Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009609.1 Hibiscus syriacus cultivar Beakdansim tig00116995_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: 1078827
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 5
Found at i:805610 original size:34 final size:34
Alignment explanation
Indices: 805571--805639 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
805561 TTTCAAGCTG
*
805571 TGAATGACAAAAAGAATAAAGTTATTATTTATAT
1 TGAATGACAAAAAGAATAAAGTTATTATCTATAT
*
805605 TGAATGACAAAAAGAATAGAGTTATTATCTATAT
1 TGAATGACAAAAAGAATAAAGTTATTATCTATAT
805639 T
1 T
805640 TCAATTACTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.48, C:0.04, G:0.13, T:0.35
Consensus pattern (34 bp):
TGAATGACAAAAAGAATAAAGTTATTATCTATAT
Found at i:805751 original size:239 final size:239
Alignment explanation
Indices: 805332--806050 Score: 1276
Period size: 242 Copynumber: 3.0 Consensus size: 239
805322 TTATTTTTAT
* * * *
805332 TGAATGACAAAAAGAATGGAGTTAATATTTATATTGGATGACAAAAAGAATAGAGTTGTTATCTA
1 TGAATGACAAAAAGAATAGAGTTATTATTTATATTGAATGACAAAAAGAATAGAGTTATTATCTA
805397 TATTTCAATTACTCATGTAACAATATTGTTGCAACACCTATACTTCTTCTGTCTTTGTTTGTAGC
66 TATTTCAATTACTCATGTAACAATATTGTTGCAACACCTATACTTCTTCTGTCTTTGTTTGTAGC
*
805462 TTTACAAAACAGAAATACTTGGAAAAAGAGAAAGATCGATGGACCAATTGACGTTGATGCTAAAG
131 TTTACAAAACAGAAAGACTTGGAAAAAGAGAAAGATCGATGGACCAATTGACGTTGATGCTAAAG
805527 GTACATTGCATCAGTGTATATCTTAAGTGTTATTTTTCAAGCTG
196 GTACATTGCATCAGTGTATATCTTAAGTGTTATTTTTCAAGCTG
*
805571 TGAATGACAAAAAGAATAAAGTTATTATTTATATTGAATGACAAAAAGAATAGAGTTATTATCTA
1 TGAATGACAAAAAGAATAGAGTTATTATTTATATTGAATGACAAAAAGAATAGAGTTATTATCTA
* * *
805636 TATTTCAATTACTCATGTAACAATATTTTTGCAACACCTATACTTCTTCTGCCTTTGTTTGTAAC
66 TATTTCAATTACTCATGTAACAATATTGTTGCAACACCTATACTTCTTCTGTCTTTGTTTGTAGC
805701 TTTACAAAACAGAAAGACTTGGAAAAAGAGAAAGATCGATGGACCAATTGACGTTGATGCTAAAG
131 TTTACAAAACAGAAAGACTTGGAAAAAGAGAAAGATCGATGGACCAATTGACGTTGATGCTAAAG
* * *
805766 GTACATTGCATCATTGTATATCTTTAGTGTTGTTGTTGTTCAAGCTG
196 GTACATTGCATCAGTGTATATCTTAAGTGTT-AT-TT-TTCAAGCTG
805813 TGAATGACAAAAAGAATAGAGTTATTATTTATATTGAATGACAAAAAGAATAGAGTTATTATCTA
1 TGAATGACAAAAAGAATAGAGTTATTATTTATATTGAATGACAAAAAGAATAGAGTTATTATCTA
805878 TATTTCAATTACTCATGTAACAATATTGTTGCAACACCTATACTTCTTCTGTCTTTGTTTGTAGC
66 TATTTCAATTACTCATGTAACAATATTGTTGCAACACCTATACTTCTTCTGTCTTTGTTTGTAGC
805943 TTTACAAAACAGAAAGACTTGGAAAAAGAGAAAGATCGATGGACCAATTGACGTTGATGCTAAAG
131 TTTACAAAACAGAAAGACTTGGAAAAAGAGAAAGATCGATGGACCAATTGACGTTGATGCTAAAG
* * *
806008 GTACATTGCATCAGTGTATATCTTAAGTTTTGTTGTTCAAGCT
196 GTACATTGCATCAGTGTATATCTTAAGTGTTATTTTTCAAGCT
806051 TCAAATGTTC
Statistics
Matches: 456, Mismatches: 21, Indels: 6
0.94 0.04 0.01
Matches are distributed among these distances:
239 223 0.49
240 2 0.00
241 3 0.01
242 228 0.50
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.35
Consensus pattern (239 bp):
TGAATGACAAAAAGAATAGAGTTATTATTTATATTGAATGACAAAAAGAATAGAGTTATTATCTA
TATTTCAATTACTCATGTAACAATATTGTTGCAACACCTATACTTCTTCTGTCTTTGTTTGTAGC
TTTACAAAACAGAAAGACTTGGAAAAAGAGAAAGATCGATGGACCAATTGACGTTGATGCTAAAG
GTACATTGCATCAGTGTATATCTTAAGTGTTATTTTTCAAGCTG
Found at i:805856 original size:34 final size:34
Alignment explanation
Indices: 805813--805881 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
805803 GTTCAAGCTG
*
805813 TGAATGACAAAAAGAATAGAGTTATTATTTATAT
1 TGAATGACAAAAAGAATAGAGTTATTATCTATAT
805847 TGAATGACAAAAAGAATAGAGTTATTATCTATAT
1 TGAATGACAAAAAGAATAGAGTTATTATCTATAT
805881 T
1 T
805882 TCAATTACTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.46, C:0.04, G:0.14, T:0.35
Consensus pattern (34 bp):
TGAATGACAAAAAGAATAGAGTTATTATCTATAT
Found at i:805925 original size:242 final size:241
Alignment explanation
Indices: 805332--806050 Score: 1284
Period size: 239 Copynumber: 3.0 Consensus size: 241
805322 TTATTTTTAT
* * * *
805332 TGAATGACAAAAAGAATGGAGTTAATATTTATATTGGATGACAAAAAGAATAGAGTTGTTATCTA
1 TGAATGACAAAAAGAATAGAGTTATTATTTATATTGAATGACAAAAAGAATAGAGTTATTATCTA
805397 TATTTCAATTACTCATGTAACAATATTGTTGCAACACCTATACTTCTTCTGTCTTTGTTTGTAGC
66 TATTTCAATTACTCATGTAACAATATTGTTGCAACACCTATACTTCTTCTGTCTTTGTTTGTAGC
*
805462 TTTACAAAACAGAAATACTTGGAAAAAGAGAAAGATCGATGGACCAATTGACGTTGATGCTAAAG
131 TTTACAAAACAGAAAGACTTGGAAAAAGAGAAAGATCGATGGACCAATTGACGTTGATGCTAAAG
* *
805527 GTACATTGCATCAGTGTATATCTTAAGTGTTAT-TT-TTCAAGCTG
196 GTACATTGCATCAGTGTATATCTTTAGTGTTTTGTTGTTCAAGCTG
*
805571 TGAATGACAAAAAGAATAAAGTTATTATTTATATTGAATGACAAAAAGAATAGAGTTATTATCTA
1 TGAATGACAAAAAGAATAGAGTTATTATTTATATTGAATGACAAAAAGAATAGAGTTATTATCTA
* * *
805636 TATTTCAATTACTCATGTAACAATATTTTTGCAACACCTATACTTCTTCTGCCTTTGTTTGTAAC
66 TATTTCAATTACTCATGTAACAATATTGTTGCAACACCTATACTTCTTCTGTCTTTGTTTGTAGC
805701 TTTACAAAACAGAAAGACTTGGAAAAAGAGAAAGATCGATGGACCAATTGACGTTGATGCTAAAG
131 TTTACAAAACAGAAAGACTTGGAAAAAGAGAAAGATCGATGGACCAATTGACGTTGATGCTAAAG
*
805766 GTACATTGCATCATTGTATATCTTTAGTGTTGTTGTTGTTCAAGCTG
196 GTACATTGCATCAGTGTATATCTTTAGTGTT-TTGTTGTTCAAGCTG
805813 TGAATGACAAAAAGAATAGAGTTATTATTTATATTGAATGACAAAAAGAATAGAGTTATTATCTA
1 TGAATGACAAAAAGAATAGAGTTATTATTTATATTGAATGACAAAAAGAATAGAGTTATTATCTA
805878 TATTTCAATTACTCATGTAACAATATTGTTGCAACACCTATACTTCTTCTGTCTTTGTTTGTAGC
66 TATTTCAATTACTCATGTAACAATATTGTTGCAACACCTATACTTCTTCTGTCTTTGTTTGTAGC
805943 TTTACAAAACAGAAAGACTTGGAAAAAGAGAAAGATCGATGGACCAATTGACGTTGATGCTAAAG
131 TTTACAAAACAGAAAGACTTGGAAAAAGAGAAAGATCGATGGACCAATTGACGTTGATGCTAAAG
*
806008 GTACATTGCATCAGTGTATATC-TTA-AGTTTTGTTGTTCAAGCT
196 GTACATTGCATCAGTGTATATCTTTAGTGTTTTGTTGTTCAAGCT
806051 TCAAATGTTC
Statistics
Matches: 459, Mismatches: 18, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
239 229 0.50
240 4 0.01
241 5 0.01
242 221 0.48
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.35
Consensus pattern (241 bp):
TGAATGACAAAAAGAATAGAGTTATTATTTATATTGAATGACAAAAAGAATAGAGTTATTATCTA
TATTTCAATTACTCATGTAACAATATTGTTGCAACACCTATACTTCTTCTGTCTTTGTTTGTAGC
TTTACAAAACAGAAAGACTTGGAAAAAGAGAAAGATCGATGGACCAATTGACGTTGATGCTAAAG
GTACATTGCATCAGTGTATATCTTTAGTGTTTTGTTGTTCAAGCTG
Found at i:806252 original size:192 final size:193
Alignment explanation
Indices: 805878--806252 Score: 524
Period size: 192 Copynumber: 1.9 Consensus size: 193
805868 TTATTATCTA
* **
805878 TATTTCAATTACTCATGTAACAATATTGTTGCAACACCTATACTTCTTCTGTCTTTGTTTGTAGC
1 TATTTCAATTACTAATGTAACAATATTGTT-CAACACCTATACTTCTTCTGTCTTAATTTGTAGC
*
805943 TTTACAAAACAGAAAGACTTGGAAAAAGAGAAAGATCGATGGACCAATTGACGTTGATGCTAAAG
65 TTTACAAAACAGAAAGACTTGGAAAAAGAGAAAGATCGATGGACCAATTGACGTTGATGCTAAAC
* * * * *
806008 GTACATTGCATCAGTGTATATCTTAAGTTTTGTTGTTCAAGCTTCAAATGTTCATGTAACTTTG
130 GTACATGGAATCAGTGTACATCTTAAGTGTTGTTATTCAAGCTTCAAATGTTCATGTAACTTTG
*
806072 TATTTCAATTACTAATGTAACAATATTGTT-AACACCTATACTTCTTTTGTCTTACAATTTGTAG
1 TATTTCAATTACTAATGTAACAATATTGTTCAACACCTATACTTCTTCTGTCTT--AATTTGTAG
* ** *
806136 CTTTACAAAATC-GCAAGACTTGG-AAAAGA-AAAGATCGATTTACTAATTGACGTTGATGCTAA
64 CTTTACAAAA-CAGAAAGACTTGGAAAAAGAGAAAGATCGATGGACCAATTGACGTTGATGCTAA
* * * *
806198 ACGTACATGGAATCAGTTTACATCTTAGGTGTTGTTATTGAAGCTTCTAATGTTC
128 ACGTACATGGAATCAGTGTACATCTTAAGTGTTGTTATTCAAGCTTCAAATGTTC
806253 TTCATTTAAC
Statistics
Matches: 160, Mismatches: 18, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
192 97 0.61
193 6 0.04
194 56 0.35
195 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (193 bp):
TATTTCAATTACTAATGTAACAATATTGTTCAACACCTATACTTCTTCTGTCTTAATTTGTAGCT
TTACAAAACAGAAAGACTTGGAAAAAGAGAAAGATCGATGGACCAATTGACGTTGATGCTAAACG
TACATGGAATCAGTGTACATCTTAAGTGTTGTTATTCAAGCTTCAAATGTTCATGTAACTTTG
Found at i:808060 original size:394 final size:395
Alignment explanation
Indices: 807333--808121 Score: 1555
Period size: 394 Copynumber: 2.0 Consensus size: 395
807323 AAAGTTTTCT
807333 TTTGATTTTTGTTTAGAGGGATATTATTGAAAATATTAACAAGTCGGTTTTAAGTTCTGTAATTT
1 TTTGATTTTTGTTTAGAGGGATATTATTGAAAATATTAACAAGTCGGTTTTAAGTTCTGTAATTT
807398 CTACTTTCTGCTAATTCTTCATGCTAATACTAAATTTCTTTAAAGGACTTTATTTATTTGTTTTT
66 CTACTTTCTGCTAATTCTTCATGCTAATACTAAATTTCTTTAAAGGACTTTATTTATTTGTTTTT
807463 AACTTACAGGAAAGAGAGAATGCTAAAGTTGTCATTTCCCCTGATTTTATGTTTTAGAGGTATGC
131 AACTTACAGGAAAGAGAGAATGCTAAAGTTGTCATTTCCCCTGATTTTATGTTTTAGAGGTATGC
807528 ATAGTACAGAAAGTCAATTAACTTCTTCAAAAACCTGCCTCAAGTTCATTGTAAGTACTCCATAT
196 ATAGTACAGAAAGTCAATTAACTTCTTCAAAAACCTGCCTCAAGTTCATTGTAAGTACTCCATAT
807593 TTTGTTGCTTGATTTTTCTTGTCTAATTAGAAGTCCTAGACTTTGTCCCTGAGTGATATATTAAA
261 TTTGTTGCTTGATTTTTCTTGTCTAATTAGAAGTCCTAGACTTTGTCCCTGAGTGATATATTAAA
807658 AAGATCCTAAACCTC-TGTGTATTGTTCTATTAAAATG-TTGCAGAATGAGCGGGTTGATCTGAT
326 AAGATCCTAAACCTCTTGTGTATTGTTCTATTAAAATGTTTGCAGAATGAGCGGGTTGATCTGAT
807721 ATCAG
391 ATCAG
807726 TTTGATTTTTGTTTAGAGGGATATTATTGAAAATATTAACAAGTCGGTTTTAAGTTCTGTAATTT
1 TTTGATTTTTGTTTAGAGGGATATTATTGAAAATATTAACAAGTCGGTTTTAAGTTCTGTAATTT
807791 CTACTTTCTGCTAATTCTTCATGCTAATACTAAATTTCTTTAAAGGACTTTATTTATTTGTTTTT
66 CTACTTTCTGCTAATTCTTCATGCTAATACTAAATTTCTTTAAAGGACTTTATTTATTTG-TTTT
807856 TAACTTACAGGAAAGAGAGAATGCTAAAGTTGTCATTTCCCCTGATTTTATGTTTTAGAGGTATG
130 TAACTTACAGGAAAGAGAGAATGCTAAAGTTGTCATTTCCCCTGATTTTATGTTTTAGAGGTATG
807921 CATAGTACAGAAAGTCAATTAACTTCTTCAAAAACCTGCCTCAAGTTCATTGTAAGTACTCCATA
195 CATAGTACAGAAAGTCAATTAACTTCTTCAAAAACCTGCCTCAAGTTCATTGTAAGTACTCCATA
807986 TTTTGTTGCTTGATTTTTCTTGTCTAATTAGAAGTCCTAGACTTTGTCCCTGAGTGATATATTAA
260 TTTTGTTGCTTGATTTTTCTTGTCTAATTAGAAGTCCTAGACTTTGTCCCTGAGTGATATATTAA
808051 AAAGATCCTAAACCTCTTGTGTATTGTTCTATTAAAATGTTTGCAGAATGAGCGGGTTGATCTGA
325 AAAGATCCTAAACCTCTTGTGTATTGTTCTATTAAAATGTTTGCAGAATGAGCGGGTTGATCTGA
808116 TATCAG
390 TATCAG
808122 ATGATGATGG
Statistics
Matches: 393, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
393 125 0.32
394 215 0.55
395 22 0.06
396 31 0.08
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (395 bp):
TTTGATTTTTGTTTAGAGGGATATTATTGAAAATATTAACAAGTCGGTTTTAAGTTCTGTAATTT
CTACTTTCTGCTAATTCTTCATGCTAATACTAAATTTCTTTAAAGGACTTTATTTATTTGTTTTT
AACTTACAGGAAAGAGAGAATGCTAAAGTTGTCATTTCCCCTGATTTTATGTTTTAGAGGTATGC
ATAGTACAGAAAGTCAATTAACTTCTTCAAAAACCTGCCTCAAGTTCATTGTAAGTACTCCATAT
TTTGTTGCTTGATTTTTCTTGTCTAATTAGAAGTCCTAGACTTTGTCCCTGAGTGATATATTAAA
AAGATCCTAAACCTCTTGTGTATTGTTCTATTAAAATGTTTGCAGAATGAGCGGGTTGATCTGAT
ATCAG
Found at i:811438 original size:87 final size:88
Alignment explanation
Indices: 811259--811438 Score: 276
Period size: 87 Copynumber: 2.1 Consensus size: 88
811249 CGCTCCCAGA
*
811259 TCTTTATCCAGTTCAGGCATTAGCTGTCTCCAAAATTAACCAACCTTTCTATCCCACTCAGATAT
1 TCTTTATCCAGTTCAGGCATTAGCTGTCTCCAAAATTAACCAACCTTTCCATCCCACTCAGATAT
* * * *
811324 GGGAGAATTACAGTAATTTGTTT
66 GGGAAAATTACAGTAAATTGATG
811347 TCTTTATCCA-TTCAAGGCATTAGCTGTCTCCAAAATTAACC-ACCTTTCCATCCCACTCAGATA
1 TCTTTATCCAGTTC-AGGCATTAGCTGTCTCCAAAATTAACCAACCTTTCCATCCCACTCAGATA
811410 TGGGAAAATTACAGTAAAATT-ATG
65 TGGGAAAATTACAGT-AAATTGATG
811434 TCTTT
1 TCTTT
811439 TGACATATTA
Statistics
Matches: 85, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
87 44 0.52
88 41 0.48
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.34
Consensus pattern (88 bp):
TCTTTATCCAGTTCAGGCATTAGCTGTCTCCAAAATTAACCAACCTTTCCATCCCACTCAGATAT
GGGAAAATTACAGTAAATTGATG
Found at i:813232 original size:16 final size:16
Alignment explanation
Indices: 813213--813246 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
813203 TTGACTCCTT
*
813213 AAGGAATTGGAATCTG
1 AAGGAATTGAAATCTG
813229 AAGGAATTGAAATCTG
1 AAGGAATTGAAATCTG
813245 AA
1 AA
813247 TATGAAACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.44, C:0.06, G:0.26, T:0.24
Consensus pattern (16 bp):
AAGGAATTGAAATCTG
Found at i:813808 original size:28 final size:29
Alignment explanation
Indices: 813748--813833 Score: 92
Period size: 27 Copynumber: 3.1 Consensus size: 29
813738 AAGCCCGAAC
*
813748 CCGAATATCACACTTAAAAAATC-CGA-T
1 CCGAATATCACACTTAAAAAAACTCGACT
*
813775 CCGAATATTACACTTAAAAAAACTCGACT
1 CCGAATATCACACTTAAAAAAACTCGACT
* * *
813804 -TGAATATCAAACTTAACAAAA-TCGAC-
1 CCGAATATCACACTTAAAAAAACTCGACT
813830 CCGA
1 CCGA
813834 CCCGATCCCA
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
27 28 0.57
28 20 0.41
29 1 0.02
ACGTcount: A:0.45, C:0.24, G:0.08, T:0.22
Consensus pattern (29 bp):
CCGAATATCACACTTAAAAAAACTCGACT
Found at i:813880 original size:28 final size:29
Alignment explanation
Indices: 813849--813929 Score: 103
Period size: 28 Copynumber: 2.8 Consensus size: 29
813839 TCCCAATTTT
813849 TTTTTAAAAAAAAACCGA-CCGATCCCGA
1 TTTTTAAAAAAAAACCGACCCGATCCCGA
* *
813877 TTTTTTAAAAAAAACCGACCCGATCCCGGTT
1 TTTTTAAAAAAAAACCGACCCGATCCC-G-A
*
813908 TTTTTTAAAAAAAA-CGACCCGA
1 TTTTTAAAAAAAAACCGACCCGA
813930 ATATCACACT
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
28 17 0.35
29 8 0.17
30 9 0.19
31 14 0.29
ACGTcount: A:0.40, C:0.23, G:0.11, T:0.26
Consensus pattern (29 bp):
TTTTTAAAAAAAAACCGACCCGATCCCGA
Found at i:813927 original size:30 final size:30
Alignment explanation
Indices: 813830--813929 Score: 125
Period size: 29 Copynumber: 3.3 Consensus size: 30
813820 CAAAATCGAC
*
813830 CCGACCCGATCCCAATTTTTTTTTAAAAAAAAA
1 CCGACCCGATCCC--GTTTTTTTT-AAAAAAAA
*
813863 CCGA-CCGATCCCG-ATTTTTTAAAAAAAA
1 CCGACCCGATCCCGTTTTTTTTAAAAAAAA
813891 CCGACCCGATCCCGGTTTTTTTTAAAAAAAA
1 CCGACCCGATCCC-GTTTTTTTTAAAAAAAA
813922 -CGACCCGA
1 CCGACCCGA
813930 ATATCACACT
Statistics
Matches: 61, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
28 12 0.20
29 14 0.23
30 9 0.15
31 14 0.23
32 8 0.13
33 4 0.07
ACGTcount: A:0.36, C:0.27, G:0.11, T:0.26
Consensus pattern (30 bp):
CCGACCCGATCCCGTTTTTTTTAAAAAAAA
Found at i:814791 original size:97 final size:100
Alignment explanation
Indices: 814687--815077 Score: 413
Period size: 97 Copynumber: 3.9 Consensus size: 100
814677 TCTTATTGTC
*
814687 TTGCTGTAAATTTAGTTTATTTGCTTCTTTGTTTCAATTGATCATA-TCAGTCTTG-TT-TGGAT
1 TTGCTGTAAATTTAGTTTATTTGATTCTTTGTTTCAATTGATCATATTCAGTCTTGCTTCTGGAT
814749 TTACTGTTTGTTGCAAAATTATTGGTTGTTTTTTT
66 TTACTGTTTGTTGCAAAATTATTGGTTGTTTTTTT
* *
814784 TTGCTGTAAATTTAGTTTATTTGCTTCTTTGATTT-AATTGATCAT-GTCAGTCTTGCTTCTGGA
1 TTGCTGTAAATTTAGTTTATTTGATTCTTTG-TTTCAATTGATCATATTCAGTCTTGCTTCTGGA
* *
814847 TTTACTGTATGTTGCAAAATTATTGGTTTATTTATTTATTTATT
65 TTTACTGTTTGTTGCAAAATTATTGG-----TT-GTT-TTT-TT
* * * * * *
814891 TTGCTTTTAAATTTAGTTTATTTGATTGTATGTTTC-TTTCGATCGTATTCAGTCATGCTTCT-G
1 TTGC-TGTAAATTTAGTTTATTTGATTCTTTGTTTCAATT-GATCATATTCAGTCTTGCTTCTGG
* * *
814954 TTTTATTGTTTGTTGCAAAAATA-TGGTTG-TTTTTT
64 ATTTACTGTTTGTTGCAAAATTATTGGTTGTTTTTTT
* * ** * *
814989 TTGCTTTAAATTTAGTTTATTTGATTGTTTGTTTCTCTCGATCATATTCAGTCTTGCTTCTGGTT
1 TTGCTGTAAATTTAGTTTATTTGATTCTTTGTTTCAATTGATCATATTCAGTCTTGCTTCTGGAT
* *
815054 TTAACTTTTTGTTGCGAAATTATT
66 TT-ACTGTTTGTTGCAAAATTATT
815078 AGTTTGTCGA
Statistics
Matches: 250, Mismatches: 24, Indels: 37
0.80 0.08 0.12
Matches are distributed among these distances:
97 100 0.40
98 17 0.07
99 47 0.19
100 2 0.01
102 2 0.01
104 2 0.01
105 2 0.01
106 3 0.01
107 14 0.06
108 48 0.19
109 13 0.05
ACGTcount: A:0.19, C:0.10, G:0.16, T:0.55
Consensus pattern (100 bp):
TTGCTGTAAATTTAGTTTATTTGATTCTTTGTTTCAATTGATCATATTCAGTCTTGCTTCTGGAT
TTACTGTTTGTTGCAAAATTATTGGTTGTTTTTTT
Found at i:823725 original size:21 final size:20
Alignment explanation
Indices: 823699--823738 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
823689 GAAAAGTTTT
823699 ATAAAATATAA-TTATATAAAA
1 ATAAAAT-TAACTTA-ATAAAA
823720 ATAAAATTAACTTAATAAA
1 ATAAAATTAACTTAATAAA
823739 CTAAAAGGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAAAATTAACTTAATAAAA
Found at i:824948 original size:360 final size:363
Alignment explanation
Indices: 824210--824899 Score: 1205
Period size: 360 Copynumber: 1.9 Consensus size: 363
824200 ATAATAAATT
824210 TACATGAAAACATAA--TTTTTCTTTTTTAAAAAGGTGTTCCGGTTTTTTCTCTCTTTAAAAAGG
1 TACATGAAAACATAATTTTTTTCTTTTTTAAAAAGGTGTTCCGGTTTTTTCTCTCTTTAAAAAGG
824273 GTTGATTTGTTTCTGATTTAGTTTCTTGAAGTTTTTTCCCCTGATTTAGGGTTTCCGAAAAATTG
66 GTTGATTTGTTTCTGATTTAGTTTCTTGAAGTTTTTTCCCCTGATTTAGGGTTTCCGAAAAATTG
824338 AAATTGAGACGGAGCGCATAAGTAATTCGGATGGTTTAAAATTCAGAGATAAACTGTGAGATTAG
131 AAATTGAGACGGAGCGCATAAGTAATTCGGATGGTTTAAAATTCAGAGATAAACTGTGAGATTAG
824403 TTATTATTGTCGCTCGTGAAGCTCTTAAGTTCTTTCATAATTAACATCACGTTTAAACAAAAAAT
196 TTATTATTGTCGCTCGTGAAGCTCTTAAGTTCTTTCATAATTAACATCACGTTTAAACAAAAAAT
824468 ATATTAATAAATATAGTAACGATCATCATTATATCAATAAAAAAATATATTAATGTAATTTAAAA
261 ATATTAATAAATATAGTAACGATCATCATTATATCAATAAAAAAATATATTAATGTAATTTAAAA
* * * *
824533 ATGAGAAAATCGCCTCAGTGACCAAAAAAAAGTTATAA
326 ATCAGAAAATCGCCTCAATGACCAAAAAAAAGTAAAAA
824571 TACATGAAAACATAATTTTTTTCTTTTTTAAAAAGGTGTTCCGG-TTTTTCTCTCTTTAAAAAGG
1 TACATGAAAACATAATTTTTTTCTTTTTTAAAAAGGTGTTCCGGTTTTTTCTCTCTTTAAAAAGG
824635 GTTGATTTGTTTCTGATTTAGTTTCTTG-AG-TTTTTCCCCTGATTTAGGGTTTCCGAAAAATTG
66 GTTGATTTGTTTCTGATTTAGTTTCTTGAAGTTTTTTCCCCTGATTTAGGGTTTCCGAAAAATTG
824698 AAATTGAGACGGAGCGCATAAGTAATTCGGATGGTTTAAAATTCAGAGATAAACTGTGAGATTAA
131 AAATTGAGACGGAGCGCATAAGTAATTCGGATGGTTTAAAATTCAGAGATAAACTGTGAGATT-A
824763 GTTATTATTGTCGCTCGTGAAGCTCTTAAAGTTCTTTCATAA-TAACATCACGTTTAAACAAAAA
195 GTTATTATTGTCGCTCGTGAAGCTCTT-AAGTTCTTTCATAATTAACATCACGTTTAAACAAAAA
* * *
824827 ATATATTAAATTATTATAGTAACGATCAATAATATTATATCAAT-AAAAAATAATATTAATGTAA
259 ATATATT-AATAAATATAGTAACGATC-AT--CATTATATCAATAAAAAAAT-ATATTAATGTAA
824891 TTTAAAAAT
319 TTTAAAAAT
824900 TCAAGAATGA
Statistics
Matches: 317, Mismatches: 3, Indels: 14
0.95 0.01 0.04
Matches are distributed among these distances:
360 96 0.30
361 74 0.23
362 79 0.25
363 29 0.09
364 7 0.02
365 32 0.10
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (363 bp):
TACATGAAAACATAATTTTTTTCTTTTTTAAAAAGGTGTTCCGGTTTTTTCTCTCTTTAAAAAGG
GTTGATTTGTTTCTGATTTAGTTTCTTGAAGTTTTTTCCCCTGATTTAGGGTTTCCGAAAAATTG
AAATTGAGACGGAGCGCATAAGTAATTCGGATGGTTTAAAATTCAGAGATAAACTGTGAGATTAG
TTATTATTGTCGCTCGTGAAGCTCTTAAGTTCTTTCATAATTAACATCACGTTTAAACAAAAAAT
ATATTAATAAATATAGTAACGATCATCATTATATCAATAAAAAAATATATTAATGTAATTTAAAA
ATCAGAAAATCGCCTCAATGACCAAAAAAAAGTAAAAA
Found at i:828845 original size:31 final size:32
Alignment explanation
Indices: 828810--828869 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 32
828800 AATAAGTACT
* * *
828810 TAGGAATTACAACACCCAAAAAC-TCCCTTAA
1 TAGGAAGTACAAAACCAAAAAACATCCCTTAA
*
828841 TAGGAAGTAGAAAACCAAAAAACATCCCT
1 TAGGAAGTACAAAACCAAAAAACATCCCT
828870 AAACAACAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 19 0.79
32 5 0.21
ACGTcount: A:0.48, C:0.25, G:0.10, T:0.17
Consensus pattern (32 bp):
TAGGAAGTACAAAACCAAAAAACATCCCTTAA
Found at i:835790 original size:35 final size:35
Alignment explanation
Indices: 835751--835821 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 35
835741 CATTCACACT
*
835751 TTTCTTATTTC-CCTTCTTCTTCCACGCCTAATTCC
1 TTTCTTATTTCTCCTT-TTCTTCCACGCATAATTCC
* *
835786 TTTCTTATTTCTCGTTTTCTTTCACGCATAATTCC
1 TTTCTTATTTCTCCTTTTCTTCCACGCATAATTCC
835821 T
1 T
835822 GTTATAATCC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
35 29 0.91
36 3 0.09
ACGTcount: A:0.13, C:0.31, G:0.04, T:0.52
Consensus pattern (35 bp):
TTTCTTATTTCTCCTTTTCTTCCACGCATAATTCC
Found at i:855290 original size:22 final size:21
Alignment explanation
Indices: 855261--855306 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
855251 ATTATGATGA
855261 AATAAATTTAAAA-GCAAAATT
1 AATAAA-TTAAAATGCAAAATT
*
855282 AATATAATTAAAATGTAAAATT
1 AATA-AATTAAAATGCAAAATT
855304 AAT
1 AAT
855307 TTACTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (21 bp):
AATAAATTAAAATGCAAAATT
Found at i:855530 original size:49 final size:49
Alignment explanation
Indices: 855459--855580 Score: 122
Period size: 49 Copynumber: 2.5 Consensus size: 49
855449 GCAGTAAAGC
* * * ** *
855459 GCGC-CCCCTACACCGCGTTATACGATGATTTGGTGCCACGTGGGATATA
1 GCGCTCCCCTGCAGCGCGCTATACGATGAGCTGGCGCCACGTGGG-TATA
* * * *
855508 GTGC-CCCCTGTATCGCGCTATACGGTGAGCTGGCGCCACGTGGGTATA
1 GCGCTCCCCTGCAGCGCGCTATACGATGAGCTGGCGCCACGTGGGTATA
*
855556 GCGCTGCCCTGCAGCGCGCTATACG
1 GCGCTCCCCTGCAGCGCGCTATACG
855581 CCACGTAGGG
Statistics
Matches: 59, Mismatches: 13, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
48 7 0.12
49 52 0.88
ACGTcount: A:0.16, C:0.31, G:0.30, T:0.22
Consensus pattern (49 bp):
GCGCTCCCCTGCAGCGCGCTATACGATGAGCTGGCGCCACGTGGGTATA
Found at i:855670 original size:49 final size:51
Alignment explanation
Indices: 855592--855714 Score: 191
Period size: 49 Copynumber: 2.5 Consensus size: 51
855582 CACGTAGGGG
855592 TATAGCGC-GGATCAGGTACCGCGCTATACCTTTACTCCT-A-ATAATTTTA
1 TATAGCGCGGGA-CAGGTACCGCGCTATACCTTTACTCCTGACATAATTTTA
*
855641 TATAGCGCGGGGCAGGTACCGCGAC-ATACCTTTACTCCTGACATAATTTTA
1 TATAGCGCGGGACAGGTACCGCG-CTATACCTTTACTCCTGACATAATTTTA
855692 TATAGCGCGGGACAGGTACCGCG
1 TATAGCGCGGGACAGGTACCGCG
855715 TTTTGTATAA
Statistics
Matches: 68, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
49 33 0.49
50 4 0.06
51 31 0.46
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (51 bp):
TATAGCGCGGGACAGGTACCGCGCTATACCTTTACTCCTGACATAATTTTA
Found at i:861484 original size:107 final size:109
Alignment explanation
Indices: 861295--861505 Score: 354
Period size: 107 Copynumber: 1.9 Consensus size: 109
861285 AATTACAAAA
* * *
861295 ATTAATTCTTAATCTAATAATCATGCATTAAATGAATTAACTAATTATTAATAATAATTTAAATT
1 ATTAATTATTAA-CTAATAATCATGCATTAAATGAAATAACTAAATATTAATAATAATTTAAATT
*
861360 AAATTAAAACGTTAAAATGTTACCGTATCAGTAAAGTGTTGAAAT
65 AAATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTTGAAAT
*
861405 ATTAATTATTAA-TAATAATCATGCATTAAAT-AAATAACTAAATATTACTAATAATTTAAATTA
1 ATTAATTATTAACTAATAATCATGCATTAAATGAAATAACTAAATATTAATAATAATTTAAATTA
861468 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGT
861506 AGAGATATAT
Statistics
Matches: 96, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
107 66 0.69
108 19 0.20
110 11 0.11
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.37
Consensus pattern (109 bp):
ATTAATTATTAACTAATAATCATGCATTAAATGAAATAACTAAATATTAATAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTTGAAAT
Found at i:865591 original size:23 final size:23
Alignment explanation
Indices: 865546--865590 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
865536 TCTCTAAAAA
865546 ATAAATTAAAAATAATAATTTTT
1 ATAAATTAAAAATAATAATTTTT
* *
865569 ATAAATT-AGAATAATATTTTTT
1 ATAAATTAAAAATAATAATTTTT
865591 TTTCTAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
ATAAATTAAAAATAATAATTTTT
Found at i:868061 original size:20 final size:20
Alignment explanation
Indices: 868038--868319 Score: 398
Period size: 20 Copynumber: 14.3 Consensus size: 20
868028 ATTCGTATGG
*
868038 GTAAATCGCAATGCGTATCC
1 GTAAATCGCAACGCGTATCC
868058 GT-AATCGCAACGCGTATCC
1 GTAAATCGCAACGCGTATCC
868077 GTAAATCGCAACGCGTATCC
1 GTAAATCGCAACGCGTATCC
*
868097 GTAAATCGCAACGTGTATCC
1 GTAAATCGCAACGCGTATCC
868117 GTAAATCGCAACGCGTATCC
1 GTAAATCGCAACGCGTATCC
*
868137 GTAAATCGCAATGCGTATCC
1 GTAAATCGCAACGCGTATCC
868157 GTAAATCGCAACGCGTATCC
1 GTAAATCGCAACGCGTATCC
868177 GTAAATCGCAACGCGTATCC
1 GTAAATCGCAACGCGTATCC
868197 GTAAATCGCAA--CG-ATCC
1 GTAAATCGCAACGCGTATCC
868214 GTAAATCGCAACGCGTATCC
1 GTAAATCGCAACGCGTATCC
*
868234 GT-AATCGCAACG-ATAATCC
1 GTAAATCGCAACGCGT-ATCC
* * *
868253 GTAAATCGCAACGAGAATCT
1 GTAAATCGCAACGCGTATCC
*
868273 GTAAATCGCAACG-ATAATCC
1 GTAAATCGCAACGCGT-ATCC
* * *
868293 GTAAATCGCAACGAGAATCT
1 GTAAATCGCAACGCGTATCC
868313 GTAAATC
1 GTAAATC
868320 AACAACACTG
Statistics
Matches: 238, Mismatches: 15, Indels: 18
0.88 0.06 0.07
Matches are distributed among these distances:
17 15 0.06
18 3 0.01
19 36 0.15
20 184 0.77
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.21
Consensus pattern (20 bp):
GTAAATCGCAACGCGTATCC
Found at i:869032 original size:24 final size:24
Alignment explanation
Indices: 868993--869039 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
868983 AAATTTGGTC
868993 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
869017 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
869040 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:871552 original size:19 final size:19
Alignment explanation
Indices: 871530--871860 Score: 432
Period size: 19 Copynumber: 18.4 Consensus size: 19
871520 CGGAAAATAC
*
871530 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
871549 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
871563 AATCGCAATGCAGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
871583 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
871597 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
871616 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
871635 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
871649 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
871668 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
871687 AATCG-AA-CCGACAT---
1 AATCGCAATGCGAAATGAA
*
871701 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
871720 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
871739 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
871758 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
871777 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
871796 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
871815 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
871834 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
871853 AATCGCAA
1 AATCGCAA
871861 CGAGATAATC
Statistics
Matches: 276, Mismatches: 15, Indels: 42
0.83 0.05 0.13
Matches are distributed among these distances:
14 37 0.13
15 4 0.01
16 10 0.04
17 9 0.03
18 5 0.02
19 198 0.72
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:871898 original size:52 final size:53
Alignment explanation
Indices: 871558--871882 Score: 460
Period size: 52 Copynumber: 6.0 Consensus size: 53
871548 AAATCCCAAC
*
871558 ATGAAAATCGCAATGCAGAAATGAAAATCGCAA-CGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
*
871611 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
* * *
871663 ATGAAAATCGCAATGCGAAATGAAAATCG-AACCGACATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
* *
871715 ATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG--A-GAAAATCGCAATGCGAA
*
871772 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG--A-GAAAATCGCAATGCGAA
*
871829 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
871881 AT
1 AT
871883 TATAAACGCA
Statistics
Matches: 254, Mismatches: 12, Indels: 13
0.91 0.04 0.05
Matches are distributed among these distances:
51 2 0.01
52 127 0.50
53 19 0.07
54 2 0.01
55 2 0.01
56 1 0.00
57 101 0.40
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (53 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
Found at i:871998 original size:19 final size:19
Alignment explanation
Indices: 871889--871990 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
871879 AAATTATAAA
871889 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
871908 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
871928 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
871944 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
871961 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
871980 CGCATTGCGAT
1 CGCATTGCGAT
871991 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:872115 original size:14 final size:14
Alignment explanation
Indices: 872096--872132 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
872086 CATCAATTAC
872096 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
872110 ACAAATCATCTTTT
1 ACAAATCAACTTTT
872124 ACAAATCAA
1 ACAAATCAA
872133 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:872144 original size:12 final size:12
Alignment explanation
Indices: 872127--872199 Score: 53
Period size: 12 Copynumber: 6.0 Consensus size: 12
872117 ATCTTTTACA
872127 AATCAATTAAAC
1 AATCAATTAAAC
*
872139 AATCAA--AAATTG
1 AATCAATTAAA--C
**
872151 AATCAACTTTTAC
1 AATCAA-TTAAAC
872164 AAATCAATTAAAC
1 A-ATCAATTAAAC
*
872177 AATCAA-AAAAC
1 AATCAATTAAAC
872188 AATCAATTAAAC
1 AATCAATTAAAC
872200 TATTGAATCA
Statistics
Matches: 46, Mismatches: 8, Indels: 14
0.68 0.12 0.21
Matches are distributed among these distances:
10 3 0.07
11 10 0.22
12 21 0.46
13 6 0.13
14 5 0.11
15 1 0.02
ACGTcount: A:0.58, C:0.16, G:0.01, T:0.25
Consensus pattern (12 bp):
AATCAATTAAAC
Found at i:872161 original size:38 final size:38
Alignment explanation
Indices: 872113--872185 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
872103 AACTTTTACA
*
872113 AATCATCTTTTACAAATCAATTAAACAATCAAAAATTG
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
872151 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
872186 ACAATCAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.53, C:0.16, G:0.01, T:0.29
Consensus pattern (38 bp):
AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
Found at i:874069 original size:14 final size:14
Alignment explanation
Indices: 874050--874106 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
874040 GCGAAATGAA
*
874050 AATCGCAACGACAG
1 AATCGCAACGAAAG
874064 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
874081 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
874097 AATCGCAACG
1 AATCGCAACG
874107 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:874077 original size:33 final size:33
Alignment explanation
Indices: 874031--874123 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
874021 GCGAAACCAA
*
874031 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
874064 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
874097 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
874124 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:874088 original size:19 final size:19
Alignment explanation
Indices: 873994--874128 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
873984 TAGTTTACTT
* *
873994 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
874014 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
874033 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
874052 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
874066 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
874085 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
874099 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
874118 TCGCAATGCGA
1 TCGCAACGCGA
874129 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:874146 original size:19 final size:19
Alignment explanation
Indices: 874124--874252 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
874114 AAAATCGCAA
874124 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
874143 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
874157 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
874176 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
874190 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
874209 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
874228 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
874248 TGCGA
1 TGCGA
874253 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:874166 original size:33 final size:33
Alignment explanation
Indices: 874124--874215 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
874114 AAAATCGCAA
874124 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
874157 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
874190 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
874216 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:874455 original size:93 final size:93
Alignment explanation
Indices: 874296--874674 Score: 744
Period size: 93 Copynumber: 4.1 Consensus size: 93
874286 TTGAATGGAT
874296 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
874361 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
874389 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
874454 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
874482 AAATTTACTTTCAACCAAAAGACAAAAC-AAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
874545 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
874573 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
874638 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
874666 AAATTTACT
1 AAATTTACT
874675 AAGCAATCTA
Statistics
Matches: 284, Mismatches: 0, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
91 81 0.29
92 20 0.07
93 183 0.64
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:874607 original size:184 final size:186
Alignment explanation
Indices: 874296--874674 Score: 744
Period size: 184 Copynumber: 2.0 Consensus size: 186
874286 TTGAATGGAT
874296 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
874361 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
874426 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
874482 AAATTTACTTTCAACCAAAAGACAAAAC-AAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
874545 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
874610 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
874666 AAATTTACT
1 AAATTTACT
874675 AAGCAATCTA
Statistics
Matches: 193, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
184 155 0.80
185 10 0.05
186 28 0.15
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:876395 original size:14 final size:14
Alignment explanation
Indices: 876376--876465 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
876366 TTGAAATGAA
876376 AATCGCAACGAGAG
1 AATCGCAACGAGAG
876390 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
*
876407 ACAATCGCAACGATAG
1 --AATCGCAACGAGAG
*
876423 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
876442 AATCGCAACGAGAG
1 AATCGCAACGAGAG
876456 AATCGCAACG
1 AATCGCAACG
876466 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 28 0.45
15 1 0.02
16 8 0.13
17 7 0.11
18 1 0.02
19 17 0.27
ACGTcount: A:0.42, C:0.23, G:0.24, T:0.10
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:876413 original size:33 final size:33
Alignment explanation
Indices: 876368--876482 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
876358 TCTTTTGGTT
876368 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* * *
876401 GAGATGACAATCGCAACGATAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
876434 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
876467 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
876483 TGCGATTTTG
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 76 1.00
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:876414 original size:19 final size:19
Alignment explanation
Indices: 876371--876487 Score: 84
Period size: 19 Copynumber: 6.9 Consensus size: 19
876361 TTTGGTTGAA
876371 ATGAAAATCGCAA--CGAG
1 ATGAAAATCGCAACGCGAG
876388 A-G--AATCGCAACGCGAG
1 ATGAAAATCGCAACGCGAG
*
876404 ATGACAATCGCAA--C--G
1 ATGAAAATCGCAACGCGAG
* *
876419 AT-AGAATCGCAACGCGAA
1 ATGAAAATCGCAACGCGAG
876437 ATGAAAATCGCAA--CGAG
1 ATGAAAATCGCAACGCGAG
*
876454 A-G--AATCGCAACGCGAA
1 ATGAAAATCGCAACGCGAG
*
876470 ATGAAAATCGCAATGCGA
1 ATGAAAATCGCAACGCGA
876488 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 6, Indels: 28
0.70 0.05 0.25
Matches are distributed among these distances:
14 25 0.32
15 3 0.04
16 12 0.15
17 8 0.10
18 2 0.03
19 29 0.37
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.11
Consensus pattern (19 bp):
ATGAAAATCGCAACGCGAG
Found at i:876518 original size:14 final size:14
Alignment explanation
Indices: 876499--876553 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
876489 TTTGGTTTCG
876499 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
876513 CGTTGCGATTTCCATTTCG
1 CGTTGCGA-TT-C---TCT
876532 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
876546 CGTTGCGA
1 CGTTGCGA
876554 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 10 0.29
ACGTcount: A:0.09, C:0.27, G:0.24, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:876712 original size:31 final size:32
Alignment explanation
Indices: 876674--876742 Score: 104
Period size: 33 Copynumber: 2.2 Consensus size: 32
876664 AATACTAACT
876674 TGAAAATCGCAACG-AGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAAGAATAGCAACGCGAAA
* *
876705 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGA-AGAATAGCAACGCGAAA
876738 TGAAA
1 TGAAA
876743 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
31 14 0.41
33 20 0.59
ACGTcount: A:0.48, C:0.19, G:0.22, T:0.12
Consensus pattern (32 bp):
TGAAAATCGCAACGAAGAATAGCAACGCGAAA
Found at i:876975 original size:22 final size:22
Alignment explanation
Indices: 876923--876977 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
876913 TGGTTGTGAG
**
876923 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
876945 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
876967 GGATTTCTTCG
1 GGATTTCTTCG
876978 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:877148 original size:20 final size:20
Alignment explanation
Indices: 877123--877316 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
877113 CTTTAAATAT
877123 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
877143 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
877165 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
877184 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
877204 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
877224 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
877244 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
877264 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
877284 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
877304 CGCGTTGCGATTT
1 CGCGTTGCGATTT
877317 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:877310 original size:60 final size:60
Alignment explanation
Indices: 877123--877316 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
877113 CTTTAAATAT
**
877123 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
877184 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
877244 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
877304 CGCGTTGCGATTT
1 CGCGTTGCGATTT
877317 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:877333 original size:21 final size:20
Alignment explanation
Indices: 877309--877385 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
877299 ATATTCGCGT
877309 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
877330 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
877350 TCGCGATTTT-CAAGAATCGCGT
1 T-GCGATTTTGGAA-AATCGC-A
877372 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
877386 CTGATTTGCG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
TGCGATTTTGGAAAATCGCA
Found at i:877396 original size:20 final size:20
Alignment explanation
Indices: 877371--877422 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
877361 AAGAATCGCG
*
877371 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
877391 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
877411 TTGCGATTCTGG
1 TTGCGATTCTGG
877423 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:878167 original size:14 final size:14
Alignment explanation
Indices: 878148--878183 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
878138 ATTGTTTAAT
878148 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
878162 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
878176 TGATTTGT
1 TGATTTGT
878184 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:878384 original size:19 final size:19
Alignment explanation
Indices: 878362--878512 Score: 80
Period size: 19 Copynumber: 8.7 Consensus size: 19
878352 CGAAATTAAA
878362 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
878381 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
878396 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
878414 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
878428 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
878447 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
878462 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
878480 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
878499 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
878513 GGACATTAAG
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:878408 original size:33 final size:32
Alignment explanation
Indices: 878366--878492 Score: 193
Period size: 33 Copynumber: 3.9 Consensus size: 32
878356 ATTAAATTCG
878366 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
878399 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
878432 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
878465 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
878493 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:878455 original size:66 final size:66
Alignment explanation
Indices: 878359--878491 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
878349 ACGCGAAATT
*
878359 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
878424 G
66 G
*
878425 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
878490 G
66 G
878491 A
1 A
878492 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:880797 original size:12 final size:12
Alignment explanation
Indices: 880780--880804 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
880770 TCTTCGGGGA
880780 CTTTTTCTTCTT
1 CTTTTTCTTCTT
880792 CTTTTTCTTCTT
1 CTTTTTCTTCTT
880804 C
1 C
880805 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:881013 original size:24 final size:24
Alignment explanation
Indices: 880979--881032 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
880969 CTGAAACATC
* *
880979 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
881003 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
881027 ATCAAA
1 ATCAAA
881033 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:882117 original size:20 final size:20
Alignment explanation
Indices: 882092--882149 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
882082 ATTCATTTGA
*
882092 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATAG
882112 CTATCGCAACGCGAAAATAG
1 CTATCGCAACGCGAAAATAG
* *
882132 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
882150 CGCAATGCGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.40, C:0.22, G:0.21, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATAG
Found at i:882192 original size:14 final size:14
Alignment explanation
Indices: 882173--882226 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
882163 GAAAATCGCA
882173 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
882187 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
882204 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
882220 TTGCGAT
1 TTGCGAT
882227 AGCCATTTCG
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:882192 original size:33 final size:33
Alignment explanation
Indices: 882155--882225 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
882145 AAAATCGCAA
882155 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
** ** **
882188 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
882221 TGCGA
1 TGCGA
882226 TAGCCATTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
Found at i:882226 original size:33 final size:33
Alignment explanation
Indices: 882168--882245 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
882158 GAAATGAAAA
***
882168 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
882201 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
*
882234 TCGCGTTGCGAT
1 TCGCATTGCGAT
882246 AGTCTGTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.13, C:0.23, G:0.22, T:0.42
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
Found at i:884268 original size:20 final size:19
Alignment explanation
Indices: 884233--884299 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
884223 GAAACTTAAA
*
884233 ATCGCAACTCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
884252 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
884272 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
884291 ATCGCAACG
1 ATCGCAACG
884300 ACAAAATCGC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
19 23 0.57
20 17 0.43
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.16
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:884307 original size:14 final size:14
Alignment explanation
Indices: 884288--884345 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
884278 ATGCGAAATG
884288 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
884302 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
884318 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
884334 AAAATCGCAACG
1 AAAATCGCAACG
884346 CGAAACACAA
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:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:884330 original size:32 final size:33
Alignment explanation
Indices: 884272--884350 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
884262 GGAAATGGCT
*
884272 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
884305 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
884337 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
884351 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:884379 original size:19 final size:16
Alignment explanation
Indices: 884357--884452 Score: 65
Period size: 19 Copynumber: 5.7 Consensus size: 16
884347 GAAACACAAA
884357 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGA-TTT-ATT
*
884376 TCGCGTTGCGATTT-TG
1 TCGC-TTGCGATTTATT
884392 TCG-TTGCGATTTCATT
1 TCGCTTGCGATTT-ATT
*
884408 TCGCGTTGCGATTT-TG
1 TCGC-TTGCGATTTATT
884424 TCG-TTGCGATTTTTATT
1 TCGCTTGCGA--TTTATT
884441 TCGCATTGCGAT
1 TCGC-TTGCGAT
884453 AGCCATTTCC
Statistics
Matches: 63, Mismatches: 5, Indels: 20
0.72 0.06 0.23
Matches are distributed among these distances:
14 15 0.24
16 15 0.24
17 5 0.08
18 12 0.19
19 16 0.25
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (16 bp):
TCGCTTGCGATTTATT
Found at i:884398 original size:14 final size:14
Alignment explanation
Indices: 884379--884436 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
884369 TTTCATTTCG
884379 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
884393 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
884409 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
884425 CGTTGCGATTTT
1 CGTTGCGATTTT
884437 TATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:884409 original size:32 final size:33
Alignment explanation
Indices: 884362--884452 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
884352 ACAAATCGCA
884362 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
884395 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
* *
884427 TTGCGATTTTTATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
884453 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 32 0.58
33 23 0.42
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:884460 original size:19 final size:20
Alignment explanation
Indices: 884438--884480 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
884428 TGCGATTTTT
884438 ATTT-CGCATTGCGATAGCC
1 ATTTCCGCATTGCGATAGCC
* *
884457 ATTTCCGCGTTGCGATAGTC
1 ATTTCCGCATTGCGATAGCC
884477 ATTT
1 ATTT
884481 TCGTGTTGCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (20 bp):
ATTTCCGCATTGCGATAGCC
Found at i:884471 original size:20 final size:20
Alignment explanation
Indices: 884446--884491 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
884436 TTATTTCGCA
884446 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* * *
884466 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGCCATTTCCGCG
884486 TTGCGA
1 TTGCGA
884492 AAGTAAACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:884991 original size:18 final size:18
Alignment explanation
Indices: 884965--885009 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
884955 GTCGATCAGA
*
884965 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
884983 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
885001 TGATGGCTC
1 TGATGGCTC
885010 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:886884 original size:20 final size:20
Alignment explanation
Indices: 886859--886911 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
886849 GATTATGTAT
*
886859 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTAAG
886879 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTAAG
*
886899 TATCTCGTTGCGA
1 TATCGCGTTGCGA
886912 TTTTTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTAAG
Found at i:886966 original size:20 final size:20
Alignment explanation
Indices: 886922--887014 Score: 105
Period size: 20 Copynumber: 4.5 Consensus size: 20
886912 TTTTTTATTA
*
886922 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACCAAT
**
886943 TCGCATTGCGATTTACTTAT
1 TCGCATTGCGATTTACCAAT
*
886963 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACCAAT
* **
886984 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACCAAT
887004 TCGCATTGCGA
1 TCGCATTGCGA
887015 ATTGGGAAAA
Statistics
Matches: 60, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
20 33 0.55
21 27 0.45
ACGTcount: A:0.19, C:0.25, G:0.17, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACCAAT
Found at i:886967 original size:41 final size:41
Alignment explanation
Indices: 886915--887017 Score: 174
Period size: 41 Copynumber: 2.6 Consensus size: 41
886905 GTTGCGATTT
*
886915 TTTA-TTA-TCGCATTGCGATTTTCCCAATTCGCATTGCGA
1 TTTACTTATTCGCATTGCGAATTTCCCAATTCGCATTGCGA
*
886954 TTTACTTATTCGCATTGCGAATTTCCCAATTCGCGTTGCGA
1 TTTACTTATTCGCATTGCGAATTTCCCAATTCGCATTGCGA
886995 TTTACTTATTCGCATTGCGAATT
1 TTTACTTATTCGCATTGCGAATT
887018 GGGAAAATCG
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
39 4 0.07
40 3 0.05
41 53 0.88
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.42
Consensus pattern (41 bp):
TTTACTTATTCGCATTGCGAATTTCCCAATTCGCATTGCGA
Found at i:897662 original size:31 final size:31
Alignment explanation
Indices: 897627--897910 Score: 514
Period size: 31 Copynumber: 9.2 Consensus size: 31
897617 GGTCACAATA
897627 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
897658 TAAACTGTTCATATGTGCCTTTAAACATATA
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
897689 TAAACTGTTCATATGTGCCTTTAAACATATA
1 TAAACTGTTCATATGTGCCTTTAAACATATG
897720 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
897751 TAAATTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
* *
897782 TAAAATATTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
897813 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
897844 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
897875 TAAAATGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
897906 TAAAC
1 TAAAC
897911 CCTCGACTCT
Statistics
Matches: 244, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 244 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.39
Consensus pattern (31 bp):
TAAACTGTTCATATGTGCCTTTAAACATATG
Found at i:898475 original size:64 final size:64
Alignment explanation
Indices: 898309--898529 Score: 223
Period size: 64 Copynumber: 3.5 Consensus size: 64
898299 TAATAAAGGT
* * * ** * * **
898309 ATGCATCGATGCACTAATGATGCATCGGTGCATAAAAGGTATTCGATGTAGTATTATTGCTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTATTATTATTAATGGG
* ** *
898373 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCAGTCGATGT-TTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTATT-ATTATTAATGGG
* * **
898437 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTCTTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGT-ATTATTATTAATGGG
**
898500 AGTGCATCGATGCACTACCAATGCATCGAT
1 A-TGCATCGATGCACTACTTATGCATCGAT
898530 ACACCTTCAA
Statistics
Matches: 132, Mismatches: 21, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
63 3 0.02
64 124 0.94
65 3 0.02
66 2 0.02
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTATTATTATTAATGGG
Found at i:901392 original size:31 final size:31
Alignment explanation
Indices: 901357--901578 Score: 399
Period size: 31 Copynumber: 7.2 Consensus size: 31
901347 GGTCACAATA
901357 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
901388 TAAACTGTTCATATGTGCCTTTAAACATATA
1 TAAACTGTTCATATGTGCCTTTAAACATATG
901419 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
* *
901450 TAAACTGTTCATATATCCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
* *
901481 TAAAATGTCCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
901512 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
901543 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
901574 TAAAC
1 TAAAC
901579 CCTCGACTCT
Statistics
Matches: 181, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 181 1.00
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (31 bp):
TAAACTGTTCATATGTGCCTTTAAACATATG
Found at i:901511 original size:16 final size:16
Alignment explanation
Indices: 901490--901574 Score: 56
Period size: 16 Copynumber: 5.4 Consensus size: 16
901480 GTAAAATGTC
901490 CATATGTGCCTTTAAA
1 CATATGTGCCTTTAAA
**
901506 CATATGTAAACTGTT---
1 CATATGT-GCCT-TTAAA
901521 CATATGTGCCTTTAAA
1 CATATGTGCCTTTAAA
**
901537 CATATGTAAACTGTT---
1 CATATGT-GCCT-TTAAA
901552 CATATGTGCCTTTAAA
1 CATATGTGCCTTTAAA
901568 CATATGT
1 CATATGT
901575 AAACCCTCGA
Statistics
Matches: 51, Mismatches: 8, Indels: 20
0.65 0.10 0.25
Matches are distributed among these distances:
13 4 0.08
14 4 0.08
15 14 0.27
16 21 0.41
17 4 0.08
18 4 0.08
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (16 bp):
CATATGTGCCTTTAAA
Found at i:904274 original size:16 final size:15
Alignment explanation
Indices: 904246--904306 Score: 61
Period size: 16 Copynumber: 3.9 Consensus size: 15
904236 TAAGTTGGGA
904246 TTAGATTGT-ATTTACT
1 TTAGATT-TAATTTA-T
904262 TTAGATTTAATTTAT
1 TTAGATTTAATTTAT
*
904277 ATTAAATTTAATTTTAT
1 -TTAGATTTAA-TTTAT
*
904294 TTGGATTTAATTT
1 TTAGATTTAATTT
904307 CGTTCTATGA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
15 5 0.13
16 29 0.74
17 5 0.13
ACGTcount: A:0.31, C:0.02, G:0.08, T:0.59
Consensus pattern (15 bp):
TTAGATTTAATTTAT
Found at i:904275 original size:11 final size:11
Alignment explanation
Indices: 904255--904306 Score: 52
Period size: 11 Copynumber: 4.8 Consensus size: 11
904245 ATTAGATTGT
*
904255 ATTTACTTTAG
1 ATTTAATTTAG
*
904266 ATTTAATTTAT
1 ATTTAATTTAG
*
904277 ATTAAATTTA-
1 ATTTAATTTAG
* *
904287 ATTTTATTTGG
1 ATTTAATTTAG
904298 ATTTAATTT
1 ATTTAATTT
904307 CGTTCTATGA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
10 7 0.21
11 26 0.79
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.60
Consensus pattern (11 bp):
ATTTAATTTAG
Found at i:912633 original size:2 final size:2
Alignment explanation
Indices: 912626--912661 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
912616 ATTTTCATCA
912626 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
912662 TATTTATTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:912716 original size:6 final size:6
Alignment explanation
Indices: 912679--912713 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
912669 TATTATTACC
*
912679 ATCATG ATCATG ATCATG ATCATG ATCATT ATCAT
1 ATCATG ATCATG ATCATG ATCATG ATCATG ATCAT
912714 TATATATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.37
Consensus pattern (6 bp):
ATCATG
Found at i:912888 original size:3 final size:3
Alignment explanation
Indices: 912874--912948 Score: 136
Period size: 3 Copynumber: 25.7 Consensus size: 3
912864 TACTACTATC
912874 ATT A-T ATT -TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
912920 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
912949 CATCATTTTT
Statistics
Matches: 70, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
2 4 0.06
3 66 0.94
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:913443 original size:15 final size:15
Alignment explanation
Indices: 913423--913464 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
913413 CTTTGGTATT
913423 ATTTAAATTTTTGTC
1 ATTTAAATTTTTGTC
*
913438 ATTTAAA-TTTTGTT
1 ATTTAAATTTTTGTC
*
913452 ATTTTAATTTTTG
1 ATTTAAATTTTTG
913465 CCTTTATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.26, C:0.02, G:0.07, T:0.64
Consensus pattern (15 bp):
ATTTAAATTTTTGTC
Found at i:914090 original size:138 final size:139
Alignment explanation
Indices: 913830--914094 Score: 343
Period size: 138 Copynumber: 1.9 Consensus size: 139
913820 GACAAATTCC
* * * *
913830 ATAATTGATTAAAATTAATTAGGATTACTATTACAGCTTTCACTTTAGGCCTAATTTCAAACTTA
1 ATAATTGATTAAAATTAATTAGGAATAATATTACAGCCTCCACTTTAGGCCTAATTTCAAACTTA
* ** * * *
913895 GTCCTTAAAATTAGGGGAATTTTTAATTTGGTCATCATTTTTGCTCGATGTTCCATTTTAATTAT
66 GTCCTTAAAATTAGAGGAATGCTTAATTTGGTCATCACTTATGCTCGAGGTTCCATTTTAATTAT
913960 TCGAATCAA
131 TCGAATCAA
* * * * * *
913969 ATAATTGGTTAAAATTAATTAGGAATAATATTAGAGCCTCCATTTTAGGCTTAATTTTATA-TTA
1 ATAATTGATTAAAATTAATTAGGAATAATATTACAGCCTCCACTTTAGGCCTAATTTCAAACTTA
* * * *
914033 GTCCTTTAATTTATAGGAATGCTTAATTTGGTCCTCACTTATGCTCGAGGTTCCATTTTAAT
66 GTCCTTAAAATTAGAGGAATGCTTAATTTGGTCATCACTTATGCTCGAGGTTCCATTTTAAT
914095 CAAACAAAAT
Statistics
Matches: 106, Mismatches: 20, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
138 55 0.52
139 51 0.48
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (139 bp):
ATAATTGATTAAAATTAATTAGGAATAATATTACAGCCTCCACTTTAGGCCTAATTTCAAACTTA
GTCCTTAAAATTAGAGGAATGCTTAATTTGGTCATCACTTATGCTCGAGGTTCCATTTTAATTAT
TCGAATCAA
Found at i:917377 original size:32 final size:33
Alignment explanation
Indices: 917307--917379 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 33
917297 CTAAATCTGA
*
917307 ACCCGACCCGAATATCACACATAAAAAACCCCG
1 ACCCGACCCAAATATCACACATAAAAAACCCCG
* * *
917340 A-CCGACTCAAATATCACACTTACAAAA-CCCG
1 ACCCGACCCAAATATCACACATAAAAAACCCCG
917371 ACCCGACCC
1 ACCCGACCC
917380 GACCCCGAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
31 5 0.15
32 28 0.82
33 1 0.03
ACGTcount: A:0.40, C:0.41, G:0.08, T:0.11
Consensus pattern (33 bp):
ACCCGACCCAAATATCACACATAAAAAACCCCG
Found at i:917489 original size:31 final size:32
Alignment explanation
Indices: 917438--917510 Score: 130
Period size: 32 Copynumber: 2.3 Consensus size: 32
917428 TTAAAAAACC
917438 CCGACCCGAACCCAATTTTTTTAAAAAAAAAT
1 CCGACCCGAACCCAATTTTTTTAAAAAAAAAT
*
917470 CCGACCCGATCCCAATTTTTTT-AAAAAAAAT
1 CCGACCCGAACCCAATTTTTTTAAAAAAAAAT
917501 CCGACCCGAA
1 CCGACCCGAA
917511 TACCAAAAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
31 18 0.46
32 21 0.54
ACGTcount: A:0.40, C:0.29, G:0.08, T:0.23
Consensus pattern (32 bp):
CCGACCCGAACCCAATTTTTTTAAAAAAAAAT
Found at i:918816 original size:16 final size:16
Alignment explanation
Indices: 918784--918823 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
918774 TTTACTTCAG
918784 AATGATT-AAACGTTA
1 AATGATTCAAACGTTA
*
918799 AATGATTCAAATGTTA
1 AATGATTCAAACGTTA
918815 AATGATTCA
1 AATGATTCA
918824 GAGGCTCTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 7 0.30
16 16 0.70
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.35
Consensus pattern (16 bp):
AATGATTCAAACGTTA
Found at i:919838 original size:10 final size:10
Alignment explanation
Indices: 919823--919847 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
919813 TGATAATTTG
919823 TATTATCTTA
1 TATTATCTTA
919833 TATTATCTTA
1 TATTATCTTA
919843 TATTA
1 TATTA
919848 AATTATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (10 bp):
TATTATCTTA
Found at i:924837 original size:42 final size:43
Alignment explanation
Indices: 924739--924858 Score: 170
Period size: 42 Copynumber: 2.8 Consensus size: 43
924729 ACATGTTAGG
* * * *
924739 GTTTTGTGATCCGAATTTCGTTTTAAATTTATGTTATATGTTAGA
1 GTTTTGTGACCCGAATTTCG-TTTGAATTCATATTATATGTTA-A
924784 GTTTTGTGACCCGAATTTCGTTTGAATTCATATTATATGTT-A
1 GTTTTGTGACCCGAATTTCGTTTGAATTCATATTATATGTTAA
*
924826 GTTTTGTGACCCAAATTTCGTTTGAATTCATAT
1 GTTTTGTGACCCGAATTTCGTTTGAATTCATAT
924859 AGTATGATAA
Statistics
Matches: 70, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
42 33 0.47
44 18 0.26
45 19 0.27
ACGTcount: A:0.24, C:0.11, G:0.17, T:0.48
Consensus pattern (43 bp):
GTTTTGTGACCCGAATTTCGTTTGAATTCATATTATATGTTAA
Found at i:928803 original size:20 final size:20
Alignment explanation
Indices: 928763--928804 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
928753 TTCGCGTTGC
* **
928763 ATTTCGCGTTGTGATTTTCT
1 ATTTCGCGTTGCGATAGTCT
928783 ATTTCGCGTTGCGATAGTCT
1 ATTTCGCGTTGCGATAGTCT
928803 AT
1 AT
928805 AATGTCGTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.14, C:0.17, G:0.21, T:0.48
Consensus pattern (20 bp):
ATTTCGCGTTGCGATAGTCT
Found at i:929369 original size:33 final size:32
Alignment explanation
Indices: 929325--929433 Score: 112
Period size: 33 Copynumber: 3.3 Consensus size: 32
929315 ATTGGGTTCT
*
929325 GGTCGGGTTTTTTTAAGTTTGATATTCGGATC
1 GGTCGGGTTTTTTTAAGTATGATATTCGGATC
* * * * *
929357 GGTTTGGTTTTTTTTAAGCATAATATTCGGGTC
1 GG-TCGGGTTTTTTTAAGTATGATATTCGGATC
*
929390 GGTCGGGTTTTTTTAAGTGTGATATTCAGG-TC
1 GGTCGGGTTTTTTTAAGTATGATATTC-GGATC
929422 GGGTTCGGGTTT
1 -GG-TCGGGTTT
929434 AGGGTGAAAA
Statistics
Matches: 62, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
32 24 0.39
33 30 0.48
34 8 0.13
ACGTcount: A:0.15, C:0.09, G:0.30, T:0.46
Consensus pattern (32 bp):
GGTCGGGTTTTTTTAAGTATGATATTCGGATC
Found at i:931494 original size:3 final size:3
Alignment explanation
Indices: 931486--931552 Score: 120
Period size: 3 Copynumber: 23.0 Consensus size: 3
931476 ATATTCAAAC
931486 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
931534 A-A ATA ATA ATA ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA
931553 TAGCTTCTCA
Statistics
Matches: 62, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 4 0.06
3 58 0.94
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:936442 original size:9 final size:9
Alignment explanation
Indices: 936430--936463 Score: 50
Period size: 9 Copynumber: 3.6 Consensus size: 9
936420 AATTTTTTAA
936430 AAAATATAT
1 AAAATATAT
936439 AAAATATATTT
1 AAAATATA--T
936450 AAAATATAT
1 AAAATATAT
936459 AAAAT
1 AAAAT
936464 CGAGCTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 14 0.61
11 9 0.39
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
AAAATATAT
Found at i:936944 original size:6 final size:6
Alignment explanation
Indices: 936933--936967 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
936923 TAGCATTCGT
936933 GGACCC GGACCC GGACCC GGACCC GGACCC GGACC
1 GGACCC GGACCC GGACCC GGACCC GGACCC GGACC
936968 AGGATCCATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.17, C:0.49, G:0.34, T:0.00
Consensus pattern (6 bp):
GGACCC
Found at i:938522 original size:2 final size:2
Alignment explanation
Indices: 938515--938568 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
938505 ATTGATTTTA
938515 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
938557 AT AT AT AT AT AT
1 AT AT AT AT AT AT
938569 TGTCTCCTCT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:939885 original size:17 final size:17
Alignment explanation
Indices: 939850--939888 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
939840 GGAAATTATA
939850 TAAT-TATATTAGTTAC
1 TAATGTATATTAGTTAC
939866 TAATGTATAGTTAGTT-C
1 TAATGTATA-TTAGTTAC
939883 TAATGT
1 TAATGT
939889 GTGTTTTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.19
17 11 0.52
18 6 0.29
ACGTcount: A:0.33, C:0.05, G:0.13, T:0.49
Consensus pattern (17 bp):
TAATGTATATTAGTTAC
Found at i:942087 original size:13 final size:13
Alignment explanation
Indices: 942069--942105 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
942059 CTTCAATTAT
942069 GATGATTGAATAA
1 GATGATTGAATAA
942082 GATGATTGAATAA
1 GATGATTGAATAA
942095 GATGATTGAAT
1 GATGATTGAAT
942106 GTTAATTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.43, C:0.00, G:0.24, T:0.32
Consensus pattern (13 bp):
GATGATTGAATAA
Found at i:957422 original size:21 final size:21
Alignment explanation
Indices: 957397--957505 Score: 110
Period size: 21 Copynumber: 5.0 Consensus size: 21
957387 ATTATCCAAT
*
957397 AAACTTGACATCCATAATAAC
1 AAACTTGAAATCCATAATAAC
* * *
957418 AAACTTAAAATCCATAACAAG
1 AAACTTGAAATCCATAATAAC
957439 AAACTTGAAATCCATAATAATAAATC
1 AAACTTGAAATCC---ATAAT-AA-C
* **
957465 AAAGTTGGCATCCATAATAAC
1 AAACTTGAAATCCATAATAAC
957486 AAACTTGAAATCCATAATAA
1 AAACTTGAAATCCATAATAA
957506 TAAATCAAAA
Statistics
Matches: 70, Mismatches: 13, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
21 47 0.67
22 2 0.03
23 5 0.07
24 4 0.06
25 2 0.03
26 10 0.14
ACGTcount: A:0.51, C:0.18, G:0.06, T:0.24
Consensus pattern (21 bp):
AAACTTGAAATCCATAATAAC
Found at i:957570 original size:15 final size:15
Alignment explanation
Indices: 957550--957581 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
957540 AGAACCAAAT
957550 ATAACTAAGTTCTAC
1 ATAACTAAGTTCTAC
957565 ATAACTAAGTTCTAC
1 ATAACTAAGTTCTAC
957580 AT
1 AT
957582 TGTAGTAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.19, G:0.06, T:0.34
Consensus pattern (15 bp):
ATAACTAAGTTCTAC
Found at i:957852 original size:40 final size:41
Alignment explanation
Indices: 957611--957901 Score: 173
Period size: 40 Copynumber: 7.1 Consensus size: 41
957601 AGAACATATG
* * * * **
957611 ACTAAAGTACGAGTATTTAGTGGCGTTTGTGCTTAAAATACC
1 ACTAAAGTACGAGTATTTAGCGGCGTTTAT-ATAAAAACGCC
* * * * * * *
957653 ACTAAATTA-TAATA-TTAGTGGCGTTTGTACTTAAAATGCC
1 ACTAAAGTACGAGTATTTAGCGGCGTTTATA-TAAAAACGCC
* * * **
957693 ACTAAAGTACGAGTTTTTGGCGGCGTTTGA-ATACAAATACC
1 ACTAAAGTACGAGTATTTAGCGGCGTTT-ATATAAAAACGCC
* * * * *
957734 ACTAAAGTAC-ATTATTTACCGGCATTTATATAAAAATGTC
1 ACTAAAGTACGAGTATTTAGCGGCGTTTATATAAAAACGCC
* *** * * *
957774 ACTATAGTACGAGTATTTAGCGTAATTGATGCT-TAAACGCC
1 ACTAAAGTACGAGTATTTAGCGGCGTTTAT-ATAAAAACGCC
* *
957815 ACTAAAGTAC-AGTATTTAGCGACGTTTATATAAAAACGCT
1 ACTAAAGTACGAGTATTTAGCGGCGTTTATATAAAAACGCC
* *
957855 ACTAAAGTACAAGTATTTACCGGCGTTTAT-TCAAAAACGCC
1 ACTAAAGTACGAGTATTTAGCGGCGTTTATAT-AAAAACGCC
*
957896 GCTAAA
1 ACTAAA
957902 AATACGGCTA
Statistics
Matches: 194, Mismatches: 45, Indels: 21
0.75 0.17 0.08
Matches are distributed among these distances:
39 2 0.01
40 92 0.47
41 80 0.41
42 20 0.10
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (41 bp):
ACTAAAGTACGAGTATTTAGCGGCGTTTATATAAAAACGCC
Found at i:957893 original size:81 final size:81
Alignment explanation
Indices: 957732--957901 Score: 180
Period size: 81 Copynumber: 2.1 Consensus size: 81
957722 AATACAAATA
* * * * * * *
957732 CCACTAAAGTACATTATTTACCGGCATTTATATAAAAATGTCACTATAGTACGAGTATTTAGCGT
1 CCACTAAAGTACAGTATTTACCGACATTTATATAAAAACGTCACTAAAGTACAAGTATTTACCGG
**
957797 AATTGATGCTTAAACG
66 AATTGATGCAAAAACG
* *
957813 CCACTAAAGTACAGTATTTAGCGACGTTTATATAAAAACG-CTACTAAAGTACAAGTATTTACCG
1 CCACTAAAGTACAGTATTTACCGACATTTATATAAAAACGTC-ACTAAAGTACAAGTATTTACCG
** * *
957877 GCGTTTATTCAAAAACG
65 GAATTGATGCAAAAACG
*
957894 CCGCTAAA
1 CCACTAAA
957902 AATACGGCTA
Statistics
Matches: 72, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
80 1 0.01
81 71 0.99
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (81 bp):
CCACTAAAGTACAGTATTTACCGACATTTATATAAAAACGTCACTAAAGTACAAGTATTTACCGG
AATTGATGCAAAAACG
Found at i:957901 original size:41 final size:40
Alignment explanation
Indices: 957732--957901 Score: 139
Period size: 41 Copynumber: 4.2 Consensus size: 40
957722 AATACAAATA
* * * *
957732 CCACTAAAGTACATTATTTACCGGCATTTATATAAAAATG
1 CCACTAAAGTACAGTATTTACCGACGTTTATATAAAAACG
* * * * * * *
957772 TCACTATAGTACGAGTATTTAGCGTA-ATTGATGCT-TAAACG
1 CCACTAAAGTAC-AGTATTTACCG-ACGTTTAT-ATAAAAACG
*
957813 CCACTAAAGTACAGTATTTAGCGACGTTTATATAAAAACG
1 CCACTAAAGTACAGTATTTACCGACGTTTATATAAAAACG
* *
957853 CTACTAAAGTACAAGTATTTACCGGCGTTTAT-TCAAAAACG
1 CCACTAAAGTAC-AGTATTTACCGACGTTTATAT-AAAAACG
*
957894 CCGCTAAA
1 CCACTAAA
957902 AATACGGCTA
Statistics
Matches: 103, Mismatches: 20, Indels: 13
0.76 0.15 0.10
Matches are distributed among these distances:
39 2 0.02
40 42 0.41
41 58 0.56
42 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (40 bp):
CCACTAAAGTACAGTATTTACCGACGTTTATATAAAAACG
Found at i:961210 original size:96 final size:96
Alignment explanation
Indices: 961101--961292 Score: 384
Period size: 96 Copynumber: 2.0 Consensus size: 96
961091 GAAAGTGAGT
961101 CCCACTATAAGTACCTTTCTTTTTTAATTTTGTCTCTAAATCACATAACCTCAAACAAACTATCA
1 CCCACTATAAGTACCTTTCTTTTTTAATTTTGTCTCTAAATCACATAACCTCAAACAAACTATCA
961166 AACAATGGTTAATAGGTAATTATGATCTAAA
66 AACAATGGTTAATAGGTAATTATGATCTAAA
961197 CCCACTATAAGTACCTTTCTTTTTTAATTTTGTCTCTAAATCACATAACCTCAAACAAACTATCA
1 CCCACTATAAGTACCTTTCTTTTTTAATTTTGTCTCTAAATCACATAACCTCAAACAAACTATCA
961262 AACAATGGTTAATAGGTAATTATGATCTAAA
66 AACAATGGTTAATAGGTAATTATGATCTAAA
961293 TCCATTTTAT
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 96 1.00
ACGTcount: A:0.38, C:0.20, G:0.07, T:0.35
Consensus pattern (96 bp):
CCCACTATAAGTACCTTTCTTTTTTAATTTTGTCTCTAAATCACATAACCTCAAACAAACTATCA
AACAATGGTTAATAGGTAATTATGATCTAAA
Found at i:965745 original size:16 final size:16
Alignment explanation
Indices: 965724--965758 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
965714 ATCCCAATGA
965724 ACAACGAAGGGAGTAG
1 ACAACGAAGGGAGTAG
965740 ACAACGAAGGGAGTAG
1 ACAACGAAGGGAGTAG
965756 ACA
1 ACA
965759 CTAGTCAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.14, G:0.34, T:0.06
Consensus pattern (16 bp):
ACAACGAAGGGAGTAG
Found at i:970584 original size:90 final size:89
Alignment explanation
Indices: 970431--970603 Score: 256
Period size: 90 Copynumber: 1.9 Consensus size: 89
970421 TAACACACCC
* * * *
970431 TTTTATAGCCAAGTTACCCTAGTCATATTAGGGTTTTTATTATTTTAAATTAATTAAATCTATAT
1 TTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTATAT
*
970496 TTAATTAATTAGAATTTAATAATCT
66 TTAATTAATT-GAAATTAATAATCT
* * * *
970521 TTTTATATCTAAGTTACCCTAATTATATCATGGATTTTATTATTTCAAATTAATTAAATCTATAT
1 TTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTATAT
970586 TTAATTAATTGAAATTAA
66 TTAATTAATTGAAATTAA
970604 ATATTCCGGA
Statistics
Matches: 74, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
89 7 0.09
90 67 0.91
ACGTcount: A:0.37, C:0.09, G:0.06, T:0.48
Consensus pattern (89 bp):
TTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTATAT
TTAATTAATTGAAATTAATAATCT
Found at i:974025 original size:4 final size:4
Alignment explanation
Indices: 974016--974041 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
974006 ATTAAACAAA
974016 ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT AT
974042 AGGAGTGTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:982772 original size:16 final size:16
Alignment explanation
Indices: 982751--982783 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
982741 ATAAGCACCG
982751 CTAATTCCAATCATGT
1 CTAATTCCAATCATGT
982767 CTAATTCCAATCATGT
1 CTAATTCCAATCATGT
982783 C
1 C
982784 ATTTTATGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.27, G:0.06, T:0.36
Consensus pattern (16 bp):
CTAATTCCAATCATGT
Found at i:984635 original size:24 final size:24
Alignment explanation
Indices: 984608--984667 Score: 111
Period size: 24 Copynumber: 2.5 Consensus size: 24
984598 GGCTTATCTC
*
984608 CTTCTCCAATTTCAGTCTTATTTT
1 CTTCTCCCATTTCAGTCTTATTTT
984632 CTTCTCCCATTTCAGTCTTATTTT
1 CTTCTCCCATTTCAGTCTTATTTT
984656 CTTCTCCCATTT
1 CTTCTCCCATTT
984668 GTGTATGCAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.13, C:0.30, G:0.03, T:0.53
Consensus pattern (24 bp):
CTTCTCCCATTTCAGTCTTATTTT
Found at i:986544 original size:24 final size:24
Alignment explanation
Indices: 986517--986567 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
986507 TGCCTGGAGG
*
986517 AGGAGGAGGTGGTGGTCGTCCACC
1 AGGAGGAGGCGGTGGTCGTCCACC
* * *
986541 AGGAGGTGGCGGTGGTGGTGCACC
1 AGGAGGAGGCGGTGGTCGTCCACC
986565 AGG
1 AGG
986568 TAGTGGAGGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.16, C:0.18, G:0.51, T:0.16
Consensus pattern (24 bp):
AGGAGGAGGCGGTGGTCGTCCACC
Found at i:986573 original size:24 final size:24
Alignment explanation
Indices: 986517--986579 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
986507 TGCCTGGAGG
* *
986517 AGGAGGAGGTGGTGGTCGTCCACC
1 AGGAGGTGGAGGTGGTCGTCCACC
* * *
986541 AGGAGGTGGCGGTGGTGGTGCACC
1 AGGAGGTGGAGGTGGTCGTCCACC
986565 AGGTA-GTGGAGGTGG
1 AGG-AGGTGGAGGTGG
986580 AGCAGGAAGT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
24 32 0.97
25 1 0.03
ACGTcount: A:0.16, C:0.14, G:0.52, T:0.17
Consensus pattern (24 bp):
AGGAGGTGGAGGTGGTCGTCCACC
Found at i:988806 original size:15 final size:15
Alignment explanation
Indices: 988786--988815 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
988776 ATCAATTTAA
*
988786 CTTCTTCCTCCTCCT
1 CTTCTTCCTCATCCT
988801 CTTCTTCCTCATCCT
1 CTTCTTCCTCATCCT
988816 GTAAAATGCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.03, C:0.50, G:0.00, T:0.47
Consensus pattern (15 bp):
CTTCTTCCTCATCCT
Found at i:993255 original size:51 final size:51
Alignment explanation
Indices: 993195--993291 Score: 149
Period size: 51 Copynumber: 1.9 Consensus size: 51
993185 AAATACCTTC
*
993195 CCTAACCCACTAAACATTAAACAAATCCTCAACTAATCTACTAAAATAAAA
1 CCTAACCCACTAAACATTAAACAAATCCTCAACTAATCCACTAAAATAAAA
** * *
993246 CCTAACCCACTATCCATTAAACAAATCCTCCACTACTCCACTAAAA
1 CCTAACCCACTAAACATTAAACAAATCCTCAACTAATCCACTAAAA
993292 ATTCATCATA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 41 1.00
ACGTcount: A:0.45, C:0.33, G:0.00, T:0.22
Consensus pattern (51 bp):
CCTAACCCACTAAACATTAAACAAATCCTCAACTAATCCACTAAAATAAAA
Found at i:993723 original size:25 final size:25
Alignment explanation
Indices: 993645--993723 Score: 90
Period size: 25 Copynumber: 3.1 Consensus size: 25
993635 TATGATGGAT
993645 TTTTAGTGGAGTAGTGGAGGATTTG
1 TTTTAGTGGAGTAGTGGAGGATTTG
* * *
993670 -TTTAATAGA-TAGTGGGTTAGGTTTTG
1 TTTTAGTGGAGTAGT-GG--AGGATTTG
993696 TTTTAGTGGAGTAGTGGAGGATTTG
1 TTTTAGTGGAGTAGTGGAGGATTTG
993721 TTT
1 TTT
993724 AATGTTTAGT
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
23 4 0.09
24 9 0.21
25 10 0.23
26 7 0.16
27 9 0.21
28 4 0.09
ACGTcount: A:0.20, C:0.00, G:0.35, T:0.44
Consensus pattern (25 bp):
TTTTAGTGGAGTAGTGGAGGATTTG
Found at i:998773 original size:84 final size:84
Alignment explanation
Indices: 998632--998803 Score: 308
Period size: 84 Copynumber: 2.0 Consensus size: 84
998622 TATTAAATAT
* * * *
998632 TTTATTAAATGATATATTTCACATTAAATATTTTATATATCTATCAAATAATTTGTTATCTCCTG
1 TTTATTAAAAGATACATTTCACATTAAATATTTTATATATCTATCAAATAAGTTGTTATCTCCTA
998697 AAATAAAACGTGTCATACA
66 AAATAAAACGTGTCATACA
998716 TTTATTAAAAGATACATTTCACATTAAATATTTTATATATCTATCAAATAAGTTGTTATCTCCTA
1 TTTATTAAAAGATACATTTCACATTAAATATTTTATATATCTATCAAATAAGTTGTTATCTCCTA
998781 AAATAAAACGTGTCATACA
66 AAATAAAACGTGTCATACA
998800 TTTA
1 TTTA
998804 AACAAAAATA
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 84 1.00
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.42
Consensus pattern (84 bp):
TTTATTAAAAGATACATTTCACATTAAATATTTTATATATCTATCAAATAAGTTGTTATCTCCTA
AAATAAAACGTGTCATACA
Found at i:1016817 original size:60 final size:60
Alignment explanation
Indices: 1016724--1016841 Score: 182
Period size: 60 Copynumber: 2.0 Consensus size: 60
1016714 TCTCAAAGAC
*
1016724 TAGGAAGGAGCCCGATGAAGGTGGGTTGGAGGGAGAAGCGGATACTGAGAACAGAAGAAA
1 TAGGAAGGAGCCCGATGAAGGTGCGTTGGAGGGAGAAGCGGATACTGAGAACAGAAGAAA
* * * * *
1016784 TAGGAAGGAGCCTGATGATGGTTCGTTGGAGGGAGAAGTGGATACTGGGAACAGAAGA
1 TAGGAAGGAGCCCGATGAAGGTGCGTTGGAGGGAGAAGCGGATACTGAGAACAGAAGA
1016842 TCTAATTTAG
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.34, C:0.09, G:0.42, T:0.15
Consensus pattern (60 bp):
TAGGAAGGAGCCCGATGAAGGTGCGTTGGAGGGAGAAGCGGATACTGAGAACAGAAGAAA
Found at i:1021422 original size:2 final size:2
Alignment explanation
Indices: 1021415--1021456 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1021405 GAGATTAATG
1021415 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
1021457 GTTGAAAACA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1027573 original size:20 final size:21
Alignment explanation
Indices: 1027527--1027586 Score: 68
Period size: 20 Copynumber: 2.8 Consensus size: 21
1027517 ACCCCCATGA
*
1027527 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC-CT-AAG
1027550 GGGAACCGATTCCCCCCT-AG
1 GGGAACCGATTCCCCCCTAAG
* *
1027570 GGGAATCGATACCCCCC
1 GGGAACCGATTCCCCCC
1027587 CGGGGGGTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 17 0.50
22 1 0.03
23 16 0.47
ACGTcount: A:0.22, C:0.37, G:0.25, T:0.17
Consensus pattern (21 bp):
GGGAACCGATTCCCCCCTAAG
Found at i:1027592 original size:20 final size:20
Alignment explanation
Indices: 1027548--1027591 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1027538 CCCCCTTTGA
* *
1027548 AGGGGAACCGATTCCCCCCT
1 AGGGGAACCGATACCCCCCC
*
1027568 AGGGGAATCGATACCCCCCC
1 AGGGGAACCGATACCCCCCC
1027588 -GGGG
1 AGGGG
1027592 GGTTCTGGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.20, C:0.36, G:0.32, T:0.11
Consensus pattern (20 bp):
AGGGGAACCGATACCCCCCC
Found at i:1028387 original size:21 final size:21
Alignment explanation
Indices: 1028361--1028402 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1028351 ATCAGATTGT
*
1028361 CCAGGGGGTACAGATTCCCCC
1 CCAGGGGGAACAGATTCCCCC
*
1028382 CCAGGGGGAATAGATTCCCCC
1 CCAGGGGGAACAGATTCCCCC
1028403 TAGGAGGTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.36, G:0.29, T:0.14
Consensus pattern (21 bp):
CCAGGGGGAACAGATTCCCCC
Found at i:1028401 original size:20 final size:20
Alignment explanation
Indices: 1028361--1028421 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
1028351 ATCAGATTGT
*
1028361 CCAGGGGGTACAGATTCCCCC
1 CCAGGGGGTATAGATT-CCCC
*
1028382 CCAGGGGGAATAGATTCCCC
1 CCAGGGGGTATAGATTCCCC
* * *
1028402 CTAGGAGGTATCGATTCCCC
1 CCAGGGGGTATAGATTCCCC
1028422 GGGAACAGAT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
20 20 0.59
21 14 0.41
ACGTcount: A:0.21, C:0.33, G:0.28, T:0.18
Consensus pattern (20 bp):
CCAGGGGGTATAGATTCCCC
Found at i:1028434 original size:15 final size:15
Alignment explanation
Indices: 1028414--1028469 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
1028404 AGGAGGTATC
1028414 GATTCCCCGGGAACA
1 GATTCCCCGGGAACA
*
1028429 GATTCCCCCAGGGGTATC-
1 GATT-CCCC--GGG-AACA
*
1028447 GATTCCCCGGGTACA
1 GATTCCCCGGGAACA
1028462 GATTCCCC
1 GATTCCCC
1028470 CTGCATGGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
14 1 0.03
15 15 0.45
16 4 0.12
17 4 0.12
18 7 0.21
19 2 0.06
ACGTcount: A:0.20, C:0.36, G:0.25, T:0.20
Consensus pattern (15 bp):
GATTCCCCGGGAACA
Found at i:1028450 original size:33 final size:35
Alignment explanation
Indices: 1028387--1028471 Score: 138
Period size: 33 Copynumber: 2.5 Consensus size: 35
1028377 CCCCCCCAGG
*
1028387 GGGAATAGATTCCCCCTAGGAGGTATCGATTCCCC
1 GGGAACAGATTCCCCCTAGGAGGTATCGATTCCCC
1028422 GGGAACAGATTCCCCC-AGG-GGTATCGATTCCCC
1 GGGAACAGATTCCCCCTAGGAGGTATCGATTCCCC
*
1028455 GGGTACAGATTCCCCCT
1 GGGAACAGATTCCCCCT
1028472 GCATGGTTTG
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
33 29 0.62
34 3 0.06
35 15 0.32
ACGTcount: A:0.21, C:0.32, G:0.26, T:0.21
Consensus pattern (35 bp):
GGGAACAGATTCCCCCTAGGAGGTATCGATTCCCC
Found at i:1028452 original size:18 final size:18
Alignment explanation
Indices: 1028379--1028454 Score: 61
Period size: 19 Copynumber: 4.2 Consensus size: 18
1028369 TACAGATTCC
* *
1028379 CCCCCAGGGGGAATAGATT
1 CCCCCA-GGGGTATCGATT
1028398 CCCCCTAGGAGGTATCGATT
1 CCCCC-AGG-GGTATCGATT
*
1028418 -CCCC--GGG-AACAGATT
1 CCCCCAGGGGTATC-GATT
1028433 CCCCCAGGGGTATCGATT
1 CCCCCAGGGGTATCGATT
1028451 CCCC
1 CCCC
1028455 GGGTACAGAT
Statistics
Matches: 46, Mismatches: 4, Indels: 15
0.71 0.06 0.23
Matches are distributed among these distances:
14 2 0.04
15 6 0.13
16 5 0.11
18 11 0.24
19 13 0.28
20 9 0.20
ACGTcount: A:0.21, C:0.34, G:0.26, T:0.18
Consensus pattern (18 bp):
CCCCCAGGGGTATCGATT
Found at i:1028609 original size:21 final size:21
Alignment explanation
Indices: 1028583--1028624 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1028573 ATTTGAATAT
*
1028583 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
1028604 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
1028625 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:1028926 original size:34 final size:32
Alignment explanation
Indices: 1028887--1028956 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
1028877 TTTTGTAAAG
* *
1028887 GGGAAATGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
1028921 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
1028953 GGGA
1 GGGA
1028957 GTTTGTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Done.