Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009605.1 Hibiscus syriacus cultivar Beakdansim tig00116989_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: 9158330
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 35
Found at i:1574346 original size:21 final size:21
Alignment explanation
Indices: 1574320--1574361 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1574310 TGTAAATCAA
1574320 TTGTACCATTTC-ATTTCAAAT
1 TTGTA-CATTTCTATTTCAAAT
*
1574341 TTGTACTTTTCTATTTCAAAT
1 TTGTACATTTCTATTTCAAAT
1574362 CATATCATCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.26, C:0.17, G:0.05, T:0.52
Consensus pattern (21 bp):
TTGTACATTTCTATTTCAAAT
Found at i:1582815 original size:6 final size:6
Alignment explanation
Indices: 1582804--1582828 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1582794 CTAGTAATGG
1582804 AGAAGC AGAAGC AGAAGC AGAAGC A
1 AGAAGC AGAAGC AGAAGC AGAAGC A
1582829 CGATTGAGTT
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:0.52, C:0.16, G:0.32, T:0.00
Consensus pattern (6 bp):
AGAAGC
Found at i:1584686 original size:14 final size:14
Alignment explanation
Indices: 1584667--1584694 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1584657 TGCGTGTGCA
1584667 CATGCGCATGCGCG
1 CATGCGCATGCGCG
1584681 CATGCGCATGCGCG
1 CATGCGCATGCGCG
1584695 TGTGTTCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.36, G:0.36, T:0.14
Consensus pattern (14 bp):
CATGCGCATGCGCG
Found at i:1586909 original size:26 final size:26
Alignment explanation
Indices: 1586880--1586936 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
1586870 CGAATTTCCT
1586880 TGATATGACAAACATCAATCAAGAAC
1 TGATATGACAAACATCAATCAAGAAC
*
1586906 TGATATGACACACATCAATCAAGAAC
1 TGATATGACAAACATCAATCAAGAAC
1586932 TGATA
1 TGATA
1586937 AGTTTTAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.21
Consensus pattern (26 bp):
TGATATGACAAACATCAATCAAGAAC
Found at i:1591716 original size:193 final size:192
Alignment explanation
Indices: 1591443--1591835 Score: 547
Period size: 193 Copynumber: 2.0 Consensus size: 192
1591433 ACATTTATAT
* ** *
1591443 ATAACGTCACTTATAATTAATATTCAATGACAACTAATTATGTCACTAAATTATGTAAAATTTTG
1 ATAACGTCACTTATAATTAATATTCAATGACAACTAATTACGTCACTAAATTAAATAAAATTTCG
* **
1591508 TTATTGATGATTTATATCGTCACGGATAATACATTAAAATCAACCAATATGTGACGAAAGAGATA
66 TTATTGATAATTTATATCGTCACAAATAATACATTAAAATCAACCAATATGTGACGAAAGAGATA
* *
1591573 TTGTCAAATTTTTAGTGACATAATATAAATATTACTTAATAATATTATGAATGACGTTTATGC
131 TTGTCAAATTTTTAGTGACATAATAT-AATATTACCTAATAATATTATGAATGACGATTATGC
* ** **
1591636 ATAACGTCACTTTATAATTTATATTTTATGACAGA-TGGTTACGTCACTAAATTAAATAAAA-TT
1 ATAACGTCAC-TTATAATTAATATTCAATGACA-ACTAATTACGTCACTAAATTAAATAAAATTT
* * **
1591699 CGTTATTGATAATTTATATTGTCACAAATAATGCATTAAAATCAACTTATATGTGACGAAAGAGA
64 CGTTATTGATAATTTATATCGTCACAAATAATACATTAAAATCAACCAATATGTGACGAAAGAGA
* * * *
1591764 TATTGTCACATTTTTAGTGACATAATATATTGTTACCTAATAATATTATGAATGATGATTATGC
129 TATTGTCAAATTTTTAGTGACATAATATAATATTACCTAATAATATTATGAATGACGATTATGC
1591828 ATAACGTC
1 ATAACGTC
1591836 GCCATATATA
Statistics
Matches: 176, Mismatches: 22, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
192 39 0.22
193 96 0.55
194 40 0.23
195 1 0.01
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (192 bp):
ATAACGTCACTTATAATTAATATTCAATGACAACTAATTACGTCACTAAATTAAATAAAATTTCG
TTATTGATAATTTATATCGTCACAAATAATACATTAAAATCAACCAATATGTGACGAAAGAGATA
TTGTCAAATTTTTAGTGACATAATATAATATTACCTAATAATATTATGAATGACGATTATGC
Found at i:1592761 original size:18 final size:19
Alignment explanation
Indices: 1592725--1592769 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
1592715 TATGATTTCA
**
1592725 AAAATAAAAATTACTCTTT
1 AAAATAAAAATTAAACTTT
1592744 AAAATAAAAA-TAAACTTT
1 AAAATAAAAATTAAACTTT
*
1592762 ATAATAAA
1 AAAATAAA
1592770 TATCAAAAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAATAAAAATTAAACTTT
Found at i:1594318 original size:13 final size:13
Alignment explanation
Indices: 1594300--1594324 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1594290 ATTATATAAG
1594300 TTCATGAATGTGT
1 TTCATGAATGTGT
1594313 TTCATGAATGTG
1 TTCATGAATGTG
1594325 ATTAAGGCCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.24, T:0.44
Consensus pattern (13 bp):
TTCATGAATGTGT
Found at i:1595048 original size:20 final size:20
Alignment explanation
Indices: 1595023--1595060 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1595013 AAATATAGAA
*
1595023 AATTTAGATAAATTAAAAAT
1 AATTTAAATAAATTAAAAAT
*
1595043 AATTTAAATAATTTAAAA
1 AATTTAAATAAATTAAAA
1595061 TAGTAAAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (20 bp):
AATTTAAATAAATTAAAAAT
Found at i:1595524 original size:16 final size:17
Alignment explanation
Indices: 1595486--1595525 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
1595476 AATAACCATA
1595486 TTAATTATATTTATTTC
1 TTAATTATATTTATTTC
1595503 TT-ATTATA-TTATTT-
1 TTAATTATATTTATTTC
1595517 TTAAATTAT
1 TT-AATTAT
1595526 TTAAAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 2 0.10
15 6 0.29
16 11 0.52
17 2 0.10
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (17 bp):
TTAATTATATTTATTTC
Found at i:1596217 original size:22 final size:22
Alignment explanation
Indices: 1596191--1596239 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
1596181 TAATTTATAT
1596191 TAATTTACCAACTATA-TTTAAA
1 TAATTTACCAA-TATACTTTAAA
**
1596213 TAATTTATTAATATACTTTAAA
1 TAATTTACCAATATACTTTAAA
1596235 TAATT
1 TAATT
1596240 CACTAACTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (22 bp):
TAATTTACCAATATACTTTAAA
Found at i:1596251 original size:22 final size:22
Alignment explanation
Indices: 1596203--1596253 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
1596193 ATTTACCAAC
* *
1596203 TATA-TTTAAATAATTTATTAA
1 TATACTTTAAATAATTCACTAA
1596224 TATACTTTAAATAATTCACTAA
1 TATACTTTAAATAATTCACTAA
1596246 CT-TACTTT
1 -TATACTTT
1596254 CTATATATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 4 0.15
22 21 0.81
23 1 0.04
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (22 bp):
TATACTTTAAATAATTCACTAA
Found at i:1608583 original size:56 final size:56
Alignment explanation
Indices: 1608405--1608667 Score: 359
Period size: 56 Copynumber: 4.7 Consensus size: 56
1608395 CCTGCTACCA
* * * * * *
1608405 ATACGGAAATTTATACACTTAGTATAAATTTCCT-AGTTTTGCATATATAGTGCCC
1 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCC
* * * *
1608460 ATACAGAAATTCATCAACTTAGTATGAATTTCTTAA-ATTTACACATAAAGTGCCC
1 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCC
** * * * *
1608515 ATACAAAAATTCATCTACTAAGTATGAATTTCTTAAGTTTTACACATATATTGCTC
1 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCC
1608571 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCC
1 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCC
*
1608627 ATACGAAAATTCATCCACTTAGTATGAATTTCTTAAGTTTT
1 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTT
1608668 TGCACACGTA
Statistics
Matches: 182, Mismatches: 24, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
55 76 0.42
56 106 0.58
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.37
Consensus pattern (56 bp):
ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCC
Found at i:1609143 original size:20 final size:20
Alignment explanation
Indices: 1609097--1609146 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1609087 TGTATTGAAT
* * *
1609097 GGTATCAATACTTTCCCTTT
1 GGTATCGATACTCTCCCTTC
1609117 GGTATCGATACTCTCCCTTC
1 GGTATCGATACTCTCCCTTC
1609137 GGTATCGATA
1 GGTATCGATA
1609147 TTGATTGAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.20, C:0.26, G:0.16, T:0.38
Consensus pattern (20 bp):
GGTATCGATACTCTCCCTTC
Found at i:1611948 original size:15 final size:15
Alignment explanation
Indices: 1611928--1611961 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1611918 AAAATGAGAA
1611928 AAAAGAAGAAAAAAT
1 AAAAGAAGAAAAAAT
* *
1611943 AAAAGAAGTAAAAGT
1 AAAAGAAGAAAAAAT
1611958 AAAA
1 AAAA
1611962 ATAAACAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (15 bp):
AAAAGAAGAAAAAAT
Found at i:1611975 original size:20 final size:21
Alignment explanation
Indices: 1611937--1611975 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
1611927 AAAAAGAAGA
* *
1611937 AAAAATAAAAGAAGTAAAAGT
1 AAAAATAAAACAAGAAAAAGT
1611958 AAAAAT-AAACAAGAAAAA
1 AAAAATAAAACAAGAAAAA
1611976 AGAATGAAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.77, C:0.03, G:0.10, T:0.10
Consensus pattern (21 bp):
AAAAATAAAACAAGAAAAAGT
Found at i:1612276 original size:23 final size:22
Alignment explanation
Indices: 1612247--1612293 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
1612237 AAATAATAGT
*
1612247 AATAATAAGTATTAAAATAA-AAA
1 AATAAT-AGTAAT-AAATAAGAAA
1612270 AATAATAGTAATAAATAAGAAA
1 AATAATAGTAATAAATAAGAAA
1612292 AA
1 AA
1612294 AACAGAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 6 0.27
22 10 0.45
23 6 0.27
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.23
Consensus pattern (22 bp):
AATAATAGTAATAAATAAGAAA
Found at i:1612303 original size:21 final size:21
Alignment explanation
Indices: 1612261--1612305 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1612251 ATAAGTATTA
* *
1612261 AAATAAAAAAATAATAGTAAT
1 AAATAAAAAAATAACAGAAAT
1612282 AAATAAGAAAAA-AACAGAAAT
1 AAATAA-AAAAATAACAGAAAT
1612303 AAA
1 AAA
1612306 AGAAATTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.16
Consensus pattern (21 bp):
AAATAAAAAAATAACAGAAAT
Found at i:1612344 original size:2 final size:2
Alignment explanation
Indices: 1612337--1612371 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1612327 TATCAAAGTA
1612337 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1612372 AATAAAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1612413 original size:22 final size:22
Alignment explanation
Indices: 1612371--1612421 Score: 52
Period size: 23 Copynumber: 2.2 Consensus size: 22
1612361 ATATATATAT
1612371 AAATAAAAAAATAAAGTATAAAT-G
1 AAAT-AAAAAATAAAG-AT-AATGG
1612395 AAATAAAAAATAATA-ATAATGG
1 AAATAAAAAATAA-AGATAATGG
1612417 AAATA
1 AAATA
1612422 TAAGTAAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
21 3 0.12
22 8 0.32
23 9 0.36
24 5 0.20
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.22
Consensus pattern (22 bp):
AAATAAAAAATAAAGATAATGG
Found at i:1613767 original size:33 final size:34
Alignment explanation
Indices: 1613691--1613776 Score: 129
Period size: 34 Copynumber: 2.5 Consensus size: 34
1613681 AACTCGAGGG
* *
1613691 TTTGTTGTTTTAAGAGAAATATTTTCAAAGGTTTT
1 TTTG-TGTTTCAAGAGAAATAATTTCAAAGGTTTT
*
1613726 TTTTTGTTTCAAGAGAAATAATTTCAAAGG-TTT
1 TTTGTGTTTCAAGAGAAATAATTTCAAAGGTTTT
1613759 TTTGTGTTTCAAGAGAAA
1 TTTGTGTTTCAAGAGAAA
1613777 CTGTATTCAA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
33 20 0.43
34 24 0.51
35 3 0.06
ACGTcount: A:0.31, C:0.05, G:0.17, T:0.47
Consensus pattern (34 bp):
TTTGTGTTTCAAGAGAAATAATTTCAAAGGTTTT
Found at i:1613786 original size:34 final size:33
Alignment explanation
Indices: 1613691--1613788 Score: 108
Period size: 34 Copynumber: 2.8 Consensus size: 33
1613681 AACTCGAGGG
* *
1613691 TTTGTTGTTTTAAGAGAAATATTTTCAAAGGTTTT
1 TTTG-TGTTTCAAGAGAAAT-TATTCAAAGGTTTT
* *
1613726 TTTTTGTTTCAAGAGAAATAATTTCAAAGG-TTT
1 TTTGTGTTTCAAGAGAAATTA-TTCAAAGGTTTT
1613759 TTTGTGTTTCAAGAGAAACTGTATTCAAAG
1 TTTGTGTTTCAAGAGAAA-T-TATTCAAAG
1613789 ATTGAAGTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
33 20 0.37
34 30 0.56
35 4 0.07
ACGTcount: A:0.32, C:0.06, G:0.17, T:0.45
Consensus pattern (33 bp):
TTTGTGTTTCAAGAGAAATTATTCAAAGGTTTT
Found at i:1614033 original size:102 final size:102
Alignment explanation
Indices: 1613910--1614277 Score: 386
Period size: 102 Copynumber: 3.6 Consensus size: 102
1613900 AAGGAAACTA
* * * *
1613910 TTTTCAAAGTTTATGCTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTATGTTTCAAGGGAAGC
1 TTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTATGTTTCAAGGGAACC
* * * *
1613975 TATCTCATGAGTGACAAAATTCATTTTAAGGGAAATG
66 TATCTCAAGAGAGACAAAATTCATCTCAAGGGAAATG
* *
1614012 TTTTCAATGTTTATGTTTCAAGAGAACCTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAACC
1 TTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTATGTTTCAAGGGAACC
*
1614077 TATCTCAAGGGAGACAAAATTCATCTCAAGGGAAATG
66 TATCTCAAGAGAGACAAAATTCATCTCAAGGGAAATG
* * * **
1614114 TTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGTGACAAAACTTA-G-TTCTAAAAGAA
1 TTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTATGTTTC-AAGGGAA
** * * * ** * **
1614177 AATGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAACA
64 CCTATCTCAAGAGAGACAAAATTCATCTCAAGGGAAATG
* * * * *
1614216 TATTCAAAGATTT-TGTTTCAAGAGAAACTATCTCAAGAGAGATAAAATTCA--TTTCAAGGGAA
1 TTTTCAATG-TTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT-ATGTTTCAAGGGAA
1614278 ATGTTTTCAA
Statistics
Matches: 228, Mismatches: 33, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
101 10 0.04
102 213 0.93
103 5 0.02
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (102 bp):
TTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTATGTTTCAAGGGAACC
TATCTCAAGAGAGACAAAATTCATCTCAAGGGAAATG
Found at i:1614076 original size:37 final size:37
Alignment explanation
Indices: 1614025--1614097 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
1614015 TCAATGTTTA
*
1614025 TGTTTCAAGAGAACCTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGAGAACCTATCTCAAGGGAGACAAAATTT
*
1614062 TGTTTCAAGGGAACCTATCTCAAGGGAGACAAAATT
1 TGTTTCAAGAGAACCTATCTCAAGGGAGACAAAATT
1614098 CATCTCAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (37 bp):
TGTTTCAAGAGAACCTATCTCAAGGGAGACAAAATTT
Found at i:1614277 original size:65 final size:66
Alignment explanation
Indices: 1614181--1614343 Score: 170
Period size: 65 Copynumber: 2.5 Consensus size: 66
1614171 AAAGAAAATG
* * *
1614181 TCTCAAGGGAGACGAAATTT-GTTTCAAGGGAAACATATTCAAAGATTT-TGTTTCAAGAGAAAC
1 TCTCAAGAGAGACAAAATTTCATTTCAAGGGAAACATATTCAAAG-TTTATGTTTCAAGAGAAAC
1614244 TA
65 TA
* ** * * **
1614246 TCTCAAGAGAGATAAAA-TTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCATTAGAAACT
1 TCTCAAGAGAGACAAAATTTCATTTCAAGGGAAACATATTCAAAGTTTATGTTTCAAGAGAAACT
*
1614310 G
66 A
* **
1614311 TCTCAAGGGAGACAAAATTTTGTTTCAAGGGAA
1 TCTCAAGAGAGACAAAATTTCATTTCAAGGGAA
1614344 CCTATCTCAA
Statistics
Matches: 80, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
64 5 0.06
65 62 0.77
66 13 0.16
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.32
Consensus pattern (66 bp):
TCTCAAGAGAGACAAAATTTCATTTCAAGGGAAACATATTCAAAGTTTATGTTTCAAGAGAAACT
A
Found at i:1614277 original size:269 final size:267
Alignment explanation
Indices: 1613952--1614476 Score: 861
Period size: 269 Copynumber: 2.0 Consensus size: 267
1613942 TCAAGGGAGA
* * * * *
1613952 CAAAATTATGTTTCAAGGGAAGCTATCTCATGAGTGACAAAATTCATTTTAAGGGAAATGTTTTC
1 CAAAATTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTC
*
1614017 AATGTTTATGTTTCAAGAGAACCTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAACCTATCT
66 AATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAACCTATCT
*
1614082 CAAGGGAGACAAAATTCATCTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCT
131 CAAGAGAGACAAAATTCATCTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCT
* * *
1614147 CAAGAGTGACAAAACTTAGTTCTAAAAGAAAATGTCTCAAGGGAGACGAAATTTGTTTCAAGGGA
196 CAAGAGAGACAAAACCTAGTTCTAAAAGAAAATGTCTAAAGGGAGACG-AATTTGTTTCAAGGGA
1614212 AACATATT
260 AACATATT
* *
1614220 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGATAAAATTCATTTCAAGGGAAATGTTTT
1 CAAA-ATTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTT
**
1614285 CAATGTTTATGTTTCATTAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAACCTATC
65 CAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAACCTATC
* * * *
1614350 TCAAGAGAGACAAAATTCATTTCAAGGGAAATTTTTTCAATTTTTATGTTTCAAGAGAAACTGTC
130 TCAAGAGAGACAAAATTCATCTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATC
*
1614415 TCAAGAGAGACGAAACCTAGTTCTAAAAGAAAATGTCTAAAGGGAGACGAATTTGTTTCAAG
195 TCAAGAGAGACAAAACCTAGTTCTAAAAGAAAATGTCTAAAGGGAGACGAATTTGTTTCAAG
1614477 AGAGACAAAA
Statistics
Matches: 237, Mismatches: 19, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
268 17 0.07
269 220 0.93
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (267 bp):
CAAAATTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTC
AATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAACCTATCT
CAAGAGAGACAAAATTCATCTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCT
CAAGAGAGACAAAACCTAGTTCTAAAAGAAAATGTCTAAAGGGAGACGAATTTGTTTCAAGGGAA
ACATATT
Found at i:1614331 original size:102 final size:103
Alignment explanation
Indices: 1614220--1614425 Score: 333
Period size: 102 Copynumber: 2.0 Consensus size: 103
1614210 GAAACATATT
*
1614220 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGATAAAATTCATTTCAAGGGAAATGTTTT
1 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTT
** *
1614285 CAATGTTTATGTTTCATTAGAAACTGTCTCAAGGGAGA
66 CAATGTTTATGTTTCAAGAGAAACTGTCTCAAGAGAGA
* * *
1614323 CAAA-ATTTTGTTTCAAGGGAACCTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATTTTTT
1 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTT
*
1614387 CAATTTTTATGTTTCAAGAGAAACTGTCTCAAGAGAGA
66 CAATGTTTATGTTTCAAGAGAAACTGTCTCAAGAGAGA
1614425 C
1 C
1614426 GAAACCTAGT
Statistics
Matches: 95, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
102 91 0.96
103 4 0.04
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (103 bp):
CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTT
CAATGTTTATGTTTCAAGAGAAACTGTCTCAAGAGAGA
Found at i:1614354 original size:167 final size:166
Alignment explanation
Indices: 1614054--1614425 Score: 467
Period size: 167 Copynumber: 2.2 Consensus size: 166
1614044 TCAAGGGAGA
* * *
1614054 CAAAATTTTGTTTCAAGGGAACCTATCTCAAGGGAGACAAAATTCATCTCAAGGGAAATGTTTTC
1 CAAAATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATCTCAAGGGAAATGTTTTC
* *
1614119 AATGTTTATGTTTCAAGAGAAACTATCTCAAGAGTGACAAAACTTAGTTCTAAAAGAAAATGTCT
66 AATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCTAAAAGAAAATATCT
* * **
1614184 CAAGGGAGACGAAATTTGTTTCAAGGGAAACATATT
131 CAAGAGAGACAAAATTCATTTCAAGGGAAACATATT
* *
1614220 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGATAAAATTCATTTCAAGGGAAATGTTTT
1 CAAA-ATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATCTCAAGGGAAATGTTTT
** * * * * ** **
1614285 CAATGTTTATGTTTCATTAGAAACTGTCTCAAGGGAGACAAAATTTTGTT-TCAAGGGAACCTAT
65 CAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCT-AAAAGAAAATAT
** *
1614349 CTCAAGAGAGACAAAATTCATTTCAAGGGAAATTTTTT
129 CTCAAGAGAGACAAAATTCATTTCAAGGGAAACATATT
** *
1614387 CAATTTTTATGTTTCAAGAGAAACTGTCTCAAGAGAGAC
1 CAAAATTT-TGTTTCAAGAGAAACTATCTCAAGAGAGAC
1614426 GAAACCTAGT
Statistics
Matches: 175, Mismatches: 28, Indels: 5
0.84 0.13 0.02
Matches are distributed among these distances:
166 8 0.05
167 167 0.95
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (166 bp):
CAAAATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATCTCAAGGGAAATGTTTTC
AATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCTAAAAGAAAATATCT
CAAGAGAGACAAAATTCATTTCAAGGGAAACATATT
Found at i:1614462 original size:102 final size:102
Alignment explanation
Indices: 1614230--1614462 Score: 270
Period size: 102 Copynumber: 2.3 Consensus size: 102
1614220 CAAAGATTTT
* * * *
1614230 GTTTCAAGAGAAACTATCTCAAGAGAGATAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTAT
1 GTTTCAAAAGAAAATATCTAAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTAT
** * ** *
1614295 GTTTCATTAGAAACTGTCTCAAGGGAGACAAAATTTT
66 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACCTA
** ** * * *
1614332 GTTTCAAGGGAACCTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATTTTTTCAATTTTTAT
1 GTTTCAAAAGAAAATATCTAAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTAT
*
1614397 GTTTCAAGAGAAACTGTCTCAAGAGAGACGAAACCTA
66 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACCTA
* *
1614434 G-TTCTAAAAGAAAATGTCTAAAGGGAGAC
1 GTTTC-AAAAGAAAATATCTAAAGAGAGAC
1614463 GAATTTGTTT
Statistics
Matches: 111, Mismatches: 19, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
101 3 0.03
102 108 0.97
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.30
Consensus pattern (102 bp):
GTTTCAAAAGAAAATATCTAAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTAT
GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACCTA
Found at i:1614629 original size:72 final size:74
Alignment explanation
Indices: 1614505--1614647 Score: 202
Period size: 72 Copynumber: 1.9 Consensus size: 74
1614495 AAAAAACAGT
* *
1614505 CTTGAGTGAAATGAAATGCCTTCTTTTGAGTGAAAACGGTCTCAAGTGAGACAAAGTCTGTTTTA
1 CTTGAGTGAAATGAAAT-CCTTCTTTCGAGTGAAAAC-GTCTCAAGTGAGACAAAGTATGTTTTA
1614570 AGAAAAGCAAA
64 AGAAAAGCAAA
* *
1614581 CTTGAGTGAAAT-AAAT-CTTCTTTCGAGTAGAACAC-TGTCAAGTGAGACAAAGTATGTTTTAA
1 CTTGAGTGAAATGAAATCCTTCTTTCGAGT-GAAAACGTCTCAAGTGAGACAAAGTATGTTTTAA
1614643 GAAAA
65 GAAAA
1614648 ACAATCTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
72 30 0.48
73 11 0.18
74 5 0.08
75 4 0.06
76 12 0.19
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.29
Consensus pattern (74 bp):
CTTGAGTGAAATGAAATCCTTCTTTCGAGTGAAAACGTCTCAAGTGAGACAAAGTATGTTTTAAG
AAAAGCAAA
Found at i:1615894 original size:17 final size:17
Alignment explanation
Indices: 1615872--1615911 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
1615862 ATTGCCAAGT
1615872 GTTTGAGCAATATCATG
1 GTTTGAGCAATATCATG
1615889 GTTTGAGCAATATCATG
1 GTTTGAGCAATATCATG
1615906 GTTTGA
1 GTTTGA
1615912 ATTTAATCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.28, C:0.10, G:0.25, T:0.38
Consensus pattern (17 bp):
GTTTGAGCAATATCATG
Found at i:1618383 original size:64 final size:63
Alignment explanation
Indices: 1618279--1618418 Score: 151
Period size: 64 Copynumber: 2.2 Consensus size: 63
1618269 TTGTTTAAGG
* * *
1618279 TGCATCGATGCACATGAAGTGCATCGATGCATTAATTTAAAAAGAAAACATCGAATACA-ATCGA
1 TGCATCGATGCATAAGAAGTGCATCGATGCACTAATTTAAAAA-AAAACATCGAATA-AGATCGA
* * * **
1618343 TGCATCGATGCATAAGGAGTGCATCGATGCACCCT-A-TTAAATACAAACATCGAATAAGATTTA
1 TGCATCGATGCATAAGAAGTGCATCGATGCA--CTAATTTAAAAAAAAACATCGAATAAGATCGA
1618406 TGCATCGATGCAT
1 TGCATCGATGCAT
1618419 GGTGTAATGC
Statistics
Matches: 65, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
62 1 0.02
63 28 0.43
64 34 0.52
65 1 0.02
66 1 0.02
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.25
Consensus pattern (63 bp):
TGCATCGATGCATAAGAAGTGCATCGATGCACTAATTTAAAAAAAAACATCGAATAAGATCGA
Found at i:1619051 original size:103 final size:103
Alignment explanation
Indices: 1618872--1619197 Score: 598
Period size: 103 Copynumber: 3.2 Consensus size: 103
1618862 GTAGAGGGTC
*
1618872 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTTTTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
1618937 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
*
1618975 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAATAGGTGTGAGGTCTGTTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
1619040 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
* * *
1619078 TATGTGGTCATTCGGGACATATATGTATTCTTTAGAACATGTGTGAGGTCTGTTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
1619143 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
*
1619181 TATGTGGTCCTTAGGGA
1 TATGTGGTCCTTCGGGA
1619198 TAACTTTATA
Statistics
Matches: 215, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 215 1.00
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:1619235 original size:23 final size:23
Alignment explanation
Indices: 1619209--1619263 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
1619199 AACTTTATAT
* * *
1619209 GGCACTTCGGTGCATTTCTATGC
1 GGCACTTCGGTACAATTCTACGC
* *
1619232 GGCACTACGGTACAATTCTACGT
1 GGCACTTCGGTACAATTCTACGC
1619255 GGCACTTCG
1 GGCACTTCG
1619264 TTGTATTTAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.18, C:0.27, G:0.25, T:0.29
Consensus pattern (23 bp):
GGCACTTCGGTACAATTCTACGC
Found at i:1626152 original size:103 final size:103
Alignment explanation
Indices: 1625973--1626298 Score: 580
Period size: 103 Copynumber: 3.2 Consensus size: 103
1625963 GTAGAGGGTC
*
1625973 TATGTGGTCCTTCGGGACATATATGTATTCTTTAGAACAGGTGTGAGGTCTGTTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
*
1626038 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATAA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
*
1626076 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCCGTTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
1626141 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
*
1626179 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAAGTCTGTTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
*
1626244 TTGATCTTTGGCATATGTATATGATTATTAAGGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
* * *
1626282 TATATGGTTCTTAGGGA
1 TATGTGGTCCTTCGGGA
1626299 TAACTTTATA
Statistics
Matches: 214, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 214 1.00
ACGTcount: A:0.26, C:0.12, G:0.25, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:1626346 original size:23 final size:23
Alignment explanation
Indices: 1626310--1626377 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 23
1626300 AACTTTATAT
* * *
1626310 GGAACTTCGATGCATTTCTATGC
1 GGAACTACGGTGCATTTCTACGC
* * *
1626333 GGCACTACGGTGCAATTCTACGT
1 GGAACTACGGTGCATTTCTACGC
* *
1626356 GGAACTTCGGTGCATTTATACG
1 GGAACTACGGTGCATTTCTACG
1626378 AGCTGTGGTG
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (23 bp):
GGAACTACGGTGCATTTCTACGC
Found at i:1631106 original size:14 final size:14
Alignment explanation
Indices: 1631089--1631127 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1631079 TAAAAGAAGT
1631089 AAAAGTAAAAAGAA
1 AAAAGTAAAAAGAA
*
1631103 AAAAGAAAAAAGAA
1 AAAAGTAAAAAGAA
**
1631117 TGAAGTAAAAA
1 AAAAGTAAAAA
1631128 ATCTAATAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (14 bp):
AAAAGTAAAAAGAA
Found at i:1636268 original size:28 final size:28
Alignment explanation
Indices: 1636185--1636270 Score: 70
Period size: 28 Copynumber: 3.1 Consensus size: 28
1636175 CATACGGAAA
1636185 TTCATCCACTTAGTATGAATTTCTTAAG
1 TTCATCCACTTAGTATGAATTTCTTAAG
* * * * * *
1636213 TT-TTACACATA-TAGTG-CTCATACGTAAG
1 TTCATCCACTTAGTA-TGAAT--TTCTTAAG
1636241 TTCATCCACTTAGTATGAATTTCTTAAG
1 TTCATCCACTTAGTATGAATTTCTTAAG
1636269 TT
1 TT
1636271 TTACACATAT
Statistics
Matches: 40, Mismatches: 12, Indels: 12
0.62 0.19 0.19
Matches are distributed among these distances:
26 3 0.08
27 8 0.20
28 18 0.45
29 8 0.20
30 3 0.08
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (28 bp):
TTCATCCACTTAGTATGAATTTCTTAAG
Found at i:1636340 original size:56 final size:56
Alignment explanation
Indices: 1635848--1636327 Score: 702
Period size: 56 Copynumber: 8.6 Consensus size: 56
1635838 ACCAATACAG
* * * *
1635848 AAATTTATACACTTAGTATAAATTTCCT-AGTTTTACACATATAGTGCCCATAC-A
1 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCCATACGA
* * * *
1635902 TAAATTCATCCACTTAGTATGAATTTCATAA-ATTTACACATAAAGAGCCCATAC-A
1 -AAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCCATACGA
*
1635957 GAAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCCATA-AA
1 -AAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCCATACGA
* *
1636013 GAAATTCATCCACTTAGTATGAATTCCTTAAGTTTTACACATATAGTGCCCATACGG
1 -AAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCCATACGA
*
1636070 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCCATATGA
1 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCCATACGA
* * *
1636126 AAATTAATCCACTGAGTATGAATTTCTTAAGTTTTACACATATAGTGCCCATACGG
1 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCCATACGA
* *
1636182 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCTCATACGT
1 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCCATACGA
*
1636238 AAGTTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAGTG-CCATACGA
1 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCCATACGA
* * *
1636293 AAATTTATCTACTTAGTATGAATTTATTAAGTTTT
1 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTT
1636328 TGCACACTTA
Statistics
Matches: 388, Mismatches: 33, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
55 111 0.29
56 277 0.71
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.37
Consensus pattern (56 bp):
AAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCCATACGA
Found at i:1636772 original size:20 final size:20
Alignment explanation
Indices: 1636733--1636769 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1636723 CTGTTTTGAA
*
1636733 TGGTATCAATACCTTCCCTT
1 TGGTATCAATACCTCCCCTT
1636753 TGGTATCAATA-CTCCCC
1 TGGTATCAATACCTCCCC
1636770 CTTCAGTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.22, C:0.32, G:0.11, T:0.35
Consensus pattern (20 bp):
TGGTATCAATACCTCCCCTT
Found at i:1640599 original size:3 final size:3
Alignment explanation
Indices: 1640591--1640637 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
1640581 AATATTTACC
1640591 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1640638 ATATATTATT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1652024 original size:21 final size:24
Alignment explanation
Indices: 1651996--1652054 Score: 88
Period size: 21 Copynumber: 2.6 Consensus size: 24
1651986 AAACTGAAGG
*
1651996 AGTAGTATCGGTACTAC-ACTT-C
1 AGTAGTATCGGTACTACTACTTAA
1652018 A-TAGTATCGGTACTACTACTTAA
1 AGTAGTATCGGTACTACTACTTAA
1652041 AGTAGTATCGGTAC
1 AGTAGTATCGGTAC
1652055 AATGTATAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
21 15 0.45
22 5 0.15
23 1 0.03
24 12 0.36
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Consensus pattern (24 bp):
AGTAGTATCGGTACTACTACTTAA
Found at i:1664018 original size:30 final size:30
Alignment explanation
Indices: 1663982--1664082 Score: 118
Period size: 30 Copynumber: 3.5 Consensus size: 30
1663972 ATCCCCACGA
* *
1663982 TATTATCCTCCTTCGCAACCCAAGCCACAG
1 TATTATCCTCCTTCGCAACCCGAGCCGCAG
*
1664012 TATTATCCT-C--CGCAATCCGAGCCGCAG
1 TATTATCCTCCTTCGCAACCCGAGCCGCAG
* * *
1664039 TATTTTCCTCCTCCGCAACCTGAGCCGCAG
1 TATTATCCTCCTTCGCAACCCGAGCCGCAG
*
1664069 TATTATCCACCTTC
1 TATTATCCTCCTTC
1664083 ACAAGATCGT
Statistics
Matches: 59, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
27 22 0.37
28 1 0.02
29 1 0.02
30 35 0.59
ACGTcount: A:0.22, C:0.39, G:0.13, T:0.27
Consensus pattern (30 bp):
TATTATCCTCCTTCGCAACCCGAGCCGCAG
Found at i:1664034 original size:27 final size:26
Alignment explanation
Indices: 1663990--1664076 Score: 84
Period size: 27 Copynumber: 3.1 Consensus size: 26
1663980 GATATTATCC
* * *
1663990 TCCTTCGCAACCCAAGCCACAGTATTA
1 TCCTCCGCAA-CCGAGCCGCAGTATTA
*
1664017 TCCTCCGCAATCCGAGCCGCAGTATTTTCC
1 TCCTCCGCAA-CCGAGCCGCAGTA--TT-A
1664047 TCCTCCGCAACCTGAGCCGCAGTATTA
1 TCCTCCGCAACC-GAGCCGCAGTATTA
1664074 TCC
1 TCC
1664077 ACCTTCACAA
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
27 23 0.46
28 2 0.04
29 4 0.08
30 21 0.42
ACGTcount: A:0.22, C:0.39, G:0.15, T:0.24
Consensus pattern (26 bp):
TCCTCCGCAACCGAGCCGCAGTATTA
Found at i:1675271 original size:23 final size:23
Alignment explanation
Indices: 1675245--1675292 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
1675235 ATAAAATACA
*
1675245 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
** *
1675268 ATAATGTAATAGGTAGTGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
1675291 AT
1 AT
1675293 TTACCTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:1675739 original size:22 final size:23
Alignment explanation
Indices: 1675711--1675772 Score: 90
Period size: 22 Copynumber: 2.7 Consensus size: 23
1675701 ATATAACCAC
1675711 TACCTATTACATTATATAA-AGA
1 TACCTATTACATTATATAAGAGA
* *
1675733 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAGAGA
*
1675756 TACCTATTACATCATAT
1 TACCTATTACATTATAT
1675773 TTTTACCTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
22 19 0.53
23 17 0.47
ACGTcount: A:0.39, C:0.19, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAGAGA
Found at i:1675763 original size:23 final size:22
Alignment explanation
Indices: 1675701--1675772 Score: 90
Period size: 23 Copynumber: 3.2 Consensus size: 22
1675691 ACACTTTACA
*
1675701 ATATAACCACTACCTATTACATT
1 ATATAA-CGCTACCTATTACATT
* *
1675724 ATATAAAGATACCTATTACATT
1 ATATAACGCTACCTATTACATT
*
1675746 ATATAAGCGCTACCTATTACATC
1 ATATAA-CGCTACCTATTACATT
1675769 ATAT
1 ATAT
1675773 TTTTACCTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
22 19 0.45
23 23 0.55
ACGTcount: A:0.40, C:0.21, G:0.04, T:0.35
Consensus pattern (22 bp):
ATATAACGCTACCTATTACATT
Found at i:1676248 original size:39 final size:39
Alignment explanation
Indices: 1676194--1676277 Score: 141
Period size: 39 Copynumber: 2.2 Consensus size: 39
1676184 AAGTTGTAGA
*
1676194 TTTGATTTCCTTTTGCTTGGCATCATATGAGATTTGAAT
1 TTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGAAT
* *
1676233 TTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTGGAT
1 TTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGAAT
1676272 TTTGAT
1 TTTGAT
1676278 GAGCATCGGA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.18, C:0.14, G:0.19, T:0.49
Consensus pattern (39 bp):
TTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGAAT
Found at i:1676553 original size:18 final size:18
Alignment explanation
Indices: 1676530--1676566 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1676520 GCCGAAATAT
1676530 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
1676548 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
1676566 A
1 A
1676567 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:1677029 original size:23 final size:23
Alignment explanation
Indices: 1677002--1677060 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
1676992 ATATAAACGA
* *
1677002 ATTACATTATATAAGCGCTACCT
1 ATTACATTATATAAACGATACCT
1677025 ATTACATTATATAAACGATACCT
1 ATTACATTATATAAACGATACCT
1677048 ATTACATTATATA
1 ATTACATTATATA
1677061 CTTATAGTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.37
Consensus pattern (23 bp):
ATTACATTATATAAACGATACCT
Found at i:1680167 original size:182 final size:183
Alignment explanation
Indices: 1679539--1680563 Score: 1882
Period size: 182 Copynumber: 5.6 Consensus size: 183
1679529 ACACATTTTA
* *
1679539 GACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAA
1 GACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATACA
*
1679604 ACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATG
66 ACCGGTATATTTATACCTGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATG
*
1679669 TGTAAATGTCGACACTTTTTTAAATCGTATCGACATATTTTTCTTCCAATATG
131 TGTAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATG
1679722 GACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATACA
1 GACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATACA
*
1679787 ACCGGTATATTTATACATGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATG
66 ACCGGTATATTTATACCTGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATG
1679852 TGTAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATG
131 TGTAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATG
1679905 GACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATACA
1 GACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATACA
*
1679970 ACAGGTATA-TTATACCTGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATG
66 ACCGGTATATTTATACCTGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATG
1680034 TGTAAATGTCGACAC-TTTTTAAATCGTATCGACACATTTTTCTTCCAATATG
131 TGTAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATG
1680086 GACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATACA
1 GACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATACA
1680151 ACCGGTATATTTATACCTGTTATATTAC-AAATTATCTATTACATTATAATTATGGGTTCCGATG
66 ACCGGTATATTTATACCTGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATG
1680215 TGTAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATG
131 TGTAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATG
*
1680268 GACATAAAGTACCGACACAATATTTAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATACA
1 GACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATACA
1680333 ACCGGTATATTTATACCTGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATG
66 ACCGGTATATTTATACCTGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATG
1680398 TGT-AATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATG
131 TGTAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATG
* *
1680450 GACATAAAGTACCGACACAATATTAAAAAGTGTCGATATA-GTTGTAGACCTATTCGCGCATAAA
1 GACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATACA
* * * * *
1680514 ACCGGTATATTTATACCGGTTATATTGCAAATTTACCTATT-TATTATAAT
66 ACCGGTATATTTATACCTGTTATATTACAAAATTATCTATTACATTATAAT
1680564 ATGTTGAAAG
Statistics
Matches: 822, Mismatches: 17, Indels: 9
0.97 0.02 0.01
Matches are distributed among these distances:
180 8 0.01
181 220 0.27
182 304 0.37
183 290 0.35
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (183 bp):
GACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATACA
ACCGGTATATTTATACCTGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATG
TGTAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATG
Found at i:1682542 original size:391 final size:393
Alignment explanation
Indices: 1681821--1683088 Score: 2417
Period size: 391 Copynumber: 3.2 Consensus size: 393
1681811 TTTAAATTAG
1681821 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1681886 ATTGTACCGGTTAGATTGAAAAATTACATA-TACATTATACTTTGGGTTCGATGATTTTGGGATC
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTGGGTTCGATGATTTTGGGATC
1681950 GACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATAA
131 GACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATAA
1682015 ATATCGACAC-AACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTAT
196 ATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTAT
1682079 AATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
261 AATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
1682144 TCGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAAT
326 TCGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAAT
1682209 AAA
391 AAA
1682212 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1682277 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTGGGTTCGATGATTTTGGGATC
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTGGGTTCGATGATTTTGGGATC
1682342 GACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTG-TTTCCATTCATTCTGGAAATAA
131 GACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATAA
1682406 ATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTAT
196 ATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTAT
1682471 AATTGTACCGGTTAGA-TGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
261 AATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
1682535 TCGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAAT
326 TCGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAAT
1682600 AAA
391 AAA
1682603 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
*
1682668 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTTGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATAC-TTTGGGTTCGATGATTTTGGGAT
1682733 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAT
130 CGACACTTTTTATATATGGATCGACACTTTAT-GGTGCACCCTGTTTTCCATTCATTCTGGAAAT
1682798 AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGT
194 AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGT
1682863 ATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
259 ATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
1682928 GATCGACAC-TTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGA
324 GATCGACACTTTTTATATATGGATCGACACTTTAT-GGTGCACCCTGTTTTCCATTCATTCTGGA
1682992 AA-AAA
388 AATAAA
* **
1682997 AATCGACACAAACTATA-TAGTGTCGACACATTATTTAGACATATTCTCACAT-AAATTGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1683060 ATTGTACCGGTTAGATTGAAAAATTACAT
66 ATTGTACCGGTTAGATTGAAAAATTACAT
1683089 CCTTTTGGCC
Statistics
Matches: 866, Mismatches: 4, Indels: 13
0.98 0.00 0.01
Matches are distributed among these distances:
391 349 0.40
392 238 0.27
393 46 0.05
394 147 0.17
395 86 0.10
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (393 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTGGGTTCGATGATTTTGGGATC
GACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATAA
ATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTAT
AATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
TCGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAAT
AAA
Found at i:1682943 original size:197 final size:197
Alignment explanation
Indices: 1681821--1683088 Score: 2412
Period size: 196 Copynumber: 6.5 Consensus size: 197
1681811 TTTAAATTAG
1681821 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1681886 ATTGTACCGGTTAGATTGAAAAATTACATA-TACATTATAC-TTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
1681949 CGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATA
131 CGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATA
1682014 AA
196 AA
1682016 TATCGACAC-AACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1682080 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
1682145 CGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATA
131 CGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATA
1682210 AA
196 AA
1682212 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1682277 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATAC-TTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
1682341 CGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTG-TTTCCATTCATTCTGGAAATA
131 CGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATA
1682405 AA
196 AA
1682407 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1682472 ATTGTACCGGTTAGA-TGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
1682536 CGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATA
131 CGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATA
1682601 AA
196 AA
1682603 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
*
1682668 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTTGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
1682733 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAT
131 CGACACTTTTTATATATGGATCGACACTTTAT-GGTGCACCCTGTTTTCCATTCATTCTGGAAAT
1682798 AAA
195 AAA
1682801 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1682866 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
1682931 CGACAC-TTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAA-
131 CGACACTTTTTATATATGGATCGACACTTTAT-GGTGCACCCTGTTTTCCATTCATTCTGGAAAT
1682994 AAA
195 AAA
* **
1682997 AATCGACACAAACTATA-TAGTGTCGACACATTATTTAGACATATTCTCACAT-AAATTGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1683060 ATTGTACCGGTTAGATTGAAAAATTACAT
66 ATTGTACCGGTTAGATTGAAAAATTACAT
1683089 CCTTTTGGCC
Statistics
Matches: 1061, Mismatches: 5, Indels: 15
0.98 0.00 0.01
Matches are distributed among these distances:
194 148 0.14
195 223 0.21
196 287 0.27
197 233 0.22
198 170 0.16
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (197 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAATA
AA
Found at i:1683256 original size:19 final size:19
Alignment explanation
Indices: 1683210--1683258 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
1683200 TTATATTCAC
*
1683210 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
1683229 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
1683248 ATACAAAATTA
1 ATACAAAATTA
1683259 ACCCTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:1687438 original size:17 final size:18
Alignment explanation
Indices: 1687416--1687457 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 18
1687406 ATATATCCGG
1687416 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
1687433 TATCATTTGATACCGGTTT
1 TATCATTT-ATACCGGTTT
1687452 TATCAT
1 TATCAT
1687458 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 8 0.35
19 15 0.65
ACGTcount: A:0.21, C:0.17, G:0.12, T:0.50
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:1687475 original size:20 final size:19
Alignment explanation
Indices: 1687421--1687466 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
1687411 TCCGGTATCA
1687421 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
**
1687440 TGATACCGGTTTTATCATAT
1 TTTTACCGGTTTTATCAT-T
1687460 TTTTACC
1 TTTTACC
1687467 TGTTATATCG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.20, C:0.17, G:0.11, T:0.52
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:1687614 original size:20 final size:20
Alignment explanation
Indices: 1687588--1687633 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
1687578 CACTTTTAAA
1687588 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
1687607 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
1687628 TTTACC
1 TTTACC
1687634 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:1688309 original size:17 final size:17
Alignment explanation
Indices: 1688261--1688300 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
1688251 GGATAGATAC
1688261 TTACCGATAACCAAAGT
1 TTACCGATAACCAAAGT
1688278 TTACCGATAACCAAAGT
1 TTACCGATAACCAAAGT
1688295 TTACCG
1 TTACCG
1688301 GTTACCAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (17 bp):
TTACCGATAACCAAAGT
Found at i:1689445 original size:30 final size:30
Alignment explanation
Indices: 1689409--1689509 Score: 118
Period size: 30 Copynumber: 3.5 Consensus size: 30
1689399 ATCCCCACGA
* *
1689409 TATTATCCTCCTTCGCAACCCAAGCCACAG
1 TATTATCCTCCTTCGCAACCCGAGCCGCAG
*
1689439 TATTATCCT-C--CGCAATCCGAGCCGCAG
1 TATTATCCTCCTTCGCAACCCGAGCCGCAG
* * *
1689466 TATTTTCCTCCTCCGCAACCTGAGCCGCAG
1 TATTATCCTCCTTCGCAACCCGAGCCGCAG
*
1689496 TATTATCCACCTTC
1 TATTATCCTCCTTC
1689510 ACAGGATCGT
Statistics
Matches: 59, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
27 22 0.37
28 1 0.02
29 1 0.02
30 35 0.59
ACGTcount: A:0.22, C:0.39, G:0.13, T:0.27
Consensus pattern (30 bp):
TATTATCCTCCTTCGCAACCCGAGCCGCAG
Found at i:1689461 original size:27 final size:26
Alignment explanation
Indices: 1689417--1689503 Score: 84
Period size: 27 Copynumber: 3.1 Consensus size: 26
1689407 GATATTATCC
* * *
1689417 TCCTTCGCAACCCAAGCCACAGTATTA
1 TCCTCCGCAA-CCGAGCCGCAGTATTA
*
1689444 TCCTCCGCAATCCGAGCCGCAGTATTTTCC
1 TCCTCCGCAA-CCGAGCCGCAGTA--TT-A
1689474 TCCTCCGCAACCTGAGCCGCAGTATTA
1 TCCTCCGCAACC-GAGCCGCAGTATTA
1689501 TCC
1 TCC
1689504 ACCTTCACAG
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
27 23 0.46
28 2 0.04
29 4 0.08
30 21 0.42
ACGTcount: A:0.22, C:0.39, G:0.15, T:0.24
Consensus pattern (26 bp):
TCCTCCGCAACCGAGCCGCAGTATTA
Found at i:1704792 original size:20 final size:21
Alignment explanation
Indices: 1704754--1704792 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1704744 CATCAAGGTC
1704754 TTTGTTGAGGCCATGAAATCT
1 TTTGTTGAGGCCATGAAATCT
1704775 TTTGTTGAGGCCAT-AAAT
1 TTTGTTGAGGCCATGAAAT
1704793 TACTGCAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (21 bp):
TTTGTTGAGGCCATGAAATCT
Found at i:1710893 original size:23 final size:23
Alignment explanation
Indices: 1710859--1710903 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
1710849 TTTTAAACTT
1710859 AAAATAATTTCAAAACAATTTTAC
1 AAAATAATTTC-AAACAATTTTAC
*
1710883 AAAAT-ATTTCAAACCATTTTA
1 AAAATAATTTCAAACAATTTTA
1710904 AAGCCAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 10 0.50
23 5 0.25
24 5 0.25
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (23 bp):
AAAATAATTTCAAACAATTTTAC
Found at i:1716826 original size:21 final size:21
Alignment explanation
Indices: 1716800--1716902 Score: 100
Period size: 21 Copynumber: 4.8 Consensus size: 21
1716790 TTTGGTGTAG
1716800 AGGGAATCGATACCCCCTTGA
1 AGGGAATCGATACCCCCTTGA
1716821 AGGGAATCGATACCCCCTTGA
1 AGGGAATCGATACCCCCTTGA
* * *
1716842 AGGGGAACCGATTTCCCCTTTGA
1 A-GGGAATCGA-TACCCCCTTGA
* * *
1716865 AGGGGAACCGATTCCCTC-TGTA
1 A-GGGAATCGATACCCCCTTG-A
*
1716887 GGGGAATCGATACCCC
1 AGGGAATCGATACCCC
1716903 TGAGGTTTTG
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
21 36 0.51
22 14 0.20
23 20 0.29
ACGTcount: A:0.25, C:0.28, G:0.26, T:0.20
Consensus pattern (21 bp):
AGGGAATCGATACCCCCTTGA
Found at i:1720364 original size:21 final size:21
Alignment explanation
Indices: 1720348--1720387 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1720338 ATCAAAACAT
*
1720348 AAAAGAAAAAAGGCAAAAAAA
1 AAAAAAAAAAAGGCAAAAAAA
*
1720369 AAAAAAAAAAATGCAAAAA
1 AAAAAAAAAAAGGCAAAAA
1720388 TCACAAACGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.82, C:0.05, G:0.10, T:0.03
Consensus pattern (21 bp):
AAAAAAAAAAAGGCAAAAAAA
Found at i:1735446 original size:25 final size:25
Alignment explanation
Indices: 1735414--1735470 Score: 105
Period size: 25 Copynumber: 2.3 Consensus size: 25
1735404 ATATCAAGTT
1735414 TCATTAATGTTAAAATGGACATTTC
1 TCATTAATGTTAAAATGGACATTTC
*
1735439 TCATTAATGTTAAAATGGATATTTC
1 TCATTAATGTTAAAATGGACATTTC
1735464 TCATTAA
1 TCATTAA
1735471 ATAAATATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.42
Consensus pattern (25 bp):
TCATTAATGTTAAAATGGACATTTC
Found at i:1743287 original size:20 final size:21
Alignment explanation
Indices: 1743264--1743343 Score: 67
Period size: 20 Copynumber: 3.8 Consensus size: 21
1743254 TTGGTGCAGA
1743264 GGGAATCGATACCCCCATGA-
1 GGGAATCGATACCCCCATGAG
* *
1743284 GGGAA-CTGATTCCCCCTTTGAAG
1 GGGAATC-GATACCCCC-ATG-AG
* *
1743307 GGGAATCGATTCCCCCCA-CAG
1 GGGAATCGA-TACCCCCATGAG
1743328 GGGAATCGATACCCCC
1 GGGAATCGATACCCCC
1743344 TGGGGTTCTG
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
19 1 0.02
20 19 0.40
21 13 0.27
22 1 0.02
23 7 0.15
24 7 0.15
ACGTcount: A:0.25, C:0.33, G:0.25, T:0.17
Consensus pattern (21 bp):
GGGAATCGATACCCCCATGAG
Found at i:1746634 original size:2 final size:2
Alignment explanation
Indices: 1746627--1746673 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
1746617 TAAATGTTTA
* *
1746627 TG TG TG TG TG TG TT TG TG TT TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1746669 TG TG T
1 TG TG T
1746674 ATGTATTTGC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.00, G:0.45, T:0.55
Consensus pattern (2 bp):
TG
Found at i:1750077 original size:30 final size:29
Alignment explanation
Indices: 1750017--1750080 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
1750007 AAATTATATG
* * *
1750017 ACTTTTTAAAATTATATTTTTGGTCTTAA
1 ACTTTTTAAAATTATACTTTAGCTCTTAA
1750046 ACTTTTTAAAATTTATACTTTAGCTAC-TAA
1 ACTTTTTAAAA-TTATACTTTAGCT-CTTAA
1750076 ACTTT
1 ACTTT
1750081 CAAAACTTAC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 11 0.37
30 18 0.60
31 1 0.03
ACGTcount: A:0.33, C:0.11, G:0.05, T:0.52
Consensus pattern (29 bp):
ACTTTTTAAAATTATACTTTAGCTCTTAA
Found at i:1751386 original size:19 final size:19
Alignment explanation
Indices: 1751362--1751400 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1751352 CCTAAATTGA
1751362 GATTGTATT-TGCTTAATTT
1 GATTGT-TTATGCTTAATTT
1751381 GATTGTTTATGCTTAATTT
1 GATTGTTTATGCTTAATTT
1751400 G
1 G
1751401 TTCATCTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 2 0.11
19 17 0.89
ACGTcount: A:0.21, C:0.05, G:0.18, T:0.56
Consensus pattern (19 bp):
GATTGTTTATGCTTAATTT
Found at i:1758805 original size:20 final size:20
Alignment explanation
Indices: 1758780--1758818 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1758770 TTATGAATCT
*
1758780 AAAAATGAGTTATAAGTCTG
1 AAAAATAAGTTATAAGTCTG
*
1758800 AAAAATAAGTTATGAGTCT
1 AAAAATAAGTTATAAGTCT
1758819 AAATTAAGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.05, G:0.18, T:0.31
Consensus pattern (20 bp):
AAAAATAAGTTATAAGTCTG
Found at i:1763617 original size:33 final size:32
Alignment explanation
Indices: 1763560--1763623 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
1763550 AACAGCACCG
1763560 TGAACAGTGCATGATACACTGCTACAGTAACA
1 TGAACAGTGCATGATACACTGCTACAGTAACA
*
1763592 TGAACAGTGTACA-GATGCACTGCTACAGTAAC
1 TGAACAGTG--CATGATACACTGCTACAGTAAC
1763624 TGCTACAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 9 0.31
33 18 0.62
34 2 0.07
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (32 bp):
TGAACAGTGCATGATACACTGCTACAGTAACA
Found at i:1764109 original size:45 final size:43
Alignment explanation
Indices: 1764019--1764159 Score: 166
Period size: 47 Copynumber: 3.3 Consensus size: 43
1764009 TATAAAATCT
* * * *
1764019 CTTACCATTTATACCATAAGCTTGAAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTATC--AATA
1764064 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTATCAATA
*
1764109 CTTGCCA-TTATT-CATAAGCTCGTAAGCTTA-TTT-TC-ATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTATCAATA
1764147 CTTACCATTTATT
1 CTTACCATTTATT
1764160 AACCAATAAA
Statistics
Matches: 87, Mismatches: 6, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
38 9 0.10
39 7 0.08
40 3 0.03
41 18 0.21
42 3 0.03
44 2 0.02
45 20 0.23
47 25 0.29
ACGTcount: A:0.32, C:0.21, G:0.07, T:0.40
Consensus pattern (43 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTATCAATA
Found at i:1764286 original size:47 final size:45
Alignment explanation
Indices: 1764210--1764335 Score: 166
Period size: 47 Copynumber: 2.8 Consensus size: 45
1764200 TATAAAATCT
* * *
1764210 CTTACCATTTATACCATAAGCTTGAAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
1764255 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
*
1764302 CTTGCCA-TTATT-CATAAGCTCGTAAGCTTATTTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTT
1764336 CATACTTACC
Statistics
Matches: 73, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
43 22 0.30
44 3 0.04
45 10 0.14
46 2 0.03
47 36 0.49
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:1764495 original size:40 final size:40
Alignment explanation
Indices: 1764416--1764496 Score: 92
Period size: 40 Copynumber: 2.0 Consensus size: 40
1764406 ATAGGAGTAA
* * * *
1764416 AATATTGCACCTAAGTGCTAAGGTCGAGCTTTGCTCACCT
1 AATAATGCACCTAAGTGCTAAGGTCGAGATTTACCCACCT
* *
1764456 AATAATGCACCGT-AGTGCTGAGGTCGGGATTTACCCACCT
1 AATAATGCACC-TAAGTGCTAAGGTCGAGATTTACCCACCT
1764496 A
1 A
1764497 GTACACCGTA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
40 33 0.97
41 1 0.03
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.27
Consensus pattern (40 bp):
AATAATGCACCTAAGTGCTAAGGTCGAGATTTACCCACCT
Found at i:1778744 original size:66 final size:66
Alignment explanation
Indices: 1778671--1778859 Score: 229
Period size: 66 Copynumber: 2.8 Consensus size: 66
1778661 TTGATCTCAC
* * *
1778671 TTGAGATTGTTTTCCTAAAAACAAATTTTGTCTAGCTTGAGACAATTTCTCTTTAAACATCAA-C
1 TTGAGATTGTTTTCCTCAAAACAAATTTTGTCTCGCTTGAGACAATTTCTCTTGAAACAT-AAGC
1778735 CT
65 CT
* * * * *
1778737 TTGAGATTG-TTTCTCTCCAAACAAATTTTCTCTCGCTAGAGATAGTTTCTCTTGAAACATAAGC
1 TTGAGATTGTTTTC-CTCAAAACAAATTTTGTCTCGCTTGAGACAATTTCTCTTGAAACATAAGC
1778801 CT
65 CT
* * * *
1778803 TTGAGATTGTTTTTCTCGAAACAAAGTTTTGTCTCGATTGAGACAATTTCCCTTGAA
1 TTGAGATTGTTTTCCTCAAAACAAA-TTTTGTCTCGCTTGAGACAATTTCTCTTGAA
1778860 GCCCAAATTT
Statistics
Matches: 103, Mismatches: 16, Indels: 7
0.82 0.13 0.06
Matches are distributed among these distances:
65 6 0.06
66 69 0.67
67 28 0.27
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.39
Consensus pattern (66 bp):
TTGAGATTGTTTTCCTCAAAACAAATTTTGTCTCGCTTGAGACAATTTCTCTTGAAACATAAGCC
T
Found at i:1778927 original size:102 final size:104
Alignment explanation
Indices: 1778801--1779007 Score: 251
Period size: 102 Copynumber: 2.0 Consensus size: 104
1778791 AAACATAAGC
* ** ** * *
1778801 CTTTGAGATTGTTTTTCTCGAAACAAAGTTTTGTCTCGATTGAGACAAT-TTCCCTTGAAGCCCA
1 CTTTGAGATTGTTTTCCTAAAAACAAA-TTCCGTCTCGATTGAGACAATGTTCCCTTGAAACACA
* *
1778865 AATTTT-AAAGTTGTTTCACTTGAAACAAAA-TTTATCTCA
65 AATTTTGAAA-TTATTTCACTCGAAACAAAATTTTATCTCA
* * *
1778904 CTTT-AGATTGTTTTCCTAAAAACAAATTCCGTCTCGCTTGAGATAGTGTTCCCTTGAAACACAA
1 CTTTGAGATTGTTTTCCTAAAAACAAATTCCGTCTCGATTGAGACAATGTTCCCTTGAAACACAA
*
1778968 ATTTTGAAATTATTTCCCTCGAAACAAAATTTTATCTCA
66 ATTTTGAAATTATTTCACTCGAAACAAAATTTTATCTCA
1779007 C
1 C
1779008 ATGAGATAGC
Statistics
Matches: 88, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
101 16 0.18
102 55 0.62
103 17 0.19
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (104 bp):
CTTTGAGATTGTTTTCCTAAAAACAAATTCCGTCTCGATTGAGACAATGTTCCCTTGAAACACAA
ATTTTGAAATTATTTCACTCGAAACAAAATTTTATCTCA
Found at i:1778995 original size:234 final size:235
Alignment explanation
Indices: 1778566--1779022 Score: 632
Period size: 234 Copynumber: 1.9 Consensus size: 235
1778556 TTGTCTATCA
** *
1778566 CCTTGGAGATTGTTTCTCTCGAAACAAAGTTTCGTCTCTCTTGATACAATTTCCCTTGAAGCCCA
1 CCTTGGAGATTGTTTCTCTCGAAACAAAGTTTCGTCTCGATTGAGACAATTTCCCTTGAAGCCCA
** *
1778631 AATTTTGGAGTTGTTTCACTTGTAACAAAATTGATCTCACTTGAGATTGTTTTCCTAAAAACAAA
66 AATTTTAAAGTTGTTTCACTTGAAACAAAATTGATCTCACTTGAGATTGTTTTCCTAAAAACAAA
** * * * * * *
1778696 TTTTGTCTAGCTTGAGACAATTTCTCTTTAAACATCAACCTTTGAGATTGTTTCTCTCCAAAC-A
131 TTCCGTCTAGCTTGAGACAATTTCCCTTGAAACATCAAACTTTGAAATTATTTCCCTCCAAACAA
* * *
1778760 AATTTTCTCTCGC-TAGAGATAGTTTCTCTTGAAACATAAG
196 AATTTTATCTCACAT-GAGATAGCTTCTCTTGAAACATAAG
* * *
1778800 CCTTTGAGATTGTTTTTCTCGAAACAAAGTTTTGTCTCGATTGAGACAATTTCCCTTGAAGCCCA
1 CCTTGGAGATTGTTTCTCTCGAAACAAAGTTTCGTCTCGATTGAGACAATTTCCCTTGAAGCCCA
* *
1778865 AATTTTAAAGTTGTTTCACTTGAAACAAAATTTATCTCACTTTAGATTGTTTTCCTAAAAACAAA
66 AATTTTAAAGTTGTTTCACTTGAAACAAAATTGATCTCACTTGAGATTGTTTTCCTAAAAACAAA
* * * * *
1778930 TTCCGTCTCGCTTGAGATAGTGTTCCCTTGAAACA-CAAATTTTGAAATTATTTCCCTCGAAACA
131 TTCCGTCTAGCTTGAGACAAT-TTCCCTTGAAACATCAAACTTTGAAATTATTTCCCTCCAAACA
1778994 AAATTTTATCTCACATGAGATAGCTTCTC
195 AAATTTTATCTCACATGAGATAGCTTCTC
1779023 ACGAAACAAA
Statistics
Matches: 193, Mismatches: 27, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
234 157 0.81
235 35 0.18
236 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (235 bp):
CCTTGGAGATTGTTTCTCTCGAAACAAAGTTTCGTCTCGATTGAGACAATTTCCCTTGAAGCCCA
AATTTTAAAGTTGTTTCACTTGAAACAAAATTGATCTCACTTGAGATTGTTTTCCTAAAAACAAA
TTCCGTCTAGCTTGAGACAATTTCCCTTGAAACATCAAACTTTGAAATTATTTCCCTCCAAACAA
AATTTTATCTCACATGAGATAGCTTCTCTTGAAACATAAG
Found at i:1779916 original size:207 final size:207
Alignment explanation
Indices: 1779563--1779941 Score: 575
Period size: 207 Copynumber: 1.8 Consensus size: 207
1779553 TCATATGAGG
* * *
1779563 CCAAAACTCTTCAACATGGATGAACAGTGTCATCTTCAACACCAGATTATCTCTAGATTACTCGA
1 CCAAAACTCTTCAACATGGATGAACAGTGTCATCTTCAACACCAGATTATCTCCAGATTACACAA
* * *
1779628 CTTCCTCAACAAGAAGGGACAGGTCCATCTGAAATCGACCAAAACTCTTCAATATGGATGAGTAG
66 CTTCCTCAACAAGAAGGAACACGTCCATCTGAAATCGACCAAAACTCTTCAACATGGATGAGTAG
* *
1779693 TGTCGTCTTAAACACCAAATTATCTCTAGATTGACTCGACTTCTACAATGAGAATGAACAACATC
131 TGTCATCTTAAACACCAAATTATCTCTAGATTGACCCGACTTCTACAATGAGAATGAACAACATC
1779758 ATATGAAAGAGT
196 ATATGAAAGAGT
* **
1779770 CCAAAACTCTTCAACATGGATGAGCAGTGTTGTCTTCAACACCAGATTATCTCCAGATTGACACA
1 CCAAAACTCTTCAACATGGATGAACAGTGTCATCTTCAACACCAGATTATCTCCAGATT-ACACA
* *
1779835 ACTTCGTCAACAAGAAGGAACAACGT-CATCTGAAAGT-GACCAGAACTCTTCAACATGGATGAG
65 ACTTCCTCAACAAGAAGGAAC-ACGTCCATCTGAAA-TCGACCAAAACTCTTCAACATGGATGAG
* *
1779898 -AGTGTCATCTTCAACACCAAATTTTCTCTAGATTGACCCGACTT
128 TAGTGTCATCTTAAACACCAAATTATCTCTAGATTGACCCGACTT
1779942 TCTCAACGAG
Statistics
Matches: 154, Mismatches: 15, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
207 95 0.62
208 55 0.36
209 4 0.03
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.26
Consensus pattern (207 bp):
CCAAAACTCTTCAACATGGATGAACAGTGTCATCTTCAACACCAGATTATCTCCAGATTACACAA
CTTCCTCAACAAGAAGGAACACGTCCATCTGAAATCGACCAAAACTCTTCAACATGGATGAGTAG
TGTCATCTTAAACACCAAATTATCTCTAGATTGACCCGACTTCTACAATGAGAATGAACAACATC
ATATGAAAGAGT
Found at i:1779966 original size:103 final size:103
Alignment explanation
Indices: 1779509--1779954 Score: 482
Period size: 104 Copynumber: 4.4 Consensus size: 103
1779499 TGTTATATTT
* * *
1779509 AAATTATC-C-AG-TTGACTCGAATTCCTCAACGAGAAGGAATAGTGTCATATG--AG-G-CCAA
1 AAATTATCTCTAGATTGACTCGACTT-CTCAACGAGAAGGAACAGCGTCATATGAAAGTGACCAA
*
1779567 AACTCTTCAACATGGATGAACAGTGTCATCTTCAACACC
65 AACTCTTCAACATGGATGAGCAGTGTCATCTTCAACACC
* * * *
1779606 AGATTATCTCTAGATT-ACTCGACTTCCTCAACAAGAAGGGACAG-GTCCATCTGAAA-TCGACC
1 AAATTATCTCTAGATTGACTCGACTT-CTCAACGAGAAGGAACAGCGT-CATATGAAAGT-GACC
* * * *
1779668 AAAACTCTTCAATATGGATGAGTAGTGTCGTCTTAAACACC
63 AAAACTCTTCAACATGGATGAGCAGTGTCATCTTCAACACC
* * * * * *
1779709 AAATTATCTCTAGATTGACTCGACTTCTACAATGAGAATGAACAACATCATATGAAAGAGTCCAA
1 AAATTATCTCTAGATTGACTCGACTTCT-CAACGAGAAGGAACAGCGTCATATGAAAGTGACCAA
**
1779774 AACTCTTCAACATGGATGAGCAGTGTTGTCTTCAACACC
65 AACTCTTCAACATGGATGAGCAGTGTCATCTTCAACACC
* * * * * * * *
1779813 AGATTATCTCCAGATTGACACAACTTCGTCAACAAGAAGGAACAACGTCATCTGAAAGTGACCAG
1 AAATTATCTCTAGATTGACTCGACTTC-TCAACGAGAAGGAACAGCGTCATATGAAAGTGACCAA
1779878 AACTCTTCAACATGGATGAG-AGTGTCATCTTCAACACC
65 AACTCTTCAACATGGATGAGCAGTGTCATCTTCAACACC
* *
1779916 AAATTTTCTCTAGATTGACCCGACTTTCTCAACGAGAAG
1 AAATTATCTCTAGATTGACTCGAC-TTCTCAACGAGAAG
1779955 TAATAGTGTC
Statistics
Matches: 289, Mismatches: 45, Indels: 24
0.81 0.13 0.07
Matches are distributed among these distances:
97 7 0.02
98 3 0.01
99 31 0.11
100 2 0.01
101 1 0.00
102 1 0.00
103 100 0.35
104 142 0.49
105 2 0.01
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.26
Consensus pattern (103 bp):
AAATTATCTCTAGATTGACTCGACTTCTCAACGAGAAGGAACAGCGTCATATGAAAGTGACCAAA
ACTCTTCAACATGGATGAGCAGTGTCATCTTCAACACC
Found at i:1782279 original size:56 final size:56
Alignment explanation
Indices: 1782193--1782305 Score: 226
Period size: 56 Copynumber: 2.0 Consensus size: 56
1782183 ATTTTATCCG
1782193 AAGATTTTCAAGAACACTCTATCGTAGAATGGGCGCGAAAAGCACATCTTGATCGA
1 AAGATTTTCAAGAACACTCTATCGTAGAATGGGCGCGAAAAGCACATCTTGATCGA
1782249 AAGATTTTCAAGAACACTCTATCGTAGAATGGGCGCGAAAAGCACATCTTGATCGA
1 AAGATTTTCAAGAACACTCTATCGTAGAATGGGCGCGAAAAGCACATCTTGATCGA
1782305 A
1 A
1782306 GTAGTGAAAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.23
Consensus pattern (56 bp):
AAGATTTTCAAGAACACTCTATCGTAGAATGGGCGCGAAAAGCACATCTTGATCGA
Found at i:1785741 original size:55 final size:55
Alignment explanation
Indices: 1785652--1786171 Score: 767
Period size: 55 Copynumber: 9.5 Consensus size: 55
1785642 AGAGTGTGAA
1785652 AAACTTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGCACTATATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGCACTATATGTGT
* * *
1785707 AAACATAAGAAATTCCTACTAAGTGGATGAATTTTCGTATGGGCACCATATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGCACTATATGTGT
*
1785762 AAACTTAAGAAATTCATACTAAGTGGATGAA-TTTCTGTATGGGCACTGTATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTTC-GTATGGGCACTATATGTGT
* ** *
1785817 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCCCATGGGCACTATATATGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGCACTATATGTGT
*
1785872 AAACTTAAGAAATTCATACTAAGTGGATGAATTTTTGTATGGGCACTATATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGCACTATATGTGT
* * * *
1785927 AAACTTAAGAAATTCACACTAAGTGGATGAATTTCCATATGGGCACTATATGTGA
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGCACTATATGTGT
*
1785982 AAACTTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGCGCTATATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGCACTATATGTGT
* * * * *
1786037 AAACTTAAGAAATTCATGCTAATTGGATGAATTTCCGTATGGTCACTTTATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGCACTATATGTGT
* * * *
1786092 AAATTTAAGAAATTCATACTAAGTGGATGAATTTAT-ATATGGGCACTAAATGTGCA
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTT-TCGTATGGGCACTATATGTG-T
* *
1786148 AAAC-TATGAAATTTATACTAAGTG
1 AAACTTAAGAAATTCATACTAAGTG
1786172 TATACATTTT
Statistics
Matches: 416, Mismatches: 45, Indels: 8
0.89 0.10 0.02
Matches are distributed among these distances:
54 4 0.01
55 406 0.98
56 6 0.01
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (55 bp):
AAACTTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGCACTATATGTGT
Found at i:1791775 original size:55 final size:55
Alignment explanation
Indices: 1791638--1792220 Score: 825
Period size: 55 Copynumber: 10.7 Consensus size: 55
1791628 AAGCGTGCAA
* * *
1791638 AAACATAAGAAATTCATACTAAGTGGAAGAATTTCCGTATGGACAC--TATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
* * *
1791691 AAACTTAAGAAATTTATACTAAGTGGATGAATTTCCATATGGGCACTATATCTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
* * *
1791746 AAACTTAAAAAATTCATACTAAGTTGATGAATTTTCGTATGGGCACTATATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
**
1791801 AAACTTAAGAAATTCATACTAAGTGGATGAATTTATGTATGGGCACTATATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
* *
1791856 AAACTTAAGAAATTCATACTAAGTGGAGGAATTTCCGCATGGGCACTATATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
* * *
1791911 AAACTTAATAAATTCATACTAAGTGGACGAATTTTCGTATGGGCACTATATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
*
1791966 AAACTTAAGAAAATCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
* * *
1792021 AAACTTAAAAAATTCATACTAAGTGGATGAA-TTCCGTATGGGAACTATATGTGC
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
* *
1792075 AAACTTAAGAAATTCATACTAAGTGGATGAAATAT-CGTATGGGCACTTTATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATG-AATTTCCGTATGGGCACTATATGTGT
* * * ** *
1792130 AAATTTAAGAAATTCATACTATGTGGATGAAATTCTATATGGGCACTATATGTGAA
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTG-T
* * * *
1792186 AAAC-TAGGAAATTCAAACTAAGTGTATAAATTTCC
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCC
1792221 ATATTGGTAG
Statistics
Matches: 471, Mismatches: 53, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
53 41 0.09
54 52 0.11
55 374 0.79
56 4 0.01
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.32
Consensus pattern (55 bp):
AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
Found at i:1792977 original size:8 final size:9
Alignment explanation
Indices: 1792948--1792976 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
1792938 CATGGAACCT
1792948 AAAGAGTTA
1 AAAGAGTTA
1792957 AAAGAGTTA
1 AAAGAGTTA
1792966 AAAGAGTTA
1 AAAGAGTTA
1792975 AA
1 AA
1792977 GGCGTAGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.21, T:0.21
Consensus pattern (9 bp):
AAAGAGTTA
Found at i:1796837 original size:18 final size:18
Alignment explanation
Indices: 1796814--1796857 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
1796804 AGGGCAAGTG
1796814 ATTTGATTTTAATGATTA
1 ATTTGATTTTAATGATTA
1796832 ATTTGATTTTAATGATTA
1 ATTTGATTTTAATGATTA
1796850 ATTTGATT
1 ATTTGATT
1796858 AATCAACTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (18 bp):
ATTTGATTTTAATGATTA
Found at i:1798969 original size:20 final size:20
Alignment explanation
Indices: 1798946--1799003 Score: 71
Period size: 21 Copynumber: 2.9 Consensus size: 20
1798936 ATTCCCCATG
*
1798946 AAAAAGTATTGATCCCTCTC
1 AAAAAGGATTGATCCCTCTC
** *
1798966 AAAAAGGATCAATCCCTTTTC
1 AAAAAGGATTGATCCC-TCTC
1798987 AAAAAGGATTGATCCCT
1 AAAAAGGATTGATCCCT
1799004 TCGCTATTGA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
20 14 0.45
21 17 0.55
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (20 bp):
AAAAAGGATTGATCCCTCTC
Found at i:1799458 original size:17 final size:17
Alignment explanation
Indices: 1799436--1799468 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1799426 TTACTTAATG
1799436 TTCTTCTTCATTTAGCA
1 TTCTTCTTCATTTAGCA
1799453 TTCTTCTTCATTTAGC
1 TTCTTCTTCATTTAGC
1799469 CTTTTCAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.15, C:0.24, G:0.06, T:0.55
Consensus pattern (17 bp):
TTCTTCTTCATTTAGCA
Found at i:1801179 original size:21 final size:21
Alignment explanation
Indices: 1801121--1801181 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
1801111 ATTCCCCGTG
* *
1801121 AAAAAGTATTGATCCC-TCTC
1 AAAAAGGATTGATCCCTTCTA
** *
1801141 AAAAAGGATCAATCCCTTTTA
1 AAAAAGGATTGATCCCTTCTA
1801162 AAAAAGGATTGATCCCTTCT
1 AAAAAGGATTGATCCCTTCT
1801182 CTATTGAGCC
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
20 13 0.41
21 19 0.59
ACGTcount: A:0.38, C:0.21, G:0.11, T:0.30
Consensus pattern (21 bp):
AAAAAGGATTGATCCCTTCTA
Found at i:1803639 original size:49 final size:48
Alignment explanation
Indices: 1803486--1803686 Score: 231
Period size: 49 Copynumber: 4.0 Consensus size: 48
1803476 GAATACCATG
** * *
1803486 AGTGGCACCTTTTATGTTGAAAATGCACCATTATGCATTTAACTTTCATT
1 AGTGGCA-CTTTTATGCCG-AAATACACCGTTATGCATTTAACTTTCATT
1803536 AGTGGCACATTTTATGCCGAAATACACCTTTGTTATGCATTTAACTTTCATT
1 AGTGGCAC-TTTTATGCCGAAATACACC---GTTATGCATTTAACTTTCATT
*
1803588 AGTGACACTTTTTATGCCGAAATACACCGTTATGCATTTAACTTTCATT
1 AGTGGCAC-TTTTATGCCGAAATACACCGTTATGCATTTAACTTTCATT
** * ** *
1803637 AGTGGCACTTTTATGTCAAAAATGCACATTTATGCATTAAACTTTCATT
1 AGTGGCACTTTTATG-CCGAAATACACCGTTATGCATTTAACTTTCATT
1803686 A
1 A
1803687 TAGAGCAATT
Statistics
Matches: 133, Mismatches: 13, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
48 7 0.05
49 65 0.49
50 15 0.11
52 46 0.35
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.39
Consensus pattern (48 bp):
AGTGGCACTTTTATGCCGAAATACACCGTTATGCATTTAACTTTCATT
Found at i:1809231 original size:14 final size:14
Alignment explanation
Indices: 1809211--1809243 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1809201 GAAGACTTTC
1809211 AATCATT-ACCATA
1 AATCATTAACCATA
1809224 ACATCATTAACCATA
1 A-ATCATTAACCATA
1809239 AATCA
1 AATCA
1809244 GCCTCCATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.06
14 10 0.56
15 7 0.39
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.27
Consensus pattern (14 bp):
AATCATTAACCATA
Found at i:1810242 original size:20 final size:20
Alignment explanation
Indices: 1810217--1810289 Score: 128
Period size: 20 Copynumber: 3.6 Consensus size: 20
1810207 TCTTTCTGTA
*
1810217 TATTTTTCCCAAATATCCTT
1 TATTTTTCCCAATTATCCTT
1810237 TATTTTTCCCAATTATCCTT
1 TATTTTTCCCAATTATCCTT
1810257 TATTTTTCCCAATTATCCTT
1 TATTTTTCCCAATTATCCTT
*
1810277 TATTTGTCCCAAT
1 TATTTTTCCCAAT
1810290 GTATGTTAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.22, C:0.25, G:0.01, T:0.52
Consensus pattern (20 bp):
TATTTTTCCCAATTATCCTT
Found at i:1810720 original size:10 final size:9
Alignment explanation
Indices: 1810690--1810716 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
1810680 CAGGTCGTTG
1810690 CCGGTCAAA
1 CCGGTCAAA
1810699 CCGGTCAAA
1 CCGGTCAAA
1810708 CCGGTCAAA
1 CCGGTCAAA
1810717 ACCGATTTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.22, T:0.11
Consensus pattern (9 bp):
CCGGTCAAA
Found at i:1811561 original size:50 final size:49
Alignment explanation
Indices: 1811419--1811567 Score: 219
Period size: 49 Copynumber: 3.0 Consensus size: 49
1811409 GGTTGTTACA
* *
1811419 AGTGGCACCTTTTATGTCGAAATGCACTGTTATGCATTTAACTTTCAAT
1 AGTGGCACCTTTTATGTCGAAATGCACCGTTATGCATTTAACTTTCATT
* * *
1811468 AGTGGCACCTTTTATGTCGAAATACAGCGTTATGCATTTAACTTTTATT
1 AGTGGCACCTTTTATGTCGAAATGCACCGTTATGCATTTAACTTTCATT
*
1811517 AGTGGCACCTTTTATG-CAAAAAATGCACCGTTATGCATTTAACTTTCATT
1 AGTGGCACCTTTTATGTC--GAAATGCACCGTTATGCATTTAACTTTCATT
1811567 A
1 A
1811568 TAGAGCAGTA
Statistics
Matches: 89, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
48 1 0.01
49 60 0.67
50 28 0.31
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.38
Consensus pattern (49 bp):
AGTGGCACCTTTTATGTCGAAATGCACCGTTATGCATTTAACTTTCATT
Found at i:1816110 original size:20 final size:20
Alignment explanation
Indices: 1816085--1816142 Score: 84
Period size: 20 Copynumber: 3.0 Consensus size: 20
1816075 CACCTGAATA
1816085 TAAAGTTTCGAAACTTTGTG
1 TAAAGTTTCGAAACTTTGTG
1816105 TAAAGTTTCGAAACTATTGTG
1 TAAAGTTTCGAAACT-TTGTG
*
1816126 -AAAGTGTCGAAA-TTTGT
1 TAAAGTTTCGAAACTTTGT
1816143 AAACATACTT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
18 4 0.11
19 1 0.03
20 26 0.72
21 5 0.14
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.38
Consensus pattern (20 bp):
TAAAGTTTCGAAACTTTGTG
Found at i:1820274 original size:22 final size:21
Alignment explanation
Indices: 1820248--1820294 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
1820238 ATGACCTGCG
*
1820248 GAAAATTCAAAACATGAAATAA
1 GAAAATTCAAAACATCAAAT-A
* *
1820270 GAAAATTCCAAGCATCAAATA
1 GAAAATTCAAAACATCAAATA
1820291 GAAA
1 GAAA
1820295 CAATTGTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.60, C:0.13, G:0.11, T:0.17
Consensus pattern (21 bp):
GAAAATTCAAAACATCAAATA
Found at i:1822222 original size:22 final size:23
Alignment explanation
Indices: 1822174--1822258 Score: 61
Period size: 22 Copynumber: 3.8 Consensus size: 23
1822164 TCATATAGCT
*
1822174 AAAGTGTCTTAG-AATGAGTACT
1 AAAGTGTCTTAGCAATGAGTACG
*
1822196 AAAGTGTCTTAGCATTGA-TACG
1 AAAGTGTCTTAGCAATGAGTACG
* * * *
1822218 GAAGTG-CATTAGCACT-AATACT
1 AAAGTGTC-TTAGCAATGAGTACG
* *
1822240 AAAGTGTCCTAGCACTGAG
1 AAAGTGTCTTAGCAATGAG
1822259 GGGGGATATA
Statistics
Matches: 50, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
21 2 0.04
22 42 0.84
23 6 0.12
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.28
Consensus pattern (23 bp):
AAAGTGTCTTAGCAATGAGTACG
Found at i:1826343 original size:82 final size:82
Alignment explanation
Indices: 1826193--1826383 Score: 240
Period size: 82 Copynumber: 2.3 Consensus size: 82
1826183 CACAGTTAAT
* * *
1826193 ATCTAACTTGCATTAATGGCACCTTTTTGCCAAAAAGCACAGTTAGCCATTTAATCTTTCATCTC
1 ATCTAA-TTGCATTATTGGCACCTTTCTGCCAAAAAGCACAGTTAGCCATTTAATCTTTCATCCC
*
1826258 AAAGGCATTTAACCTTTC
65 AAAGGCATTTAACATTTC
** * * * *
1826276 ATCTAATTGGCATTATTGGCACCTTTCTG-TTAAATGCATAGTTAGGCATTTAGTCTTTCATCCC
1 ATCTAATT-GCATTATTGGCACCTTTCTGCCAAAAAGCACAGTTAGCCATTTAATCTTTCATCCC
*
1826340 AAAGGTATTTAACATTTC
65 AAAGGCATTTAACATTTC
* *
1826358 ATCTAACTACATTATTGGCACCTTTC
1 ATCTAATTGCATTATTGGCACCTTTC
1826384 ATCTAACTGC
Statistics
Matches: 94, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
81 17 0.18
82 53 0.56
83 24 0.26
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (82 bp):
ATCTAATTGCATTATTGGCACCTTTCTGCCAAAAAGCACAGTTAGCCATTTAATCTTTCATCCCA
AAGGCATTTAACATTTC
Found at i:1826406 original size:26 final size:26
Alignment explanation
Indices: 1826347--1826409 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
1826337 CCCAAAGGTA
*
1826347 TTTAACATTTCATCTAACTACATTAT
1 TTTAACCTTTCATCTAACTACATTAT
*** *
1826373 TGGCACCTTTCATCTAACTGCATTAT
1 TTTAACCTTTCATCTAACTACATTAT
1826399 TTTAACCTTTC
1 TTTAACCTTTC
1826410 TGGCAAATGC
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.27, C:0.24, G:0.05, T:0.44
Consensus pattern (26 bp):
TTTAACCTTTCATCTAACTACATTAT
Found at i:1826408 original size:107 final size:109
Alignment explanation
Indices: 1826269--1826491 Score: 306
Period size: 107 Copynumber: 2.1 Consensus size: 109
1826259 AAGGCATTTA
* * ** * * *
1826269 ACCTTTCATCTAATTGGCATTATTGGCACCTTTCTGTTAAATGCATAGTTAGGCATTTAGTCTTT
1 ACCTTTCATCTAACTGGCATTATTGGAACCTTTCTGGCAAATGCACAGCTAGGCATTTAGTATTT
* *
1826334 CATCCCAAAGGTATTTAACATTTCATCTAACTA-CATTATTGGC
66 CATCCCAAAGGCATTTAACATTTCATCTAACTAGCATTATAGGC
** * *
1826377 ACCTTTCATCTAACT-GCATTATTTTAACCTTTCTGGCAAATGCACAGCTATGTATTTAGTATTT
1 ACCTTTCATCTAACTGGCATTATTGGAACCTTTCTGGCAAATGCACAGCTAGGCATTTAGTATTT
*
1826441 CATCTCAAAGGCATTTAACATTTCATCTAACTAGCATTATAGGC
66 CATCCCAAAGGCATTTAACATTTCATCTAACTAGCATTATAGGC
1826485 ACCTTTC
1 ACCTTTC
1826492 TACCAAATGC
Statistics
Matches: 100, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
107 70 0.70
108 30 0.30
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.39
Consensus pattern (109 bp):
ACCTTTCATCTAACTGGCATTATTGGAACCTTTCTGGCAAATGCACAGCTAGGCATTTAGTATTT
CATCCCAAAGGCATTTAACATTTCATCTAACTAGCATTATAGGC
Found at i:1826499 original size:82 final size:80
Alignment explanation
Indices: 1826380--1826606 Score: 301
Period size: 82 Copynumber: 2.8 Consensus size: 80
1826370 TATTGGCACC
*** * * * *
1826380 TTTCATCTAACTGCATTATTTTAACCTTTCTGGCAAATGCACAGCTATGTATTTAGTATTTCATC
1 TTTCATCTAACTGCATTATTGGCACCTTTCTGCCAAATGCACAGCTA-GCATTTAGTCTTTCATA
1826445 TCAAAGGCATTTAACA
65 TCAAAGGCATTTAACA
* * *
1826461 TTTCATCTAACTAGCATTATAGGCACCTTTCTACCAAATGCATAGCTAGACATTTAGTCTTTCAT
1 TTTCATCTAACT-GCATTATTGGCACCTTTCTGCCAAATGCACAGCTAG-CATTTAGTCTTTCAT
*
1826526 ATCAAAGGCATTTAACC
64 ATCAAAGGCATTTAACA
* *
1826543 TTTCATCAAACTGCATTATTGGCACCTTTCTGCCAAATGCACAGCCAGGCATTTAGTCTTTCAT
1 TTTCATCTAACTGCATTATTGGCACCTTTCTGCCAAATGCACAGCTA-GCATTTAGTCTTTCAT
1826607 TTTAGAACAA
Statistics
Matches: 127, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
81 59 0.46
82 68 0.54
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.36
Consensus pattern (80 bp):
TTTCATCTAACTGCATTATTGGCACCTTTCTGCCAAATGCACAGCTAGCATTTAGTCTTTCATAT
CAAAGGCATTTAACA
Found at i:1832710 original size:20 final size:20
Alignment explanation
Indices: 1832663--1832720 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
1832653 CGATACTTTT
* * *
1832663 CAAGTGTTTTGAAACTATCT
1 CAAGAGTTTTGAAACTTTCC
1832683 CAAGAGTTTTGAAACTTTCC
1 CAAGAGTTTTGAAACTTTCC
*
1832703 CTAA-AGTTTTGATACTTT
1 C-AAGAGTTTTGAAACTTT
1832721 GTGTCCAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 31 0.94
21 2 0.06
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (20 bp):
CAAGAGTTTTGAAACTTTCC
Found at i:1843775 original size:2 final size:2
Alignment explanation
Indices: 1843768--1843823 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
1843758 TTACACGGGC
1843768 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
1843810 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
1843824 CGACACATTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1846464 original size:27 final size:27
Alignment explanation
Indices: 1846434--1846488 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
1846424 TTGAATGCTT
**
1846434 GAATTTTATGTATTAGGTTGAAATTAA
1 GAATTTTAAATATTAGGTTGAAATTAA
1846461 GAATTTTAAATATTAGGTTGAAATTAA
1 GAATTTTAAATATTAGGTTGAAATTAA
1846488 G
1 G
1846489 GTGAAATGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.40, C:0.00, G:0.18, T:0.42
Consensus pattern (27 bp):
GAATTTTAAATATTAGGTTGAAATTAA
Found at i:1847233 original size:15 final size:14
Alignment explanation
Indices: 1847207--1847236 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
1847197 AATCAAAATT
1847207 TATAAAAATATATA
1 TATAAAAATATATA
1847221 TATAAATAATATATA
1 TATAAA-AATATATA
1847236 T
1 T
1847237 TATATATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TATAAAAATATATA
Found at i:1848923 original size:5 final size:5
Alignment explanation
Indices: 1848727--1848920 Score: 370
Period size: 5 Copynumber: 38.8 Consensus size: 5
1848717 GAAGAGTGTT
1848727 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
1848777 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
1848827 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
* *
1848877 ATATC ATATC ATATC ATATC ATATC ATATC ATATT ATATT ATAT
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATAT
1848921 TATTTTATAT
Statistics
Matches: 188, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
5 188 1.00
ACGTcount: A:0.40, C:0.19, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATC
Found at i:1848928 original size:5 final size:5
Alignment explanation
Indices: 1848725--1849020 Score: 198
Period size: 5 Copynumber: 58.8 Consensus size: 5
1848715 ATGAAGAGTG
* * * * * * * * *
1848725 TTATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
* * * * * * * * * *
1848775 TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
* * * * * * * * * *
1848825 TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
* * * * * * * *
1848875 TCATA TCATA TCATA TCATA TCATA TCATA TCATA TTATA TTATA TTATT
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
* *
1848925 TTATA TTATA TTATGA TTATA TTATA TTATA TTATA -TATTA TGATT TTATA
1 TTATA TTATA TTAT-A TTATA TTATA TTATA TTATA TTA-TA TTATA TTATA
*
1848976 TTTTTA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTAT
1 -TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTAT
1849021 GGCTTTAAAA
Statistics
Matches: 277, Mismatches: 10, Indels: 8
0.94 0.03 0.03
Matches are distributed among these distances:
4 2 0.01
5 265 0.96
6 10 0.04
ACGTcount: A:0.39, C:0.12, G:0.01, T:0.49
Consensus pattern (5 bp):
TTATA
Found at i:1848974 original size:46 final size:46
Alignment explanation
Indices: 1848887--1849012 Score: 166
Period size: 46 Copynumber: 2.7 Consensus size: 46
1848877 ATATCATATC
* * * * *
1848887 ATATCATATCATATCATATCATATTATATTATATTATTTTATA-TT
1 ATATTATATTATATTATATTATATTATATTATATGATTTTATATTT
1848932 ATATTATGATTATATTATATTATATTATA-TATTATGATTTTATATTT
1 ATATTAT-ATTATATTATATTATATTATATTA-TATGATTTTATATTT
*
1848979 TTATTATATTATATTATATTATATTATATTATAT
1 ATATTATATTATATTATATTATATTATATTATAT
1849013 TATATTATGG
Statistics
Matches: 71, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
45 8 0.11
46 53 0.75
47 10 0.14
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (46 bp):
ATATTATATTATATTATATTATATTATATTATATGATTTTATATTT
Found at i:1848975 original size:41 final size:41
Alignment explanation
Indices: 1848902--1849021 Score: 163
Period size: 41 Copynumber: 2.9 Consensus size: 41
1848892 ATATCATATC
*
1848902 ATATCATATTATATTATATTATT-TTATATTATATTATGATT
1 ATATTATATTATATTATA-TATTATTATATTATATTATGATT
* * * *
1848943 ATATTATATTATATTATATATTATGATTTTATATTTTTATT
1 ATATTATATTATATTATATATTATTATATTATATTATGATT
1848984 ATATTATATTATATTATAT-TATATTATATTATATTATG
1 ATATTATATTATATTATATAT-TATTATATTATATTATG
1849022 GCTTTAAAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
40 5 0.07
41 63 0.93
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.60
Consensus pattern (41 bp):
ATATTATATTATATTATATATTATTATATTATATTATGATT
Found at i:1849036 original size:46 final size:46
Alignment explanation
Indices: 1848940--1849041 Score: 107
Period size: 46 Copynumber: 2.2 Consensus size: 46
1848930 TTATATTATG
* ** ** *
1848940 ATTATATTATATTATATTATATATTATGATTTTATATTTTTATTAT
1 ATTATATTATATTATATTATATATTATGATATTATAGCTTTAAAAA
* *
1848986 ATTATATTATATTATATTATAT-TATATTATATTATGGCTTTAAAAA
1 ATTATATTATATTATATTATATAT-TATGATATTATAGCTTTAAAAA
*
1849032 ATTATTTTAT
1 ATTATATTAT
1849042 TAAATGACGC
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
45 1 0.02
46 45 0.98
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (46 bp):
ATTATATTATATTATATTATATATTATGATATTATAGCTTTAAAAA
Found at i:1850921 original size:101 final size:101
Alignment explanation
Indices: 1850801--1851001 Score: 287
Period size: 101 Copynumber: 2.0 Consensus size: 101
1850791 ACTATGTTAA
* *
1850801 TTTTTAAACATACTTTAAGGAGAGTTAGTTCATCACACTACAATCCAACACTCTAAGTGAAAGGG
1 TTTTTAAACATACTTTAAGGAGAGTCAGCTCATCACACTACAATCCAACACTCTAAGTGAAAGGG
*
1850866 AGCATACCTTCCA-CCCCGAGCTAGTTAAGTAGAGTT
66 AGCATACATTCCACCCCCGAGCTAG-TAAGTAGAGTT
* * * * * *
1850902 TTTTTAAGCATACTTTAAGGGGTGTCAGCTCATCACACTACCATCCCACACTCTAAGTTAAAGGG
1 TTTTTAAACATACTTTAAGGAGAGTCAGCTCATCACACTACAATCCAACACTCTAAGTGAAAGGG
* *
1850967 AGCATACATTTCACCCCCGAGCTAGTCAGTAGAGT
66 AGCATACATTCCACCCCCGAGCTAGTAAGTAGAGT
1851002 CATCTCGTGA
Statistics
Matches: 88, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
101 77 0.88
102 11 0.12
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.27
Consensus pattern (101 bp):
TTTTTAAACATACTTTAAGGAGAGTCAGCTCATCACACTACAATCCAACACTCTAAGTGAAAGGG
AGCATACATTCCACCCCCGAGCTAGTAAGTAGAGTT
Found at i:1852915 original size:11 final size:11
Alignment explanation
Indices: 1852880--1852928 Score: 61
Period size: 10 Copynumber: 4.8 Consensus size: 11
1852870 GAATGCTGGA
1852880 AACCGGTTTTG
1 AACCGGTTTTG
*
1852891 -ACTGG-TTT-
1 AACCGGTTTTG
1852899 AACCGGTTTTG
1 AACCGGTTTTG
1852910 AACCGGTTTTG
1 AACCGGTTTTG
1852921 -ACCGGTTT
1 AACCGGTTT
1852929 GACCGGTCAC
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
9 7 0.21
10 15 0.45
11 11 0.33
ACGTcount: A:0.16, C:0.18, G:0.27, T:0.39
Consensus pattern (11 bp):
AACCGGTTTTG
Found at i:1852931 original size:9 final size:10
Alignment explanation
Indices: 1852881--1852935 Score: 69
Period size: 9 Copynumber: 5.6 Consensus size: 10
1852871 AATGCTGGAA
1852881 ACCGGTTTTG
1 ACCGGTTTTG
* *
1852891 ACTGG-TTTA
1 ACCGGTTTTG
1852900 ACCGGTTTTG
1 ACCGGTTTTG
1852910 AACCGGTTTTG
1 -ACCGGTTTTG
1852921 ACCGG-TTTG
1 ACCGGTTTTG
1852930 ACCGGT
1 ACCGGT
1852936 CACGACCCGT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
9 16 0.42
10 12 0.32
11 10 0.26
ACGTcount: A:0.15, C:0.20, G:0.29, T:0.36
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:1852935 original size:19 final size:19
Alignment explanation
Indices: 1852880--1852935 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
1852870 GAATGCTGGA
*
1852880 AACCGGTTTTGACTGGTTT
1 AACCGGTTTTGACCGGTTT
1852899 AACCGGTTTTGAACCGGTTTT
1 AACCGGTTTTG-ACCGG-TTT
*
1852920 GACCGG-TTTGACCGGT
1 AACCGGTTTTGACCGGT
1852936 CACGACCCGT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
18 1 0.03
19 16 0.48
20 8 0.24
21 8 0.24
ACGTcount: A:0.16, C:0.20, G:0.29, T:0.36
Consensus pattern (19 bp):
AACCGGTTTTGACCGGTTT
Found at i:1852981 original size:13 final size:13
Alignment explanation
Indices: 1852938--1852970 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1852928 TGACCGGTCA
*
1852938 CGACCCGTTTACC
1 CGACCCGTTGACC
1852951 CGACCCGTTGACC
1 CGACCCGTTGACC
1852964 CGACCCG
1 CGACCCG
1852971 ACCCGTTGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.15, C:0.48, G:0.21, T:0.15
Consensus pattern (13 bp):
CGACCCGTTGACC
Found at i:1853050 original size:29 final size:29
Alignment explanation
Indices: 1852989--1853064 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
1852979 ACCGTTGACC
*** *
1852989 GGTGCTATTCTGGAAATTAATTCGGTTTT
1 GGTGCTATTCTGGAAATTAATTCGAAATG
*
1853018 GGTGCTATTCTGGGAATTAATTCGAAATG
1 GGTGCTATTCTGGAAATTAATTCGAAATG
* *
1853047 GGTGCTATTTTGGTAATT
1 GGTGCTATTCTGGAAATT
1853065 TTTTTAAAAG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.22, C:0.09, G:0.26, T:0.42
Consensus pattern (29 bp):
GGTGCTATTCTGGAAATTAATTCGAAATG
Found at i:1860014 original size:11 final size:11
Alignment explanation
Indices: 1859975--1860023 Score: 52
Period size: 10 Copynumber: 4.8 Consensus size: 11
1859965 GAACGCTGGA
1859975 AACCGGTTTTG
1 AACCGGTTTTG
*
1859986 -AGCGG-TTT-
1 AACCGGTTTTG
*
1859994 AACCGCTTTTG
1 AACCGGTTTTG
1860005 AACCGGTTTTG
1 AACCGGTTTTG
1860016 -ACCGGTTT
1 AACCGGTTT
1860024 GACCGGTCAC
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
9 6 0.19
10 15 0.48
11 10 0.32
ACGTcount: A:0.16, C:0.20, G:0.27, T:0.37
Consensus pattern (11 bp):
AACCGGTTTTG
Found at i:1860021 original size:10 final size:10
Alignment explanation
Indices: 1859976--1860030 Score: 60
Period size: 9 Copynumber: 5.6 Consensus size: 10
1859966 AACGCTGGAA
1859976 ACCGGTTTTG
1 ACCGGTTTTG
* *
1859986 AGCGG-TTTA
1 ACCGGTTTTG
*
1859995 ACCGCTTTTG
1 ACCGGTTTTG
1860005 AACCGGTTTTG
1 -ACCGGTTTTG
1860016 ACCGG-TTTG
1 ACCGGTTTTG
1860025 ACCGGT
1 ACCGGT
1860031 CACGACCCGT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
9 15 0.42
10 12 0.33
11 9 0.25
ACGTcount: A:0.15, C:0.22, G:0.29, T:0.35
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:1860030 original size:19 final size:19
Alignment explanation
Indices: 1859975--1860030 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
1859965 GAACGCTGGA
*
1859975 AACCGGTTTTGAGCGGTTT
1 AACCGGTTTTGACCGGTTT
*
1859994 AACCGCTTTTGAACCGGTTTT
1 AACCGGTTTTG-ACCGG-TTT
*
1860015 GACCGG-TTTGACCGGT
1 AACCGGTTTTGACCGGT
1860031 CACGACCCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
18 1 0.03
19 15 0.48
20 8 0.26
21 7 0.23
ACGTcount: A:0.16, C:0.21, G:0.29, T:0.34
Consensus pattern (19 bp):
AACCGGTTTTGACCGGTTT
Found at i:1860061 original size:13 final size:13
Alignment explanation
Indices: 1860043--1860073 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
1860033 CGACCCGTTT
1860043 ACCCGTTTACCCG
1 ACCCGTTTACCCG
1860056 ACCCGTTTACCCG
1 ACCCGTTTACCCG
1860069 ACCCG
1 ACCCG
1860074 ACCCGTTGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.16, C:0.48, G:0.16, T:0.19
Consensus pattern (13 bp):
ACCCGTTTACCCG
Found at i:1860074 original size:18 final size:18
Alignment explanation
Indices: 1860033--1860098 Score: 96
Period size: 18 Copynumber: 3.5 Consensus size: 18
1860023 TGACCGGTCA
1860033 CGACCCGTTTACCCGTTTACC
1 CGACCCGTTTACCCG---ACC
1860054 CGACCCGTTTACCCGACC
1 CGACCCGTTTACCCGACC
*
1860072 CGACCCGTTGACCCGACC
1 CGACCCGTTTACCCGACC
1860090 CGACCCGTT
1 CGACCCGTT
1860099 GACTGGTGCT
Statistics
Matches: 44, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
18 29 0.66
21 15 0.34
ACGTcount: A:0.15, C:0.47, G:0.18, T:0.20
Consensus pattern (18 bp):
CGACCCGTTTACCCGACC
Found at i:1860164 original size:29 final size:29
Alignment explanation
Indices: 1860103--1860169 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
1860093 CCCGTTGACT
*** *
1860103 GGTGCTATTCTAGGAATTAATTCGGTTTT
1 GGTGCTATTCTAGGAATTAATTCGAAATG
1860132 GGTGCTATTCT-GTGAATTAATTCGAAATG
1 GGTGCTATTCTAG-GAATTAATTCGAAATG
1860161 GGTGCTATT
1 GGTGCTATT
1860170 TTGGTAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 1 0.03
29 32 0.97
ACGTcount: A:0.22, C:0.10, G:0.25, T:0.42
Consensus pattern (29 bp):
GGTGCTATTCTAGGAATTAATTCGAAATG
Found at i:1866322 original size:136 final size:136
Alignment explanation
Indices: 1865906--1867107 Score: 1584
Period size: 136 Copynumber: 8.9 Consensus size: 136
1865896 AATTTAAAAT
* * * *
1865906 GAACAAGTTCTTCTGATTATGAAC-T-TTCT--C-CTATAGGAGGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAACT
** * * * *
1865966 CTCCATCAGAAATGTTAATCCCTCAAGCGAGGCGTCACTGATTCGAAATACCGTGAATCAAGTGA
66 CTCCATTGGAAATGTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATACCATGAATCGAGTGA
1866031 TAGGTC
131 TAGGTC
* * * *
1866037 AAACAAGCTCTTCTCATTATGAACTTTTTCTCCCTCTGTCGGACGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAACT
* * * * *
1866102 CTCAATTAGAAATATCAAT--C-C---CGAGGTGTCACTAATTCGAAATACCGTGAATCGAGTGA
66 CTCCATTGGAAATGTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATACCATGAATCGAGTGA
*
1866161 TAAGTC
131 TAGGTC
* * *
1866167 GGACAAGCACTTCTCATTATGAACTTCTTCTCCCTCTATCAGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAACT
* * *
1866232 CTCAATTGGAAATATCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATGCCATGAATCGAGTGA
66 CTCCATTGGAAATGTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATACCATGAATCGAGTGA
1866297 TAGGTC
131 TAGGTC
* * *
1866303 GAACAAGCTCTTCTCATTATGAACTTATTCTCCCCCTTTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAACT
* * * * *
1866368 CTCCATTGGAAACGTCAATCTCTCAAGCGAGGTGTCACTGATTTGAAATACCTTGAATTGAGTGA
66 CTCCATTGGAAATGTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATACCATGAATCGAGTGA
*
1866433 TAGCTC
131 TAGGTC
* * * * * *
1866439 GAATAAACTCTTCTCGTTATGAACTTCTTCTCCCTTTATCGGAAGAGTTCTTCTTATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAACT
* * * *
1866504 ATCCATTGGAAATGTCAATCCCTCAAGCGAGGTATCACTGATTCAAAATGCCATGAATCGAGTGA
66 CTCCATTGGAAATGTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATACCATGAATCGAGTGA
1866569 TAGGTC
131 TAGGTC
* * * *
1866575 GAACAAACTCTTCTCATTATGAACTTATTCTCCCTCTGTCGGATGAGTTCTTCTTATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAACT
* ** * * * * *
1866640 CTCAATTGGTTACGTCAATCCCTCAAGCGAGGTGTCACTAATTCAAAATATCATGAATCGAGTAA
66 CTCCATTGGAAATGTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATACCATGAATCGAGTGA
1866705 TAGGTC
131 TAGGTC
* * * *
1866711 AAACAAGCTCTTCTTATTATGAACTTCTTCTCCGTCTATCGGATGAG-TCCT-TCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAACT
* **
1866774 CTCCATTGGAAATGTCAATCCCTCAAGTGAGGTGTCACTGATTTAAAATACCATGAATCGAGTGA
66 CTCCATTGGAAATGTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATACCATGAATCGAGTGA
*
1866839 TATGTC
131 TAGGTC
* * * *
1866845 GAACAAACTCTTCTCATTATAAACTTGTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAACT
* * *
1866910 CTCCATTGGAAATGTTAATCCCTCAAGCGAGGTGTCACTGATTCAAAATATCATGAATCGAGTGA
66 CTCCATTGGAAATGTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATACCATGAATCGAGTGA
* *
1866975 TATGTT
131 TAGGTC
* * * *
1866981 GAACAAGATCTTCTCATTATGAACTTCTTCTCCCTGTGTCGGATGAGTTCTTCTAATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAACT
* * *
1867046 CTCCATTGGAAATGTCCATCCCTCAAGCGAGGTGTCACTGATTTGAAATGCCATGAATCGAG
66 CTCCATTGGAAATGTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATACCATGAATCGAG
1867108 CAACGAAAAT
Statistics
Matches: 939, Mismatches: 119, Indels: 21
0.87 0.11 0.02
Matches are distributed among these distances:
130 116 0.12
131 21 0.02
132 2 0.00
133 6 0.01
134 113 0.12
135 7 0.01
136 674 0.72
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (136 bp):
GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAACT
CTCCATTGGAAATGTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATACCATGAATCGAGTGA
TAGGTC
Done.