATCCTAATTAAAACACT
1 TAAAAACTAATTAAAACACT
*
1392243 T-AAAACTATTTAAA
1 TAAAAACTAATTAAA
1392257 CTAAAATACC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
19 10 0.36
20 3 0.11
21 12 0.43
22 3 0.11
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (20 bp):
TAAAAACTAATTAAAACACT
Found at i:1392348 original size:64 final size:69
Alignment explanation
Indices: 1392223--1392414 Score: 198
Period size: 64 Copynumber: 2.8 Consensus size: 69
1392213 TAAAACATCT
* * * * *
1392223 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATAC----CTAAAAAAT-GATATAA
1 TAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACAAAGATAAAGAATAAAAATAA
*
1392282 TATTC
65 TATCC
1392287 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAGATAAAATATAAA
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAG-----A-ATAAA
1392352 AATAATATCC
60 AATAATATCC
* *
1392362 TAAAACTTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAA
1 TAAATCCTAATTAAAATACT-AAAACCTATTTAAACTAAAATACAAAGATAAA
1392415 ATATTATGTT
Statistics
Matches: 107, Mismatches: 8, Indels: 14
0.83 0.06 0.11
Matches are distributed among these distances:
63 5 0.05
64 36 0.34
68 4 0.04
73 1 0.01
74 2 0.02
75 27 0.25
76 32 0.30
ACGTcount: A:0.57, C:0.12, G:0.02, T:0.28
Consensus pattern (69 bp):
TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAGAATAAAAATAAT
ATCC
Found at i:1397845 original size:34 final size:34
Alignment explanation
Indices: 1397797--1397864 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
1397787 TATTTGCATT
*
1397797 AAAAAAATTAACTACAACGATAAGAAAATGACAA
1 AAAAAAATTAACTACAACAATAAGAAAATGACAA
* *
1397831 AAAAAAAGTT-ACTACAATAATAAGCAAATGACAA
1 AAAAAAA-TTAACTACAACAATAAGAAAATGACAA
1397865 GAGAGCATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 28 0.93
35 2 0.07
ACGTcount: A:0.63, C:0.12, G:0.09, T:0.16
Consensus pattern (34 bp):
AAAAAAATTAACTACAACAATAAGAAAATGACAA
Found at i:1399287 original size:23 final size:22
Alignment explanation
Indices: 1399261--1399319 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 22
1399251 TTTTTAATAA
1399261 TTCTGTCTTTATGACATGTCTTC
1 TTCTGTCTTTATGACATG-CTTC
* *
1399284 TTCTGTCTTTATGGCATGCTTT
1 TTCTGTCTTTATGACATGCTTC
*
1399306 TGTATGTCTTTATG
1 T-TCTGTCTTTATG
1399320 GTACATTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
22 4 0.12
23 28 0.88
ACGTcount: A:0.12, C:0.17, G:0.17, T:0.54
Consensus pattern (22 bp):
TTCTGTCTTTATGACATGCTTC
Found at i:1400551 original size:13 final size:13
Alignment explanation
Indices: 1400533--1400557 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1400523 ACATGAATAG
1400533 AAAAAAAAAAGTA
1 AAAAAAAAAAGTA
1400546 AAAAAAAAAAGT
1 AAAAAAAAAAGT
1400558 TAGTTACAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (13 bp):
AAAAAAAAAAGTA
Found at i:1400621 original size:43 final size:43
Alignment explanation
Indices: 1400574--1400662 Score: 178
Period size: 43 Copynumber: 2.1 Consensus size: 43
1400564 CAATAATAAA
1400574 CAAATGATAAGAAAAACGTGTTGATTATATATAATGTATGCTG
1 CAAATGATAAGAAAAACGTGTTGATTATATATAATGTATGCTG
1400617 CAAATGATAAGAAAAACGTGTTGATTATATATAATGTATGCTG
1 CAAATGATAAGAAAAACGTGTTGATTATATATAATGTATGCTG
1400660 CAA
1 CAA
1400663 CTAACTATAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.43, C:0.08, G:0.18, T:0.31
Consensus pattern (43 bp):
CAAATGATAAGAAAAACGTGTTGATTATATATAATGTATGCTG
Found at i:1402327 original size:15 final size:15
Alignment explanation
Indices: 1402280--1402328 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
1402270 AAAAAACTAT
1402280 TTTTC-GCCTTTTCG
1 TTTTCAGCCTTTTCG
*
1402294 TTTCCAGCCTTTTCG
1 TTTTCAGCCTTTTCG
* *
1402309 TTTTCAGCTTTTTAG
1 TTTTCAGCCTTTTCG
1402324 TTTTC
1 TTTTC
1402329 TTTATTCTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
14 4 0.13
15 26 0.87
ACGTcount: A:0.06, C:0.24, G:0.12, T:0.57
Consensus pattern (15 bp):
TTTTCAGCCTTTTCG
Found at i:1402511 original size:21 final size:22
Alignment explanation
Indices: 1402486--1402534 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
1402476 AGTTGTGGGG
1402486 ATGTTTTTAGT-TTTTTATTAA
1 ATGTTTTTAGTATTTTTATTAA
* *
1402507 ATGTTTTTGGTATTTTTATTTA
1 ATGTTTTTAGTATTTTTATTAA
1402529 AT-TTTT
1 ATGTTTT
1402535 AAATAATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 14 0.56
22 11 0.44
ACGTcount: A:0.20, C:0.00, G:0.10, T:0.69
Consensus pattern (22 bp):
ATGTTTTTAGTATTTTTATTAA
Found at i:1402586 original size:18 final size:18
Alignment explanation
Indices: 1402563--1402597 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1402553 CCGGTTCTTC
1402563 CGACCTGTCTG-ACCGGTT
1 CGACCTGT-TGAACCGGTT
1402581 CGACCTGTTGAACCGGT
1 CGACCTGTTGAACCGGT
1402598 GAACCGGTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 14 0.88
ACGTcount: A:0.14, C:0.31, G:0.29, T:0.26
Consensus pattern (18 bp):
CGACCTGTTGAACCGGTT
Found at i:1403164 original size:20 final size:21
Alignment explanation
Indices: 1403125--1403180 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
1403115 AGGCCTGCCC
*
1403125 ATATTATTTTATTTTAAATATA
1 ATATT-TTTTATTTTAAATAAA
1403147 ATATTTTTTATTTT-AATAAA
1 ATATTTTTTATTTTAAATAAA
1403167 AGTA-TTTTTATTTT
1 A-TATTTTTTATTTT
1403181 TTATACTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 16 0.50
21 11 0.34
22 5 0.16
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (21 bp):
ATATTTTTTATTTTAAATAAA
Found at i:1403306 original size:59 final size:59
Alignment explanation
Indices: 1403205--1403318 Score: 192
Period size: 59 Copynumber: 1.9 Consensus size: 59
1403195 GTAGTCGTTG
* * *
1403205 ATACTCAAATCCAGAATCTTTATGGATAACAACCATCTCTTTAATCATTGAGGTCTCTT
1 ATACTCAAATCCAAAATCTTTATGGATAACAACCATCCCTTTAATCATTAAGGTCTCTT
*
1403264 ATACTCAAATCCAAAATCTTTATGGATAACAAGCATCCCTTTAATCATTAAGGTC
1 ATACTCAAATCCAAAATCTTTATGGATAACAACCATCCCTTTAATCATTAAGGTC
1403319 GTTTATTTCA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 51 1.00
ACGTcount: A:0.35, C:0.22, G:0.10, T:0.33
Consensus pattern (59 bp):
ATACTCAAATCCAAAATCTTTATGGATAACAACCATCCCTTTAATCATTAAGGTCTCTT
Found at i:1403509 original size:27 final size:29
Alignment explanation
Indices: 1403461--1403514 Score: 76
Period size: 27 Copynumber: 1.9 Consensus size: 29
1403451 AATTGGTTTT
*
1403461 CTGGAAATTAAATTATGTAAAATGAATAA
1 CTGGAAATTAAATTATGGAAAATGAATAA
*
1403490 CTGGAAA-T-AATTCTGGAAAATGAAT
1 CTGGAAATTAAATTATGGAAAATGAAT
1403515 TACATTTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 15 0.65
28 1 0.04
29 7 0.30
ACGTcount: A:0.48, C:0.06, G:0.17, T:0.30
Consensus pattern (29 bp):
CTGGAAATTAAATTATGGAAAATGAATAA
Found at i:1403558 original size:14 final size:14
Alignment explanation
Indices: 1403525--1403559 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1403515 TACATTTCTT
*
1403525 GAAAACGTTTTCCG
1 GAAAATGTTTTCCG
1403539 GAAAATGTTTTCCG
1 GAAAATGTTTTCCG
*
1403553 TAAAATG
1 GAAAATG
1403560 AATTACATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.31
Consensus pattern (14 bp):
GAAAATGTTTTCCG
Found at i:1403748 original size:20 final size:20
Alignment explanation
Indices: 1403723--1403762 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1403713 TATTTTAAAA
1403723 TATTAAA-ATAATTTATTTAT
1 TATTAAATATAATTT-TTTAT
*
1403743 TATTAAATATTATTTTTTAT
1 TATTAAATATAATTTTTTAT
1403763 AATTTTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TATTAAATATAATTTTTTAT
Found at i:1403899 original size:21 final size:22
Alignment explanation
Indices: 1403853--1403917 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
1403843 AGTGTTATAT
* *
1403853 TATTTTAAAAATATTAATTAGTA
1 TATTTTAAATATATTAATTA-AA
1403876 TATTTTAAATATATT-ATTAAA
1 TATTTTAAATATATTAATTAAA
*
1403897 TATTATTAGAT-TATTAATTAA
1 TATT-TTAAATATATTAATTAA
1403918 TTAAATATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
21 9 0.24
22 14 0.38
23 14 0.38
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (22 bp):
TATTTTAAATATATTAATTAAA
Found at i:1403927 original size:33 final size:33
Alignment explanation
Indices: 1403890--1403957 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
1403880 TTAAATATAT
*
1403890 TATTAAATATTATTAG-ATTATTAATTAATTAAA
1 TATTAAATAATATTAGTATTATTAA-TAATTAAA
* *
1403923 TATTAAATAATATTAGTCTTATTAATAATTTAA
1 TATTAAATAATATTAGTATTATTAATAATTAAA
1403956 TA
1 TA
1403958 ATTATTTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (33 bp):
TATTAAATAATATTAGTATTATTAATAATTAAA
Found at i:1404252 original size:42 final size:43
Alignment explanation
Indices: 1404205--1404295 Score: 132
Period size: 42 Copynumber: 2.2 Consensus size: 43
1404195 TTCCTCCAAC
* * *
1404205 CAAACACTGG-AAAACATTTTATGGAAAATGAATTACGTGAAA
1 CAAACACAGGAAAAACATTTTACGGAAAATAAATTACGTGAAA
*
1404247 CAAACA-AGGAAAAACATTTTCCGGAAAATAAATTACGTGAAA
1 CAAACACAGGAAAAACATTTTACGGAAAATAAATTACGTGAAA
1404289 CAAACAC
1 CAAACAC
1404296 GGGATTTCGA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
41 2 0.05
42 41 0.95
ACGTcount: A:0.51, C:0.15, G:0.14, T:0.20
Consensus pattern (43 bp):
CAAACACAGGAAAAACATTTTACGGAAAATAAATTACGTGAAA
Found at i:1406885 original size:3 final size:3
Alignment explanation
Indices: 1406877--1406935 Score: 91
Period size: 3 Copynumber: 19.7 Consensus size: 3
1406867 TTAATCAAAA
* * *
1406877 AAT AAT AAT GAT GAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ATT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1406925 AAT AAT AAT AA
1 AAT AAT AAT AA
1406936 AAAAAACTGG
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
AAT
Done.