Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008425.1 Hibiscus syriacus cultivar Beakdansim tig00111208_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: 2340112
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 12
Found at i:1120248 original size:75 final size:76
Alignment explanation
Indices: 1120079--1120287 Score: 290
Period size: 75 Copynumber: 2.8 Consensus size: 76
1120069 AAAACATCTT
* * *
1120079 AAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCT---A-AAA-ATAATAT-TTA
1 AAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
*
1120137 AAATAATACTCT
65 AAATAATACTCA
1120149 AAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAA
1 AAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAA
1120214 AATAATA-TCA
66 AATAATACTCA
** *
1120224 AAATTTTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAAGATAA
1 AAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
1120288 TGTTTAAAAT
Statistics
Matches: 125, Mismatches: 7, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
69 5 0.04
70 37 0.30
73 1 0.01
74 3 0.02
75 69 0.55
76 10 0.08
ACGTcount: A:0.58, C:0.13, G:0.01, T:0.28
Consensus pattern (76 bp):
AAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAA
AATAATACTCA
Found at i:1128308 original size:29 final size:30
Alignment explanation
Indices: 1128261--1128324 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 30
1128251 TTTTGATCCT
**
1128261 TAAACTTTTCAAAGTTTATACTTTAGCCAC
1 TAAACTTTTCAAAACTTATACTTTAGCCAC
* *
1128291 TAAAC-TTTCAAAACTTATATTTTAGTCAC
1 TAAACTTTTCAAAACTTATACTTTAGCCAC
1128320 TAAAC
1 TAAAC
1128325 AAAATTTGGG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 25 0.83
30 5 0.17
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.39
Consensus pattern (30 bp):
TAAACTTTTCAAAACTTATACTTTAGCCAC
Found at i:1131642 original size:16 final size:16
Alignment explanation
Indices: 1131621--1131674 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 16
1131611 AAGTCCAAGG
1131621 ACTAAAGTGTAAAAAA
1 ACTAAAGTGTAAAAAA
* **
1131637 ACTAAAGTCT-AAGGA
1 ACTAAAGTGTAAAAAA
*
1131652 CCT-AAGTGTAAAAAA
1 ACTAAAGTGTAAAAAA
1131667 ACTAAAGT
1 ACTAAAGT
1131675 CTAGGGCCTA
Statistics
Matches: 28, Mismatches: 8, Indels: 4
0.70 0.20 0.10
Matches are distributed among these distances:
14 5 0.18
15 10 0.36
16 13 0.46
ACGTcount: A:0.54, C:0.11, G:0.15, T:0.20
Consensus pattern (16 bp):
ACTAAAGTGTAAAAAA
Found at i:1131684 original size:29 final size:30
Alignment explanation
Indices: 1131608--1131730 Score: 162
Period size: 30 Copynumber: 4.1 Consensus size: 30
1131598 TAAGGAAACT
*
1131608 CTAAAGTCCAAGGA-CTAAAGTGTAAAAAAA
1 CTAAAGTCTAAGGACCT-AAGTGTAAAAAAA
1131638 CTAAAGTCTAAGGACCTAAGTGTAAAAAAA
1 CTAAAGTCTAAGGACCTAAGTGTAAAAAAA
* *
1131668 CTAAAGTCT-AGGGCCTATA-TGTAAAAAAT
1 CTAAAGTCTAAGGACCTA-AGTGTAAAAAAA
* *
1131697 CTAAAGTCTAAGGACCTAAGTGTGAAAAAT
1 CTAAAGTCTAAGGACCTAAGTGTAAAAAAA
1131727 CTAA
1 CTAA
1131731 TCCTAGAGGG
Statistics
Matches: 84, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
29 26 0.31
30 56 0.67
31 2 0.02
ACGTcount: A:0.47, C:0.14, G:0.17, T:0.22
Consensus pattern (30 bp):
CTAAAGTCTAAGGACCTAAGTGTAAAAAAA
Found at i:1132669 original size:24 final size:23
Alignment explanation
Indices: 1132642--1132686 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
1132632 TAAAGTCCCA
1132642 TCCTCTCT-TTTCGATTTTTTTCAT
1 TCCTCTCTCTTT-G-TTTTTTTCAT
1132666 TCCTCTCTCTTTGTTTTTTTC
1 TCCTCTCTCTTTGTTTTTTTC
1132687 GTTCATTTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 8 0.40
24 9 0.45
25 3 0.15
ACGTcount: A:0.04, C:0.27, G:0.04, T:0.64
Consensus pattern (23 bp):
TCCTCTCTCTTTGTTTTTTTCAT
Found at i:1134070 original size:114 final size:115
Alignment explanation
Indices: 1133927--1134185 Score: 335
Period size: 114 Copynumber: 2.2 Consensus size: 115
1133917 AGAACTTCCT
* * * * * **
1133927 CATCGGATGATTTCTTCTCATTATGAACTCTCCACTAAAAATGTTGATCCACCT-CTTTCTGTGA
1 CATCGAATGAGTTCTTCTCATTATGAACTCTCCACTAAAAATATTAACCCACCTCCTTT-TACGA
1133991 TGGAATCGAGTAAAGGTTGAAC-TTCTTCTCATTATGAACTTCTTCTCCCC
65 TGGAATCGAGTAAAGGTTGAACATTCTTCTCATTATGAACTTCTTCTCCCC
* * **
1134041 CATC-AGGTGAGTTCTTCTCATTATGAACTCTCCATTGGAAATATTAACCCACCTCCTTTTACGA
1 CATCGA-ATGAGTTCTTCTCATTATGAACTCTCCACTAAAAATATTAACCCACCTCCTTTTACGA
* * *
1134105 TGGAATTGAGTAAATGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCT
65 TGGAATCGAGTAAAGGTTGAAC-A-TTCTTCTCATTATGAACTTCTTCTCCCC
1134158 CATCGAATGAGTTCTTCTCATTATGAAC
1 CATCGAATGAGTTCTTCTCATTATGAAC
1134186 CCTTTACTGG
Statistics
Matches: 124, Mismatches: 15, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
114 67 0.54
115 4 0.03
117 52 0.42
118 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.37
Consensus pattern (115 bp):
CATCGAATGAGTTCTTCTCATTATGAACTCTCCACTAAAAATATTAACCCACCTCCTTTTACGAT
GGAATCGAGTAAAGGTTGAACATTCTTCTCATTATGAACTTCTTCTCCCC
Found at i:1134197 original size:117 final size:117
Alignment explanation
Indices: 1133897--1134225 Score: 374
Period size: 117 Copynumber: 2.9 Consensus size: 117
1133887 TGTCGTGTTC
* * *
1133897 TGAACAAGTTCTTCTCATTAAGAA---C-T-T-CCTCATCGGATGATTTCTTCTCATTATGAACT
1 TGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGAATGAGTTCTTCTCATTATGAACT
** * **
1133956 CTCCACTAAAAATGTTGATCCACCTCTTTCTGTGATGGAATCGAGTAAAGGT
66 CTCCACTGGAAATGTTGACCCACCTCTTTCTACGATGGAATCGAGTAAAGGT
* *
1134008 TGAAC---TTCTTCTCATTATGAACTTCTTCTCCCCCATC-AGGTGAGTTCTTCTCATTATGAAC
1 TGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGA-ATGAGTTCTTCTCATTATGAAC
* * * * *
1134069 TCTCCATTGGAAATATTAACCCACCTCCTTT-TACGATGGAATTGAGTAAATGT
65 TCTCCACTGGAAATGTTGACCCACCT-CTTTCTACGATGGAATCGAGTAAAGGT
*
1134122 TGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGAATGAGTTCTTCTCATTATGAACC
1 TGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGAATGAGTTCTTCTCATTATGAACT
** * * *
1134187 CTTTACTGGAAATGTTGACCCATCTCATTCTGCGATGGA
66 CTCCACTGGAAATGTTGACCCACCTCTTTCTACGATGGA
1134226 TGGAGAATTT
Statistics
Matches: 179, Mismatches: 26, Indels: 20
0.80 0.12 0.09
Matches are distributed among these distances:
108 15 0.08
111 6 0.03
112 1 0.01
113 1 0.01
114 69 0.39
115 4 0.02
116 3 0.02
117 79 0.44
118 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.36
Consensus pattern (117 bp):
TGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGAATGAGTTCTTCTCATTATGAACT
CTCCACTGGAAATGTTGACCCACCTCTTTCTACGATGGAATCGAGTAAAGGT
Found at i:1136790 original size:10 final size:10
Alignment explanation
Indices: 1136721--1136794 Score: 51
Period size: 10 Copynumber: 7.1 Consensus size: 10
1136711 TTGATATGTT
*
1136721 TTCTTTCTTC
1 TTCTTTTTTC
1136731 TTCTTTTTTC
1 TTCTTTTTTC
**
1136741 CCCTTTTTTGC
1 TTCTTTTTT-C
*
1136752 TTTCTTTTCTC
1 -TTCTTTTTTC
1136763 TCTCTCTTTTT-
1 T-TCT-TTTTTC
* *
1136774 ATGTTTTTTC
1 TTCTTTTTTC
1136784 TTCTTTTTTC
1 TTCTTTTTTC
1136794 T
1 T
1136795 ATATCTTCTT
Statistics
Matches: 48, Mismatches: 11, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
9 5 0.10
10 28 0.58
11 5 0.10
12 10 0.21
ACGTcount: A:0.01, C:0.24, G:0.03, T:0.72
Consensus pattern (10 bp):
TTCTTTTTTC
Found at i:1140348 original size:30 final size:30
Alignment explanation
Indices: 1140290--1140353 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
1140280 TATGATAACT
*
1140290 CTAAAGTCTAGGAACTAAATTGTAAAAAAA
1 CTAAAGTCTAGGAACTAAAGTGTAAAAAAA
* * *
1140320 CTAAAGTCTAGAGACCT-AAGTGTGAAAAAT
1 CTAAAGTCTAG-GAACTAAAGTGTAAAAAAA
1140350 CTAA
1 CTAA
1140354 TCCTAGAGGG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 25 0.86
31 4 0.14
ACGTcount: A:0.48, C:0.12, G:0.16, T:0.23
Consensus pattern (30 bp):
CTAAAGTCTAGGAACTAAAGTGTAAAAAAA
Found at i:1141780 original size:328 final size:331
Alignment explanation
Indices: 1141177--1141791 Score: 909
Period size: 332 Copynumber: 1.9 Consensus size: 331
1141167 CATTGGTGTC
* * * *
1141177 TTCTCTCCCTTCTCAACGGTTGGATCTACTAATGGACCTCACGAATGCCGACGAAGCCTCCAGTC
1 TTCTCTCCCTTCTCAACAGTTGGATCGACAAACGGACCTCACGAATGCCGACGAAGCCTCCAGTC
* * * * *
1141242 GATATGTAAAGTCCCCTCATCTCTCTTTACAATTTTTTTTCATTCCTCTCTCCCTTTGATTTTTT
66 GAGAGGTAAAGTCCCCTCATCTATCTTTACAATTTTTTCTCATTCCTCTCT-CCTTCGATTTTTT
* ** * *
1141307 TTGTTCATTTGCACTTGTTTTTGTTTGGTTCGAATGGATATGACCATGAAAAATATGTTTGGTTT
130 TCGTTCATTCACACTTGTATTTGTTTGGTTCGAATGGATATAACCATGAAAAATATGTTTGGTTT
* **
1141372 CTTTGTATTTTTTTGTTAGTTTTCGAATGGAATTTAAATAAAAAAATTGAAGAAAAATAGATTAT
195 CTTTGTATTTTTTTGTTAGTTTTCAAATGGAATGCAAATAAAAAAATTGAAGAAAAATAGATTAT
1141437 GGAAATGAAGTTGTATTGCCTCTTTGATGAATCAAGATCGATATGATTTTTTAATATGTGGTTCA
260 GGAAATGAAGTTGTATTGCCTCTTTGATGAATCAAGATCGATATGATTTTTTAATATGTGGTTCA
1141502 CAGTTTA
325 CAGTTTA
* *
1141509 TTCTCTCCCTTCTCAACAGTTGGATCGACAAACGGACCTCCCGAATGCCGATGAAGCCTCCAGTC
1 TTCTCTCCCTTCTCAACAGTTGGATCGACAAACGGACCTCACGAATGCCGACGAAGCCTCCAGTC
* * *
1141574 GAGAGGTAAGGTCCCCTCCTCTATCTTTTCAATTTTTTCT-ATTCCTCTCT-CTTCGATTTTTTT
66 GAGAGGTAAAGTCCCCTCATCTATCTTTACAATTTTTTCTCATTCCTCTCTCCTTCGATTTTTTT
** **
1141637 CGTTCATTCACACTTG-ATTTGTTTGGTTTTAATGGATATAAGGATGAAAAA-AGGTGTTTGGTT
131 CGTTCATTCACACTTGTATTTGTTTGGTTCGAATGGATATAACCATGAAAAATA--TGTTTGGTT
*
1141700 TCTTTTTATTTTTTTGTTAGTTTTCAAATGGAATGCAAAT-AAAAAATTGAAGAAAAATAGATGT
194 TCTTTGTATTTTTTTGTTAGTTTTCAAATGGAATGCAAATAAAAAAATTGAAGAAAAATAGAT-T
1141764 -TGGAAATGAAGTTGTATTGCCTCTTTGA
258 ATGGAAATGAAGTTGTATTGCCTCTTTGA
1141792 AATTGAATCG
Statistics
Matches: 253, Mismatches: 27, Indels: 10
0.87 0.09 0.03
Matches are distributed among these distances:
327 1 0.00
328 79 0.31
329 71 0.28
331 10 0.04
332 92 0.36
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (331 bp):
TTCTCTCCCTTCTCAACAGTTGGATCGACAAACGGACCTCACGAATGCCGACGAAGCCTCCAGTC
GAGAGGTAAAGTCCCCTCATCTATCTTTACAATTTTTTCTCATTCCTCTCTCCTTCGATTTTTTT
CGTTCATTCACACTTGTATTTGTTTGGTTCGAATGGATATAACCATGAAAAATATGTTTGGTTTC
TTTGTATTTTTTTGTTAGTTTTCAAATGGAATGCAAATAAAAAAATTGAAGAAAAATAGATTATG
GAAATGAAGTTGTATTGCCTCTTTGATGAATCAAGATCGATATGATTTTTTAATATGTGGTTCAC
AGTTTA
Found at i:1142485 original size:42 final size:42
Alignment explanation
Indices: 1142437--1142558 Score: 235
Period size: 42 Copynumber: 2.9 Consensus size: 42
1142427 GGGCGGCTCG
1142437 CTTTTAGGAAGTGGTTAAACGATAACCAGTTACATTAACACA
1 CTTTTAGGAAGTGGTTAAACGATAACCAGTTACATTAACACA
1142479 CTTTTAGGAAGTGGTTAAACGATAACCAGTTACATTAACACA
1 CTTTTAGGAAGTGGTTAAACGATAACCAGTTACATTAACACA
*
1142521 CTTTTAGGAAGTGGTTAAAGGATAACCAGTTACATTAA
1 CTTTTAGGAAGTGGTTAAACGATAACCAGTTACATTAA
1142559 ATACTGTGTT
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
42 79 1.00
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.30
Consensus pattern (42 bp):
CTTTTAGGAAGTGGTTAAACGATAACCAGTTACATTAACACA
Found at i:1144961 original size:60 final size:60
Alignment explanation
Indices: 1144847--1144983 Score: 136
Period size: 60 Copynumber: 2.3 Consensus size: 60
1144837 ATAGTCAACT
* * * * *
1144847 GATCATTTTATAACTTTTAATAATTGAGGGACTCAACAAAGCAACTCCTCATAGTTGAAG
1 GATCATTTTGTAACTTTTAATAATTAAAGGACTCAACAAAGCAAATCCTCATAGTCGAAG
* * * *
1144907 GATCATTTTGTAA-TCTTTAATAGTTAAAGGACTCAATAAAGTAATATCCT-ATAGTCGAGG
1 GATCATTTTGTAACT-TTTAATAATTAAAGGACTCAACAAAGCAA-ATCCTCATAGTCGAAG
*
1144967 GACCATTTGTGT-ACTTT
1 GATCATTT-TGTAACTTT
1144984 ACTCTAAAAA
Statistics
Matches: 63, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
59 1 0.02
60 54 0.86
61 8 0.13
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (60 bp):
GATCATTTTGTAACTTTTAATAATTAAAGGACTCAACAAAGCAAATCCTCATAGTCGAAG
Found at i:1150263 original size:33 final size:33
Alignment explanation
Indices: 1150226--1150294 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
1150216 ATACAATATT
1150226 GTCCATCAACTATATCCATATATGATCAAAAGG
1 GTCCATCAACTATATCCATATATGATCAAAAGG
1150259 GTCCATCAACTATATCCATATATGATCAAAAGG
1 GTCCATCAACTATATCCATATATGATCAAAAGG
1150292 GTC
1 GTC
1150295 TTTGCCATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.28
Consensus pattern (33 bp):
GTCCATCAACTATATCCATATATGATCAAAAGG
Found at i:1154283 original size:30 final size:30
Alignment explanation
Indices: 1154247--1154304 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
1154237 AGAGTCGAGG
*
1154247 GTTACCTATGTCCTTCGGGACATATGGACA
1 GTTACCTATGTCCTTCGGAACATATGGACA
*
1154277 GTTACCTATGTTCTTCGGAACATATGGA
1 GTTACCTATGTCCTTCGGAACATATGGA
1154305 TAGTGGTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (30 bp):
GTTACCTATGTCCTTCGGAACATATGGACA
Found at i:1154332 original size:22 final size:23
Alignment explanation
Indices: 1154290--1154369 Score: 94
Period size: 22 Copynumber: 3.5 Consensus size: 23
1154280 ACCTATGTTC
*
1154290 TTCGGAACATATGGATAGTGGTCA
1 TTCGGGACATAT-GATAGTGGTCA
1154314 TTCGGGACATAT-ATAGTGGTCA
1 TTCGGGACATATGATAGTGGTCA
* *
1154336 TTCGGGACAAATGCATA--GGTTA
1 TTCGGGACATATG-ATAGTGGTCA
1154358 TTCGGGACATAT
1 TTCGGGACATAT
1154370 TTTACATGCC
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
22 36 0.72
24 14 0.28
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.30
Consensus pattern (23 bp):
TTCGGGACATATGATAGTGGTCA
Found at i:1159891 original size:63 final size:63
Alignment explanation
Indices: 1159812--1160160 Score: 542
Period size: 63 Copynumber: 5.6 Consensus size: 63
1159802 CAAGAGTCAA
* * * *
1159812 AGAATTACCTATGTCTTTCGGGACATATGGACAGTATATCAATGTTCTACGGAATATATAGAC
1 AGAATTACCTATGTCTTTCGGGACATATGGACAGTATACCTATGTTCTACGGAACATATGGAC
* *
1159875 AGAATTACCTACGTCTTTCAGGACATATGGACAGTATACCTATGTTCTACGGAACATATGGAC
1 AGAATTACCTATGTCTTTCGGGACATATGGACAGTATACCTATGTTCTACGGAACATATGGAC
* *
1159938 CGAATTACCTATGTCTTTTGGGACATATGGACAGTATACCTATGTTCTACGGAACATATGGAC
1 AGAATTACCTATGTCTTTCGGGACATATGGACAGTATACCTATGTTCTACGGAACATATGGAC
1160001 AGAATTACCTATGTCTTTCGGGACATATGGACAGTATACCTATGTTCTACGGAACATATGGAC
1 AGAATTACCTATGTCTTTCGGGACATATGGACAGTATACCTATGTTCTACGGAACATATGGAC
* * *
1160064 AGAATTACCTATGTCTTTCGGGACATATGGATAGTATACCTATGTTCTAAGAAACATATGGAC
1 AGAATTACCTATGTCTTTCGGGACATATGGACAGTATACCTATGTTCTACGGAACATATGGAC
* *
1160127 AG-TTTACCTA-GAT-TCTTCGGGACCTATGGACAGT
1 AGAATTACCTATG-TCT-TTCGGGACATATGGACAGT
1160161 TGCCGAGGTT
Statistics
Matches: 266, Mismatches: 18, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
61 2 0.01
62 25 0.09
63 239 0.90
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (63 bp):
AGAATTACCTATGTCTTTCGGGACATATGGACAGTATACCTATGTTCTACGGAACATATGGAC
Found at i:1160155 original size:31 final size:31
Alignment explanation
Indices: 1159816--1160161 Score: 272
Period size: 31 Copynumber: 11.0 Consensus size: 31
1159806 AGTCAAAGAA
*
1159816 TTACCTATG-TCTTTCGGGACATATGGACAGT
1 TTACCTATGTTC-TACGGGACATATGGACAGT
* * * * * * *
1159847 ATATCAATGTTCTACGGAATATATAGACAGAA
1 TTACCTATGTTCTACGGGACATATGGACAG-T
* * *
1159879 TTACCTACG-TCTTTCAGGACATATGGACAGT
1 TTACCTATGTTC-TACGGGACATATGGACAGT
* * * *
1159910 ATACCTATGTTCTACGGAACATATGGACCGAA
1 TTACCTATGTTCTACGGGACATATGGACAG-T
**
1159942 TTACCTATG-TCTTTTGGGACATATGGACAGT
1 TTACCTATGTTC-TACGGGACATATGGACAGT
* * *
1159973 ATACCTATGTTCTACGGAACATATGGACAGAA
1 TTACCTATGTTCTACGGGACATATGGACAG-T
*
1160005 TTACCTATG-TCTTTCGGGACATATGGACAGT
1 TTACCTATGTTC-TACGGGACATATGGACAGT
* * *
1160036 ATACCTATGTTCTACGGAACATATGGACAGAA
1 TTACCTATGTTCTACGGGACATATGGACAG-T
* *
1160068 TTACCTATG-TCTTTCGGGACATATGGATAGT
1 TTACCTATGTTC-TACGGGACATATGGACAGT
* * **
1160099 ATACCTATGTTCTAAGAAACATATGGACAGT
1 TTACCTATGTTCTACGGGACATATGGACAGT
* *
1160130 TTACCTA-GATTCTTCGGGACCTATGGACAGT
1 TTACCTATG-TTCTACGGGACATATGGACAGT
1160161 T
1 T
1160162 GCCGAGGTTC
Statistics
Matches: 240, Mismatches: 61, Indels: 28
0.73 0.19 0.09
Matches are distributed among these distances:
30 1 0.00
31 142 0.59
32 97 0.40
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (31 bp):
TTACCTATGTTCTACGGGACATATGGACAGT
Found at i:1160830 original size:21 final size:21
Alignment explanation
Indices: 1160806--1160845 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1160796 TGCCGAAGTT
1160806 ACTGTAGCAGTACATCGATGC
1 ACTGTAGCAGTACATCGATGC
*
1160827 ACTGTAGCAGTGCATCGAT
1 ACTGTAGCAGTACATCGAT
1160846 ACACAATTGA
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:0.28, C:0.23, G:0.25, T:0.25
Consensus pattern (21 bp):
ACTGTAGCAGTACATCGATGC
Found at i:1163381 original size:13 final size:13
Alignment explanation
Indices: 1163363--1163400 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1163353 TAAGAGATGA
1163363 TATAAGAATATAT
1 TATAAGAATATAT
1163376 TATAAGAATATAT
1 TATAAGAATATAT
1163389 TATAAG-ATATAT
1 TATAAGAATATAT
1163401 GATATAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 6 0.24
13 19 0.76
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (13 bp):
TATAAGAATATAT
Found at i:1164251 original size:31 final size:31
Alignment explanation
Indices: 1164194--1164474 Score: 241
Period size: 31 Copynumber: 9.0 Consensus size: 31
1164184 GTTGAAGAAT
* * *
1164194 TACCTATG-TCTTTCGGGACATTTGGACAGTA
1 TACCTATGTTC-TACGGAACATATGGACAGTA
* *
1164225 TACGTATGTTCTACGGAACATATGGACAGAA
1 TACCTATGTTCTACGGAACATATGGACAGTA
* * *
1164256 TTACCTATG-TCTTTCGGGATATATGGACAGTA
1 -TACCTATGTTC-TACGGAACATATGGACAGTA
*
1164288 TCCCTATGTTCTACGGAACATATGGACA-TAA
1 TACCTATGTTCTACGGAACATATGGACAGT-A
* *
1164319 TTACCAATG-TCTTTCAGG-ACATATGGACAGTA
1 -TACCTATGTTC-TAC-GGAACATATGGACAGTA
* *
1164351 TACCTATGTTCTACAGAACATATGGACAGAA
1 TACCTATGTTCTACGGAACATATGGACAGTA
* * *
1164382 TTACCTATG-TCTTTCGGGACATATGAACAGTA
1 -TACCTATGTTC-TACGGAACATATGGACAGTA
* *
1164414 TACCTATGTTCTAAGGAACATATGGACAGTT
1 TACCTATGTTCTACGGAACATATGGACAGTA
* * * *
1164445 TACCTAGGTTCTTCGGGACCTATGGACAGT
1 TACCTATGTTCTACGGAACATATGGACAGT
1164475 TGTCGAGGTT
Statistics
Matches: 200, Mismatches: 36, Indels: 28
0.76 0.14 0.11
Matches are distributed among these distances:
30 2 0.01
31 121 0.61
32 74 0.37
33 3 0.01
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (31 bp):
TACCTATGTTCTACGGAACATATGGACAGTA
Found at i:1164267 original size:63 final size:63
Alignment explanation
Indices: 1164189--1164474 Score: 432
Period size: 63 Copynumber: 4.6 Consensus size: 63
1164179 CAAGAGTTGA
* *
1164189 AGAATTACCTATGTCTTTCGGGACATTTGGACAGTATACGTATGTTCTACGGAACATATGGAC
1 AGAATTACCTATGTCTTTCGGGACATATGGACAGTATACCTATGTTCTACGGAACATATGGAC
* *
1164252 AGAATTACCTATGTCTTTCGGGATATATGGACAGTATCCCTATGTTCTACGGAACATATGGAC
1 AGAATTACCTATGTCTTTCGGGACATATGGACAGTATACCTATGTTCTACGGAACATATGGAC
* * * *
1164315 ATAATTACCAATGTCTTTCAGGACATATGGACAGTATACCTATGTTCTACAGAACATATGGAC
1 AGAATTACCTATGTCTTTCGGGACATATGGACAGTATACCTATGTTCTACGGAACATATGGAC
* *
1164378 AGAATTACCTATGTCTTTCGGGACATATGAACAGTATACCTATGTTCTAAGGAACATATGGAC
1 AGAATTACCTATGTCTTTCGGGACATATGGACAGTATACCTATGTTCTACGGAACATATGGAC
* * *
1164441 AG-TTTACCTAGGT-TCTTCGGGACCTATGGACAGT
1 AGAATTACCTATGTCT-TTCGGGACATATGGACAGT
1164475 TGTCGAGGTT
Statistics
Matches: 202, Mismatches: 20, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
61 1 0.00
62 26 0.13
63 175 0.87
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (63 bp):
AGAATTACCTATGTCTTTCGGGACATATGGACAGTATACCTATGTTCTACGGAACATATGGAC
Found at i:1164374 original size:94 final size:94
Alignment explanation
Indices: 1164192--1164474 Score: 234
Period size: 94 Copynumber: 3.0 Consensus size: 94
1164182 GAGTTGAAGA
* * * * ** * *
1164192 ATTACCTATGTCTTTCGGGACATTTGGACAGTATACGTATGTTCTACGGAACATATGGACAGAAT
1 ATTACCTATGTCTTACGGAACATATGAACAGTATACCAATGTTCTAAGGAACATATGGACAGTA-
* * * * *
1164257 TACCTATG-TCTTTCGGGATATATGGACAGT
65 TACCTAGGTTC-TACAGAACATATGGACAGT
* * * *
1164287 A-TCCCTATGT-TCTACGGAACATATGGACA-TAATTACCAATGTCTTTCAGG-ACATATGGACA
1 ATTACCTATGTCT-TACGGAACATATGAACAGT-A-TACCAATGT-TCTAAGGAACATATGGACA
* *
1164348 GTATACCTATGTTCTACAGAACATATGGACAGA
62 GTATACCTAGGTTCTACAGAACATATGGACAGT
* * * *
1164381 ATTACCTATGTCTTTCGGGACATATGAACAGTATACCTATGTTCTAAGGAACATATGGACAGTTT
1 ATTACCTATGTCTTACGGAACATATGAACAGTATACCAATGTTCTAAGGAACATATGGACAGTAT
* * * *
1164446 ACCTAGGTTCTTCGGGACCTATGGACAGT
66 ACCTAGGTTCTACAGAACATATGGACAGT
1164475 TGTCGAGGTT
Statistics
Matches: 150, Mismatches: 29, Indels: 19
0.76 0.15 0.10
Matches are distributed among these distances:
93 7 0.05
94 91 0.61
95 46 0.31
96 6 0.04
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (94 bp):
ATTACCTATGTCTTACGGAACATATGAACAGTATACCAATGTTCTAAGGAACATATGGACAGTAT
ACCTAGGTTCTACAGAACATATGGACAGT
Found at i:1165145 original size:21 final size:21
Alignment explanation
Indices: 1165121--1165160 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1165111 TGTCGAAGTT
1165121 ACTGTAGCAGTACATCGATGC
1 ACTGTAGCAGTACATCGATGC
1165142 ACTGTAGCAGTACATCGAT
1 ACTGTAGCAGTACATCGAT
1165161 ACACAAACGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (21 bp):
ACTGTAGCAGTACATCGATGC
Found at i:1165215 original size:24 final size:23
Alignment explanation
Indices: 1165188--1165241 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 23
1165178 AAATTTTCAC
*
1165188 TGTTCACTATTGTTCATACGATAT
1 TGTTCACTATT-TTCATACCATAT
1165212 TGTTCAC--TTTTCATACCATAT
1 TGTTCACTATTTTCATACCATAT
1165233 T-TT-ACTATT
1 TGTTCACTATT
1165242 CATAAAAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
19 2 0.07
20 2 0.07
21 14 0.52
22 2 0.07
24 7 0.26
ACGTcount: A:0.24, C:0.19, G:0.07, T:0.50
Consensus pattern (23 bp):
TGTTCACTATTTTCATACCATAT
Found at i:1165649 original size:20 final size:20
Alignment explanation
Indices: 1165607--1165646 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1165597 GAACGTAATG
*
1165607 AGGGTACCGATACCCCAGTA
1 AGGGTACCGATACCCCACTA
*
1165627 AGGGTACTGATACCCC-CTA
1 AGGGTACCGATACCCCACTA
1165646 A
1 A
1165647 AGGAAAAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.30, C:0.30, G:0.23, T:0.17
Consensus pattern (20 bp):
AGGGTACCGATACCCCACTA
Found at i:1166957 original size:30 final size:30
Alignment explanation
Indices: 1166921--1166978 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
1166911 AGAGTCGAGG
*
1166921 GTTACCTATGTCCTTCGGGACATATGGACA
1 GTTACCTATGTCCTTCGGAACATATGGACA
*
1166951 GTTACCTATGTTCTTCGGAACATATGGA
1 GTTACCTATGTCCTTCGGAACATATGGA
1166979 TAGTGGTCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (30 bp):
GTTACCTATGTCCTTCGGAACATATGGACA
Found at i:1171649 original size:59 final size:59
Alignment explanation
Indices: 1171557--1171676 Score: 222
Period size: 59 Copynumber: 2.0 Consensus size: 59
1171547 AAAACTTTTA
* *
1171557 TAAAATTATTTATATTTTAAATTATTTACCCTCAAAGTTTTCTTAGACTATACTATACG
1 TAAAATTATTTATATTTTAAATTACTTACCCTCAAAGTTTTCCTAGACTATACTATACG
1171616 TAAAATTATTTATATTTTAAATTACTTACCCTCAAAGTTTTCCTAGACTATACTATACG
1 TAAAATTATTTATATTTTAAATTACTTACCCTCAAAGTTTTCCTAGACTATACTATACG
1171675 TA
1 TA
1171677 TAAGATTTTG
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.36, C:0.15, G:0.05, T:0.44
Consensus pattern (59 bp):
TAAAATTATTTATATTTTAAATTACTTACCCTCAAAGTTTTCCTAGACTATACTATACG
Found at i:1175526 original size:22 final size:23
Alignment explanation
Indices: 1175496--1175550 Score: 85
Period size: 22 Copynumber: 2.4 Consensus size: 23
1175486 AGATTTTTTA
* *
1175496 TGAATAGTGATGAACAGTA-CCG
1 TGAACAGTGATGAACAATACCCG
1175518 TGAACAGTGATGAACAATACCCG
1 TGAACAGTGATGAACAATACCCG
1175541 TGAACAGTGA
1 TGAACAGTGA
1175551 ATGTACCGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 17 0.57
23 13 0.43
ACGTcount: A:0.38, C:0.16, G:0.25, T:0.20
Consensus pattern (23 bp):
TGAACAGTGATGAACAATACCCG
Found at i:1176092 original size:21 final size:20
Alignment explanation
Indices: 1176066--1176104 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1176056 ATAAAAAAAT
*
1176066 ATTCTTTCCAATATACTTGCC
1 ATTCTTTCC-ATAAACTTGCC
1176087 ATTCTTTCCATAAACTTG
1 ATTCTTTCCATAAACTTG
1176105 TAAGTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.26, C:0.26, G:0.05, T:0.44
Consensus pattern (20 bp):
ATTCTTTCCATAAACTTGCC
Found at i:1177530 original size:39 final size:39
Alignment explanation
Indices: 1177476--1177560 Score: 161
Period size: 39 Copynumber: 2.2 Consensus size: 39
1177466 AATACAAAAT
*
1177476 TACCCTTAATAAAACTTTATAATCACCATTAAACCAAGA
1 TACCCATAATAAAACTTTATAATCACCATTAAACCAAGA
1177515 TACCCATAATAAAACTTTATAATCACCATTAAACCAAGA
1 TACCCATAATAAAACTTTATAATCACCATTAAACCAAGA
1177554 TACCCAT
1 TACCCAT
1177561 CCTTATCATC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.46, C:0.25, G:0.02, T:0.27
Consensus pattern (39 bp):
TACCCATAATAAAACTTTATAATCACCATTAAACCAAGA
Found at i:1177547 original size:20 final size:20
Alignment explanation
Indices: 1177485--1177547 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
1177475 TTACCCTTAA
1177485 TAAAACTTTATAATCACCAT
1 TAAAACTTTATAATCACCAT
* ***
1177505 TAAACCAAGAT-A-C-CCAT
1 TAAAACTTTATAATCACCAT
1177522 AATAAAACTTTATAATCACCAT
1 --TAAAACTTTATAATCACCAT
1177544 TAAA
1 TAAA
1177548 CCAAGATACC
Statistics
Matches: 30, Mismatches: 8, Indels: 10
0.62 0.17 0.21
Matches are distributed among these distances:
17 4 0.13
18 1 0.03
19 8 0.27
20 12 0.40
21 1 0.03
22 4 0.13
ACGTcount: A:0.49, C:0.21, G:0.02, T:0.29
Consensus pattern (20 bp):
TAAAACTTTATAATCACCAT
Found at i:1183226 original size:24 final size:24
Alignment explanation
Indices: 1183199--1183266 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 24
1183189 AGCTCGTATA
1183199 AATTTGCACCGAAGTGCCACGTAG
1 AATTTGCACCGAAGTGCCACGTAG
* *
1183223 AATTTGTC-CCAAAG-GACCGCGTAG
1 AATTTG-CACCGAAGTG-CCACGTAG
*
1183247 AATTTTGCACCGTAGTGCCA
1 AA-TTTGCACCGAAGTGCCA
1183267 TATAATATTG
Statistics
Matches: 34, Mismatches: 5, Indels: 9
0.71 0.10 0.19
Matches are distributed among these distances:
23 1 0.03
24 21 0.62
25 11 0.32
26 1 0.03
ACGTcount: A:0.28, C:0.25, G:0.24, T:0.24
Consensus pattern (24 bp):
AATTTGCACCGAAGTGCCACGTAG
Found at i:1183296 original size:48 final size:48
Alignment explanation
Indices: 1183201--1183296 Score: 115
Period size: 48 Copynumber: 2.0 Consensus size: 48
1183191 CTCGTATAAA
* *
1183201 TTTGCACCGAAGTGCCACGTAGAATTTGTCCCAAAGGACCGCGTAGAAT
1 TTTGCACCGAAGTGCCAC-TAGAATTTGTCCCAAAGGACCACATAGAAT
* *
1183250 TTTGCACCGTAGTGCCA-TATAATATTGT-CCATAAGGACCACATAGAA
1 TTTGCACCGAAGTGCCACTAGAAT-TTGTCCCA-AAGGACCACATAGAA
1183297 ATTCCTTAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
47 8 0.20
48 17 0.41
49 16 0.39
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (48 bp):
TTTGCACCGAAGTGCCACTAGAATTTGTCCCAAAGGACCACATAGAAT
Found at i:1183559 original size:30 final size:30
Alignment explanation
Indices: 1183514--1183572 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
1183504 ATCGCGTAGA
* *
1183514 CATATTATTTCCATACCTTTATCACATAGG
1 CATATCATTTACATACCTTTATCACATAGG
1183544 CATATCATTTACATACCTTTATCACATAG
1 CATATCATTTACATACCTTTATCACATAG
1183573 CTCATATAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (30 bp):
CATATCATTTACATACCTTTATCACATAGG
Found at i:1183627 original size:29 final size:30
Alignment explanation
Indices: 1183594--1183666 Score: 139
Period size: 29 Copynumber: 2.5 Consensus size: 30
1183584 TTTTCTGCAT
1183594 ATTCATGTCATGTAATACATAT-AATATGA
1 ATTCATGTCATGTAATACATATAAATATGA
1183623 ATTCATGTCATGTAATACATATAAATATGA
1 ATTCATGTCATGTAATACATATAAATATGA
1183653 ATTCATGTCATGTA
1 ATTCATGTCATGTA
1183667 TCATAATATG
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 22 0.51
30 21 0.49
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (30 bp):
ATTCATGTCATGTAATACATATAAATATGA
Found at i:1183628 original size:24 final size:28
Alignment explanation
Indices: 1183598--1183666 Score: 95
Period size: 30 Copynumber: 2.4 Consensus size: 28
1183588 CTGCATATTC
1183598 ATGTCATGTAATACATAT-AATATGAATT
1 ATGTCATGTAATACATATAAATATGAA-T
1183626 CATGTCATGTAATACATATAAATATGAATT
1 -ATGTCATGTAATACATATAAATATGAA-T
1183656 CATGTCATGTA
1 -ATGTCATGTA
1183667 TCATAATATG
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
29 18 0.46
30 21 0.54
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.38
Consensus pattern (28 bp):
ATGTCATGTAATACATATAAATATGAAT
Found at i:1185240 original size:15 final size:14
Alignment explanation
Indices: 1185222--1185268 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
1185212 ATCATATGAA
*
1185222 ATGTGATAGAGAGCT
1 ATGTGATA-AGAACT
1185237 ATGTGA-AAGAACT
1 ATGTGATAAGAACT
*
1185250 ATGTGATATGAA-T
1 ATGTGATAAGAACT
1185263 ATGTGA
1 ATGTGA
1185269 ATGTGTAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 18 0.62
14 5 0.17
15 6 0.21
ACGTcount: A:0.38, C:0.04, G:0.28, T:0.30
Consensus pattern (14 bp):
ATGTGATAAGAACT
Found at i:1185385 original size:18 final size:18
Alignment explanation
Indices: 1185364--1185408 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1185354 CGCGGTCCTC
*
1185364 CGGGACATAGTGGTCATT
1 CGGGACATAATGGTCATT
*
1185382 CGGGACATAATGGTCCTT
1 CGGGACATAATGGTCATT
1185400 CGGGACATA
1 CGGGACATA
1185409 TGTGTTATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.24
Consensus pattern (18 bp):
CGGGACATAATGGTCATT
Found at i:1186120 original size:19 final size:19
Alignment explanation
Indices: 1186096--1186133 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1186086 AACATAAATG
1186096 AATAACATGTATTTTGTTA
1 AATAACATGTATTTTGTTA
1186115 AATAACATGTATTTTGTTA
1 AATAACATGTATTTTGTTA
1186134 TATAGAAGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.05, G:0.11, T:0.47
Consensus pattern (19 bp):
AATAACATGTATTTTGTTA
Found at i:1187608 original size:23 final size:23
Alignment explanation
Indices: 1187577--1187627 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
1187567 GTTTAGGTAT
* * *
1187577 TTTTCTAATTTTGTATCTCAAAA
1 TTTTATAATTTAGTACCTCAAAA
*
1187600 TTTTATAATTTAGTACCTCAAAT
1 TTTTATAATTTAGTACCTCAAAA
1187623 TTTTA
1 TTTTA
1187628 ATATAAATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.31, C:0.12, G:0.04, T:0.53
Consensus pattern (23 bp):
TTTTATAATTTAGTACCTCAAAA
Found at i:1190717 original size:21 final size:21
Alignment explanation
Indices: 1190676--1190717 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1190666 TTTTTATTAA
*
1190676 ATTTTAGATTTTTTAAGAATT
1 ATTTTAGATTTTTAAAGAATT
* *
1190697 ATTTTATATTTTTAAATAATT
1 ATTTTAGATTTTTAAAGAATT
1190718 TTTATTCTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (21 bp):
ATTTTAGATTTTTAAAGAATT
Found at i:1195105 original size:24 final size:25
Alignment explanation
Indices: 1195063--1195123 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 25
1195053 TTTTTTAATT
* *
1195063 TTATTAGTTTAATTTAATATATAAAA
1 TTATTA-TATAATTAAATATATAAAA
* *
1195089 TTATTA-ATAATTAAATATGTAATA
1 TTATTATATAATTAAATATATAAAA
1195113 TTATTATATAA
1 TTATTATATAA
1195124 AAAAATAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 20 0.67
25 4 0.13
26 6 0.20
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (25 bp):
TTATTATATAATTAAATATATAAAA
Found at i:1197103 original size:32 final size:32
Alignment explanation
Indices: 1197067--1197138 Score: 117
Period size: 32 Copynumber: 2.2 Consensus size: 32
1197057 TAATGTTGGG
**
1197067 TTTGATTCCTATTTTTTACCTCCTATTTTGCA
1 TTTGATTCCTATTTTCGACCTCCTATTTTGCA
*
1197099 TTTGATTCCTATTTTCGACCTCCTATTTTGCG
1 TTTGATTCCTATTTTCGACCTCCTATTTTGCA
1197131 TTTGATTC
1 TTTGATTC
1197139 TTTTCCCCTG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.14, C:0.22, G:0.10, T:0.54
Consensus pattern (32 bp):
TTTGATTCCTATTTTCGACCTCCTATTTTGCA
Found at i:1197152 original size:20 final size:20
Alignment explanation
Indices: 1197127--1197164 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1197117 CCTCCTATTT
*
1197127 TGCGTTTGATTCTTTTCCCC
1 TGCGTTAGATTCTTTTCCCC
1197147 TGCGTTAGATTCTTTTCC
1 TGCGTTAGATTCTTTTCC
1197165 TGGTAGTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.08, C:0.26, G:0.16, T:0.50
Consensus pattern (20 bp):
TGCGTTAGATTCTTTTCCCC
Found at i:1199087 original size:11 final size:11
Alignment explanation
Indices: 1199071--1199098 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1199061 GGAAAGTAAT
1199071 GTTTGTTAGCA
1 GTTTGTTAGCA
1199082 GTTTGTTAGCA
1 GTTTGTTAGCA
1199093 GTTTGT
1 GTTTGT
1199099 GTGTGCATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.14, C:0.07, G:0.29, T:0.50
Consensus pattern (11 bp):
GTTTGTTAGCA
Found at i:1202095 original size:13 final size:13
Alignment explanation
Indices: 1202077--1202102 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1202067 AAGGTGTGAA
1202077 CACTGGTAGCAAC
1 CACTGGTAGCAAC
1202090 CACTGGTAGCAAC
1 CACTGGTAGCAAC
1202103 AAAAACAACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.31, G:0.23, T:0.15
Consensus pattern (13 bp):
CACTGGTAGCAAC
Found at i:1213206 original size:3 final size:3
Alignment explanation
Indices: 1213200--1213286 Score: 174
Period size: 3 Copynumber: 29.0 Consensus size: 3
1213190 ACAAAATCAT
1213200 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1213248 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1213287 AGGTAGGCAG
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 84 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1214435 original size:6 final size:6
Alignment explanation
Indices: 1214424--1214448 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1214414 AATTATTTTA
1214424 TTATAT TTATAT TTATAT TTATAT T
1 TTATAT TTATAT TTATAT TTATAT T
1214449 GTACTTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTATAT
Found at i:1215419 original size:15 final size:15
Alignment explanation
Indices: 1215379--1215422 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
1215369 GATGCTAACA
1215379 AGTAACAACAAATTG
1 AGTAACAACAAATTG
*
1215394 A-T-A-TA-AAATTG
1 AGTAACAACAAATTG
1215405 AGTAACAACAAATTG
1 AGTAACAACAAATTG
1215420 AGT
1 AGT
1215423 CCACAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 8
0.70 0.06 0.24
Matches are distributed among these distances:
11 7 0.30
12 2 0.09
13 2 0.09
14 2 0.09
15 10 0.43
ACGTcount: A:0.52, C:0.09, G:0.14, T:0.25
Consensus pattern (15 bp):
AGTAACAACAAATTG
Found at i:1215626 original size:21 final size:21
Alignment explanation
Indices: 1215587--1215627 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1215577 GGTAAAAAAT
* *
1215587 TACCTAAAACATTATTATTTC
1 TACCTAAAACATCAATATTTC
1215608 TACCTAAAACATCAATATTT
1 TACCTAAAACATCAATATTT
1215628 TTTAACATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.20, G:0.00, T:0.39
Consensus pattern (21 bp):
TACCTAAAACATCAATATTTC
Found at i:1216676 original size:19 final size:21
Alignment explanation
Indices: 1216643--1216682 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1216633 ATTAGGTAGC
*
1216643 AAAATTAATATTTTTA-ATAA
1 AAAAATAATATTTTTAGATAA
1216663 AAAAATAATA-TTTTAGATAA
1 AAAAATAATATTTTTAGATAA
1216683 TACTTTAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (21 bp):
AAAAATAATATTTTTAGATAA
Found at i:1223191 original size:22 final size:20
Alignment explanation
Indices: 1223149--1223189 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1223139 ATATTTTTTC
*
1223149 TCTATATTTTTTTAGTTAAA
1 TCTATATTTTTTTAGTAAAA
*
1223169 TCTATATTTTATTTTGTAAAA
1 TCTATATTTT-TTTAGTAAAA
1223190 ATAAAATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.59
Consensus pattern (20 bp):
TCTATATTTTTTTAGTAAAA
Found at i:1226954 original size:10 final size:9
Alignment explanation
Indices: 1226935--1226969 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
1226925 ATTTTATTTT
1226935 AAAAAATAA
1 AAAAAATAA
*
1226944 AAAAAATTA
1 AAAAAATAA
1226953 AAAAAATAA
1 AAAAAATAA
*
1226962 GAAAAATA
1 AAAAAATA
1226970 TAACAATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (9 bp):
AAAAAATAA
Found at i:1228505 original size:30 final size:31
Alignment explanation
Indices: 1228436--1228514 Score: 108
Period size: 31 Copynumber: 2.6 Consensus size: 31
1228426 AGTTTCAAAA
* *
1228436 GTAAC-AAATCGGTCACTAATGTTATTAATTT
1 GTAACAAAAT-GGTCACTAACGTTATCAATTT
*
1228467 GTAACAAAATGGTCACTAACGTTATCGATTT
1 GTAACAAAATGGTCACTAACGTTATCAATTT
1228498 G-AACAAAATGGTCACTA
1 GTAACAAAATGGTCACTA
1228515 TACCGCCATC
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
30 16 0.36
31 24 0.55
32 4 0.09
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (31 bp):
GTAACAAAATGGTCACTAACGTTATCAATTT
Found at i:1231255 original size:21 final size:22
Alignment explanation
Indices: 1231229--1231269 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1231219 AAAAAATTAG
1231229 ATCGA-TTTTTATCCGATTTGA
1 ATCGATTTTTTATCCGATTTGA
1231250 ATCGATTTTTTATCCGATTT
1 ATCGATTTTTTATCCGATTT
1231270 TGTGCATGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.22, C:0.15, G:0.12, T:0.51
Consensus pattern (22 bp):
ATCGATTTTTTATCCGATTTGA
Found at i:1231439 original size:17 final size:18
Alignment explanation
Indices: 1231407--1231440 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1231397 TTTCCTTTAT
*
1231407 AGTTTCATGTCTATAGCG
1 AGTTTCATGACTATAGCG
1231425 AGTTTCA-GACTATAGC
1 AGTTTCATGACTATAGC
1231441 ATATTGCTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (18 bp):
AGTTTCATGACTATAGCG
Found at i:1232871 original size:34 final size:34
Alignment explanation
Indices: 1232820--1232885 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
1232810 ACCCGACCCG
* *
1232820 AAAACATTTTATATATAATTAATATAAAATATAT
1 AAAACATTATATATATAACTAATATAAAATATAT
*
1232854 AAAATATTATATATATAACTAATATAAAATAT
1 AAAACATTATATATATAACTAATATAAAATAT
1232886 TATATATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (34 bp):
AAAACATTATATATATAACTAATATAAAATATAT
Found at i:1233107 original size:15 final size:14
Alignment explanation
Indices: 1233084--1233116 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1233074 AAAATAAGTT
*
1233084 AAAATA-AAAACAA
1 AAAATACAAAAAAA
1233097 AAAATACAAAAAAA
1 AAAATACAAAAAAA
1233111 AAAATA
1 AAAATA
1233117 GGCATTTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.85, C:0.06, G:0.00, T:0.09
Consensus pattern (14 bp):
AAAATACAAAAAAA
Found at i:1233373 original size:24 final size:24
Alignment explanation
Indices: 1233346--1233399 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
1233336 ATTTATGAAT
*
1233346 TTAAATTTAATGAAAAT-ATATAAA
1 TTAAATATAAT-AAAATAATATAAA
* *
1233370 TTAAAAATAATAAAATAATATATA
1 TTAAATATAATAAAATAATATAAA
1233394 TTAAAT
1 TTAAAT
1233400 GAGTTTTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
23 5 0.20
24 20 0.80
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (24 bp):
TTAAATATAATAAAATAATATAAA
Found at i:1245160 original size:372 final size:372
Alignment explanation
Indices: 1244475--1245218 Score: 1398
Period size: 372 Copynumber: 2.0 Consensus size: 372
1244465 CTCCACCGAT
1244475 TGGAACACAACCAGACACGCATTCTTAGCAAAACCCCACCTCACAACCTTTACGTTGATACCGTC
1 TGGAACACAACCAGACACGCATTCTTAGCAAAACCCCACCTCACAACCTTTACGTTGATACCGTC
* * *
1244540 ATTCCTTAATGCTTTCTGCATAACATGAAATTCAAAAATATCTTTACAAATACTAGTAAGTGACG
66 ATTCCTTAATGCTTTCTACACAACATGAAATTCAAAAATATCTTTACAAATACCAGTAAGTGACG
*
1244605 ATCTAAGCCAGACCCTATCCTCCACCGGGATAAAAACATCCTTAGTGTTTTTCAACTCCTTTGAA
131 ATCTAAGCCAGACCCTATCCTCCACCGGGATAAAAACATCCTTAGTGTTTTTCAACTCCTTCGAA
* *
1244670 TTAAAATTACTTCCTTCTTGCACACCATCTGACTCTTTAAGCATCCCGACAACCGCTTCCTTATA
196 TTAAAATGACTTCCTTCTTGCACACCATCTGACTCTTTAAGCATCCCAACAACCGCTTCCTTATA
*
1244735 AGACTTACCATCATGAAACTTATCCAGCATCTCCATCTTCCTCACCCTTCCATCTGGAGAAGGCA
261 AGACCTACCATCATGAAACTTATCCAGCATCTCCATCTTCCTCACCCTTCCATCTGGAGAAGGCA
*
1244800 ATCTTCCAGCCTTTTCCCCACTGAATCCACCATTCTTTACCCCATCA
326 ATCTTCCAGCCTTTTCCCCACTGAATCCACCACTCTTTACCCCATCA
1244847 TGGAACACAACCAGACACGCATTCTTAGCAAAACCCCACCTCACAACCTTTACGTTGATACCGTC
1 TGGAACACAACCAGACACGCATTCTTAGCAAAACCCCACCTCACAACCTTTACGTTGATACCGTC
1244912 ATTCCTTAATGCTTTCTACACAACATGAAATTCAAAAATATCTTTACAAATACCAGTAAGTGACG
66 ATTCCTTAATGCTTTCTACACAACATGAAATTCAAAAATATCTTTACAAATACCAGTAAGTGACG
*
1244977 ATCTAAGCCAGACTCTATCCTCCACCGGGATAAAAACATCCTTAGTGTTTTTCAACTCCTTCGAA
131 ATCTAAGCCAGACCCTATCCTCCACCGGGATAAAAACATCCTTAGTGTTTTTCAACTCCTTCGAA
1245042 TTAAAATGACTTCCTTCTTGCACACCATCTGACTCTTTAAGCATCCCAACAACCGCTTCCTTATA
196 TTAAAATGACTTCCTTCTTGCACACCATCTGACTCTTTAAGCATCCCAACAACCGCTTCCTTATA
1245107 AGACCTACCATCATGAAACTTATCCAGCATCTCCATCTTCCTCACCCTTCCATCTGGAGAAGGCA
261 AGACCTACCATCATGAAACTTATCCAGCATCTCCATCTTCCTCACCCTTCCATCTGGAGAAGGCA
*
1245172 ATCTTCCAGCCTTTTCCCCACTGAATTCACCACTCTTTACCCCATCA
326 ATCTTCCAGCCTTTTCCCCACTGAATCCACCACTCTTTACCCCATCA
1245219 ACCCTCCCAT
Statistics
Matches: 362, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
372 362 1.00
ACGTcount: A:0.30, C:0.32, G:0.10, T:0.28
Consensus pattern (372 bp):
TGGAACACAACCAGACACGCATTCTTAGCAAAACCCCACCTCACAACCTTTACGTTGATACCGTC
ATTCCTTAATGCTTTCTACACAACATGAAATTCAAAAATATCTTTACAAATACCAGTAAGTGACG
ATCTAAGCCAGACCCTATCCTCCACCGGGATAAAAACATCCTTAGTGTTTTTCAACTCCTTCGAA
TTAAAATGACTTCCTTCTTGCACACCATCTGACTCTTTAAGCATCCCAACAACCGCTTCCTTATA
AGACCTACCATCATGAAACTTATCCAGCATCTCCATCTTCCTCACCCTTCCATCTGGAGAAGGCA
ATCTTCCAGCCTTTTCCCCACTGAATCCACCACTCTTTACCCCATCA
Found at i:1251507 original size:39 final size:39
Alignment explanation
Indices: 1251435--1251525 Score: 112
Period size: 39 Copynumber: 2.3 Consensus size: 39
1251425 AAGAAGCTCA
* * * *
1251435 TATTCGAATCGGGGTACCAGTGATAGATGAGCATGTGTT
1 TATTCGAATCAGGGTACAAGTGATAGATGAGCATATGTC
* *
1251474 TATTCGAATCAGGGTGCAAGTGTTAGA-GAAGCATATGTC
1 TATTCGAATCAGGGTACAAGTGATAGATG-AGCATATGTC
1251513 TATTCGAATCAGG
1 TATTCGAATCAGG
1251526 ATACGAGCAA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
38 1 0.02
39 44 0.98
ACGTcount: A:0.29, C:0.13, G:0.29, T:0.30
Consensus pattern (39 bp):
TATTCGAATCAGGGTACAAGTGATAGATGAGCATATGTC
Found at i:1254445 original size:35 final size:35
Alignment explanation
Indices: 1254399--1254469 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
1254389 CAAAAATACC
1254399 TTATTATTCTATTCAAAAATATTTCTTTTATTAGT
1 TTATTATTCTATTCAAAAATATTTCTTTTATTAGT
1254434 TTATTATTCTATTCAAAAATATTTCTTTTATTAGT
1 TTATTATTCTATTCAAAAATATTTCTTTTATTAGT
1254469 T
1 T
1254470 AGATTTGATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.31, C:0.08, G:0.03, T:0.58
Consensus pattern (35 bp):
TTATTATTCTATTCAAAAATATTTCTTTTATTAGT
Found at i:1256573 original size:2 final size:2
Alignment explanation
Indices: 1256568--1256612 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1256558 GAATGCAATC
1256568 AT AT AT AT AT 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 AT AT AT AT AT
1256610 AT A
1 AT A
1256613 AACTTTATGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1261565 original size:2 final size:2
Alignment explanation
Indices: 1261558--1261598 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1261548 GTACACGGGA
1261558 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1261599 AGCAGGCAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1270933 original size:39 final size:39
Alignment explanation
Indices: 1270875--1271072 Score: 155
Period size: 39 Copynumber: 5.3 Consensus size: 39
1270865 ACCCTACCAT
* * * * *
1270875 TACAAGTCACCACCGCCTCCTCCCAAGGAGGCATACAAA
1 TACAAGTCTCTACCACCTCCTCCCAAGGAGTCATACAAG
* * *
1270914 TACAAGTCTCTACCTCCTCCTCCTAAGGAATCATACAAG
1 TACAAGTCTCTACCACCTCCTCCCAAGGAGTCATACAAG
* * * *
1270953 TATAATTCTCCACCTCCTCCTCCCAAGGA---AT-C-A-
1 TACAAGTCTCTACCACCTCCTCCCAAGGAGTCATACAAG
*
1270986 TACAAG--TCT-CCACCTCCTCCCAATGAGTCATACAAG
1 TACAAGTCTCTACCACCTCCTCCCAAGGAGTCATACAAG
* * *
1271022 TACAA-TCTCCGTCTCCACCTCCTCCTAAGGAGCCATACAAG
1 TACAAGTCT-C-T-ACCACCTCCTCCCAAGGAGTCATACAAG
1271063 TACAAGTCTC
1 TACAAGTCTC
1271073 CTCCTCCACC
Statistics
Matches: 127, Mismatches: 19, Indels: 24
0.75 0.11 0.14
Matches are distributed among these distances:
30 15 0.12
31 2 0.02
33 6 0.05
34 2 0.02
35 2 0.02
36 7 0.06
37 1 0.01
38 1 0.01
39 58 0.46
41 30 0.24
42 3 0.02
ACGTcount: A:0.30, C:0.37, G:0.11, T:0.22
Consensus pattern (39 bp):
TACAAGTCTCTACCACCTCCTCCCAAGGAGTCATACAAG
Found at i:1271026 original size:36 final size:36
Alignment explanation
Indices: 1270890--1271148 Score: 181
Period size: 36 Copynumber: 7.1 Consensus size: 36
1270880 GTCACCACCG
* * *
1270890 CCTCCTCCCAAGGAGGCATACAAATACAAGTCTCTA
1 CCTCCTCCCAAGGAGTCATACAAGTACAAGTCTCCA
* * *
1270926 CCTCCTCCTCCTAAGGAATCATACAAGTATAATTCTCCA
1 CCTCCT-C-CC-AAGGAGTCATACAAGTACAAGTCTCCA
1270965 CCTCCTCCTCCCAAGGA---AT-C-A-TACAAGTCTCCA
1 ---CCTCCTCCCAAGGAGTCATACAAGTACAAGTCTCCA
*
1270998 CCTCCTCCCAATGAGTCATACAAGTACAATCTCCGTCTCCA
1 CCTCCTCCCAAGGAGTCATACAAGTACAA-----GTCTCCA
* * *
1271039 CCTCCTCCTAAGGAGCCATACAAGTACAAGTCTCCT
1 CCTCCTCCCAAGGAGTCATACAAGTACAAGTCTCCA
* **** * * *
1271075 CCTCCACCCCCTCATGT-ATATAAGTACGAGTCTCCT
1 CCTCCTCCCAAGGA-GTCATACAAGTACAAGTCTCCA
* *
1271111 CCTCCTCCCAAGGAGCCATACAAGTACAAGTCACCA
1 CCTCCTCCCAAGGAGTCATACAAGTACAAGTCTCCA
1271147 CC
1 CC
1271149 GCCACCCCCA
Statistics
Matches: 172, Mismatches: 32, Indels: 38
0.71 0.13 0.16
Matches are distributed among these distances:
30 13 0.08
33 12 0.07
34 2 0.01
35 3 0.02
36 70 0.41
37 2 0.01
38 2 0.01
39 26 0.15
40 2 0.01
41 34 0.20
42 6 0.03
ACGTcount: A:0.29, C:0.38, G:0.11, T:0.22
Consensus pattern (36 bp):
CCTCCTCCCAAGGAGTCATACAAGTACAAGTCTCCA
Found at i:1271059 original size:41 final size:42
Alignment explanation
Indices: 1270991--1271087 Score: 135
Period size: 41 Copynumber: 2.3 Consensus size: 42
1270981 AATCATACAA
* *
1270991 GTCTCCACCTCCTCCCAATGAGTCATACAAGTACAA-TCTCC
1 GTCTCCACCTCCTCCCAAGGAGCCATACAAGTACAAGTCTCC
*
1271032 GTCTCCACCTCCTCCTAAGGAGCCATACAAGTACAAGTCTCC
1 GTCTCCACCTCCTCCCAAGGAGCCATACAAGTACAAGTCTCC
*
1271074 -TCCTCCACCCCCTC
1 GT-CTCCACCTCCTC
1271088 ATGTATATAA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
41 34 0.68
42 16 0.32
ACGTcount: A:0.24, C:0.43, G:0.10, T:0.23
Consensus pattern (42 bp):
GTCTCCACCTCCTCCCAAGGAGCCATACAAGTACAAGTCTCC
Found at i:1271135 original size:113 final size:108
Alignment explanation
Indices: 1270890--1271142 Score: 283
Period size: 110 Copynumber: 2.3 Consensus size: 108
1270880 GTCACCACCG
* * * *
1270890 CCTCCTCCCAAGGAGGCATACAAATACAAGTCTCTACCTCCTCCTCCTAAGGAATCATACAAGTA
1 CCTCCTCCCAAGGAGCCATACAAGTACAAGTCTCTACCACCTCCTCCTAAGGAACCATACAAGTA
* * * * *
1270955 TAATTCTCCACCTCCTCCTCCCAAGGAATCATACAAGTCTCCA
66 CAAGTCTCCACCTCCACCCCCCAAGGAATAATACAAGTCTCCA
* * * *
1270998 CCTCCTCCCAATGAGTCATACAAGTACAA-TCTCCGTCTCCACCTCCTCCTAAGGAGCCATACAA
1 CCTCCTCCCAAGGAGCCATACAAGTACAAGTCT-C-T-ACCACCTCCTCCTAAGGAACCATACAA
* * * * *
1271062 GTACAAGTCTCCTCCTCCACCCCCTCATGTATATAAGTACGAGTCTCCT
63 GTACAAGTCTCCACCTCCACCCCC-CAAGGA-ATAA-TACAAGTCTCCA
1271111 CCTCCTCCCAAGGAGCCATACAAGTACAAGTC
1 CCTCCTCCCAAGGAGCCATACAAGTACAAGTC
1271143 ACCACCGCCA
Statistics
Matches: 119, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
107 3 0.03
108 27 0.23
109 1 0.01
110 42 0.35
111 4 0.03
112 3 0.03
113 37 0.31
114 2 0.02
ACGTcount: A:0.28, C:0.37, G:0.11, T:0.23
Consensus pattern (108 bp):
CCTCCTCCCAAGGAGCCATACAAGTACAAGTCTCTACCACCTCCTCCTAAGGAACCATACAAGTA
CAAGTCTCCACCTCCACCCCCCAAGGAATAATACAAGTCTCCA
Found at i:1271172 original size:72 final size:72
Alignment explanation
Indices: 1271032--1271185 Score: 193
Period size: 72 Copynumber: 2.1 Consensus size: 72
1271022 TACAATCTCC
* * * * * * *
1271032 GTCTCCACCTCCTCCTAAGGAGCCATACAAGTACAAGTCTCCTCCTCCACCCCCTCATGTATATA
1 GTCTCCACCTCCTCCCAAGGAGCCATACAAGTACAAGTCACCACCGCCACCCCCACACGTATACA
1271097 AGTACGA
66 AGTACGA
* *
1271104 GTCTCCTCCTCCTCCCAAGGAGCCATACAAGTACAAGTCACCACCGCCACCCCCAC-CGATCTAC
1 GTCTCCACCTCCTCCCAAGGAGCCATACAAGTACAAGTCACCACCGCCACCCCCACACG-TATAC
*
1271168 AAGTACAA
65 AAGTACGA
*
1271176 ATCTCCACCT
1 GTCTCCACCT
1271186 TCACCACCAT
Statistics
Matches: 69, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
71 1 0.01
72 68 0.99
ACGTcount: A:0.27, C:0.41, G:0.12, T:0.20
Consensus pattern (72 bp):
GTCTCCACCTCCTCCCAAGGAGCCATACAAGTACAAGTCACCACCGCCACCCCCACACGTATACA
AGTACGA
Found at i:1272817 original size:4 final size:4
Alignment explanation
Indices: 1272808--1272842 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
1272798 ATTCGTATAG
1272808 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1272843 TATTGTTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:1277548 original size:30 final size:30
Alignment explanation
Indices: 1277462--1277535 Score: 141
Period size: 30 Copynumber: 2.5 Consensus size: 30
1277452 CTTAATTTTA
1277462 TCTTAAAAATTAAATAAATACCTAAATAAT
1 TCTTAAAAATTAAATAAATACCTAAATAAT
1277492 TCTTAAAAATTAAATAAATACCTAAATAAT
1 TCTTAAAAATTAAATAAATACCTAAATAAT
1277522 TCTTAAAAA-TAAAT
1 TCTTAAAAATTAAAT
1277536 TATACTTTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 5 0.11
30 39 0.89
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (30 bp):
TCTTAAAAATTAAATAAATACCTAAATAAT
Found at i:1277946 original size:27 final size:27
Alignment explanation
Indices: 1277908--1277973 Score: 132
Period size: 27 Copynumber: 2.4 Consensus size: 27
1277898 CAAAACAGTG
1277908 CTGAATGATTCAACACAGAAGTATATT
1 CTGAATGATTCAACACAGAAGTATATT
1277935 CTGAATGATTCAACACAGAAGTATATT
1 CTGAATGATTCAACACAGAAGTATATT
1277962 CTGAATGATTCA
1 CTGAATGATTCA
1277974 GAGTCATTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.30
Consensus pattern (27 bp):
CTGAATGATTCAACACAGAAGTATATT
Found at i:1278064 original size:15 final size:16
Alignment explanation
Indices: 1278026--1278066 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
1278016 ACAGAGCCTC
*
1278026 TGAATCATTCAGCATT
1 TGAATCATTCAGCACT
*
1278042 TGAATCATTCAGCGCT
1 TGAATCATTCAGCACT
1278058 T-AATCATTC
1 TGAATCATTC
1278067 TGAAGTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (16 bp):
TGAATCATTCAGCACT
Found at i:1278446 original size:26 final size:26
Alignment explanation
Indices: 1278410--1278472 Score: 126
Period size: 26 Copynumber: 2.4 Consensus size: 26
1278400 AGACAAATTG
1278410 GTGACGATTAGTTTCATTCTGTTTGA
1 GTGACGATTAGTTTCATTCTGTTTGA
1278436 GTGACGATTAGTTTCATTCTGTTTGA
1 GTGACGATTAGTTTCATTCTGTTTGA
1278462 GTGACGATTAG
1 GTGACGATTAG
1278473 CCCCTATTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.21, C:0.11, G:0.25, T:0.43
Consensus pattern (26 bp):
GTGACGATTAGTTTCATTCTGTTTGA
Found at i:1279094 original size:39 final size:39
Alignment explanation
Indices: 1279036--1279342 Score: 249
Period size: 36 Copynumber: 8.3 Consensus size: 39
1279026 ACCCTACCAT
* ** * *
1279036 TACAAGTCACCACGGCCTCCTCCCAAGGAGGCATACAAA
1 TACAAGTCTCCACCTCCTCCTCCCAAGGAGTCATACAAG
* *
1279075 TACAAGTCTCCACCTCCTCCTCCCAAGGAATCATATAAG
1 TACAAGTCTCCACCTCCTCCTCCCAAGGAGTCATACAAG
* *
1279114 TATAATTCTCCACCTCCTCCTCCCAAGGA---AT-C-A-
1 TACAAGTCTCCACCTCCTCCTCCCAAGGAGTCATACAAG
*
1279147 TACAAGTCTCCACCTCCTCCT---AAGGAGCCATACAAG
1 TACAAGTCTCCACCTCCTCCTCCCAAGGAGTCATACAAG
* * * *
1279183 TACAAGTCTCCGCCTCCACCTCCTC---CAGT-TTACAAG
1 TACAAGTCTCCACCTCCTCCTCC-CAAGGAGTCATACAAG
*
1279219 TACAAGTCTCCACCTCCTCAT---AAGGAGTCATACAAG
1 TACAAGTCTCCACCTCCTCCTCCCAAGGAGTCATACAAG
* * * *
1279255 TACAAGTCTCCTCCTCCACC-CCCTCA--TGTC-TACAAG
1 TACAAGTCTCCACCTCCTCCTCCC-AAGGAGTCATACAAG
* * *
1279291 TACAAGTCTCCTCCTCCTCCTCCCAAGGAGCCATACAAA
1 TACAAGTCTCCACCTCCTCCTCCCAAGGAGTCATACAAG
*
1279330 TACAAGTCACCAC
1 TACAAGTCTCCAC
1279343 AGTCACCCCC
Statistics
Matches: 212, Mismatches: 34, Indels: 44
0.73 0.12 0.15
Matches are distributed among these distances:
30 5 0.02
33 21 0.10
34 2 0.01
35 4 0.02
36 94 0.44
37 8 0.04
38 2 0.01
39 76 0.36
ACGTcount: A:0.29, C:0.38, G:0.11, T:0.21
Consensus pattern (39 bp):
TACAAGTCTCCACCTCCTCCTCCCAAGGAGTCATACAAG
Found at i:1279157 original size:33 final size:33
Alignment explanation
Indices: 1279074--1279167 Score: 125
Period size: 39 Copynumber: 2.7 Consensus size: 33
1279064 AGGCATACAA
1279074 ATACAAGTCTCCACCTCCTCCTCCCAAGGAATC
1 ATACAAGTCTCCACCTCCTCCTCCCAAGGAATC
*
1279107 ATATAAGTATAATTCTCCACCTCCTCCTCCCAAGGAATC
1 ATACAAG------TCTCCACCTCCTCCTCCCAAGGAATC
1279146 ATACAAGTCTCCACCTCCTCCT
1 ATACAAGTCTCCACCTCCTCCT
1279168 AAGGAGCCAT
Statistics
Matches: 53, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
33 21 0.40
39 32 0.60
ACGTcount: A:0.28, C:0.39, G:0.07, T:0.26
Consensus pattern (33 bp):
ATACAAGTCTCCACCTCCTCCTCCCAAGGAATC
Found at i:1279350 original size:75 final size:71
Alignment explanation
Indices: 1279147--1279379 Score: 279
Period size: 72 Copynumber: 3.2 Consensus size: 71
1279137 CAAGGAATCA
* *
1279147 TACAAGTCTCCACCTCCTCCTAAGGAGCCATACAAGTACAAGTCTCCGCCTCCACCTCCTCCAGT
1 TACAAGTCTCCACCTCCTCCTAAGGAGCCATACAAGTACAAGTCTCCACCTCCACCCCCT-CAGT
*
1279212 TTACAAG
65 CTACAAG
* * *
1279219 TACAAGTCTCCACCTCCTCATAAGGAGTCATACAAGTACAAGTCTCCTCCTCCACCCCCTCATGT
1 TACAAGTCTCCACCTCCTCCTAAGGAGCCATACAAGTACAAGTCTCCACCTCCACCCCCTCA-GT
1279284 CTACAAG
65 CTACAAG
* * * * *
1279291 TACAAGTCTCCTCCTCCTCCTCCCAAGGAGCCATACAAATACAAGTCACCACAGT-CACCCCCAC
1 TACAAGTCTCCACCTCCTCCT---AAGGAGCCATACAAGTACAAGTCTCCAC-CTCCACCCCC-T
*
1279355 CGGTCTACAAG
61 CAGTCTACAAG
*
1279366 TACAAATCTCCACC
1 TACAAGTCTCCACC
1279380 CCCACCACCA
Statistics
Matches: 139, Mismatches: 16, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
71 2 0.01
72 83 0.60
75 52 0.37
76 2 0.01
ACGTcount: A:0.28, C:0.39, G:0.11, T:0.21
Consensus pattern (71 bp):
TACAAGTCTCCACCTCCTCCTAAGGAGCCATACAAGTACAAGTCTCCACCTCCACCCCCTCAGTC
TACAAG
Found at i:1289062 original size:111 final size:111
Alignment explanation
Indices: 1288829--1289332 Score: 550
Period size: 111 Copynumber: 4.5 Consensus size: 111
1288819 TTGCATATCG
** * *
1288829 GATATTCCCTTTACAAGAAATAGAACAAATCTCTCTCTTCCAAGATTTGATATTCCCTTTGAAGA
1 GATATT-CCTTTACAAGAAGCAGAACAAATCACTCTCTTCCAAGATTTGATATTCCCTTAGAAGA
*
1288894 AGCGGAACAAGTCTACCCCGATTCAATGTAT-AACTCCCCCAGATAT
65 AGCGGAACAAGTCTACCCCGATTCAATGGATCAACTCCCCCAGATAT
* *
1288940 GATATTCCCTTTACAAGAAGCATAACAAATCACTCTCTTCCAAGATCTGATATTCCCTTAGAAGA
1 GATATT-CCTTTACAAGAAGCAGAACAAATCACTCTCTTCCAAGATTTGATATTCCCTTAGAAGA
* * *
1289005 AGCGGAACAAGTCTACCACAATTAAATGGATCAACTCCCCCAGATAT
65 AGCGGAACAAGTCTACCCCGATTCAATGGATCAACTCCCCCAGATAT
* * * * *
1289052 TATATTCCTTTTACAAGAAAC-GAACATATCCCTCTCTTCTAAGATTTGATATTCCCTTAGAAGA
1 GATATTCC-TTTACAAGAAGCAGAACAAATCACTCTCTTCCAAGATTTGATATTCCCTTAGAAGA
* * * * *
1289116 AGTGGAACAAGTCTACCCCGATTCAATGGATAAAGCTCCCCTATATCT
65 AGCGGAACAAGTCTACCCCGATTCAATGGATCAA-CTCCCCCAGATAT
* * * * * * * *
1289164 GATATTTCTTT-CAGAAAATGC-GAAACAAGTCCCTATTTTCCAAGATTTGATATTCCCTGAG-T
1 GATATTCCTTTACA-AGAA-GCAG-AACAAATCACTCTCTTCCAAGATTTGATATTCCCTTAGAA
* * * * *
1289226 GACAGGGGAATAAATCTGCCCCGATTCAATGGATCAACTCCCCCAGATCT
63 GA-AGCGGAACAAGTCTACCCCGATTCAATGGATCAACTCCCCCAGATAT
* * * * * *
1289276 GATATTCCCTTAGAAGAAGCGGAACATATCACTCTCTTCTAAGAATTGATATTCCCT
1 GATATTCCTTTACAAGAAGCAGAACAAATCACTCTCTTCCAAGATTTGATATTCCCT
1289333 GGCCCAATCG
Statistics
Matches: 330, Mismatches: 54, Indels: 18
0.82 0.13 0.04
Matches are distributed among these distances:
110 2 0.01
111 191 0.58
112 75 0.23
113 62 0.19
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.29
Consensus pattern (111 bp):
GATATTCCTTTACAAGAAGCAGAACAAATCACTCTCTTCCAAGATTTGATATTCCCTTAGAAGAA
GCGGAACAAGTCTACCCCGATTCAATGGATCAACTCCCCCAGATAT
Found at i:1289303 original size:224 final size:222
Alignment explanation
Indices: 1288829--1289332 Score: 588
Period size: 224 Copynumber: 2.3 Consensus size: 222
1288819 TTGCATATCG
* * * * *
1288829 GATATTCC-CTTTACAAGAAATAGAACAAATCTCTCTCTTCCAAGATTTGATATTCCCTTTGAAG
1 GATATTCCTC-TTACAAGAAA-CGAACATATCACTCTCTTCTAAGATTTGATATTCCCTTAGAAG
* *
1288893 AAGCGGAACAAGTCTACCCCGATTCAATGTATAACTCCCCCAGATATGATATTCCCTTTACAAGA
64 AAGCGGAACAAGTCTACCCCGATTCAATGGATAACTCCCCCAGATATGATATTCCCTTTACAAAA
* * *
1288958 AGCATAACAAATCACTCTCTTCCAAGATCTGATATTCCCTTAGAAGAAGCGGAACAAGTCTACCA
129 AGCATAACAAATCACTATCTTCCAAGATCTGATATTCCCTGAGAAGAAGCGGAACAAATCTACCA
1289023 CAATTAAATGGATCAACTCCCCCAGATAT
194 CAATTAAATGGATCAACTCCCCCAGATAT
* * *
1289052 TATATTCCTTTTACAAGAAACGAACATATCCCTCTCTTCTAAGATTTGATATTCCCTTAGAAGAA
1 GATATTCCTCTTACAAGAAACGAACATATCACTCTCTTCTAAGATTTGATATTCCCTTAGAAGAA
* * * * *
1289117 GTGGAACAAGTCTACCCCGATTCAATGGATAAAGCTCCCCTATATCTGATATT-TCTTT-CAGAA
66 GCGGAACAAGTCTACCCCGATTCAATGGAT-AA-CTCCCCCAGATATGATATTCCCTTTACA-AA
* * * * * * *
1289180 AATGCGA-AACAAGTCCCTATTTTCCAAGATTTGATATTCCCTGAG-TGACAGGGGAATAAATCT
128 AA-GC-ATAACAAATCACTATCTTCCAAGATCTGATATTCCCTGAGAAGA-AGCGGAACAAATCT
* * * * *
1289243 GCCCCGATTCAATGGATCAACTCCCCCAGATCT
190 ACCACAATTAAATGGATCAACTCCCCCAGATAT
* * *
1289276 GATATTCC-CTTAGAAGAAGCGGAACATATCACTCTCTTCTAAGAATTGATATTCCCT
1 GATATTCCTCTTACAAGAAAC-GAACATATCACTCTCTTCTAAGATTTGATATTCCCT
1289333 GGCCCAATCG
Statistics
Matches: 238, Mismatches: 35, Indels: 15
0.83 0.12 0.05
Matches are distributed among these distances:
222 70 0.29
223 37 0.16
224 130 0.55
225 1 0.00
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.29
Consensus pattern (222 bp):
GATATTCCTCTTACAAGAAACGAACATATCACTCTCTTCTAAGATTTGATATTCCCTTAGAAGAA
GCGGAACAAGTCTACCCCGATTCAATGGATAACTCCCCCAGATATGATATTCCCTTTACAAAAAG
CATAACAAATCACTATCTTCCAAGATCTGATATTCCCTGAGAAGAAGCGGAACAAATCTACCACA
ATTAAATGGATCAACTCCCCCAGATAT
Found at i:1289987 original size:4 final size:4
Alignment explanation
Indices: 1289978--1290004 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1289968 TTGATTTTGA
1289978 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1290005 AGTGAATCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:1297772 original size:19 final size:19
Alignment explanation
Indices: 1297745--1297797 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 19
1297735 ATTCCTGCTT
* * *
1297745 AGCTACCAATTTCAACTCA
1 AGCTGCCAACTTCAACCCA
1297764 AGCTGCCAACTTCAACCCA
1 AGCTGCCAACTTCAACCCA
*
1297783 AGTTGCCAACTTCAA
1 AGCTGCCAACTTCAA
1297798 AGATTCTCTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.34, C:0.34, G:0.09, T:0.23
Consensus pattern (19 bp):
AGCTGCCAACTTCAACCCA
Found at i:1297868 original size:10 final size:9
Alignment explanation
Indices: 1297848--1297872 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1297838 GAAACTTCCC
1297848 TTTTTTATT
1 TTTTTTATT
1297857 TTTTTTATT
1 TTTTTTATT
1297866 TTTTTTA
1 TTTTTTA
1297873 CCTTTTTACA
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:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTTATT
Found at i:1298198 original size:39 final size:39
Alignment explanation
Indices: 1298140--1298237 Score: 124
Period size: 39 Copynumber: 2.5 Consensus size: 39
1298130 ACCCTACCAT
* * *
1298140 TACAAGTCACCACCGCCTCCTCCCAAAGAGGCATACAAA
1 TACAAGTCTCCACCTCCTCCTCCCAAAGAAGCATACAAA
* * *
1298179 TACAAGTCTCCACCTCCTCCTCCCAAGGAATCATACAAG
1 TACAAGTCTCCACCTCCTCCTCCCAAAGAAGCATACAAA
* *
1298218 TATAATTCTCCACCTCCTCC
1 TACAAGTCTCCACCTCCTCC
1298238 CAATGAATCA
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 51 1.00
ACGTcount: A:0.31, C:0.40, G:0.09, T:0.20
Consensus pattern (39 bp):
TACAAGTCTCCACCTCCTCCTCCCAAAGAAGCATACAAA
Found at i:1298215 original size:33 final size:33
Alignment explanation
Indices: 1298178--1298267 Score: 108
Period size: 36 Copynumber: 2.6 Consensus size: 33
1298168 AGGCATACAA
1298178 ATACAAGTCTCCACCTCCTCCTCCCAAGGAATC
1 ATACAAGTCTCCACCTCCTCCTCCCAAGGAATC
* * * * *
1298211 ATACAAGTATAATTCTCCACCTCCTCCCAATGAATC
1 ATACAAG--T-CTCCACCTCCTCCTCCCAAGGAATC
1298247 ATACAAGTCTCCACCTCCTCC
1 ATACAAGTCTCCACCTCCTCC
1298268 CAAGGAGCCA
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
33 16 0.36
34 1 0.02
35 1 0.02
36 27 0.60
ACGTcount: A:0.29, C:0.40, G:0.07, T:0.24
Consensus pattern (33 bp):
ATACAAGTCTCCACCTCCTCCTCCCAAGGAATC
Found at i:1298246 original size:36 final size:35
Alignment explanation
Indices: 1298194--1298300 Score: 125
Period size: 36 Copynumber: 3.1 Consensus size: 35
1298184 GTCTCCACCT
1298194 CCTCCTCCCAAGGAATCATACAAGTATAATTCTCCA
1 CCTCCTCCCAAGGAATCATACAAGTATAA-TCTCCA
*
1298230 CCTCCTCCCAATGAATCATACAAG-----TCTCCA
1 CCTCCTCCCAAGGAATCATACAAGTATAATCTCCA
** *
1298260 CCTCCTCCCAAGGAGCCATACAAGTATAAGTCTCCG
1 CCTCCTCCCAAGGAATCATACAAGTATAA-TCTCCA
1298296 CCTCC
1 CCTCC
1298301 ACCTCCTCCA
Statistics
Matches: 60, Mismatches: 5, Indels: 12
0.78 0.06 0.16
Matches are distributed among these distances:
30 27 0.45
36 33 0.55
ACGTcount: A:0.29, C:0.38, G:0.10, T:0.22
Consensus pattern (35 bp):
CCTCCTCCCAAGGAATCATACAAGTATAATCTCCA
Found at i:1298258 original size:30 final size:30
Alignment explanation
Indices: 1298178--1298284 Score: 106
Period size: 30 Copynumber: 3.3 Consensus size: 30
1298168 AGGCATACAA
1298178 ATACAAGTCTCCACCTCCTCCTCCCAAGGAATC
1 ATACAAGTCTCCA---CCTCCTCCCAAGGAATC
*
1298211 ATACAAGTATAATTCTCCACCTCCTCCCAATGAATC
1 ATACAAG------TCTCCACCTCCTCCCAAGGAATC
**
1298247 ATACAAGTCTCCACCTCCTCCCAAGGAGCC
1 ATACAAGTCTCCACCTCCTCCCAAGGAATC
1298277 ATACAAGT
1 ATACAAGT
1298285 ATAAGTCTCC
Statistics
Matches: 64, Mismatches: 4, Indels: 15
0.77 0.05 0.18
Matches are distributed among these distances:
30 28 0.44
33 7 0.11
36 23 0.36
39 6 0.09
ACGTcount: A:0.31, C:0.37, G:0.09, T:0.22
Consensus pattern (30 bp):
ATACAAGTCTCCACCTCCTCCCAAGGAATC
Found at i:1298287 original size:66 final size:66
Alignment explanation
Indices: 1298178--1298513 Score: 230
Period size: 66 Copynumber: 4.9 Consensus size: 66
1298168 AGGCATACAA
** * *
1298178 ATACAAGTCTCCACCTCCTCCTCCCAAGGAATCATACAAGTATAATTCTCCACCTCCTCC-CAAT
1 ATACAAGTCTCCA---CCTCCTCCCAAGGAGCCATACAAGTATAAGTCTCCACCTCCACCTC-AT
*
1298242 -GAAT
62 CCAAT
* *
1298246 CATACAAGTCTCCACCTCCTCCCAAGGAGCCATACAAGTATAAGTCTCCGCCTCCACCTCCTCCA
1 -ATACAAGTCTCCACCTCCTCCCAAGGAGCCATACAAGTATAAGTCTCCACCTCCACCTCATCCA
*
1298311 GT
65 AT
* * * * * * *
1298313 TTACAAGTCTCCCCCTCCTCCTAAGGAGCCATACAAGTACAAGTCTCCTCCACCCCCTCATGTCT
1 ATACAAGTCTCCACCTCCTCCCAAGGAGCCATACAAGTATAAGTCTCCACCTCCACCTCA--TC-
1298378 ACAA-
63 -CAAT
* * * * * *
1298382 GTACAAATCTCCTCCTCCCCCTCCCAAGGAGCCATACAAGTACAAGTCACCACCGCCACCTCCAC
1 ATACAAGTCTCCACCT---CCTCCCAAGGAGCCATACAAGTATAAGTCTCCACCTCCACCT-CA-
1298447 CGGTCTACAA-
61 ---TC--CAAT
* * * * * *
1298457 GTACAAGTCTCCTCCTCCTCCCAATGAGCCATACAAGTACAAGTCACCACCGCCACC
1 ATACAAGTCTCCACCTCCTCCCAAGGAGCCATACAAGTATAAGTCTCCACCTCCACC
1298514 CCCACCGGTC
Statistics
Matches: 227, Mismatches: 28, Indels: 21
0.82 0.10 0.08
Matches are distributed among these distances:
66 92 0.41
67 3 0.01
68 2 0.01
69 26 0.11
70 2 0.01
72 77 0.34
73 2 0.01
75 23 0.10
ACGTcount: A:0.28, C:0.41, G:0.11, T:0.21
Consensus pattern (66 bp):
ATACAAGTCTCCACCTCCTCCCAAGGAGCCATACAAGTATAAGTCTCCACCTCCACCTCATCCAA
T
Found at i:1298354 original size:36 final size:36
Alignment explanation
Indices: 1298314--1298501 Score: 129
Period size: 36 Copynumber: 5.2 Consensus size: 36
1298304 TCCTCCAGTT
*
1298314 TACAAGTCTCCCCCTCCTCCTAAGGAGCCATACAAG
1 TACAAGTCTCCCCCTCCTCCCAAGGAGCCATACAAG
* * * * *
1298350 TACAAGTCTCCTCCACC-CCCTCA--TGTC-TACAAG
1 TACAAGTCTCCCCCTCCTCCC-AAGGAGCCATACAAG
* *
1298383 TACAAATCTCCTCCTCCCCCTCCCAAGGAGCCATACAAG
1 TACAAGTCT-C-CC-CCTCCTCCCAAGGAGCCATACAAG
* * ** *
1298422 TACAAGTCACCACCGCCACCT-CCACCG-GTC-TACAAG
1 TACAAGTC-TC-CC-CCTCCTCCCAAGGAGCCATACAAG
* *
1298458 TACAAGTCTCCTCCTCCTCCCAATGAGCCATACAAG
1 TACAAGTCTCCCCCTCCTCCCAAGGAGCCATACAAG
1298494 TACAAGTC
1 TACAAGTC
1298502 ACCACCGCCA
Statistics
Matches: 114, Mismatches: 26, Indels: 24
0.70 0.16 0.15
Matches are distributed among these distances:
33 19 0.17
34 8 0.07
35 6 0.05
36 49 0.43
37 5 0.04
38 6 0.05
39 21 0.18
ACGTcount: A:0.28, C:0.41, G:0.12, T:0.20
Consensus pattern (36 bp):
TACAAGTCTCCCCCTCCTCCCAAGGAGCCATACAAG
Found at i:1298417 original size:72 final size:74
Alignment explanation
Indices: 1298321--1298540 Score: 272
Period size: 72 Copynumber: 3.0 Consensus size: 74
1298311 GTTTACAAGT
* * * * *
1298321 CTCC-CCCTCCTCCTAAGGAGCCATACAAGTACAAGTCTCCTCCACCCCCT-CA-TGTCTACAAG
1 CTCCTCCC-CCTCCCAAGGAGCCATACAAGTACAAGTCACCACCACCACCTCCACGGTCTACAAG
1298383 TACAAATCTC
65 TACAAATCTC
*
1298393 CTCCTCCCCCTCCCAAGGAGCCATACAAGTACAAGTCACCACCGCCACCTCCACCGGTCTACAAG
1 CTCCTCCCCCTCCCAAGGAGCCATACAAGTACAAGTCACCACCACCACCTCCA-CGGTCTACAAG
*
1298458 TACAAGTCTC
65 TACAAATCTC
* * * *
1298468 CTCCT---CCTCCCAATGAGCCATACAAGTACAAGTCACCACCGCCACCCCCACCGGTCTACAAA
1 CTCCTCCCCCTCCCAAGGAGCCATACAAGTACAAGTCACCACCACCACCTCCA-CGGTCTACAAG
1298530 TACAAATCTC
65 TACAAATCTC
1298540 C
1 C
1298541 ACCCCCACCA
Statistics
Matches: 133, Mismatches: 11, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
72 105 0.79
73 5 0.04
75 23 0.17
ACGTcount: A:0.28, C:0.43, G:0.11, T:0.18
Consensus pattern (74 bp):
CTCCTCCCCCTCCCAAGGAGCCATACAAGTACAAGTCACCACCACCACCTCCACGGTCTACAAGT
ACAAATCTC
Found at i:1298528 original size:36 final size:36
Alignment explanation
Indices: 1298416--1298555 Score: 131
Period size: 36 Copynumber: 3.9 Consensus size: 36
1298406 CAAGGAGCCA
*
1298416 TACAAGTACAAGTCACCACCGCCACCTCCACCGGTC
1 TACAAGTACAAGTCACCACCGCCACCCCCACCGGTC
* * * * ** *
1298452 TACAAGTACAAGTCTCCTCC-TC-CTCCCAATGAGCC
1 TACAAGTACAAGTCACCACCGCCACCCCCACCG-GTC
1298487 ATACAAGTACAAGTCACCACCGCCACCCCCACCGGTC
1 -TACAAGTACAAGTCACCACCGCCACCCCCACCGGTC
* * * * *
1298524 TACAAATACAAATCTCCACCCCCACCACCACC
1 TACAAGTACAAGTCACCACCGCCACCCCCACC
1298556 CCATTATGTC
Statistics
Matches: 80, Mismatches: 20, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
34 5 0.06
35 3 0.04
36 63 0.79
37 3 0.04
38 6 0.08
ACGTcount: A:0.30, C:0.45, G:0.10, T:0.15
Consensus pattern (36 bp):
TACAAGTACAAGTCACCACCGCCACCCCCACCGGTC
Found at i:1298528 original size:66 final size:66
Alignment explanation
Indices: 1298248--1298528 Score: 244
Period size: 72 Copynumber: 4.1 Consensus size: 66
1298238 CAATGAATCA
* * * * * * * *
1298248 TACAAGTCTCCACCTCCTCCCAAGGAGCCATACAAGTATAAGTCTCCGCCTCCACCTCCTCCAGT
1 TACAAGTCTCCTCCTCCTCCCAAGGAGCCATACAAGTACAAGTCACCACCGCCACCCCCACCGGT
*
1298313 T
66 C
* * * * * **
1298314 TACAAGTCTCCCCCTCCTCCTAAGGAGCCATACAAGTACAAGT---CTCCTCCACCCCCTCATGT
1 TACAAGTCTCCTCCTCCTCCCAAGGAGCCATACAAGTACAAGTCACCACCGCCACCCCCACCGGT
1298376 C
66 C
1298377 TACAAGTACAAATCTCCTCCTCCCCCTCCCAAGGAGCCATACAAGTACAAGTCACCACCGCCACC
1 TACAAG------TCTCCTCCT---CCTCCCAAGGAGCCATACAAGTACAAGTCACCACCGCCACC
*
1298442 TCCACCGGTCTAC
57 CCCACCGG--T-C
*
1298455 AAGTACAAGTCTCCTCCTCCTCCCAATGAGCCATACAAGTACAAGTCACCACCGCCACCCCCACC
1 ---TACAAGTCTCCTCCTCCTCCCAAGGAGCCATACAAGTACAAGTCACCACCGCCACCCCCACC
1298520 GGTC
63 GGTC
1298524 TACAA
1 TACAA
1298529 ATACAAATCT
Statistics
Matches: 179, Mismatches: 18, Indels: 36
0.77 0.08 0.15
Matches are distributed among these distances:
63 21 0.12
66 45 0.25
69 9 0.05
70 1 0.01
72 74 0.41
75 21 0.12
77 1 0.01
78 1 0.01
81 6 0.03
ACGTcount: A:0.27, C:0.42, G:0.12, T:0.19
Consensus pattern (66 bp):
TACAAGTCTCCTCCTCCTCCCAAGGAGCCATACAAGTACAAGTCACCACCGCCACCCCCACCGGT
C
Found at i:1300233 original size:24 final size:23
Alignment explanation
Indices: 1300206--1300251 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1300196 TGAAAATTAG
1300206 TTTTCACCTCATAAATTATATAAA
1 TTTTCACCT-ATAAATTATATAAA
* * *
1300230 TTTTCTCCTTTAAATTTTATAA
1 TTTTCACCTATAAATTATATAA
1300252 GTTTACCCCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (23 bp):
TTTTCACCTATAAATTATATAAA
Found at i:1302405 original size:15 final size:15
Alignment explanation
Indices: 1302385--1302413 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1302375 TTCATTTCAT
1302385 TTTCATATTCTTTTC
1 TTTCATATTCTTTTC
1302400 TTTCATATTCTTTT
1 TTTCATATTCTTTT
1302414 TATATAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTCATATTCTTTTC
Found at i:1305295 original size:32 final size:32
Alignment explanation
Indices: 1305111--1305297 Score: 137
Period size: 32 Copynumber: 5.9 Consensus size: 32
1305101 GTATAGTATT
* * * *
1305111 GTCAGTGTTGCATTTAGATAATTCACAACACA
1 GTCAGTGTTGTATTCAGATAATGCACAACAGA
* * *
1305143 GTCAGTATTGAATTCACATAA--CAC-ACAGTA
1 GTCAGTGTTGTATTCAGATAATGCACAACAG-A
* * * * *
1305173 GATTAGTATTGCATCCAGATAATGCACATCAGA
1 G-TCAGTGTTGTATTCAGATAATGCACAACAGA
* * *
1305206 GTCAGTGTTGTATTTAGATAATGAACACCAGA
1 GTCAGTGTTGTATTCAGATAATGCACAACAGA
**** *
1305238 GTCAACAATGCATTCAGATAATGCACAACAGA
1 GTCAGTGTTGTATTCAGATAATGCACAACAGA
* *
1305270 GTTAGTGTTGTATTCAGATAGTGCACAA
1 GTCAGTGTTGTATTCAGATAATGCACAA
1305298 GAGCAACAAT
Statistics
Matches: 118, Mismatches: 32, Indels: 10
0.74 0.20 0.06
Matches are distributed among these distances:
29 3 0.03
30 5 0.04
31 16 0.14
32 86 0.73
33 5 0.04
34 3 0.03
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.28
Consensus pattern (32 bp):
GTCAGTGTTGTATTCAGATAATGCACAACAGA
Found at i:1305324 original size:64 final size:63
Alignment explanation
Indices: 1305188--1305308 Score: 165
Period size: 64 Copynumber: 1.9 Consensus size: 63
1305178 GTATTGCATC
* * * *
1305188 CAGATAATGCACATCAGAGTCAGTGTTGTATTTAGATAATGAACACCAGAGTCAACAATGCATT
1 CAGATAATGCACAACAGAGTCAGTGTTGTATTCAGATAATG-ACACAAGAGTCAACAATACATT
* *
1305252 CAGATAATGCACAACAGAGTTAGTGTTGTATTCAGATAGTG-CACAAGAG-CAACAATA
1 CAGATAATGCACAACAGAGTCAGTGTTGTATTCAGATAATGACACAAGAGTCAACAATA
1305309 TCACATTTAT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
61 7 0.14
62 7 0.14
64 37 0.73
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.25
Consensus pattern (63 bp):
CAGATAATGCACAACAGAGTCAGTGTTGTATTCAGATAATGACACAAGAGTCAACAATACATT
Found at i:1309766 original size:20 final size:21
Alignment explanation
Indices: 1309741--1309792 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1309731 TTTTCCCAAC
*
1309741 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1309761 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1309782 TCGCAATGCGA
1 TCGCAATGCGA
1309793 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1309806 original size:20 final size:20
Alignment explanation
Indices: 1309781--1309894 Score: 140
Period size: 20 Copynumber: 5.7 Consensus size: 20
1309771 AATTGGGAAA
1309781 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
1309801 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
1309821 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
1309841 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
1309862 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
1309882 TTCGCAACGCGAT
1 ATCGCAATGCGAT
1309895 TTACATAGCG
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
19 2 0.02
20 65 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:1310488 original size:19 final size:19
Alignment explanation
Indices: 1310466--1310630 Score: 125
Period size: 19 Copynumber: 9.1 Consensus size: 19
1310456 GAAACCAAAA
*
1310466 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1310485 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
1310504 TCGCGTTGTGATTTTTATT
1 TCGCGTTGCGATTTTCATT
1310523 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
1310537 TCTCGTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
1310556 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
1310570 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
* *
1310589 TCCACGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
1310609 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1310629 TC
1 TC
1310631 AACCAAAAGA
Statistics
Matches: 116, Mismatches: 18, Indels: 24
0.73 0.11 0.15
Matches are distributed among these distances:
14 19 0.16
16 4 0.03
17 4 0.03
19 57 0.49
20 31 0.27
21 1 0.01
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1310546 original size:38 final size:38
Alignment explanation
Indices: 1310466--1310630 Score: 125
Period size: 33 Copynumber: 4.6 Consensus size: 38
1310456 GAAACCAAAA
* * *
1310466 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATG
* *
1310504 TCGCGTTGTGATTTTTATTTCGCGTTGCGATTCTC---
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATG
* **
1310539 T--CGTCGCGATAGTCATTTCGCGTTGCGATTCTC---
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATG
** * *
1310572 T--CGTTGCGATAGTCATTTCCACGTTGCGATTCTCATTA
1 TCGCGTTGCGATTTTCATTT-CGCGTTGCGATTCTCA-TG
*
1310610 TCTCGTTGCGATTTTCATTTC
1 TCGCGTTGCGATTTTCATTTC
1310631 AACCAAAAGA
Statistics
Matches: 107, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
33 44 0.41
34 14 0.13
35 1 0.01
38 32 0.30
39 1 0.01
40 15 0.14
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATG
Found at i:1310562 original size:33 final size:33
Alignment explanation
Indices: 1310520--1310605 Score: 145
Period size: 33 Copynumber: 2.6 Consensus size: 33
1310510 TGTGATTTTT
1310520 ATTTCGCGTTGCGATTCTCTCGTCGCGATAGTC
1 ATTTCGCGTTGCGATTCTCTCGTCGCGATAGTC
*
1310553 ATTTCGCGTTGCGATTCTCTCGTTGCGATAGTC
1 ATTTCGCGTTGCGATTCTCTCGTCGCGATAGTC
*
1310586 ATTTCCACGTTGCGATTCTC
1 ATTT-CGCGTTGCGATTCTC
1310606 ATTATCTCGT
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
33 36 0.72
34 14 0.28
ACGTcount: A:0.13, C:0.27, G:0.22, T:0.38
Consensus pattern (33 bp):
ATTTCGCGTTGCGATTCTCTCGTCGCGATAGTC
Found at i:1310607 original size:20 final size:20
Alignment explanation
Indices: 1310573--1310630 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
1310563 GCGATTCTCT
**
1310573 CGTTGCGATAGTCATTTCCA
1 CGTTGCGATTCTCATTTCCA
*
1310593 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCA
*
1310613 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
1310631 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.16, C:0.24, G:0.17, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCA
Found at i:1312797 original size:21 final size:21
Alignment explanation
Indices: 1312773--1312839 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1312763 TCATTCCTCG
1312773 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
1312794 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
1312815 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
1312836 AGAG
1 AGAG
1312840 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:1312797 original size:42 final size:42
Alignment explanation
Indices: 1312721--1312839 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
1312711 GACTCGCCTG
* * * * * * *
1312721 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
1312763 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
1312805 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
1312840 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:1314217 original size:14 final size:14
Alignment explanation
Indices: 1314198--1314233 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1314188 ATTGTTTAAT
1314198 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
1314212 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
1314226 TGATTTGT
1 TGATTTGT
1314234 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:1314385 original size:33 final size:33
Alignment explanation
Indices: 1314340--1314403 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
1314330 AAAAAGTACT
*
1314340 ATCGCAATGCGAAATGAAAATCACAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCACAACGAGAGA
*
1314373 ATCGCAACGCGAAATGAAAATCGCAACGAGA
1 ATCGCAACGCGAAATGAAAATCACAACGAGA
1314404 AATTAAATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.47, C:0.20, G:0.22, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCACAACGAGAGA
Found at i:1314415 original size:19 final size:19
Alignment explanation
Indices: 1314340--1314406 Score: 63
Period size: 19 Copynumber: 3.8 Consensus size: 19
1314330 AAAAAGTACT
* *
1314340 ATCGCAATGCGAAATGAAA
1 ATCGCAACGAGAAATGAAA
*
1314359 ATCACAACGAG--A-G--A
1 ATCGCAACGAGAAATGAAA
*
1314373 ATCGCAACGCGAAATGAAA
1 ATCGCAACGAGAAATGAAA
1314392 ATCGCAACGAGAAAT
1 ATCGCAACGAGAAAT
1314407 TAAATTCGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
14 10 0.27
16 2 0.05
17 2 0.05
19 23 0.62
ACGTcount: A:0.48, C:0.19, G:0.21, T:0.12
Consensus pattern (19 bp):
ATCGCAACGAGAAATGAAA
Found at i:1314433 original size:19 final size:19
Alignment explanation
Indices: 1314411--1314561 Score: 80
Period size: 19 Copynumber: 8.7 Consensus size: 19
1314401 AGAAATTAAA
1314411 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1314430 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
1314445 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
1314463 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
1314477 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1314496 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
1314511 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
1314529 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
1314548 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
1314562 AGACATTAAG
Statistics
Matches: 95, Mismatches: 21, Indels: 31
0.65 0.14 0.21
Matches are distributed among these distances:
14 28 0.29
16 6 0.06
17 6 0.06
19 45 0.47
20 10 0.11
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:1314457 original size:33 final size:32
Alignment explanation
Indices: 1314415--1314541 Score: 193
Period size: 33 Copynumber: 3.9 Consensus size: 32
1314405 ATTAAATTCG
1314415 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
1314448 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
1314481 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
1314514 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1314542 AGTAATTTCC
Statistics
Matches: 86, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
31 3 0.03
33 80 0.93
35 3 0.03
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:1314491 original size:66 final size:66
Alignment explanation
Indices: 1314408--1314540 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
1314398 ACGAGAAATT
*
1314408 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1314473 G
66 G
*
1314474 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1314539 G
66 G
1314540 A
1 A
1314541 TAGTAATTTC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:1317853 original size:20 final size:20
Alignment explanation
Indices: 1317828--1317876 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
1317818 TTATCTCTCG
1317828 TTGCGAAAGTCAGAATCGCA
1 TTGCGAAAGTCAGAATCGCA
*
1317848 TTGCGAAAGTCAGAATCGCG
1 TTGCGAAAGTCAGAATCGCA
*
1317868 TTACGAAAG
1 TTGCGAAAG
1317877 GCAATCATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.20
Consensus pattern (20 bp):
TTGCGAAAGTCAGAATCGCA
Found at i:1318127 original size:19 final size:20
Alignment explanation
Indices: 1318089--1318138 Score: 84
Period size: 19 Copynumber: 2.5 Consensus size: 20
1318079 ATTCATTTGA
*
1318089 CTATCGCAACGTGAAAATGG
1 CTATCGCAACGCGAAAATGG
1318109 CTATCGCAACGCG-AAATGG
1 CTATCGCAACGCGAAAATGG
1318128 CTATCGCAACG
1 CTATCGCAACG
1318139 ACAAAATCGC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.32, C:0.26, G:0.24, T:0.18
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:1318205 original size:19 final size:19
Alignment explanation
Indices: 1318164--1318228 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 19
1318154 GAAATGAAAA
1318164 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
1318180 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
1318197 TCGTATTGCAATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1318216 TCGCATTACGATT
1 TCGCATTGCGATT
1318229 CTCTCGTTGC
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
14 11 0.28
16 3 0.08
17 3 0.08
19 23 0.57
ACGTcount: A:0.17, C:0.20, G:0.15, T:0.48
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1318259 original size:20 final size:20
Alignment explanation
Indices: 1318234--1318272 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1318224 CGATTCTCTC
1318234 GTTGCGATAGTCAGTTTTGT
1 GTTGCGATAGTCAGTTTTGT
*
1318254 GTTGCGATAGTCTGTTTTG
1 GTTGCGATAGTCAGTTTTG
1318273 CCTTCAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.10, G:0.31, T:0.46
Consensus pattern (20 bp):
GTTGCGATAGTCAGTTTTGT
Found at i:1318374 original size:14 final size:15
Alignment explanation
Indices: 1318355--1318392 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
1318345 CATCAATTAA
1318355 ACAAATCAAT-ATTT
1 ACAAATCAATCATTT
*
1318369 ACAAATC-ATCTTTT
1 ACAAATCAATCATTT
1318383 ACAAATCAAT
1 ACAAATCAAT
1318393 TAAACAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 2 0.10
14 17 0.81
15 2 0.10
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.34
Consensus pattern (15 bp):
ACAAATCAATCATTT
Found at i:1320283 original size:20 final size:20
Alignment explanation
Indices: 1320260--1320313 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
1320250 GAAACTTAAA
1320260 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
1320280 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGAAAATGACT
*
1320300 ATCGCAATGCGAAA
1 ATCGCAACGCGAAA
1320314 TAAAAATCGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1320322 original size:19 final size:19
Alignment explanation
Indices: 1320300--1320381 Score: 68
Period size: 19 Copynumber: 4.6 Consensus size: 19
1320290 GGAAATGGCT
1320300 ATCGCAATGCGAAATAAAA
1 ATCGCAATGCGAAATAAAA
*
1320319 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATAAAA
*
1320333 ATCGCAATGCGAAAT-GAA
1 ATCGCAATGCGAAATAAAA
* * *
1320351 ATCGCAACGCGAAACACAA
1 ATCGCAATGCGAAATAAAA
*
1320370 ATCGCATTGCGA
1 ATCGCAATGCGA
1320382 TTTTCATTTC
Statistics
Matches: 50, Mismatches: 7, Indels: 12
0.72 0.10 0.17
Matches are distributed among these distances:
14 10 0.20
15 1 0.02
16 2 0.04
17 2 0.04
18 16 0.32
19 19 0.38
ACGTcount: A:0.45, C:0.23, G:0.18, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATAAAA
Found at i:1320412 original size:14 final size:14
Alignment explanation
Indices: 1320393--1320450 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1320383 TTTCATTTCG
1320393 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1320407 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1320423 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
1320439 CGTTGCGATTTT
1 CGTTGCGATTTT
1320451 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1320423 original size:32 final size:33
Alignment explanation
Indices: 1320376--1320466 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
1320366 ACAAATCGCA
*
1320376 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1320409 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1320441 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
1320467 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:1320485 original size:20 final size:19
Alignment explanation
Indices: 1320451--1320505 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
1320441 TTGCGATTTT
1320451 CATTTCGCATTGCGATAGC
1 CATTTCGCATTGCGATAGC
* *
1320470 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCATTGCGATAGC
*
1320490 CATTTTCGTATTGCGA
1 CA-TTTCGCATTGCGA
1320506 AAGTAAACTA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 5 0.17
20 22 0.73
21 3 0.10
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (19 bp):
CATTTCGCATTGCGATAGC
Found at i:1321013 original size:18 final size:18
Alignment explanation
Indices: 1320987--1321031 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1320977 GTCGATCAGA
*
1320987 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
1321005 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
1321023 TGATGGCTC
1 TGATGGCTC
1321032 CCGAAGTGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Done.