Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold35
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: 4812169
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 17994 characters in sequence are not A, C, G, or T
File 8 of 30
Found at i:1149360 original size:32 final size:33
Alignment explanation
Indices: 1149321--1149382 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 33
1149311 CAATTGAATG
1149321 TGTATCGATACCAAG-AACATGTATCGATACAA
1 TGTATCGATACCAAGCAACATGTATCGATACAA
* *
1149353 TGTATCGATACTAAGCAATATGTATCGATA
1 TGTATCGATACCAAGCAACATGTATCGATA
1149383 TATTTGGGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 14 0.52
33 13 0.48
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (33 bp):
TGTATCGATACCAAGCAACATGTATCGATACAA
Found at i:1152004 original size:13 final size:13
Alignment explanation
Indices: 1151986--1152010 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1151976 AATAGTGCCC
1151986 ATGTATCGATACA
1 ATGTATCGATACA
1151999 ATGTATCGATAC
1 ATGTATCGATAC
1152011 TAAGAGCGCA
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1158213 original size:32 final size:33
Alignment explanation
Indices: 1158177--1158241 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
1158167 ACAATTTAAT
1158177 ATGTATCGATACCAAG-AACATGTATCAATACA
1 ATGTATCGATACCAAGCAACATGTATCAATACA
* * *
1158209 ATGTATCGATACTAAGCAATATGTATCGATACA
1 ATGTATCGATACCAAGCAACATGTATCAATACA
1158242 TCTGGGTATG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
ATGTATCGATACCAAGCAACATGTATCAATACA
Found at i:1160164 original size:20 final size:20
Alignment explanation
Indices: 1160141--1160213 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
1160131 ACAATTCAAA
*
1160141 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGAAAT
***
1160161 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGAA-AT
*
1160182 GTATCGATACATGTTGTAAT
1 GTATCGATACATGTTGAAAT
1160202 GTATCGATACAT
1 GTATCGATACAT
1160214 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (20 bp):
GTATCGATACATGTTGAAAT
Found at i:1160185 original size:21 final size:21
Alignment explanation
Indices: 1160159--1160234 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1160149 ACATGTTGCA
1160159 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
1160180 ATGTATCGATACATGTTGTA-
1 ATGTATCGATACATGAAAAAG
*
1160200 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
1160221 ATGTATCGATACAT
1 ATGTATCGATACAT
1160235 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:1160192 original size:41 final size:41
Alignment explanation
Indices: 1160141--1160234 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
1160131 ACAATTCAAA
*
1160141 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
*
1160182 GTATCGATACATGTTGTAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1160223 GTATCGATACAT
1 GTATCGATACAT
1160235 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:1160291 original size:13 final size:13
Alignment explanation
Indices: 1160273--1160298 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1160263 TACAGCAAGT
1160273 ATGTATCGATACA
1 ATGTATCGATACA
1160286 ATGTATCGATACA
1 ATGTATCGATACA
1160299 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1162547 original size:21 final size:21
Alignment explanation
Indices: 1162514--1162558 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1162504 TTGCAAGTTG
*
1162514 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1162536 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
1162556 AAA
1 AAA
1162559 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1164382 original size:15 final size:15
Alignment explanation
Indices: 1164362--1164392 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1164352 TAAAAATGTC
*
1164362 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1164377 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1164392 C
1 C
1164393 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1166486 original size:20 final size:21
Alignment explanation
Indices: 1166407--1166485 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 21
1166397 AATGTCCAAA
*
1166407 ATGTATCGATACATGTTTT-T
1 ATGTATCGATACATCTTTTCT
* *
1166427 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACATCT----TTTCT
1166452 ATGTATCGATACAT-TTTTCT
1 ATGTATCGATACATCTTTTCT
*
1166472 TTGTATCGATACAT
1 ATGTATCGATACAT
1166486 TGTATCGATA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
20 31 0.65
24 3 0.06
25 14 0.29
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTCT
Found at i:1166490 original size:13 final size:13
Alignment explanation
Indices: 1166472--1166510 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1166462 ACATTTTTCT
1166472 TTGTATCGATACA
1 TTGTATCGATACA
1166485 TTGTATCGATACA
1 TTGTATCGATACA
*
1166498 CTGTATCGATACA
1 TTGTATCGATACA
1166511 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1168990 original size:20 final size:20
Alignment explanation
Indices: 1168967--1169039 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1168957 ACAATTCAAA
1168967 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
1168987 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
1169008 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
1169028 GTATCGATACAT
1 GTATCGATACAT
1169040 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1169011 original size:21 final size:21
Alignment explanation
Indices: 1168985--1169060 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1168975 ACATGTTGCA
1168985 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
1169006 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
1169026 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
1169047 ATGTATCGATACAT
1 ATGTATCGATACAT
1169061 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:1169018 original size:41 final size:41
Alignment explanation
Indices: 1168967--1169060 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
1168957 ACAATTCAAA
*
1168967 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1169008 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1169049 GTATCGATACAT
1 GTATCGATACAT
1169061 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:1169117 original size:13 final size:13
Alignment explanation
Indices: 1169099--1169124 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1169089 TACAGCAAGT
1169099 ATGTATCGATACA
1 ATGTATCGATACA
1169112 ATGTATCGATACA
1 ATGTATCGATACA
1169125 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1172606 original size:78 final size:78
Alignment explanation
Indices: 1172477--1172633 Score: 278
Period size: 78 Copynumber: 2.0 Consensus size: 78
1172467 AAATATATAT
1172477 GACATATTGTAAGACCCAAATGAAAAAAGTAATGAAGATGGAACATAAAAAATGATAGCCTTGTT
1 GACATATTGTAAGACCCAAATGAAAAAAGTAATGAAGATGGAACATAAAAAATGATAGCCTTGTT
*
1172542 AAAATTGATTAAA
66 AAAATTGATCAAA
* * *
1172555 GACATATTGTAAGGCCCAAATGAAAGAAGTAATGAAGATGGAACATAAAAAATGGTAGCCTTGTT
1 GACATATTGTAAGACCCAAATGAAAAAAGTAATGAAGATGGAACATAAAAAATGATAGCCTTGTT
1172620 AAAATTGATCAAA
66 AAAATTGATCAAA
1172633 G
1 G
1172634 CTTTCCTTTT
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 75 1.00
ACGTcount: A:0.48, C:0.10, G:0.19, T:0.24
Consensus pattern (78 bp):
GACATATTGTAAGACCCAAATGAAAAAAGTAATGAAGATGGAACATAAAAAATGATAGCCTTGTT
AAAATTGATCAAA
Found at i:1173695 original size:28 final size:28
Alignment explanation
Indices: 1173596--1174497 Score: 826
Period size: 28 Copynumber: 32.5 Consensus size: 28
1173586 ATCGATACAT
* **
1173596 TTTTAAAGTCCATAACTCTATGGCACCC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
* *
1173624 TTTT-CAGTCCACAACTTCGTGGCACCC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
1173651 TTTT-AAGTCCACAACTCCGTGGCACCC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
* * **
1173678 TTTTAAAGTCCATAACTCCATGGCATAC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
*
1173706 TTTTAAAGTCCACAACTCCTTGGCACCC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
* *
1173734 TTTTAAAGTCCACAACTCCATGGCATCC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
*
1173762 TTTTAAAGTCCA-AACTCCGTGGCATCC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
* * *
1173789 -TTTAAATTCCACAACTCCATGGCATCC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
* *
1173816 TTTTAAAGTCCATAACTCCGTGGCATCC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
*
1173844 TTTTAAAGTCCATAACTCCGTGGCACCC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
*
1173872 TTTTAAAGTCCACAACTCTGTGGCACCC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
*
1173900 TTTTAAAGTCCACAACTCCGTGGCACCT
1 TTTTAAAGTCCACAACTCCGTGGCACCC
**
1173928 TTTTAAAGTCCACAACTCTATGGCACCC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
*
1173956 TTTTAAAGTCCACAACTCTGTGGCACCC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
* *
1173984 TTTT-AAGTCCACAACTTCGTGGCTCCC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
* *
1174011 TTTTAAAGTCCACAACTTCGTGGCACCA
1 TTTTAAAGTCCACAACTCCGTGGCACCC
*
1174039 TTTTAAAGTCCACAACTTCGTGGCACCC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
* * *
1174067 GTTT-AAGCCCACAACTCCATGGCACCC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
1174094 TTTT-AAGTCCACAACTCCGTGGCACCC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
*
1174121 TTTT-AAGTCCACAACTCCGTGGCGGCCC
1 TTTTAAAGTCCACAACTCCGTGGC-ACCC
* *
1174149 TTTTTAAGTCCACAACTCCGTGGCACAC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
* ** * * *
1174177 TTTT-AAGCCCACAGGTCAGTGGCATCA
1 TTTTAAAGTCCACAACTCCGTGGCACCC
* *
1174204 ATTT-ATGTCCACAACTCCGTGGCACCC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
* ** * *
1174231 TTTT-AAGTCCACAAGTTAGTGGCATCA
1 TTTTAAAGTCCACAACTCCGTGGCACCC
* * * * * *
1174258 TTTCAAAGCCCACAAGTCAGTAGCATCC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
* **
1174286 TTTTCAAAGCCCACGAA-TTAGTGGCACCC
1 TTTT-AAAGTCCAC-AACTCCGTGGCACCC
* ** * * *
1174315 TTTCAAAACCCACAAGTCAGTGGCA-TC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
* * * *
1174342 TTTTCAAAGCCCACAAGTCGGTGG-AACC
1 TTTT-AAAGTCCACAACTCCGTGGCACCC
** * * ** *
1174370 TTTTCATCGCCCACAAGTTAGTGGCATCC
1 TTTT-AAAGTCCACAACTCCGTGGCACCC
* * * **
1174399 TTTCAAAGCCCACAAGTTAGTGGCATCCC
1 TTTTAAAGTCCACAACTCCGTGGCA-CCC
* * * ** *
1174428 -TTCAAAGCCCACAAGTTAGTGGCATCC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
* * * *
1174455 TTTTAAAGCCCACAAGTCAGTGGCATCC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
* *
1174483 TTTCAAAGCCCACAA
1 TTTTAAAGTCCACAA
1174498 GTTAGTGGCA
Statistics
Matches: 759, Mismatches: 100, Indels: 30
0.85 0.11 0.03
Matches are distributed among these distances:
26 10 0.01
27 233 0.31
28 466 0.61
29 48 0.06
30 2 0.00
ACGTcount: A:0.26, C:0.32, G:0.15, T:0.27
Consensus pattern (28 bp):
TTTTAAAGTCCACAACTCCGTGGCACCC
Found at i:1173806 original size:110 final size:109
Alignment explanation
Indices: 1173596--1174244 Score: 804
Period size: 110 Copynumber: 5.9 Consensus size: 109
1173586 ATCGATACAT
* ** * * *
1173596 TTTTAAAGTCCATAACTCTATGGCACCCTTTTCAGTCCACAACTTCGTGGCACCCTTTTAAGTCC
1 TTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCATGGCACCCTTTTAAGTCC
* * *
1173661 ACAACTCCGTGGCACCCTTTTAAAGTCCATAACTCCATGGCATAC
66 ACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCA-CC
* *
1173706 TTTTAAAGTCCACAACTCCTTGGCACCCTTTTAAAGTCCACAACTCCATGGCATCCTTTTAAAGT
1 TTTTAAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCATGGCACCCTTTT-AAGT
* * *
1173771 CCA-AACTCCGTGGCATCC-TTTAAATTCCACAACTCCATGGCATCC
64 CCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCA-CC
* * * *
1173816 TTTTAAAGTCCATAACTCCGTGGCATCCTTTTAAAGTCCATAACTCCGTGGCACCCTTTTAAAGT
1 TTTTAAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCATGGCACCCTTTT-AAGT
*
1173881 CCACAACTCTGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACC
64 CCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACC
** **
1173927 TTTTTAAAGTCCACAACTCTATGGCACCCTTTTAAAGTCCACAACTCTGTGGCACCCTTTTAAGT
1 -TTTTAAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCATGGCACCCTTTTAAGT
* * *
1173992 CCACAACTTCGTGGCTCCCTTTTAAAGTCCACAACTTCGTGGCACC
64 CCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACC
* * *
1174038 ATTTTAAAGTCCACAACTTCGTGGCACCCGTTTAAGCCCACAACTCCATGGCACCCTTTTAAGTC
1 -TTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCATGGCACCCTTTTAAGTC
*
1174103 CACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCGGCCC
65 CACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGC--ACC
* * * ** * ** *
1174149 TTTTTAAGTCCACAACTCCGTGGCACACTTTTAAGCCCACAGGT-CAGTGGCATCAATTTATGTC
1 TTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCA-TGGCACCCTTTTAAGTC
1174213 CACAACTCCGTGGCACCCTTTT-AAGTCCACAA
65 CACAACTCCGTGGCACCCTTTTAAAGTCCACAA
1174245 GTTAGTGGCA
Statistics
Matches: 478, Mismatches: 53, Indels: 16
0.87 0.10 0.03
Matches are distributed among these distances:
109 20 0.04
110 247 0.52
111 128 0.27
112 83 0.17
ACGTcount: A:0.25, C:0.32, G:0.14, T:0.29
Consensus pattern (109 bp):
TTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCATGGCACCCTTTTAAGTCC
ACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACC
Found at i:1174253 original size:110 final size:111
Alignment explanation
Indices: 1173596--1174541 Score: 801
Period size: 110 Copynumber: 8.5 Consensus size: 111
1173586 ATCGATACAT
* ** *
1173596 TTTTAAAGTCCATAACTCTATGGCACCCTTTT-CAGTCCACAACTTC-GTGGCACCCTTTTAAGT
1 TTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAAC-TCAGTGGCACCCTTTTAAGT
* **
1173659 CCACAACTCCGTGGCACCCTTTTAAAGTCCATAACTCCA-TGGCATAC
65 CCACAACTCCGTGGCACCCTTTTAAAGTCCACAACT-CAGTGGCACCC
* *
1173706 TTTTAAAGTCCACAACTCCTTGGCACCCTTTTAAAGTCCACAACTCCA-TGGCATCCTTTTAAAG
1 TTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACT-CAGTGGCACCCTTTT-AAG
* * *
1173770 TCCA-AACTCCGTGGCATCC-TTTAAATTCCACAACTCCA-TGGCATCC
64 TCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACT-CAGTGGCACCC
* * * *
1173816 TTTTAAAGTCCATAACTCCGTGGCATCCTTTTAAAGTCCATAACTCCGTGGCACCCTTTTAAAGT
1 TTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCAGTGGCACCCTTTT-AAGT
* * *
1173881 CCACAACTCTGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCT
65 CCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCAGTGGCACCC
** *
1173928 TTTTAAAGTCCACAACTCTATGGCACCCTTTTAAAGTCCACAACTCTGTGGCACCCTTTTAAGTC
1 TTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCAGTGGCACCCTTTTAAGTC
* * *
1173993 CACAACTTCGTGGCTCCCTTTTAAAGTCCACAACTTC-GTGGCACCA
66 CACAACTCCGTGGCACCCTTTTAAAGTCCACAAC-TCAGTGGCACCC
* * *
1174039 TTTTAAAGTCCACAACTTCGTGGCACCCGTTT-AAGCCCACAACTCCA-TGGCACCCTTTTAAGT
1 TTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACT-CAGTGGCACCCTTTTAAGT
* *
1174102 CCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCGGCCC
65 CCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCAGTGGC-ACCC
* * * ** * ** *
1174149 TTTTTAAGTCCACAACTCCGTGGCACACTTTT-AAGCCCACAGGTCAGTGGCATCAATTTATGTC
1 TTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCAGTGGCACCCTTTTAAGTC
* * * *
1174213 CACAACTCCGTGGCACCCTTTT-AAGTCCACAAGTTAGTGGCATCA
66 CACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCAGTGGCACCC
* * * * * * * * *
1174258 TTTCAAAGCCCACAAGTCAGTAGCATCCTTTTCAAAGCCCACGAA-TTAGTGGCACCCTTTCAAA
1 TTTTAAAGTCCACAACTCCGTGGCACCCTTTT-AAAGTCCAC-AACTCAGTGGCACCCTTT-TAA
** * * * * * * *
1174322 ACCCACAAGTCAGTGGCA-TCTTTTCAAAGCCCACAAGTCGGTGG-AACC
63 GTCCACAACTCCGTGGCACCCTTTT-AAAGTCCACAACTCAGTGGCACCC
** * * ** * * * * * **
1174370 TTTTCATCGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCATCCCTTCAAAG
1 TTTT-AAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCAGTGGCA-CCCTTTTAAG
* * ** * * * *
1174435 CCCACAAGTTAGTGGCATCCTTTTAAAGCCCACAAGTCAGTGGCATCC
64 TCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCAGTGGCACCC
* * * ** * * * * *
1174483 TTTCAAAGCCCACAAGTTAGTGGCA-TCTTTTCAGAGCCCACAAGTCAGTGGCATCCTTT
1 TTTTAAAGTCCACAACTCCGTGGCACCCTTTT-AAAGTCCACAACTCAGTGGCACCCTTT
1174542 CAAAACCCAC
Statistics
Matches: 708, Mismatches: 103, Indels: 49
0.82 0.12 0.06
Matches are distributed among these distances:
108 2 0.00
109 44 0.06
110 253 0.36
111 157 0.22
112 198 0.28
113 54 0.08
ACGTcount: A:0.26, C:0.31, G:0.15, T:0.27
Consensus pattern (111 bp):
TTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCAGTGGCACCCTTTTAAGTC
CACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCAGTGGCACCC
Found at i:1174498 original size:28 final size:28
Alignment explanation
Indices: 1173632--1174695 Score: 631
Period size: 28 Copynumber: 38.2 Consensus size: 28
1173622 CCTTTTCAGT
* * *
1173632 CCACAACTTC-GTGGCACCCTTT-TAAGT
1 CCACAAC-TCAGTGGCATCCTTTCAAAGC
* * * *
1173659 CCACAACTCCGTGGCACCCTTTTAAAGT
1 CCACAACTCAGTGGCATCCTTTCAAAGC
* * * *
1173687 CCATAACTCCA-TGGCATACTTTTAAAGT
1 CCACAACT-CAGTGGCATCCTTTCAAAGC
** * * *
1173715 CCACAACTCCTTGGCACCCTTTTAAAGT
1 CCACAACTCAGTGGCATCCTTTCAAAGC
* *
1173743 CCACAACTCCA-TGGCATCCTTTTAAAGT
1 CCACAACT-CAGTGGCATCCTTTCAAAGC
* **
1173771 CCA-AACTCCGTGGCATCCTTT-AAATT
1 CCACAACTCAGTGGCATCCTTTCAAAGC
* *
1173797 CCACAACTCCA-TGGCATCCTTTTAAAGT
1 CCACAACT-CAGTGGCATCCTTTCAAAGC
* * * *
1173825 CCATAACTCCGTGGCATCCTTTTAAAGT
1 CCACAACTCAGTGGCATCCTTTCAAAGC
* * * * *
1173853 CCATAACTCCGTGGCACCCTTTTAAAGT
1 CCACAACTCAGTGGCATCCTTTCAAAGC
* * * *
1173881 CCACAACTCTGTGGCACCCTTTTAAAGT
1 CCACAACTCAGTGGCATCCTTTCAAAGC
* * *
1173909 CCACAACTCCGTGGCA-CCTTTTTAAAGT
1 CCACAACTCAGTGGCATCC-TTTCAAAGC
* * *
1173937 CCACAACTCTA-TGGCACCCTTTTAAAGT
1 CCACAACTC-AGTGGCATCCTTTCAAAGC
* * * *
1173965 CCACAACTCTGTGGCACCCTTT-TAAGT
1 CCACAACTCAGTGGCATCCTTTCAAAGC
* *
1173992 CCACAACTTC-GTGGC-TCCCTTTTAAAGT
1 CCACAAC-TCAGTGGCAT-CCTTTCAAAGC
* *
1174020 CCACAACTTC-GTGGCA-CCATTTTAAAGT
1 CCACAAC-TCAGTGGCATCC-TTTCAAAGC
*
1174048 CCACAACTTC-GTGGCACCCGTTT--AAGC
1 CCACAAC-TCAGTGGCATCC-TTTCAAAGC
* * *
1174075 CCACAACTCCA-TGGCACCCTTT-TAAGT
1 CCACAACT-CAGTGGCATCCTTTCAAAGC
* * * *
1174102 CCACAACTCCGTGGCACCCTTT-TAAGT
1 CCACAACTCAGTGGCATCCTTTCAAAGC
* ** ** *
1174129 CCACAACTCCGTGGCGGCCCTTTTTAAGT
1 CCACAACTCAGTGGC-ATCCTTTCAAAGC
* *
1174158 CCACAACTCCGTGGCA-CACTTT-TAAGC
1 CCACAACTCAGTGGCATC-CTTTCAAAGC
** * * *
1174185 CCACAGGTCAGTGGCATCAATTT--ATGT
1 CCACAACTCAGTGGCATC-CTTTCAAAGC
* * * *
1174212 CCACAACTCCGTGGCACCCTTT-TAAGT
1 CCACAACTCAGTGGCATCCTTTCAAAGC
* * *
1174239 CCACAAGTTAGTGGCATCATTTCAAAGC
1 CCACAACTCAGTGGCATCCTTTCAAAGC
* *
1174267 CCACAAGTCAGTAGCATCCTTTTCAAAGC
1 CCACAACTCAGTGGCATCC-TTTCAAAGC
* * *
1174296 CCACGAA-TTAGTGGCACCCTTTCAAAAC
1 CCAC-AACTCAGTGGCATCCTTTCAAAGC
* *
1174324 CCACAAGTCAGTGGCATCTTTTCAAAGC
1 CCACAACTCAGTGGCATCCTTTCAAAGC
* * * **
1174352 CCACAAGTCGGTGG-AACCTTTTCATCGC
1 CCACAACTCAGTGGCATCC-TTTCAAAGC
* *
1174380 CCACAAGTTAGTGGCATCCTTTCAAAGC
1 CCACAACTCAGTGGCATCCTTTCAAAGC
* * *
1174408 CCACAAGTTAGTGGCATCCCTTCAAAGC
1 CCACAACTCAGTGGCATCCTTTCAAAGC
* * *
1174436 CCACAAGTTAGTGGCATCCTTTTAAAGC
1 CCACAACTCAGTGGCATCCTTTCAAAGC
*
1174464 CCACAAGTCAGTGGCATCCTTTCAAAGC
1 CCACAACTCAGTGGCATCCTTTCAAAGC
* * * *
1174492 CCACAAGTTAGTGGCATCTTTTCAGAGC
1 CCACAACTCAGTGGCATCCTTTCAAAGC
* *
1174520 CCACAAGTCAGTGGCATCCTTTCAAAAC
1 CCACAACTCAGTGGCATCCTTTCAAAGC
* * * *
1174548 CCACAAGAT-AATGGCATCTTTTCAGAGC
1 CCACAA-CTCAGTGGCATCCTTTCAAAGC
*
1174576 CCACAAGTCAGTGGCATCCTTTTCAAAGC
1 CCACAACTCAGTGGCATCC-TTTCAAAGC
* *
1174605 CCACGAA-TCAGTGGCACCCTTTCATAGC
1 CCAC-AACTCAGTGGCATCCTTTCAAAGC
* *
1174633 CCACAAGTCAGTGGCA-CATTTTCAAAGC
1 CCACAACTCAGTGGCATC-CTTTCAAAGC
* * * *
1174661 CCACAAGTCGGTGGCAACTTTCTCTAAAGC
1 CCACAACTCAGTGGCATCCTT-TC-AAAGC
1174691 CCACA
1 CCACA
1174696 CAAGTTGGTG
Statistics
Matches: 894, Mismatches: 99, Indels: 85
0.83 0.09 0.08
Matches are distributed among these distances:
26 18 0.02
27 199 0.22
28 582 0.65
29 81 0.09
30 14 0.02
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.26
Consensus pattern (28 bp):
CCACAACTCAGTGGCATCCTTTCAAAGC
Found at i:1174498 original size:56 final size:56
Alignment explanation
Indices: 1173600--1174695 Score: 703
Period size: 56 Copynumber: 19.7 Consensus size: 56
1173590 ATACATTTTT
* * * * * *
1173600 AAAGTCCATAACTCTA-TGGCACCCTTTT-CAGTCCACAACTTC-GTGGCACCCTTT-
1 AAAGTCCACAACTC-AGTGGCATCCTTTTAAAGCCCACAA-GTCAGTGGCATCCTTTC
* * * * * * * *
1173654 TAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCATAACTCCA-TGGCATACTTTT
1 AAAGTCCACAACTCAGTGGCATCCTTTTAAAGCCCACAAGT-CAGTGGCATCCTTTC
** * * * *
1173710 AAAGTCCACAACTCCTTGGCACCCTTTTAAAGTCCACAACTCCA-TGGCATCCTTTT
1 AAAGTCCACAACTCAGTGGCATCCTTTTAAAGCCCACAAGT-CAGTGGCATCCTTTC
* ** * *
1173766 AAAGTCCA-AACTCCGTGGCATCC-TTTAAATTCCACAACTCCA-TGGCATCCTTTT
1 AAAGTCCACAACTCAGTGGCATCCTTTTAAAGCCCACAAGT-CAGTGGCATCCTTTC
* * * * * * * *
1173820 AAAGTCCATAACTCCGTGGCATCCTTTTAAAGTCCATAACTCCGTGGCACCCTTTT
1 AAAGTCCACAACTCAGTGGCATCCTTTTAAAGCCCACAAGTCAGTGGCATCCTTTC
* * * * * *
1173876 AAAGTCCACAACTCTGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCA-CCTTTTT
1 AAAGTCCACAACTCAGTGGCATCCTTTTAAAGCCCACAAGTCAGTGGCATCC-TTTC
* * * * *
1173932 AAAGTCCACAACTCTA-TGGCACCCTTTTAAAGTCCACAACTCTGTGGCACCCTTT-
1 AAAGTCCACAACTC-AGTGGCATCCTTTTAAAGCCCACAAGTCAGTGGCATCCTTTC
* * * *
1173987 TAAGTCCACAACTTC-GTGGC-TCCCTTTTAAAGTCCACAACTTC-GTGGCA-CCATTTT
1 AAAGTCCACAAC-TCAGTGGCAT-CCTTTTAAAGCCCACAA-GTCAGTGGCATCC-TTTC
* * * *
1174043 AAAGTCCACAACTTC-GTGGCACCCGTTT-AAGCCCACAACTCCA-TGGCACCCTTT-
1 AAAGTCCACAAC-TCAGTGGCATCCTTTTAAAGCCCACAAGT-CAGTGGCATCCTTTC
* * * * * * ** *
1174097 TAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCGGCCCTTTT
1 AAAGTCCACAACTCAGTGGCATCCTTTTAAAGCCCACAAGTCAGTGGC-ATCCTTTC
* * * *
1174153 TAAGTCCACAACTCCGTGGCA-CACTTTT-AAGCCCACAGGTCAGTGGCATCAATTT-
1 AAAGTCCACAACTCAGTGGCATC-CTTTTAAAGCCCACAAGTCAGTGGCATC-CTTTC
* * * * * *
1174208 -ATGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAAGTTAGTGGCATCATTTC
1 AAAGTCCACAACTCAGTGGCATCCTTTTAAAGCCCACAAGTCAGTGGCATCCTTTC
* * * * *
1174262 AAAGCCCACAAGTCAGTAGCATCCTTTTCAAAGCCCACGAA-TTAGTGGCACCCTTTC
1 AAAGTCCACAACTCAGTGGCATCCTTTT-AAAGCCCAC-AAGTCAGTGGCATCCTTTC
** * * *
1174319 AAAACCCACAAGTCAGTGGCAT-CTTTTCAAAGCCCACAAGTCGGTGG-AACCTTTTC
1 AAAGTCCACAACTCAGTGGCATCCTTTT-AAAGCCCACAAGTCAGTGGCATCC-TTTC
** * * * * * *
1174375 ATCGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCATCCCTTC
1 AAAGTCCACAACTCAGTGGCATCCTTTTAAAGCCCACAAGTCAGTGGCATCCTTTC
* * *
1174431 AAAGCCCACAAGTTAGTGGCATCCTTTTAAAGCCCACAAGTCAGTGGCATCCTTTC
1 AAAGTCCACAACTCAGTGGCATCCTTTTAAAGCCCACAAGTCAGTGGCATCCTTTC
* * * *
1174487 AAAGCCCACAAGTTAGTGGCAT-CTTTTCAGAGCCCACAAGTCAGTGGCATCCTTTC
1 AAAGTCCACAACTCAGTGGCATCCTTTT-AAAGCCCACAAGTCAGTGGCATCCTTTC
** * * *
1174543 AAAACCCACAAGAT-AATGGCAT-CTTTTCAGAGCCCACAAGTCAGTGGCATCCTTTTC
1 AAAGTCCACAA-CTCAGTGGCATCCTTTT-AAAGCCCACAAGTCAGTGGCATCC-TTTC
* * * * *
1174600 AAAGCCCACGAA-TCAGTGGCACCCTTTCATAGCCCACAAGTCAGTGGCA-CATTTTC
1 AAAGTCCAC-AACTCAGTGGCATCCTTTTAAAGCCCACAAGTCAGTGGCATC-CTTTC
* * * * *
1174656 AAAGCCCACAAGTCGGTGGCAACTTTCTCTAAAGCCCACA
1 AAAGTCCACAACTCAGTGGCATCCTT-T-TAAAGCCCACA
1174696 CAAGTTGGTG
Statistics
Matches: 903, Mismatches: 92, Indels: 90
0.83 0.08 0.08
Matches are distributed among these distances:
53 7 0.01
54 147 0.16
55 150 0.17
56 492 0.54
57 90 0.10
58 17 0.02
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.26
Consensus pattern (56 bp):
AAAGTCCACAACTCAGTGGCATCCTTTTAAAGCCCACAAGTCAGTGGCATCCTTTC
Found at i:1175089 original size:11 final size:11
Alignment explanation
Indices: 1175075--1175099 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1175065 AAAAAAATAC
1175075 AAAAAAAGAAA
1 AAAAAAAGAAA
1175086 AAAAAAAGAAA
1 AAAAAAAGAAA
1175097 AAA
1 AAA
1175100 GGGGTACAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:1175613 original size:28 final size:28
Alignment explanation
Indices: 1175541--1175940 Score: 537
Period size: 27 Copynumber: 14.5 Consensus size: 28
1175531 ATCAATACAT
* **
1175541 TTTTAAAGTCCATAACTCTATGGCACCC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
*
1175569 TTTT-AAGTCCACAACTCTGTGGCACCC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
1175596 TTTTAAAGTCCACAACTCCGTGGCA-CC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
1175623 TTTTAAAGTCCACAACTCCGTGGCACCC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
**
1175651 TTTTAAAGTCCACAACTCTATGGCACCC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
1175679 TTTTAAAGTCCACAACTCCGTGGCACCC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
*
1175707 TTTT-AAGTCCACAACTCCGTGGCTCCC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
* * *
1175734 TTTTAAAATCCACAACTTCGTGGCACCA
1 TTTTAAAGTCCACAACTCCGTGGCACCC
1175762 TTTTAAAGTCCACAACTCCGTGGCACCC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
*
1175790 TTTT-AAGCCCACAACTCCGTGGCACCC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
*
1175817 TTTT-AAGTCCACAACTCCGTGGCGGCCC
1 TTTTAAAGTCCACAACTCCGTGGC-ACCC
* *
1175845 TTTTTAAGTCCACAACTCCGTGGCACAC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
* ** * * *
1175873 TTTT-AAGCCCACAGGTCAGTGGCATCA
1 TTTTAAAGTCCACAACTCCGTGGCACCC
*
1175900 ATTT-AAGTCCACAACTCCGTGGCACCC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
*
1175927 TTTT-AATTCCACAA
1 TTTTAAAGTCCACAA
1175941 GTTAGTGGCA
Statistics
Matches: 331, Mismatches: 36, Indels: 11
0.88 0.10 0.03
Matches are distributed among these distances:
27 170 0.51
28 142 0.43
29 19 0.06
ACGTcount: A:0.25, C:0.33, G:0.14, T:0.27
Consensus pattern (28 bp):
TTTTAAAGTCCACAACTCCGTGGCACCC
Found at i:1175687 original size:83 final size:83
Alignment explanation
Indices: 1175541--1176316 Score: 531
Period size: 83 Copynumber: 9.3 Consensus size: 83
1175531 ATCAATACAT
* * *
1175541 TTTTAAAGTCCATAACTCTA-TGGCACCCTTTT-AAGTCCACAACTCTGTGGCACCCTTTTAAAG
1 TTTTAAAGCCCACAACTC-AGTGGCACCCTTTTAAAGTCCACAACTCTATGGCACCCTTTTAAAG
1175604 TCCACAACTCCGTGGCACC
65 TCCACAACTCCGTGGCACC
* *
1175623 TTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCTATGGCACCCTTTTAAAGT
1 TTTTAAAGCCCACAACTCAGTGGCACCCTTTTAAAGTCCACAACTCTATGGCACCCTTTTAAAGT
1175688 CCACAACTCCGTGGCACCC
66 CCACAACTCCGTGGCA-CC
* * * * * *
1175707 TTTT-AAGTCCACAACTCCGTGGCTCCCTTTTAAAATCCACAACT-TCGTGGCACCATTTTAAAG
1 TTTTAAAGCCCACAACTCAGTGGCACCCTTTTAAAGTCCACAACTCT-ATGGCACCCTTTTAAAG
1175770 TCCACAACTCCGTGGCACCC
65 TCCACAACTCCGTGGCA-CC
* ** * *
1175790 TTTT-AAGCCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCGGCCCTTTTTAAG
1 TTTTAAAGCCCACAACTCAGTGGCACCCTTTTAAAGTCCACAACTCTATGGC-ACCCTTTTAAAG
1175853 TCCACAACTCCGTGGCACAC
65 TCCACAACTCCGTGGCAC-C
** * ** ** *
1175873 TTTT-AAGCCCACAGGTCAGTGGCATCAATTT-AAGTCCACAACTCCGTGGCACCCTTTT-AATT
1 TTTTAAAGCCCACAACTCAGTGGCACCCTTTTAAAGTCCACAACTCTATGGCACCCTTTTAAAGT
* ** *
1175935 CCACAAGTTAGTGGCATCA
66 CCACAACTCCGTGGCA-CC
* * * * * * * * *
1175954 TTTCAAAGCCTACAAGTCAATAGCATCATTTTCAAAGCCCACGAA-T-TAGTGGCACCCTTTCAA
1 TTTTAAAGCCCACAACTCAGTGGCACCCTTTT-AAAGTCCAC-AACTCTA-TGGCACCCTTTTAA
** * * *
1176017 AACCCACAAGTCAGTGGCATC
63 AGTCCACAACTCCGTGGCACC
* * * * * * *
1176038 TTTTCGAAGCCCACAAATCGGTGGCA-CCTTTTCATAGTCCACAAGT-TAGTGGCATCCTTTCAA
1 TTTT-AAAGCCCACAACTCAGTGGCACCCTTTT-AAAGTCCACAACTCTA-TGGCACCCTTTTAA
* * * *
1176101 AGCCCACAAGTCAGTGGCATC
63 AGTCCACAACTCCGTGGCACC
* * * * * * * *
1176122 TCTTCAAAGCCCACAAGTCAGCGGCATCCTTTTAAAGCCCACAAGTC-AGTGGCATCCTTTCAAA
1 T-TTTAAAGCCCACAACTCAGTGGCACCCTTTTAAAGTCCACAACTCTA-TGGCACCCTTTTAAA
* * *** * *
1176186 GCCCACAAGTTAATGGTATC
64 GTCCACAACTCCGTGGCACC
** * * * * *
1176206 TTTTCGGAGCCCACAAGTTAGTGGCATCCTTTTCAAAGCCCACGAA-TC-AGTGGCACCCTTTCA
1 TTTT-AAAGCCCACAACTCAGTGGCACCCTTTT-AAAGTCCAC-AACTCTA-TGGCACCCTTTTA
* * * *
1176269 TAGCCCACAAGTCAGTGGCACC
62 AAGTCCACAACTCCGTGGCACC
* *
1176291 TTTTCAAAGCCCACAAGTCGGTGGCA
1 TTTT-AAAGCCCACAACTCAGTGGCA
1176317 ACTTTCTCTA
Statistics
Matches: 594, Mismatches: 78, Indels: 41
0.83 0.11 0.06
Matches are distributed among these distances:
81 19 0.03
82 77 0.13
83 224 0.38
84 166 0.28
85 106 0.18
86 2 0.00
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.26
Consensus pattern (83 bp):
TTTTAAAGCCCACAACTCAGTGGCACCCTTTTAAAGTCCACAACTCTATGGCACCCTTTTAAAGT
CCACAACTCCGTGGCACC
Found at i:1175822 original size:110 final size:109
Alignment explanation
Indices: 1175541--1175940 Score: 563
Period size: 110 Copynumber: 3.6 Consensus size: 109
1175531 ATCAATACAT
* *
1175541 TTTTAAAGTCCATAACTCTATGGCACCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGTC
1 TTTTAAAGTCCACAACTCTATGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTC
* *
1175606 CACAACTCCGTGGCACCTTTTAAAGTCCACAACTCCGTGGCACCC
65 CACAACTCCGTGGCCCCTTTTAAAGTCCACAACTCCGTGGCACCA
1175651 TTTTAAAGTCCACAACTCTATGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1 TTTTAAAGTCCACAACTCTATGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTC
* *
1175716 CACAACTCCGTGGCTCCCTTTTAAAATCCACAACTTCGTGGCACCA
65 CACAACTCCGTGGC-CCCTTTTAAAGTCCACAACTCCGTGGCACCA
** *
1175762 TTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCCGTGGCACCCTTTTAAGTCC
1 TTTTAAAGTCCACAACTCTATGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
*
1175827 ACAACTCCGTGGCGGCCCTTTTTAAGTCCACAACTCCGTGGCA-CA
66 ACAACTCCGTGGC--CCCTTTTAAAGTCCACAACTCCGTGGCACCA
* ** * ** *
1175872 CTTTT-AAGCCCACAGGTC-AGTGGCATCAATTTAAGTCCACAACTCCGTGGCACCCTTTTAATT
1 -TTTTAAAGTCCACAACTCTA-TGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGT
1175935 CCACAA
64 CCACAA
1175941 GTTAGTGGCA
Statistics
Matches: 263, Mismatches: 22, Indels: 10
0.89 0.07 0.03
Matches are distributed among these distances:
110 151 0.57
111 112 0.43
ACGTcount: A:0.25, C:0.33, G:0.14, T:0.27
Consensus pattern (109 bp):
TTTTAAAGTCCACAACTCTATGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
ACAACTCCGTGGCCCCTTTTAAAGTCCACAACTCCGTGGCACCA
Found at i:1175970 original size:28 final size:28
Alignment explanation
Indices: 1175577--1176335 Score: 447
Period size: 28 Copynumber: 27.2 Consensus size: 28
1175567 CCTTTTAAGT
* * * * *
1175577 CCACAACTCTGTGGCACCCTTTTAAAGT
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* * * *
1175605 CCACAACTCCGTGGCA-CCTTTTAAAGT
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* * * * *
1175632 CCACAACTCCGTGGCACCCTTTTAAAGT
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* * * *
1175660 CCACAACTCTA-TGGCACCCTTTTAAAGT
1 CCACAAGTC-AGTGGCATCCTTTCAAAGC
* * * * *
1175688 CCACAACTCCGTGGCACCCTTT-TAAGT
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* * * **
1175715 CCACAACTCCGTGGC-TCCCTTTTAAAAT
1 CCACAAGTCAGTGGCAT-CCTTTCAAAGC
* * *
1175743 CCACAACTTC-GTGGCA-CCATTTTAAAGT
1 CCACAA-GTCAGTGGCATCC-TTTCAAAGC
* * * *
1175771 CCACAACTCCGTGGCACCCTTT-TAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* * * * *
1175798 CCACAACTCCGTGGCACCCTTT-TAAGT
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* * ** ** *
1175825 CCACAACTCCGTGGCGGCCCTTTTTAAGT
1 CCACAAGTCAGTGGC-ATCCTTTCAAAGC
* * *
1175854 CCACAACTCCGTGGCA-CACTTT-TAAGC
1 CCACAAGTCAGTGGCATC-CTTTCAAAGC
* * *
1175881 CCACAGGTCAGTGGCATCAATTT--AAGT
1 CCACAAGTCAGTGGCATC-CTTTCAAAGC
* * * * **
1175908 CCACAACTCCGTGGCACCCTTT-TAATT
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* *
1175935 CCACAAGTTAGTGGCATCATTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* * * *
1175963 CTACAAGTCAATAGCATCATTTTCAAAGC
1 CCACAAGTCAGTGGCATC-CTTTCAAAGC
* * *
1175992 CCACGAA-TTAGTGGCACCCTTTCAAAAC
1 CCAC-AAGTCAGTGGCATCCTTTCAAAGC
* *
1176020 CCACAAGTCAGTGGCATCTTTTCGAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* * * *
1176048 CCACAAATCGGTGGCA-CCTTTTCATAGT
1 CCACAAGTCAGTGGCATCC-TTTCAAAGC
*
1176076 CCACAAGTTAGTGGCATCCTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
1176104 CCACAAGTCAGTGGCAT-CTCTTCAAAGC
1 CCACAAGTCAGTGGCATCCT-TTCAAAGC
* *
1176132 CCACAAGTCAGCGGCATCCTTTTAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
1176160 CCACAAGTCAGTGGCATCCTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* * * * **
1176188 CCACAAGTTAATGGTATCTTTTCGGAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
*
1176216 CCACAAGTTAGTGGCATCCTTTTCAAAGC
1 CCACAAGTCAGTGGCATCC-TTTCAAAGC
* *
1176245 CCACGAA-TCAGTGGCACCCTTTCATAGC
1 CCAC-AAGTCAGTGGCATCCTTTCAAAGC
1176273 CCACAAGTCAGTGGCA-CCTTTTCAAAGC
1 CCACAAGTCAGTGGCATCC-TTTCAAAGC
* * *
1176301 CCACAAGTCGGTGGCAACTTTCTCTAAAGC
1 CCACAAGTCAGTGGCATCCTT-TC-AAAGC
1176331 CCACA
1 CCACA
1176336 CAAGTTGGTG
Statistics
Matches: 616, Mismatches: 85, Indels: 58
0.81 0.11 0.08
Matches are distributed among these distances:
26 3 0.00
27 163 0.26
28 365 0.59
29 71 0.12
30 14 0.02
ACGTcount: A:0.27, C:0.32, G:0.16, T:0.25
Consensus pattern (28 bp):
CCACAAGTCAGTGGCATCCTTTCAAAGC
Found at i:1184709 original size:40 final size:40
Alignment explanation
Indices: 1184654--1184739 Score: 172
Period size: 40 Copynumber: 2.1 Consensus size: 40
1184644 TCAAGTCAAA
1184654 AGCCTCTTAAACACCTAAAGCAACATGGGGAAATCTTAGG
1 AGCCTCTTAAACACCTAAAGCAACATGGGGAAATCTTAGG
1184694 AGCCTCTTAAACACCTAAAGCAACATGGGGAAATCTTAGG
1 AGCCTCTTAAACACCTAAAGCAACATGGGGAAATCTTAGG
1184734 AGCCTC
1 AGCCTC
1184740 CAAAGGTTGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (40 bp):
AGCCTCTTAAACACCTAAAGCAACATGGGGAAATCTTAGG
Found at i:1185746 original size:34 final size:35
Alignment explanation
Indices: 1185698--1185765 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 35
1185688 TTTAGTGGTA
* *
1185698 TTTCTTTTCAAAGTCCACAACTCTGTGGCAACCTT
1 TTTCTTCTCAAAGTCCACAACTCCGTGGCAACCTT
1185733 TTTCTTCT-AAAGTCCACAACTCCGTGGCAACCT
1 TTTCTTCTCAAAGTCCACAACTCCGTGGCAACCT
1185766 ATTAAGTCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 24 0.77
35 7 0.23
ACGTcount: A:0.24, C:0.31, G:0.12, T:0.34
Consensus pattern (35 bp):
TTTCTTCTCAAAGTCCACAACTCCGTGGCAACCTT
Found at i:1185782 original size:27 final size:27
Alignment explanation
Indices: 1185740--1185836 Score: 133
Period size: 27 Copynumber: 3.6 Consensus size: 27
1185730 CTTTTTCTTC
1185740 TAAAGTCCACAACTCCGTGGCAACCTAT
1 TAAAGTCCACAACTCCGTGGCAACCT-T
* *
1185768 T-AAGTCCACAGCTCCGTGGCACCCTT
1 TAAAGTCCACAACTCCGTGGCAACCTT
* *
1185794 TAAAGTCCACAACTCTGTGGCATCCTTT
1 TAAAGTCCACAACTCCGTGGCAACC-TT
1185822 TAAAGTCCACAACTC
1 TAAAGTCCACAACTC
1185837 TGATGGGATT
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
26 2 0.03
27 42 0.68
28 18 0.29
ACGTcount: A:0.28, C:0.33, G:0.14, T:0.25
Consensus pattern (27 bp):
TAAAGTCCACAACTCCGTGGCAACCTT
Found at i:1190671 original size:20 final size:20
Alignment explanation
Indices: 1190629--1190695 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
1190619 TTCTACAATT
* *
1190629 TGTATCGATACAACAAGTTAA
1 TGTATCGATAC-ATAAGTGAA
1190650 TGTATCGATACATAAGTGAA
1 TGTATCGATACATAAGTGAA
*
1190670 TGTATCAATACATAAGTGAA
1 TGTATCGATACATAAGTGAA
*
1190690 TATATC
1 TGTATC
1190696 AATGTCGTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
20 31 0.74
21 11 0.26
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (20 bp):
TGTATCGATACATAAGTGAA
Found at i:1191808 original size:13 final size:13
Alignment explanation
Indices: 1191790--1191815 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1191780 CAATTTTTTG
1191790 TGTATCGATACAT
1 TGTATCGATACAT
1191803 TGTATCGATACAT
1 TGTATCGATACAT
1191816 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1191880 original size:21 final size:21
Alignment explanation
Indices: 1191854--1191929 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1191844 CTGCCAAGAA
*
1191854 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
1191875 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
1191895 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
1191916 ATGTATCGATACAT
1 ATGTATCGATACAT
1191930 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:1191900 original size:20 final size:20
Alignment explanation
Indices: 1191875--1191947 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1191865 CATCTTTTTT
1191875 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
1191895 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
1191916 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1191936 ATGTATCGATAC
1 ATGTATCGATAC
1191948 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:1191911 original size:41 final size:41
Alignment explanation
Indices: 1191854--1191947 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
1191844 CTGCCAAGAA
*
1191854 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1191895 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1191936 ATGTATCGATAC
1 ATGTATCGATAC
1191948 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:1194404 original size:13 final size:13
Alignment explanation
Indices: 1194386--1194424 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1194376 ATAATCACCC
*
1194386 TGTATCGATACAG
1 TGTATCGATACAA
1194399 TGTATCGATACAA
1 TGTATCGATACAA
1194412 TGTATCGATACAA
1 TGTATCGATACAA
1194425 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1194435 original size:20 final size:20
Alignment explanation
Indices: 1194410--1194488 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
1194400 GTATCGATAC
1194410 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
1194430 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
*
1194455 GATGTATCGATACACAA-AAA
1 AATGTATCGATACA-AAGAAA
*
1194475 CATGTATCGATACA
1 AATGTATCGATACA
1194489 TTTTGGACAT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
20 32 0.65
25 16 0.33
26 1 0.02
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:1196523 original size:15 final size:15
Alignment explanation
Indices: 1196503--1196533 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1196493 ATTTCGTTTG
*
1196503 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1196518 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1196533 G
1 G
1196534 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1200332 original size:13 final size:13
Alignment explanation
Indices: 1200314--1200339 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1200304 CAATTTTTTG
1200314 TGTATCGATACAT
1 TGTATCGATACAT
1200327 TGTATCGATACAT
1 TGTATCGATACAT
1200340 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1200404 original size:21 final size:21
Alignment explanation
Indices: 1200378--1200453 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1200368 CTGCCAAGAA
*
1200378 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
1200399 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
1200419 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
1200440 ATGTATCGATACAT
1 ATGTATCGATACAT
1200454 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:1200424 original size:20 final size:20
Alignment explanation
Indices: 1200399--1200471 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1200389 CATCTTTTTT
1200399 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
1200419 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
1200440 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1200460 ATGTATCGATAC
1 ATGTATCGATAC
1200472 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:1200435 original size:41 final size:41
Alignment explanation
Indices: 1200378--1200471 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
1200368 CTGCCAAGAA
*
1200378 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1200419 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1200460 ATGTATCGATAC
1 ATGTATCGATAC
1200472 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:1204126 original size:13 final size:13
Alignment explanation
Indices: 1204108--1204133 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1204098 CAATTTTTTG
1204108 TGTATCGATACAT
1 TGTATCGATACAT
1204121 TGTATCGATACAT
1 TGTATCGATACAT
1204134 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1206506 original size:21 final size:21
Alignment explanation
Indices: 1206482--1206528 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
1206472 TTTAATGCTG
1206482 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
1206502 -TATTTGAAGTGAAAAACAAGT
1 AT-TTTGAAGTGAAAAACAAGT
1206523 ATTTTG
1 ATTTTG
1206529 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 1 0.04
20 4 0.17
21 9 0.39
22 9 0.39
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:1206667 original size:13 final size:13
Alignment explanation
Indices: 1206649--1206687 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1206639 ATAATCACCC
*
1206649 TGTATCGATACAG
1 TGTATCGATACAA
1206662 TGTATCGATACAA
1 TGTATCGATACAA
1206675 TGTATCGATACAA
1 TGTATCGATACAA
1206688 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1206698 original size:20 final size:20
Alignment explanation
Indices: 1206673--1206751 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
1206663 GTATCGATAC
1206673 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
1206693 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
1206718 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
1206738 CATGTATCGATACA
1 AATGTATCGATACA
1206752 TTTTGGACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 32 0.64
25 18 0.36
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:1207304 original size:21 final size:21
Alignment explanation
Indices: 1207271--1207311 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1207261 CTAAGTAAAA
1207271 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
1207292 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
1207312 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:1207376 original size:20 final size:19
Alignment explanation
Indices: 1207351--1207421 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
1207341 ACCCTGAAAA
1207351 GTATCGATACACATTTAAAT
1 GTATCGATACACA-TTAAAT
* **
1207371 GTATCGATACAAATTGCAT
1 GTATCGATACACATTAAAT
**
1207390 AGTATCGATACACACAAATAT
1 -GTATCGATACACATTAA-AT
1207411 GTATCGATACA
1 GTATCGATACA
1207422 GGTCATTGGC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 4 0.10
20 35 0.85
21 2 0.05
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.30
Consensus pattern (19 bp):
GTATCGATACACATTAAAT
Found at i:1207517 original size:10 final size:10
Alignment explanation
Indices: 1207498--1207528 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1207488 AATCTCATTT
1207498 TCACTGTTCA
1 TCACTGTTCA
*
1207508 TCACTATTCA
1 TCACTGTTCA
1207518 TCACTGTTCA
1 TCACTGTTCA
1207528 T
1 T
1207529 GTATCGATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.23, C:0.29, G:0.06, T:0.42
Consensus pattern (10 bp):
TCACTGTTCA
Found at i:1207544 original size:22 final size:23
Alignment explanation
Indices: 1207516--1207574 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
1207506 CATCACTATT
*
1207516 CATCACTGTTCATGTATCG-ATA
1 CATCACTGTTCATGTATCGTAAA
*
1207538 CATCACTATTCATGTATCGTTAAA
1 CATCACTGTTCATGTATCG-TAAA
*
1207562 AATCACTGTTCAT
1 CATCACTGTTCAT
1207575 CACTATTCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 18 0.58
24 13 0.42
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.37
Consensus pattern (23 bp):
CATCACTGTTCATGTATCGTAAA
Found at i:1207621 original size:13 final size:13
Alignment explanation
Indices: 1207603--1207628 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1207593 ACATATTTGT
1207603 GTGTATCGATACA
1 GTGTATCGATACA
1207616 GTGTATCGATACA
1 GTGTATCGATACA
1207629 TCATAAATAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
GTGTATCGATACA
Found at i:1208170 original size:34 final size:35
Alignment explanation
Indices: 1208107--1208173 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
1208097 CTAAGTGATT
1208107 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
1208143 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
1208174 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:1210143 original size:15 final size:15
Alignment explanation
Indices: 1210123--1210153 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1210113 ATTTCGTTTG
*
1210123 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1210138 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1210153 G
1 G
1210154 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1214230 original size:13 final size:13
Alignment explanation
Indices: 1214212--1214237 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1214202 CAATTTTTTG
1214212 TGTATCGATACAT
1 TGTATCGATACAT
1214225 TGTATCGATACAT
1 TGTATCGATACAT
1214238 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1215151 original size:24 final size:24
Alignment explanation
Indices: 1215123--1215184 Score: 65
Period size: 24 Copynumber: 2.5 Consensus size: 24
1215113 TTGCCTGTTT
1215123 CTATTTC-TTCTTAATTTGCT-GCAG
1 CTATTTCTTTCTTAA-TTG-TAGCAG
* *
1215147 CTATTACTTTCTTCATTGTAGCAG
1 CTATTTCTTTCTTAATTGTAGCAG
1215171 CTATTTCGTTTCTT
1 CTATTTC-TTTCTT
1215185 TCTTCATTGC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
23 1 0.03
24 19 0.59
25 12 0.38
ACGTcount: A:0.16, C:0.21, G:0.11, T:0.52
Consensus pattern (24 bp):
CTATTTCTTTCTTAATTGTAGCAG
Found at i:1216339 original size:42 final size:41
Alignment explanation
Indices: 1216309--1217038 Score: 593
Period size: 42 Copynumber: 17.4 Consensus size: 41
1216299 GTCAATGGGC
* * ** *
1216309 AGACAAAAGGTAAAGAAGTCTTCCGGGTCAAAATCAACAGGT
1 AGACTAAAGGTAAAGAAGTC-TCAGGGTCAAAGCCGACAGGT
* * * * *
1216351 AAAC-AAATGGTAATGAAGTC-CTAGGGTCAAAGCTGATAGGC
1 AGACTAAA-GGTAAAGAAGTCTC-AGGGTCAAAGCCGACAGGT
*
1216392 AGACTAAAGGTAAAGAAATCTCTAGGGTCAAAGCCGACAGGT
1 AGACTAAAGGTAAAGAAGTCTC-AGGGTCAAAGCCGACAGGT
* *
1216434 AAACTAAAGGTAAAGAAGTCTCCAAGGTCAAAGCCGACAGGT
1 AGACTAAAGGTAAAGAAGTCT-CAGGGTCAAAGCCGACAGGT
* * * * *
1216476 AGACTAAAGGTAAAGAAGTCTCTAAGGTCAAAACCGATAAGC
1 AGACTAAAGGTAAAGAAGTCTC-AGGGTCAAAGCCGACAGGT
* * *
1216518 AGATTAAAGGTAAAGAAGTCTCTAGGGTCAAAGCCGACAAGC
1 AGACTAAAGGTAAAGAAGTCTC-AGGGTCAAAGCCGACAGGT
* * *
1216560 AGACTAAAGGTAAAGAAGTCTCTAGGGTTAAAGTCGATAGGT
1 AGACTAAAGGTAAAGAAGTCTC-AGGGTCAAAGCCGACAGGT
* * * *
1216602 AGATTAAAGGTAAAGAAGTCTCCAAGATCAAAGCCGACAAGT
1 AGACTAAAGGTAAAGAAGTCT-CAGGGTCAAAGCCGACAGGT
* * * ** *
1216644 AGACAAAAGGT-AAGAAATCTCCAAGGTCAAAGTGGACAGGC
1 AGACTAAAGGTAAAGAAGTCT-CAGGGTCAAAGCCGACAGGT
* * * *
1216685 AGAATAAAGGTAAAGAAGCCTCTAAGGTCAAAGCCAACAGGT
1 AGACTAAAGGTAAAGAAGTCTC-AGGGTCAAAGCCGACAGGT
* * ** *
1216727 AGACTAAAGGTAAAAAAAGTCTCCAAGGTCAAAATCGATAGGT
1 AGACTAAAGGT-AAAGAAGTCT-CAGGGTCAAAGCCGACAGGT
* * * *
1216770 AGACTAAAGGTAAAGAAGTCTCTAAGGTCAAAACTGACAGGC
1 AGACTAAAGGTAAAGAAGTCTC-AGGGTCAAAGCCGACAGGT
* * * * *
1216812 AGACTAAAGGTAAAGAAGTCTTTAAGGTCAAAGCTGATAGGC
1 AGACTAAAGGTAAAGAAGTC-TCAGGGTCAAAGCCGACAGGT
* * * * * * *
1216854 AAACTAAAGGTAAAAAAGTCTCTAGGGTTAAAGTCAATAGGC
1 AGACTAAAGGTAAAGAAGTCTC-AGGGTCAAAGCCGACAGGT
* * * * * * *
1216896 AAACTAAAAGTAAAAAAGTCTCCAAGGTCAAAGCCAACAAGC
1 AGACTAAAGGTAAAGAAGTCT-CAGGGTCAAAGCCGACAGGT
* * ** *
1216938 AGACAAAAGGTAAAGAAATCTCTAGGGTCAAAGCAAACATGT
1 AGACTAAAGGTAAAGAAGTCTC-AGGGTCAAAGCCGACAGGT
* * *
1216980 AGAATAAAAGGTAAAGAAGTCTCCAGGGTTAAAGCCGACAGGC
1 AGACT-AAAGGTAAAGAAGTCT-CAGGGTCAAAGCCGACAGGT
1217023 AGACTAAAGGTAAAGA
1 AGACTAAAGGTAAAGA
1217039 CTGATAGGCA
Statistics
Matches: 567, Mismatches: 103, Indels: 36
0.80 0.15 0.05
Matches are distributed among these distances:
40 1 0.00
41 66 0.12
42 427 0.75
43 71 0.13
44 2 0.00
ACGTcount: A:0.44, C:0.15, G:0.24, T:0.17
Consensus pattern (41 bp):
AGACTAAAGGTAAAGAAGTCTCAGGGTCAAAGCCGACAGGT
Found at i:1216498 original size:84 final size:84
Alignment explanation
Indices: 1216265--1217038 Score: 705
Period size: 84 Copynumber: 9.2 Consensus size: 84
1216255 AAGTCGACGA
* * * ** *
1216265 GCAGAC-AAAGGATAACGAAGTCTCCTAA-GTCAAAGTCAATGGGCAGACAAAAGGTAAAGAAGT
1 GCAGACTAAAGG-TAAAGAAGTCT-CTAAGGTCAAAGCCGACAGGCAGACTAAAGGTAAAGAAGT
** ** *
1216328 CT-TCCGGGTCAAAATCAACAG
64 CTCT-AAGGTCAAAGCCGACAG
* * * * * * *
1216349 GTAAAC-AAATGGTAATGAAGTC-CTAGGGTCAAAGCTGATAGGCAGACTAAAGGTAAAGAAATC
1 GCAGACTAAA-GGTAAAGAAGTCTCTAAGGTCAAAGCCGACAGGCAGACTAAAGGTAAAGAAGTC
*
1216412 TCTAGGGTCAAAGCCGACAG
65 TCTAAGGTCAAAGCCGACAG
* * * *
1216432 GTAAACTAAAGGTAAAGAAGTCTCCAAGGTCAAAGCCGACAGGTAGACTAAAGGTAAAGAAGTCT
1 GCAGACTAAAGGTAAAGAAGTCTCTAAGGTCAAAGCCGACAGGCAGACTAAAGGTAAAGAAGTCT
* * *
1216497 CTAAGGTCAAAACCGATAA
66 CTAAGGTCAAAGCCGACAG
* * *
1216516 GCAGATTAAAGGTAAAGAAGTCTCTAGGGTCAAAGCCGACAAGCAGACTAAAGGTAAAGAAGTCT
1 GCAGACTAAAGGTAAAGAAGTCTCTAAGGTCAAAGCCGACAGGCAGACTAAAGGTAAAGAAGTCT
* * * *
1216581 CTAGGGTTAAAGTCGATAG
66 CTAAGGTCAAAGCCGACAG
* * * * * * * *
1216600 GTAGATTAAAGGTAAAGAAGTCTCCAAGATCAAAGCCGACAAGTAGACAAAAGGT-AAGAAATCT
1 GCAGACTAAAGGTAAAGAAGTCTCTAAGGTCAAAGCCGACAGGCAGACTAAAGGTAAAGAAGTCT
* **
1216664 CCAAGGTCAAAGTGGACAG
66 CTAAGGTCAAAGCCGACAG
* * * * *
1216683 GCAGAATAAAGGTAAAGAAGCCTCTAAGGTCAAAGCCAACAGGTAGACTAAAGGTAAAAAAAGTC
1 GCAGACTAAAGGTAAAGAAGTCTCTAAGGTCAAAGCCGACAGGCAGACTAAAGGT-AAAGAAGTC
* ** *
1216748 TCCAAGGTCAAAATCGATAG
65 TCTAAGGTCAAAGCCGACAG
* * *
1216768 GTAGACTAAAGGTAAAGAAGTCTCTAAGGTCAAAACTGACAGGCAGACTAAAGGTAAAGAAGTCT
1 GCAGACTAAAGGTAAAGAAGTCTCTAAGGTCAAAGCCGACAGGCAGACTAAAGGTAAAGAAGTCT
* * *
1216833 TTAAGGTCAAAGCTGATAG
66 CTAAGGTCAAAGCCGACAG
* * * * * * * * * *
1216852 GCAAACTAAAGGTAAAAAAGTCTCTAGGGTTAAAGTCAATAGGCAAACTAAAAGTAAAAAAGTCT
1 GCAGACTAAAGGTAAAGAAGTCTCTAAGGTCAAAGCCGACAGGCAGACTAAAGGTAAAGAAGTCT
* * *
1216917 CCAAGGTCAAAGCCAACAA
66 CTAAGGTCAAAGCCGACAG
* * * ** * * *
1216936 GCAGACAAAAGGTAAAGAAATCTCTAGGGTCAAAGCAAACATGTAGAATAAAAGGTAAAGAAGTC
1 GCAGACTAAAGGTAAAGAAGTCTCTAAGGTCAAAGCCGACAGGCAGACT-AAAGGTAAAGAAGTC
* * *
1217001 TCCAGGGTTAAAGCCGACAG
65 TCTAAGGTCAAAGCCGACAG
1217021 GCAGACTAAAGGTAAAGA
1 GCAGACTAAAGGTAAAGA
1217039 CTGATAGGCA
Statistics
Matches: 569, Mismatches: 113, Indels: 15
0.82 0.16 0.02
Matches are distributed among these distances:
82 3 0.01
83 130 0.23
84 317 0.56
85 119 0.21
ACGTcount: A:0.44, C:0.16, G:0.24, T:0.17
Consensus pattern (84 bp):
GCAGACTAAAGGTAAAGAAGTCTCTAAGGTCAAAGCCGACAGGCAGACTAAAGGTAAAGAAGTCT
CTAAGGTCAAAGCCGACAG
Found at i:1216551 original size:126 final size:126
Alignment explanation
Indices: 1216265--1217038 Score: 759
Period size: 126 Copynumber: 6.1 Consensus size: 126
1216255 AAGTCGACGA
* * * ** *
1216265 GCAGAC-AAAGGATAACGAAGTCTCCTAA-GTCAAAGTCAATGGGCAGACAAAAGGTAAAGAAGT
1 GCAGACTAAAGG-TAAAGAAGTCT-CTAAGGTCAAAGCCGACAGGCAGACTAAAGGTAAAGAAGT
** ** * * * * *
1216328 CT-TCCGGGTCAAAATCAACAGGTAAAC-AAATGGTAATGAAGTC-CTAGGGTCAAAGCTGATAG
64 CTCT-AAGGTCAAAGCCAACAGGTAGACTAAA-GGTAAAGAAGTCTCCAAGGTCAAAGCCGATAG
* * * *
1216390 GCAGACTAAAGGTAAAGAAATCTCTAGGGTCAAAGCCGACAGGTAAACTAAAGGTAAAGAAGTCT
1 GCAGACTAAAGGTAAAGAAGTCTCTAAGGTCAAAGCCGACAGGCAGACTAAAGGTAAAGAAGTCT
* * * * *
1216455 CCAAGGTCAAAGCCGACAGGTAGACTAAAGGTAAAGAAGTCTCTAAGGTCAAAACCGATAA
66 CTAAGGTCAAAGCCAACAGGTAGACTAAAGGTAAAGAAGTCTCCAAGGTCAAAGCCGATAG
* * *
1216516 GCAGATTAAAGGTAAAGAAGTCTCTAGGGTCAAAGCCGACAAGCAGACTAAAGGTAAAGAAGTCT
1 GCAGACTAAAGGTAAAGAAGTCTCTAAGGTCAAAGCCGACAGGCAGACTAAAGGTAAAGAAGTCT
* * * * * * * * *
1216581 CTAGGGTTAAAGTCGATAGGTAGATTAAAGGTAAAGAAGTCTCCAAGATCAAAGCCGACAA
66 CTAAGGTCAAAGCCAACAGGTAGACTAAAGGTAAAGAAGTCTCCAAGGTCAAAGCCGATAG
* * * * ** * *
1216642 GTAGACAAAAGGT-AAGAAATCTCCAAGGTCAAAGTGGACAGGCAGAATAAAGGTAAAGAAGCCT
1 GCAGACTAAAGGTAAAGAAGTCTCTAAGGTCAAAGCCGACAGGCAGACTAAAGGTAAAGAAGTCT
* **
1216706 CTAAGGTCAAAGCCAACAGGTAGACTAAAGGTAAAAAAAGTCTCCAAGGTCAAAATCGATAG
66 CTAAGGTCAAAGCCAACAGGTAGACTAAAGGT-AAAGAAGTCTCCAAGGTCAAAGCCGATAG
* * *
1216768 GTAGACTAAAGGTAAAGAAGTCTCTAAGGTCAAAACTGACAGGCAGACTAAAGGTAAAGAAGTCT
1 GCAGACTAAAGGTAAAGAAGTCTCTAAGGTCAAAGCCGACAGGCAGACTAAAGGTAAAGAAGTCT
* ** * * * * * * * * *
1216833 TTAAGGTCAAAGCTGATAGGCAAACTAAAGGTAAAAAAGTCTCTAGGGTTAAAGTCAATAG
66 CTAAGGTCAAAGCCAACAGGTAGACTAAAGGTAAAGAAGTCTCCAAGGTCAAAGCCGATAG
* * * * * * * *
1216894 GCAAACTAAAAGTAAAAAAGTCTCCAAGGTCAAAGCCAACAAGCAGACAAAAGGTAAAGAAATCT
1 GCAGACTAAAGGTAAAGAAGTCTCTAAGGTCAAAGCCGACAGGCAGACTAAAGGTAAAGAAGTCT
* * * * * * *
1216959 CTAGGGTCAAAGCAAACATGTAGAATAAAAGGTAAAGAAGTCTCCAGGGTTAAAGCCGACAG
66 CTAAGGTCAAAGCCAACAGGTAGACT-AAAGGTAAAGAAGTCTCCAAGGTCAAAGCCGATAG
1217021 GCAGACTAAAGGTAAAGA
1 GCAGACTAAAGGTAAAGA
1217039 CTGATAGGCA
Statistics
Matches: 534, Mismatches: 107, Indels: 14
0.82 0.16 0.02
Matches are distributed among these distances:
124 3 0.01
125 142 0.27
126 274 0.51
127 115 0.22
ACGTcount: A:0.44, C:0.16, G:0.24, T:0.17
Consensus pattern (126 bp):
GCAGACTAAAGGTAAAGAAGTCTCTAAGGTCAAAGCCGACAGGCAGACTAAAGGTAAAGAAGTCT
CTAAGGTCAAAGCCAACAGGTAGACTAAAGGTAAAGAAGTCTCCAAGGTCAAAGCCGATAG
Found at i:1217036 original size:24 final size:25
Alignment explanation
Indices: 1217009--1217063 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
1216999 TCTCCAGGGT
1217009 TAAAG-CCGACAGGCAGACTAAAGG
1 TAAAGACCGACAGGCAGACTAAAGG
* *
1217033 TAAAGACTGATAGGCAGACTAAAGG
1 TAAAGACCGACAGGCAGACTAAAGG
1217058 TAAAGA
1 TAAAGA
1217064 AGTCTTCAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
24 5 0.18
25 23 0.82
ACGTcount: A:0.45, C:0.15, G:0.27, T:0.13
Consensus pattern (25 bp):
TAAAGACCGACAGGCAGACTAAAGG
Found at i:1217075 original size:42 final size:42
Alignment explanation
Indices: 1217029--1218315 Score: 717
Period size: 42 Copynumber: 29.9 Consensus size: 42
1217019 AGGCAGACTA
*
1217029 AAGGT-AAAGACTGATAGGCAGACTAAAGGTAAAGAAGTCT-T
1 AAGGTCAAAG-CTGACAGGCAGACTAAAGGTAAAGAAGTCTCT
* * * *
1217070 CAAGGTCAAAG-TCGACAAGCAAACTAAATGAAAAGAAGTCTCT
1 -AAGGTCAAAGCT-GACAGGCAGACTAAAGGTAAAGAAGTCTCT
* * * * *
1217113 AGGGTCAAAGATGATAGGCAAACTAAAGGTAAAGAAGTCTCC
1 AAGGTCAAAGCTGACAGGCAGACTAAAGGTAAAGAAGTCTCT
* ** *
1217155 AAGGTCAAAGCCGACAGGCAGAAAAAAGGTAAAGAAGCCTCT
1 AAGGTCAAAGCTGACAGGCAGACTAAAGGTAAAGAAGTCTCT
* * * *
1217197 AGGGTCAAAG-TCGACAGGCAGACTAAAGGTAAAAAAATCTCA
1 AAGGTCAAAGCT-GACAGGCAGACTAAAGGTAAAGAAGTCTCT
* *
1217239 AAGGTCAAAGCTGATAGGCAGACTAAAGGTAAAGAACTCTCT
1 AAGGTCAAAGCTGACAGGCAGACTAAAGGTAAAGAAGTCTCT
* * * * **
1217281 AAGGTCAAAGCCGAAAGGCAGACTAATGGTAAAG-ACTGAC-
1 AAGGTCAAAGCTGACAGGCAGACTAAAGGTAAAGAAGTCTCT
* * * * * * * **
1217321 AAGCAGACTAAAGGT-A-AAGAAGTCTCTAAGGT-CA-AAGTCGAT
1 AAG--GTC-AAAGCTGACAGGCAGACT-AAAGGTAAAGAAGTCTCT
* ** * * * * * *
1217363 -AGGTAAACTAAATGAAAGGAAGTCTCTAAGGTCAAAGCCAATAGGCAAACT
1 AAGGTCAA--AGCTGACAGGCAGACT-AAAGGT-AAAG---A-AGTC--TCT
*
1217414 AAAGGT-AAAGACTGACAGGCAGACTAAAGGTAAAGAAGTCTCC
1 -AAGGTCAAAG-CTGACAGGCAGACTAAAGGTAAAGAAGTCTCT
* * *
1217457 AAAGTCAAAG-TCGACAGGCAAACTAAAGGTAAAGAAGTTTCT
1 AAGGTCAAAGCT-GACAGGCAGACTAAAGGTAAAGAAGTCTCT
* * * *
1217499 AAGGTTAAAGCCGACAGGAAGATTAAAGGTAAAGAAGTCTCT
1 AAGGTCAAAGCTGACAGGCAGACTAAAGGTAAAGAAGTCTCT
* * * *
1217541 AAGTTCAAAGCCGACAGGTAGATTAAAGGTAAAGAAGTCTCT
1 AAGGTCAAAGCTGACAGGCAGACTAAAGGTAAAGAAGTCTCT
* * * *
1217583 AAGTTCAAAGCCGACAAGCAGACAAAAGGTAAAGAAGTCTCT
1 AAGGTCAAAGCTGACAGGCAGACTAAAGGTAAAGAAGTCTCT
* * * *
1217625 AGGGTCAAAGTTGACAGGCAGACTAAAGGTAAAGAAATCTCC
1 AAGGTCAAAGCTGACAGGCAGACTAAAGGTAAAGAAGTCTCT
* * * * * *
1217667 AAGGTCAATG-TCAAAAGGTAAACTAAAGGTAAA-AGAGTCTCC
1 AAGGTCAAAGCT-GACAGGCAGACTAAAGGTAAAGA-AGTCTCT
* * * * *
1217709 GAGGTCAAAGCTGATAAGCAGACTAAAGGTAAAAAAGTCTTT
1 AAGGTCAAAGCTGACAGGCAGACTAAAGGTAAAGAAGTCTCT
* * * * * * * *
1217751 AGGGTTGAAA-CCGATAAGCTGACTAAAGGTGACGATCGACAGGAAGACT-A
1 AAGG-TCAAAGCTGACAGGCAGACTAAAGGT----A---A-A-GAAGTCTCT
* *** * *
1217801 AAGGTAAAGAAGTCTTTGAGGTCAAAGCTGACAGGTAAACTAAATGAAAAGAAGTCTCT
1 AAGGT-CA-AAG-CTGACAGG-CAGA-CT-AAAGG---------T--AAAGAAGTCTCT
*
1217860 AAGGTCAAAGCTGACAGGCAGACTAAAGGTAAAGAAGTCTCC
1 AAGGTCAAAGCTGACAGGCAGACTAAAGGTAAAGAAGTCTCT
* ** * * *
1217902 AAAGTCAAAGCCAACAAGCAAACT-AAGGTAAAGAAGTCTTT
1 AAGGTCAAAGCTGACAGGCAGACTAAAGGTAAAGAAGTCTCT
* * * * * *
1217943 AGGGTTAAAGCTAATAGGCAGACTAAAGGTAAAAAAGTCTTT
1 AAGGTCAAAGCTGACAGGCAGACTAAAGGTAAAGAAGTCTCT
* * * *
1217985 AAGTTCAAAGCTGATAGGCAAACAAAAGGTAAAGAAGTCTCT
1 AAGGTCAAAGCTGACAGGCAGACTAAAGGTAAAGAAGTCTCT
* * * * * *
1218027 AGGGTCAAAGCTGATAGGCAAACTAATGGTAAAGAAATCTCC
1 AAGGTCAAAGCTGACAGGCAGACTAAAGGTAAAGAAGTCTCT
* * * *
1218069 AAGGTCAAAGCTGAAAGGTAAACTAAAGGTAAAGAAGTCTCC
1 AAGGTCAAAGCTGACAGGCAGACTAAAGGTAAAGAAGTCTCT
* * *
1218111 AAGGTCAAAGCTGACAAGCAGACTAAATGTAAAGAAGTCTCC
1 AAGGTCAAAGCTGACAGGCAGACTAAAGGTAAAGAAGTCTCT
** * * *
1218153 AAGGTCAAAG-TCGTTAGGCAGACCAAAGGTAAAAAAGTTTCCT
1 AAGGTCAAAGCT-GACAGGCAGACTAAAGGTAAAGAAGTCT-CT
* * * *
1218196 -AGGTTAAAGCCGACAGGCAAACTAAAGGTAAATAAGTCT-T
1 AAGGTCAAAGCTGACAGGCAGACTAAAGGTAAAGAAGTCTCT
* * * *
1218236 CAGAGTTAAAGCTGATAGGCATACTAAAGGTAAAGAAGTCTCT
1 AAG-GTCAAAGCTGACAGGCAGACTAAAGGTAAAGAAGTCTCT
** * * *
1218279 AAGGTCAAAGCCAACAAGCAGACAAAAAGTAAAGAAG
1 AAGGTCAAAGCTGACAGGCAGACTAAAGGTAAAGAAG
1218316 GGTTGGCCAG
Statistics
Matches: 968, Mismatches: 208, Indels: 138
0.74 0.16 0.11
Matches are distributed among these distances:
38 2 0.00
39 1 0.00
40 6 0.01
41 55 0.06
42 782 0.81
43 26 0.03
44 2 0.00
45 3 0.00
46 2 0.00
48 1 0.00
49 9 0.01
50 11 0.01
51 18 0.02
52 2 0.00
53 11 0.01
54 4 0.00
55 5 0.01
56 9 0.01
57 3 0.00
58 7 0.01
59 6 0.01
60 1 0.00
63 1 0.00
65 1 0.00
ACGTcount: A:0.43, C:0.15, G:0.24, T:0.18
Consensus pattern (42 bp):
AAGGTCAAAGCTGACAGGCAGACTAAAGGTAAAGAAGTCTCT
Found at i:1217088 original size:152 final size:151
Alignment explanation
Indices: 1216890--1217189 Score: 388
Period size: 152 Copynumber: 2.0 Consensus size: 151
1216880 GTTAAAGTCA
* *
1216890 ATAGGCAAACTAAAAGTAAAAAAGTCTCCAAGGTCAAAGCCAACAAGCAGACAAAAGGTAAAGAA
1 ATAGGCAAACTAAAAGTAAAAAAGTCTCCAAGGTCAAAGCCAACAAGCAAACAAAAGGAAAAGAA
* * * *
1216955 ATCTCTAGGGTCAAAGCA-AACATGTAGAA-TAAAAGGTAAAGAAGTCTCCAGGGTTAAAGCCGA
66 ATCTCTAGGGTCAAAG-ATAACAGGCA-AACT-AAAGGTAAAGAAGTCTCCAAGGTCAAAGCCGA
**
1217018 CAGGCAGACTAAAGGTAAAGACTG
128 CAGGCAGAAAAAAGGTAAAGACTG
* * * * * * * *
1217042 ATAGGCAGACTAAAGGTAAAGAAGTCTTCAAGGTCAAAGTCGACAAGCAAACTAAATGAAAAGAA
1 ATAGGCAAACTAAAAGTAAAAAAGTCTCCAAGGTCAAAGCCAACAAGCAAACAAAAGGAAAAGAA
* * *
1217107 GTCTCTAGGGTCAAAGATGATAGGCAAACTAAAGGTAAAGAAGTCTCCAAGGTCAAAGCCGACAG
66 ATCTCTAGGGTCAAAGATAACAGGCAAACTAAAGGTAAAGAAGTCTCCAAGGTCAAAGCCGACAG
1217172 GCAGAAAAAAGGTAAAGA
131 GCAGAAAAAAGGTAAAGA
1217190 AGCCTCTAGG
Statistics
Matches: 127, Mismatches: 19, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
151 52 0.41
152 75 0.59
ACGTcount: A:0.46, C:0.16, G:0.23, T:0.15
Consensus pattern (151 bp):
ATAGGCAAACTAAAAGTAAAAAAGTCTCCAAGGTCAAAGCCAACAAGCAAACAAAAGGAAAAGAA
ATCTCTAGGGTCAAAGATAACAGGCAAACTAAAGGTAAAGAAGTCTCCAAGGTCAAAGCCGACAG
GCAGAAAAAAGGTAAAGACTG
Found at i:1217306 original size:24 final size:24
Alignment explanation
Indices: 1217279--1217340 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 24
1217269 AAAGAACTCT
1217279 CTAAGGTCAAAG-CCGA-AAGGCAGA
1 CTAAGGT-AAAGACCGACAA-GCAGA
*
1217303 CTAATGGTAAAGACTGACAAGCAGA
1 CTAA-GGTAAAGACCGACAAGCAGA
1217328 CTAAAGGTAAAGA
1 CT-AAGGTAAAGA
1217341 AGTCTCTAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
24 8 0.24
25 21 0.64
26 4 0.12
ACGTcount: A:0.45, C:0.16, G:0.26, T:0.13
Consensus pattern (24 bp):
CTAAGGTAAAGACCGACAAGCAGA
Found at i:1217357 original size:109 final size:110
Alignment explanation
Indices: 1217209--1217533 Score: 392
Period size: 109 Copynumber: 3.0 Consensus size: 110
1217199 GGTCAAAGTC
* * * * * *
1217209 GACAGGCAGACTAAAGGTAAAAAAATCTCAAAGGTCAAAGCTGATAGGCAGACTAAAGGTAAAGA
1 GACAAGCAGACTAAAGGTAAAGAAGTCTCTAAGGTCAAAGCTGACAGGCAAACTAAAGGTAAAGA
* *
1217274 ACTCTCTAAGGTCAAAGCCGAAAGGCAGACTAATGGTAAAGACT-
66 AGTCTCTAAGGTCAAAGCCGAAAGGCAGACTAAAGGTAAAGACTA
* * *
1217318 GACAAGCAGACTAAAGGTAAAGAAGTCTCTAAGGTCAAAG-TCGATAGGTAAACTAAATG-AAAG
1 GACAAGCAGACTAAAGGTAAAGAAGTCTCTAAGGTCAAAGCT-GACAGGCAAACTAAAGGTAAA-
*
1217381 GAAGTCTCTAAGGTCAAAGCC-AATAGGCAAACTAAAGGTAAAGACT-
64 GAAGTCTCTAAGGTCAAAGCCGAA-AGGCAGACTAAAGGTAAAGACTA
* * *
1217427 GACAGGCAGACTAAAGGTAAAGAAGTCTCCAAAGTCAAAG-TCGACAGGCAAACTAAAGGTAAAG
1 GACAAGCAGACTAAAGGTAAAGAAGTCTCTAAGGTCAAAGCT-GACAGGCAAACTAAAGGTAAAG
* * * * *
1217491 AAGTTTCTAAGGTTAAAGCCGACAGGAAGATTAAAGGTAAAGA
65 AAGTCTCTAAGGTCAAAGCCGAAAGGCAGACTAAAGGTAAAGA
1217534 AGTCTCTAAG
Statistics
Matches: 189, Mismatches: 22, Indels: 10
0.86 0.10 0.05
Matches are distributed among these distances:
108 6 0.03
109 179 0.95
110 4 0.02
ACGTcount: A:0.45, C:0.15, G:0.24, T:0.16
Consensus pattern (110 bp):
GACAAGCAGACTAAAGGTAAAGAAGTCTCTAAGGTCAAAGCTGACAGGCAAACTAAAGGTAAAGA
AGTCTCTAAGGTCAAAGCCGAAAGGCAGACTAAAGGTAAAGACTA
Found at i:1217482 original size:151 final size:150
Alignment explanation
Indices: 1217119--1217575 Score: 439
Period size: 151 Copynumber: 3.0 Consensus size: 150
1217109 CTCTAGGGTC
* * * *
1217119 AAAGA-TGATAGGCAAACTAAAGGTAAAGAAGTCTCCAAGGTCAAAGCCGACAGGCAGAA-AAAA
1 AAAGACTGACAGGCAGACTAAAGGTAAAGAAGTCTCCAAGGTCAAAGACGACAGGCA-AACTAAA
* * * * * *
1217182 GGTAAAGAAGCCTCTAGGGTCAAAGTCGACAGGCAGACTAAAGGTAAAAAAATCTCAAAGGTCAA
65 GGTAAAGAAGTCTCTAAGGTCAAAGTCGACAGG-AAACTAAAGGTAAAGAAGTCTCTAAGGTCAA
*
1217247 AGCTGATAGGCAGACTAAAGGT
129 AGCCGATAGGCAGACTAAAGGT
** * * * * * *
1217269 AAAGAACTCTCTAAG--GTC-AAAGCCG-AAAGGCAGACT--AATGGT-AAAGACTGACAAGCAG
1 AAAG-ACTGAC-AGGCAGACTAAAG--GTAAA-GAAGTCTCCAA-GGTCAAAGAC-GACAGGCAA
* *
1217327 ACTAAAGGTAAAGAAGTCTCTAAGGTCAAAGTCGATAGGTAAACTAAATG-AAAGGAAGTCTCTA
59 ACTAAAGGTAAAGAAGTCTCTAAGGTCAAAGTCGACAGG-AAACTAAAGGTAAA-GAAGTCTCTA
* *
1217391 AGGTCAAAGCCAATAGGCAAACTAAAGGT
122 AGGTCAAAGCCGATAGGCAGACTAAAGGT
* *
1217420 AAAGACTGACAGGCAGACTAAAGGTAAAGAAGTCTCCAAAGTCAAAGTCGACAGGCAAACTAAAG
1 AAAGACTGACAGGCAGACTAAAGGTAAAGAAGTCTCCAAGGTCAAAGACGACAGGCAAACTAAAG
* * * * *
1217485 GTAAAGAAGTTTCTAAGGTTAAAGCCGACAGGAAGATTAAAGGTAAAGAAGTCTCTAAGTTCAAA
66 GTAAAGAAGTCTCTAAGGTCAAAGTCGACAGGAA-ACTAAAGGTAAAGAAGTCTCTAAGGTCAAA
* * *
1217550 GCCGACAGGTAGATTAAAGGT
130 GCCGATAGGCAGACTAAAGGT
1217571 AAAGA
1 AAAGA
1217576 AGTCTCTAAG
Statistics
Matches: 242, Mismatches: 46, Indels: 37
0.74 0.14 0.11
Matches are distributed among these distances:
149 2 0.01
150 31 0.13
151 186 0.77
152 21 0.09
153 2 0.01
ACGTcount: A:0.44, C:0.15, G:0.24, T:0.16
Consensus pattern (150 bp):
AAAGACTGACAGGCAGACTAAAGGTAAAGAAGTCTCCAAGGTCAAAGACGACAGGCAAACTAAAG
GTAAAGAAGTCTCTAAGGTCAAAGTCGACAGGAAACTAAAGGTAAAGAAGTCTCTAAGGTCAAAG
CCGATAGGCAGACTAAAGGT
Found at i:1217911 original size:277 final size:276
Alignment explanation
Indices: 1217510--1218031 Score: 659
Period size: 277 Copynumber: 1.9 Consensus size: 276
1217500 AGGTTAAAGC
* * * * *
1217510 CGACAGGAAGATTAAAGGTAAAGAAGTCTCTAAGTTCAAAGCCGACAGGTAGATTAAAGGTAAAG
1 CGACAGGAAGACTAAAGGTAAAGAAGTCTCTAAGGTCAAAGCCGACAGGTAAACTAAAGGAAAAG
* * ** ***
1217575 AAGTCTCTAAGTTCAAAGCCGACAAGCAGACAAAAGGTAAAGAAGTCTCTAGGGTCAAAGTTGAC
66 AAGTCTCTAAGGTCAAAGCCGACAAGCAGACAAAAGGTAAAGAAGTCTCCAAAGTCAAAGCCAAC
* * * * *
1217640 AGGCAGACTAAAGGTAAAGAAATCTCCAAGGTCAATG-TCAAAAGGTAAACTAAAGGTAAAAGAG
131 AAGCAAACT-AAGGTAAAGAAATCTCCAAGGTCAAAGCT-AAAAGGCAAACTAAAGGTAAAAAAG
* * * *
1217704 TCTCCGAGGTCAAAGCTGATAAGCAGACTAAAGGTAAAAAAGTCTTTAGGGTTGAAACCGATAAG
194 TCTCCAAGGTCAAAGCTGATAAGCAAACAAAAGGTAAAAAAGTCTCTAGGGTTGAAACCGATAAG
1217769 CTGACTAAAGGTGACGAT
259 CTGACTAAAGGTGACGAT
* * * *
1217787 CGACAGGAAGACTAAAGGTAAAGAAGTCTTTGAGGTCAAAGCTGACAGGTAAACTAAATGAAAAG
1 CGACAGGAAGACTAAAGGTAAAGAAGTCTCTAAGGTCAAAGCCGACAGGTAAACTAAAGGAAAAG
* * *
1217852 AAGTCTCTAAGGTCAAAGCTGACAGGCAGACTAAAGGTAAAGAAGTCTCCAAAGTCAAAGCCAAC
66 AAGTCTCTAAGGTCAAAGCCGACAAGCAGACAAAAGGTAAAGAAGTCTCCAAAGTCAAAGCCAAC
* ** * * * *
1217917 AAGCAAACTAAGGTAAAGAAGTCTTTAGGGTTAAAGCTAATAGGCAGACTAAAGGTAAAAAAGTC
131 AAGCAAACTAAGGTAAAGAAATCTCCAAGGTCAAAGCTAAAAGGCAAACTAAAGGTAAAAAAGTC
** * * *
1217982 TTTAAGTTCAAAGCTGATAGGCAAACAAAAGGTAAAGAAGTCTCTAGGGT
196 TCCAAGGTCAAAGCTGATAAGCAAACAAAAGGTAAAAAAGTCTCTAGGGT
1218032 CAAAGCTGAT
Statistics
Matches: 204, Mismatches: 40, Indels: 3
0.83 0.16 0.01
Matches are distributed among these distances:
276 85 0.42
277 119 0.58
ACGTcount: A:0.43, C:0.15, G:0.24, T:0.19
Consensus pattern (276 bp):
CGACAGGAAGACTAAAGGTAAAGAAGTCTCTAAGGTCAAAGCCGACAGGTAAACTAAAGGAAAAG
AAGTCTCTAAGGTCAAAGCCGACAAGCAGACAAAAGGTAAAGAAGTCTCCAAAGTCAAAGCCAAC
AAGCAAACTAAGGTAAAGAAATCTCCAAGGTCAAAGCTAAAAGGCAAACTAAAGGTAAAAAAGTC
TCCAAGGTCAAAGCTGATAAGCAAACAAAAGGTAAAAAAGTCTCTAGGGTTGAAACCGATAAGCT
GACTAAAGGTGACGAT
Found at i:1217927 original size:151 final size:151
Alignment explanation
Indices: 1217637--1217927 Score: 327
Period size: 151 Copynumber: 1.9 Consensus size: 151
1217627 GGTCAAAGTT
* *
1217637 GACAGGCAGACTAAAGGTAAAGAAATCTCCAAGGTCAATGTCAAAAGGTAAACTAAAGGTAAAAG
1 GACAGGAAGACTAAAGGTAAAGAAATCTCCAAGGTCAAAGTCAAAAGGTAAACTAAAGGTAAAAG
* * ** ** * * *
1217702 AGTCTCCGAGGTCAAAGCTGATAAGCAGACTAAAGGTAAAAAAGTCTTTAGGGTTGAAACCGATA
66 AGTCTCCAAGGTCAAAGCTGACAAGCAGACTAAAGGTAAAAAAGTCTCCAAAGTTCAAACCAACA
**
1217767 AGCTGACTAAAGGTGACGATC
131 AGCAAACTAAAGGTGACGATC
* *** * * *
1217788 GACAGGAAGACTAAAGGTAAAGAAGTCTTTGAGGTCAAAG-CTGACAGGTAAACTAAATG-AAAA
1 GACAGGAAGACTAAAGGTAAAGAAATCTCCAAGGTCAAAGTC-AAAAGGTAAACTAAAGGTAAAA
* * *
1217851 GAAGTCTCTAAGGTCAAAGCTGACAGGCAGACTAAAGGTAAAGAAGTCTCCAAAG-TCAAAGCCA
65 G-AGTCTCCAAGGTCAAAGCTGACAAGCAGACTAAAGGTAAAAAAGTCTCCAAAGTTCAAA-CCA
1217915 ACAAGCAAACTAA
128 ACAAGCAAACTAA
1217928 GGTAAAGAAG
Statistics
Matches: 114, Mismatches: 23, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
150 10 0.09
151 104 0.91
ACGTcount: A:0.43, C:0.16, G:0.24, T:0.17
Consensus pattern (151 bp):
GACAGGAAGACTAAAGGTAAAGAAATCTCCAAGGTCAAAGTCAAAAGGTAAACTAAAGGTAAAAG
AGTCTCCAAGGTCAAAGCTGACAAGCAGACTAAAGGTAAAAAAGTCTCCAAAGTTCAAACCAACA
AGCAAACTAAAGGTGACGATC
Found at i:1221806 original size:20 final size:20
Alignment explanation
Indices: 1221757--1221812 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
1221747 ATATAAATAG
1221757 TAAATGTATCGATACATAAA
1 TAAATGTATCGATACATAAA
* * ***
1221777 TGAATATATCGATACATGCC
1 TAAATGTATCGATACATAAA
1221797 TAAATGTATCGATACA
1 TAAATGTATCGATACA
1221813 AAACCACCCT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.30
Consensus pattern (20 bp):
TAAATGTATCGATACATAAA
Found at i:1221907 original size:43 final size:43
Alignment explanation
Indices: 1221840--1222010 Score: 135
Period size: 43 Copynumber: 3.8 Consensus size: 43
1221830 ACCAAGGAAA
* *
1221840 TGTATCGATACATTAGTCAATGTATTGATACATGCTTCCTCAT
1 TGTATCGATACATTACTCAATGTATCGATACATGCTTCCTCAT
* * * * * * * *
1221883 TATATCGATACATTTCTCATTGTATTGATATATTCTGGGTTTTTCACCCAAA
1 TGTATCGATACATTACTCAATGTATCGATACA---T--G--CTTC-CTC-AT
*
1221935 TGTATCGATACATTAGTCAATGTATCGATACATGCTTCCTCAT
1 TGTATCGATACATTACTCAATGTATCGATACATGCTTCCTCAT
* * *
1221978 TGTATCAATACATTTCTCATTGTATCGATACAT
1 TGTATCGATACATTACTCAATGTATCGATACAT
1222011 TCTAGGTTTT
Statistics
Matches: 98, Mismatches: 21, Indels: 18
0.72 0.15 0.13
Matches are distributed among these distances:
43 57 0.58
44 2 0.02
45 3 0.03
46 1 0.01
47 1 0.01
48 1 0.01
49 1 0.01
50 3 0.03
51 2 0.02
52 27 0.28
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.41
Consensus pattern (43 bp):
TGTATCGATACATTACTCAATGTATCGATACATGCTTCCTCAT
Found at i:1221912 original size:20 final size:20
Alignment explanation
Indices: 1221840--1221912 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
1221830 ACCAAGGAAA
** *
1221840 TGTATCGATACATTAGTCAA
1 TGTATCGATACATTTCTCAT
*
1221860 TGTATTGATACATGCTTCCTCAT
1 TGTATCGATACAT--TT-CTCAT
*
1221883 TATATCGATACATTTCTCAT
1 TGTATCGATACATTTCTCAT
*
1221903 TGTATTGATA
1 TGTATCGATA
1221913 TATTCTGGGT
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
20 25 0.60
21 2 0.05
22 1 0.02
23 14 0.33
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.42
Consensus pattern (20 bp):
TGTATCGATACATTTCTCAT
Found at i:1221949 original size:95 final size:95
Alignment explanation
Indices: 1221837--1222042 Score: 349
Period size: 95 Copynumber: 2.2 Consensus size: 95
1221827 ACTACCAAGG
* *
1221837 AAATGTATCGATACATTAGTCAATGTATTGATACATGCTTCCTCATTATATCGATACATTTCTCA
1 AAATGTATCGATACATTAGTCAATGTATCGATACATGCTTCCTCATTATATCAATACATTTCTCA
* * *
1221902 TTGTATTGATATATTCTGGGTTTTTCACCC
66 TTGTATCGATACATTCTAGGTTTTTCACCC
*
1221932 AAATGTATCGATACATTAGTCAATGTATCGATACATGCTTCCTCATTGTATCAATACATTTCTCA
1 AAATGTATCGATACATTAGTCAATGTATCGATACATGCTTCCTCATTATATCAATACATTTCTCA
*
1221997 TTGTATCGATACATTCTAGGTTTTTGACCC
66 TTGTATCGATACATTCTAGGTTTTTCACCC
1222027 AAATGTATCGATACAT
1 AAATGTATCGATACAT
1222043 GCAGGCAAAT
Statistics
Matches: 104, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
95 104 1.00
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (95 bp):
AAATGTATCGATACATTAGTCAATGTATCGATACATGCTTCCTCATTATATCAATACATTTCTCA
TTGTATCGATACATTCTAGGTTTTTCACCC
Found at i:1221998 original size:20 final size:20
Alignment explanation
Indices: 1221935--1222011 Score: 91
Period size: 20 Copynumber: 3.7 Consensus size: 20
1221925 TTCACCCAAA
** *
1221935 TGTATCGATACATTAGTCAA
1 TGTATCGATACATTTCTCAT
1221955 TGTATCGATACATGCTTCCTCAT
1 TGTATCGATACAT--TT-CTCAT
*
1221978 TGTATCAATACATTTCTCAT
1 TGTATCGATACATTTCTCAT
1221998 TGTATCGATACATT
1 TGTATCGATACATT
1222012 CTAGGTTTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
20 31 0.63
21 2 0.04
22 1 0.02
23 15 0.31
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (20 bp):
TGTATCGATACATTTCTCAT
Found at i:1222811 original size:16 final size:16
Alignment explanation
Indices: 1222790--1222821 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1222780 TAACATGTTT
*
1222790 CCATGACCTTTTTAGG
1 CCATGACCCTTTTAGG
1222806 CCATGACCCTTTTAGG
1 CCATGACCCTTTTAGG
1222822 ACTTTCATGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.28, G:0.19, T:0.34
Consensus pattern (16 bp):
CCATGACCCTTTTAGG
Found at i:1230212 original size:13 final size:13
Alignment explanation
Indices: 1230194--1230220 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1230184 ACAATTCTTT
1230194 ATGTATCGATACA
1 ATGTATCGATACA
1230207 ATGTATCGATACA
1 ATGTATCGATACA
1230220 A
1 A
1230221 AGCAATATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1235356 original size:3 final size:3
Alignment explanation
Indices: 1235348--1235379 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1235338 CGAGTCAACT
*
1235348 TCA TCA TCA TCA TCA TCA TCA TCT TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
1235380 TTTGATGGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.28, C:0.34, G:0.00, T:0.38
Consensus pattern (3 bp):
TCA
Found at i:1242747 original size:21 final size:21
Alignment explanation
Indices: 1242721--1242766 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
1242711 GAAAAAGAGA
1242721 ATGATGGCCTAGCGTGGTACT
1 ATGATGGCCTAGCGTGGTACT
1242742 ATGATGGCCTAGCGTGGTACT
1 ATGATGGCCTAGCGTGGTACT
1242763 ATGA
1 ATGA
1242767 CATCCTTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.22, C:0.17, G:0.33, T:0.28
Consensus pattern (21 bp):
ATGATGGCCTAGCGTGGTACT
Found at i:1244064 original size:24 final size:26
Alignment explanation
Indices: 1244035--1244096 Score: 83
Period size: 25 Copynumber: 2.5 Consensus size: 26
1244025 ATCCTTCGTA
*
1244035 AAAAAACAAAAAATAAAAA-ATCAAT
1 AAAAAACAAAAAATAAAAACAACAAT
* *
1244060 CAAAAA-AATAAATAAAAACAACAAT
1 AAAAAACAAAAAATAAAAACAACAAT
1244085 AAAAAACAAAAA
1 AAAAAACAAAAA
1244097 GGGGAAGAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
24 11 0.37
25 15 0.50
26 4 0.13
ACGTcount: A:0.81, C:0.10, G:0.00, T:0.10
Consensus pattern (26 bp):
AAAAAACAAAAAATAAAAACAACAAT
Found at i:1244065 original size:13 final size:12
Alignment explanation
Indices: 1244049--1244090 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
1244039 AACAAAAAAT
1244049 AAAAAATCAATCA
1 AAAAAATCAAT-A
*
1244062 AAAAAATAAATA
1 AAAAAATCAATA
1244074 AAAACAA-CAATA
1 AAAA-AATCAATA
1244086 AAAAA
1 AAAAA
1244091 CAAAAAGGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 1 0.04
12 13 0.50
13 12 0.46
ACGTcount: A:0.79, C:0.10, G:0.00, T:0.12
Consensus pattern (12 bp):
AAAAAATCAATA
Found at i:1245479 original size:28 final size:28
Alignment explanation
Indices: 1245447--1245500 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
1245437 ATAGCCCACT
* *
1245447 AGTCAGTGACATCTCTTCGAAGTCCAAA
1 AGTCAGTGACACCTCTTCAAAGTCCAAA
*
1245475 AGTCAGTGGCACCTCTTCAAAGTCCA
1 AGTCAGTGACACCTCTTCAAAGTCCA
1245501 TAATCAATGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.24
Consensus pattern (28 bp):
AGTCAGTGACACCTCTTCAAAGTCCAAA
Found at i:1245740 original size:32 final size:33
Alignment explanation
Indices: 1245699--1245842 Score: 161
Period size: 32 Copynumber: 4.5 Consensus size: 33
1245689 CTTTCTCAAA
* *
1245699 ACAAAAGTTGGTGGTAACCTTCTTC-AAAGCCC
1 ACAAAAGTTGGTGGCAACCCTCTTCAAAAGCCC
* *
1245731 ACAAAAGTTGGTGGCAACCCT-TTCTAAAGCCT
1 ACAAAAGTTGGTGGCAACCCTCTTCAAAAGCCC
* * * *
1245763 ACATAAGCTGGTTGCAA-CCTCTTCAAAAGCTC
1 ACAAAAGTTGGTGGCAACCCTCTTCAAAAGCCC
*
1245795 ACAAAAGTTGGTGGCAACCCTC-TCAAAAACCC
1 ACAAAAGTTGGTGGCAACCCTCTTCAAAAGCCC
* *
1245827 ACATAAGTTAGTGGCA
1 ACAAAAGTTGGTGGCA
1245843 TCTCTTTCTA
Statistics
Matches: 93, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
31 6 0.06
32 83 0.89
33 4 0.04
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (33 bp):
ACAAAAGTTGGTGGCAACCCTCTTCAAAAGCCC
Found at i:1245792 original size:64 final size:64
Alignment explanation
Indices: 1245714--1245833 Score: 179
Period size: 64 Copynumber: 1.9 Consensus size: 64
1245704 AGTTGGTGGT
* * * *
1245714 AACCTTCTTCAAAGCCCACAAAAGTTGGTGGCAACCCTTTCTAAAGCCTACATAAGCTGGTTGC
1 AACCTTCTTCAAAGCCCACAAAAGTTGGTGGCAACCCTCTCAAAAACCCACATAAGCTGGTTGC
*
1245778 AACC-TCTTCAAAAGCTCACAAAAGTTGGTGGCAACCCTCTCAAAAACCCACATAAG
1 AACCTTCTTC-AAAGCCCACAAAAGTTGGTGGCAACCCTCTCAAAAACCCACATAAG
1245834 TTAGTGGCAT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
63 5 0.10
64 45 0.90
ACGTcount: A:0.34, C:0.29, G:0.15, T:0.22
Consensus pattern (64 bp):
AACCTTCTTCAAAGCCCACAAAAGTTGGTGGCAACCCTCTCAAAAACCCACATAAGCTGGTTGC
Found at i:1247038 original size:20 final size:20
Alignment explanation
Indices: 1246972--1247048 Score: 82
Period size: 20 Copynumber: 3.7 Consensus size: 20
1246962 GCTAAGGAAA
** *
1246972 TGTATCGATACATTAGTCAA
1 TGTATCGATACATTTCTCAT
*
1246992 TGTATCGATACATGCTTCCTTAT
1 TGTATCGATACAT--TT-CTCAT
1247015 TGTATCGATACATTTCTCAT
1 TGTATCGATACATTTCTCAT
*
1247035 TGTATTGATACATT
1 TGTATCGATACATT
1247049 CTGGGTTTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
20 30 0.62
21 2 0.04
22 1 0.02
23 15 0.31
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.43
Consensus pattern (20 bp):
TGTATCGATACATTTCTCAT
Found at i:1253596 original size:17 final size:17
Alignment explanation
Indices: 1253560--1253592 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1253550 ATTCTTACCG
*
1253560 CATTCATCCACACTAAT
1 CATTCATCAACACTAAT
1253577 CATTCATCAACA-TAAT
1 CATTCATCAACACTAAT
1253593 TCATCAGAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.39, C:0.30, G:0.00, T:0.30
Consensus pattern (17 bp):
CATTCATCAACACTAAT
Found at i:1260872 original size:13 final size:12
Alignment explanation
Indices: 1260854--1260925 Score: 54
Period size: 12 Copynumber: 5.7 Consensus size: 12
1260844 ATCCTTCGTA
1260854 AAAAAACAAAAAC
1 AAAAAA-AAAAAC
** *
1260867 AAAAAATCAATC
1 AAAAAAAAAAAC
* *
1260879 AAAAAAATAAAT
1 AAAAAAAAAAAC
1260891 AAATAAATAAAAAC
1 AAA-AAA-AAAAAC
*
1260905 AACAATAAAAAAC
1 AA-AAAAAAAAAC
1260918 AAAAAAAA
1 AAAAAAAA
1260926 TGGAAGAAAG
Statistics
Matches: 45, Mismatches: 11, Indels: 7
0.71 0.17 0.11
Matches are distributed among these distances:
12 19 0.42
13 17 0.38
14 8 0.18
15 1 0.02
ACGTcount: A:0.81, C:0.10, G:0.00, T:0.10
Consensus pattern (12 bp):
AAAAAAAAAAAC
Found at i:1260902 original size:20 final size:19
Alignment explanation
Indices: 1260861--1260925 Score: 53
Period size: 20 Copynumber: 3.4 Consensus size: 19
1260851 GTAAAAAAAC
* *
1260861 AAAAACAAA-AAATCAATCA
1 AAAAAAAAATAAATAAAT-A
1260880 AAAAAATAAATAAATAAATA
1 AAAAAA-AAATAAATAAATA
* *
1260900 AAAACAACAATAAA-AAACA
1 AAAA-AAAAATAAATAAATA
1260919 AAAAAAA
1 AAAAAAA
1260926 TGGAAGAAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
18 2 0.05
19 13 0.34
20 14 0.37
21 9 0.24
ACGTcount: A:0.80, C:0.09, G:0.00, T:0.11
Consensus pattern (19 bp):
AAAAAAAAATAAATAAATA
Found at i:1262854 original size:13 final size:13
Alignment explanation
Indices: 1262836--1262860 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1262826 ACAATAAACA
1262836 TGTATCGATACAT
1 TGTATCGATACAT
1262849 TGTATCGATACA
1 TGTATCGATACA
1262861 AAGCATAATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1263460 original size:22 final size:24
Alignment explanation
Indices: 1263435--1263514 Score: 74
Period size: 31 Copynumber: 3.1 Consensus size: 24
1263425 AGGCTTTGTT
*
1263435 AAAAAAATTT-T-CCCTTTGATAA
1 AAAAAAATTTCTCCCCCTTGATAA
1263457 AAAAAAATTTCTCCCCCTTGATAA
1 AAAAAAATTTCTCCCCCTTGATAA
1263481 TCAGTTAAAAAGATTTTCTCCCCCTTGATAA
1 --A---AAAAA-A-TTTCTCCCCCTTGATAA
1263512 AAA
1 AAA
1263515 TTTATTTTCA
Statistics
Matches: 48, Mismatches: 1, Indels: 14
0.76 0.02 0.22
Matches are distributed among these distances:
22 10 0.21
23 1 0.02
24 10 0.21
26 3 0.06
29 6 0.12
30 1 0.02
31 17 0.35
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.33
Consensus pattern (24 bp):
AAAAAAATTTCTCCCCCTTGATAA
Found at i:1264594 original size:20 final size:21
Alignment explanation
Indices: 1264564--1264605 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
1264554 CCGTTTTTCT
1264564 TGATGATTTTG-A-TGAAAAA
1 TGATGATTTTGAAGTGAAAAA
1264583 TGATGTATTTTGAAGTGAAAAA
1 TGATG-ATTTTGAAGTGAAAAA
1264605 T
1 T
1264606 AAAAAATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 6 0.30
21 1 0.05
22 8 0.40
ACGTcount: A:0.40, C:0.00, G:0.21, T:0.38
Consensus pattern (21 bp):
TGATGATTTTGAAGTGAAAAA
Found at i:1264745 original size:13 final size:13
Alignment explanation
Indices: 1264727--1264752 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1264717 TAGTAACCCT
1264727 TGTATCGATACAA
1 TGTATCGATACAA
1264740 TGTATCGATACAA
1 TGTATCGATACAA
1264753 AGAATATTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1268833 original size:19 final size:19
Alignment explanation
Indices: 1268788--1268843 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
1268778 CTACCAGTTT
**
1268788 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
1268808 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
*
1268827 TATGTATCGATACAATG
1 CATGTATCGATACAATG
1268844 TATCGATACA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:1268846 original size:13 final size:13
Alignment explanation
Indices: 1268828--1268854 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1268818 TACAATGAAT
1268828 ATGTATCGATACA
1 ATGTATCGATACA
1268841 ATGTATCGATACA
1 ATGTATCGATACA
1268854 A
1 A
1268855 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1268850 original size:32 final size:33
Alignment explanation
Indices: 1268809--1268873 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
1268799 ACAATTGTCC
* *
1268809 ATGTATCGATACAATGAAT-ATGTATCGATACA
1 ATGTATCGATACAAAGAATAATGTATCAATACA
*
1268841 ATGTATCGATACAAAGCATAATGTATCAATACA
1 ATGTATCGATACAAAGAATAATGTATCAATACA
1268874 TTCAAGGGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (33 bp):
ATGTATCGATACAAAGAATAATGTATCAATACA
Found at i:1272710 original size:14 final size:13
Alignment explanation
Indices: 1272693--1272779 Score: 52
Period size: 14 Copynumber: 6.5 Consensus size: 13
1272683 TAATTTGCCA
1272693 TTGTCAAGAAATT
1 TTGTCAAGAAATT
*
1272706 GTTGTCAATAAATT
1 -TTGTCAAGAAATT
* *
1272720 TTCGTCAAGAACTA
1 TT-GTCAAGAAATT
**
1272734 TTGTTGAGAACA-T
1 TTGTCAAGAA-ATT
* *
1272747 TTGTC-TGAAACT
1 TTGTCAAGAAATT
*
1272759 TCGTCAAGAAATTT
1 TTGTCAAGAAA-TT
1272773 TTGTCAA
1 TTGTCAA
1272780 CACGAATCCT
Statistics
Matches: 54, Mismatches: 14, Indels: 10
0.69 0.18 0.13
Matches are distributed among these distances:
11 1 0.02
12 8 0.15
13 16 0.30
14 29 0.54
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (13 bp):
TTGTCAAGAAATT
Found at i:1272873 original size:27 final size:28
Alignment explanation
Indices: 1272800--1272873 Score: 114
Period size: 28 Copynumber: 2.7 Consensus size: 28
1272790 TTCTCATAGC
*
1272800 CCACTAGTCAGTGGCACCTCTTCGAAGT
1 CCACAAGTCAGTGGCACCTCTTCGAAGT
*
1272828 CCACAAGTCAGTGGCACCTTTTCGAAGT
1 CCACAAGTCAGTGGCACCTCTTCGAAGT
*
1272856 CCATAA-TCAGTGGCACCT
1 CCACAAGTCAGTGGCACCT
1272874 GCTATATATA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
27 12 0.28
28 31 0.72
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.24
Consensus pattern (28 bp):
CCACAAGTCAGTGGCACCTCTTCGAAGT
Found at i:1273100 original size:32 final size:33
Alignment explanation
Indices: 1273061--1273205 Score: 190
Period size: 32 Copynumber: 4.5 Consensus size: 33
1273051 CTTAAACGCA
* * *
1273061 CACACAAGCTAGTAGCAACCTTCTTC-AAAGCC
1 CACACAAGCTGGTGGCAACCCTCTTCAAAAGCC
* * *
1273093 CATACAAGTTGGTGGCAACCCT-TTCTAAAGCC
1 CACACAAGCTGGTGGCAACCCTCTTCAAAAGCC
1273125 CACACAAGCTGGTGGCAA-CCTCTTCAAAAGCC
1 CACACAAGCTGGTGGCAACCCTCTTCAAAAGCC
*
1273157 CACACAAGTTGGTGGCAACCCTC-TCAAAAGCC
1 CACACAAGCTGGTGGCAACCCTCTTCAAAAGCC
*
1273189 CACACAAGTTGGTGGCA
1 CACACAAGCTGGTGGCA
1273206 TCTCCTTCTA
Statistics
Matches: 101, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
31 6 0.06
32 91 0.90
33 4 0.04
ACGTcount: A:0.31, C:0.32, G:0.19, T:0.19
Consensus pattern (33 bp):
CACACAAGCTGGTGGCAACCCTCTTCAAAAGCC
Found at i:1273164 original size:64 final size:64
Alignment explanation
Indices: 1273061--1273205 Score: 220
Period size: 64 Copynumber: 2.3 Consensus size: 64
1273051 CTTAAACGCA
* * * * *
1273061 CACACAAGCTAGTAGCAACCTTCTTCAAAGCCCATACAAGTTGGTGGCAACCCTTTCTAAAGCC
1 CACACAAGCTGGTGGCAACCTTCTTCAAAGCCCACACAAGTTGGTGGCAACCCTCTCAAAAGCC
1273125 CACACAAGCTGGTGGCAACC-TCTTCAAAAGCCCACACAAGTTGGTGGCAACCCTCTCAAAAGCC
1 CACACAAGCTGGTGGCAACCTTCTTC-AAAGCCCACACAAGTTGGTGGCAACCCTCTCAAAAGCC
*
1273189 CACACAAGTTGGTGGCA
1 CACACAAGCTGGTGGCA
1273206 TCTCCTTCTA
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
63 5 0.07
64 69 0.93
ACGTcount: A:0.31, C:0.32, G:0.19, T:0.19
Consensus pattern (64 bp):
CACACAAGCTGGTGGCAACCTTCTTCAAAGCCCACACAAGTTGGTGGCAACCCTCTCAAAAGCC
Found at i:1273427 original size:52 final size:52
Alignment explanation
Indices: 1273371--1273478 Score: 137
Period size: 52 Copynumber: 2.1 Consensus size: 52
1273361 GACGCCATTG
* * * *
1273371 TCATCTTTAAGTC-CAATGTCACCGGCCTTGAATTAGCAAATTGGCACCTTTA
1 TCATCTTTAAG-CGCAATATCACCAGCCTTGAATCAGCAAATTAGCACCTTTA
* * *
1273423 TCATCTTTAAGCGCAATATCGCTAGCCTTGAATCAGCATATTAGCACCTTTA
1 TCATCTTTAAGCGCAATATCACCAGCCTTGAATCAGCAAATTAGCACCTTTA
1273475 TCAT
1 TCAT
1273479 TCTTCTCATC
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
51 1 0.02
52 47 0.98
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (52 bp):
TCATCTTTAAGCGCAATATCACCAGCCTTGAATCAGCAAATTAGCACCTTTA
Found at i:1276272 original size:17 final size:17
Alignment explanation
Indices: 1276236--1276268 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1276226 ATTCTTGCTG
*
1276236 CATTCATCCACACTAAT
1 CATTCATCAACACTAAT
1276253 CATTCATCAACA-TAAT
1 CATTCATCAACACTAAT
1276269 TCATCATAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.39, C:0.30, G:0.00, T:0.30
Consensus pattern (17 bp):
CATTCATCAACACTAAT
Found at i:1284937 original size:13 final size:13
Alignment explanation
Indices: 1284907--1284952 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
1284897 TAATTTGCCA
*
1284907 TTGTCAAGAAATTT
1 TTGTCAAG-AACTT
1284921 TTGTCAAGAACTT
1 TTGTCAAGAACTT
* *
1284934 TTGTCGAGAACGT
1 TTGTCAAGAACTT
1284947 TTGTCA
1 TTGTCA
1284953 GAAACTTCGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
13 20 0.71
14 8 0.29
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (13 bp):
TTGTCAAGAACTT
Found at i:1285067 original size:27 final size:28
Alignment explanation
Indices: 1285005--1285071 Score: 100
Period size: 28 Copynumber: 2.4 Consensus size: 28
1284995 AAAGCCCATT
* *
1285005 AGTCAGTGGCACATTTTTGAAGTTCACA
1 AGTCAGTGGCACATTTTCGAAGTCCACA
*
1285033 AGTTAGTGGCACATTTTCGAAGTCCACA
1 AGTCAGTGGCACATTTTCGAAGTCCACA
1285061 A-TCAGTGGCAC
1 AGTCAGTGGCAC
1285072 TTGCTGTATA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
27 9 0.26
28 26 0.74
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.28
Consensus pattern (28 bp):
AGTCAGTGGCACATTTTCGAAGTCCACA
Found at i:1285307 original size:32 final size:33
Alignment explanation
Indices: 1285253--1285406 Score: 181
Period size: 32 Copynumber: 4.8 Consensus size: 33
1285243 GAAAACTTTC
* * *
1285253 TCAAAAGCCTACACAAGCTGGTGGCAACCTTCT
1 TCAAAAGCCCACACAAGTTGGTGGCAACCCTCT
* * *
1285286 TC-AAAGCTCACATAAGTTGGTGACAACCCT-T
1 TCAAAAGCCCACACAAGTTGGTGGCAACCCTCT
* * * *
1285317 TCTAAAGCCTACACAAGCTAGTGGCAA-CCTCT
1 TCAAAAGCCCACACAAGTTGGTGGCAACCCTCT
*
1285349 TCAAAAGCCCACACAAGTCGGTGGCAACCCTC-
1 TCAAAAGCCCACACAAGTTGGTGGCAACCCTCT
1285381 TCAAAAGCCCACACAAGTTGGTGGCA
1 TCAAAAGCCCACACAAGTTGGTGGCA
1285407 TCTCCTTCTA
Statistics
Matches: 100, Mismatches: 18, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
31 6 0.06
32 88 0.88
33 6 0.06
ACGTcount: A:0.32, C:0.31, G:0.18, T:0.19
Consensus pattern (33 bp):
TCAAAAGCCCACACAAGTTGGTGGCAACCCTCT
Found at i:1285327 original size:64 final size:64
Alignment explanation
Indices: 1285251--1285406 Score: 215
Period size: 64 Copynumber: 2.4 Consensus size: 64
1285241 GAGAAAACTT
* * *
1285251 TCTCAAAAGCCTACACAAGCTGGTGGCAACCTTCTTC-AAAGCTCACATAAGTTGGTGACAACCC
1 TCTCAAAAGCCTACACAAGCTGGTGGCAACC-TCTTCAAAAGCCCACACAAGTCGGTGACAACCC
* * * *
1285315 TTTCTAAAGCCTACACAAGCTAGTGGCAACCTCTTCAAAAGCCCACACAAGTCGGTGGCAACCC
1 TCTCAAAAGCCTACACAAGCTGGTGGCAACCTCTTCAAAAGCCCACACAAGTCGGTGACAACCC
* *
1285379 TCTCAAAAGCCCACACAAGTTGGTGGCA
1 TCTCAAAAGCCTACACAAGCTGGTGGCA
1285407 TCTCCTTCTA
Statistics
Matches: 79, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
63 5 0.06
64 74 0.94
ACGTcount: A:0.31, C:0.31, G:0.18, T:0.20
Consensus pattern (64 bp):
TCTCAAAAGCCTACACAAGCTGGTGGCAACCTCTTCAAAAGCCCACACAAGTCGGTGACAACCC
Found at i:1285545 original size:52 final size:52
Alignment explanation
Indices: 1285468--1285683 Score: 184
Period size: 52 Copynumber: 4.2 Consensus size: 52
1285458 TCAAACCATT
* * * * * *
1285468 TCTTTCCTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTAGCACTTTTT
1 TCTTTCTTAACTCCAATATCACTGGCCTTGAATCAGCACATTAGCACCTTTG
* * * **
1285520 TCTTTCTTAAGTCCAATATCACTGGCCTTGAATCAGCATATTGGTGCCTTTG
1 TCTTTCTTAACTCCAATATCACTGGCCTTGAATCAGCACATTAGCACCTTTG
* * * * * *
1285572 TCATTT-TTAACTCCAATGTTACTAGCCATAAATCAGCACATTGGCACCTTTG
1 TC-TTTCTTAACTCCAATATCACTGGCCTTGAATCAGCACATTAGCACCTTTG
* * * * * *
1285624 TC-ATCTTTAACCCCAATATCGCTGGCCTTGAATCAGCATATTAGCATCTTTA
1 TCTTTC-TTAACTCCAATATCACTGGCCTTGAATCAGCACATTAGCACCTTTG
*
1285676 TCATTCTT
1 TCTTTCTT
1285684 CTCATCTTCA
Statistics
Matches: 129, Mismatches: 31, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
50 1 0.01
52 123 0.95
53 5 0.04
ACGTcount: A:0.24, C:0.25, G:0.13, T:0.37
Consensus pattern (52 bp):
TCTTTCTTAACTCCAATATCACTGGCCTTGAATCAGCACATTAGCACCTTTG
Found at i:1285719 original size:61 final size:59
Alignment explanation
Indices: 1285624--1285803 Score: 184
Period size: 60 Copynumber: 3.0 Consensus size: 59
1285614 GGCACCTTTG
* *
1285624 TCATCTTTAACCCCAATATCGCTGGCCTTGAATCAGCATATTAGCATCTTTATCATTCTTC
1 TCATC-TTAAGCCCAATATCGTTGG-CTTGAATCAGCATATTAGCATCTTTATCATTCTTC
* * *
1285685 TCATCTTCAAGCCCGATATCGTTGGCTGTGAATCAGCATATTGGCAAC-TTATCATTCTTC
1 TCATCTT-AAGCCCAATATCGTTGGCT-TGAATCAGCATATTAGCATCTTTATCATTCTTC
* * * * * * *
1285745 GCATCCTTAAGTCCAATGTTGTTGACTTGAATTAGCATATTTGCATTCTTT-TCATTCTT
1 TCAT-CTTAAGCCCAATATCGTTGGCTTGAATCAGCATATTAGCA-TCTTTATCATTCTT
1285804 ATATCATCTT
Statistics
Matches: 100, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
59 16 0.16
60 42 0.42
61 42 0.42
ACGTcount: A:0.23, C:0.24, G:0.13, T:0.39
Consensus pattern (59 bp):
TCATCTTAAGCCCAATATCGTTGGCTTGAATCAGCATATTAGCATCTTTATCATTCTTC
Found at i:1285800 original size:60 final size:59
Alignment explanation
Indices: 1285650--1285827 Score: 178
Period size: 60 Copynumber: 2.9 Consensus size: 59
1285640 TATCGCTGGC
* * * * *
1285650 CTTGAATCAGCATATTAGCATCTTTATCATTCTTCTCAT-CTTCAAGCCCGATATCGTTGG
1 CTTGAATCAGCATATTAGCATCTTT-TCATTCTTCTCATCCTT-AAGTCCAATGTTGTTGA
* * * *
1285710 CTGTGAATCAGCATATTGGCAACTTATCATTCTTCGCATCCTTAAGTCCAATGTTGTTGA
1 CT-TGAATCAGCATATTAGCATCTTTTCATTCTTCTCATCCTTAAGTCCAATGTTGTTGA
* * * *
1285770 CTTGAATTAGCATATTTGCATTCTTTTCATTCTTATATCATCTTTAAGTCCAATGTTG
1 CTTGAATCAGCATATTAGCA-TCTTTTCATTC-T-TCTCATCCTTAAGTCCAATGTTG
1285828 CAAGCCTTGA
Statistics
Matches: 97, Mismatches: 16, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
59 16 0.16
60 37 0.38
61 24 0.25
62 20 0.21
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.41
Consensus pattern (59 bp):
CTTGAATCAGCATATTAGCATCTTTTCATTCTTCTCATCCTTAAGTCCAATGTTGTTGA
Found at i:1286478 original size:20 final size:21
Alignment explanation
Indices: 1286434--1286486 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
1286424 TTTTACAATT
* *
1286434 TGTATCGATATAAACAGTAAA
1 TGTATCGATACAAACAATAAA
*
1286455 TGTATCGATACAAA-AATGAA
1 TGTATCGATACAAACAATAAA
1286475 TGTATCGATACA
1 TGTATCGATACA
1286487 TGCCTAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.45, C:0.11, G:0.15, T:0.28
Consensus pattern (21 bp):
TGTATCGATACAAACAATAAA
Found at i:1286599 original size:20 final size:20
Alignment explanation
Indices: 1286535--1286612 Score: 84
Period size: 20 Copynumber: 3.8 Consensus size: 20
1286525 ACCAAGGAAA
** *
1286535 TGTATCGATACATTAGTCAA
1 TGTATCGATACATTTCTCAT
*
1286555 TGTATCGATACATGCTTTTTCAT
1 TGTATCGATACA---TTTCTCAT
*
1286578 TGTATCGATATATTTCTCAT
1 TGTATCGATACATTTCTCAT
1286598 TGTATCGATACATTT
1 TGTATCGATACATTT
1286613 TGGGTTTTTA
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
20 33 0.67
23 16 0.33
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45
Consensus pattern (20 bp):
TGTATCGATACATTTCTCAT
Found at i:1295450 original size:13 final size:13
Alignment explanation
Indices: 1295432--1295456 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1295422 TACCAAGAAC
1295432 ATGTATCGATACA
1 ATGTATCGATACA
1295445 ATGTATCGATAC
1 ATGTATCGATAC
1295457 TAAGCAATAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1296770 original size:21 final size:21
Alignment explanation
Indices: 1296744--1296792 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
1296734 TCTTCCTCAA
1296744 GCTCATCATCTCGTTGTGGAG
1 GCTCATCATCTCGTTGTGGAG
1296765 GCTCATCATCTCGTTGTGGAG
1 GCTCATCATCTCGTTGTGGAG
1296786 GCTCATC
1 GCTCATC
1296793 CACTTGCCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.14, C:0.27, G:0.27, T:0.33
Consensus pattern (21 bp):
GCTCATCATCTCGTTGTGGAG
Found at i:1302620 original size:3 final size:3
Alignment explanation
Indices: 1302612--1302667 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
1302602 GTCAACTTCC
*
1302612 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCT
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1302660 TCA TCA TC
1 TCA TCA TC
1302668 TTTGATGGTT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.30, C:0.34, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:1304385 original size:32 final size:32
Alignment explanation
Indices: 1304344--1304407 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
1304334 ACAATTCACT
1304344 ATGTATCAATACCAAG-AACATGTATCGATACA
1 ATGTATCAATACCAAGCAACAT-TATCGATACA
* *
1304376 ATGTATCAATACTAAGCAATATTATCGATACA
1 ATGTATCAATACCAAGCAACATTATCGATACA
1304408 TCTGGGTGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 25 0.86
33 4 0.14
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.28
Consensus pattern (32 bp):
ATGTATCAATACCAAGCAACATTATCGATACA
Found at i:1308206 original size:13 final size:13
Alignment explanation
Indices: 1308188--1308213 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1308178 TACAGCAAGT
1308188 ATGTATCGATACA
1 ATGTATCGATACA
1308201 ATGTATCGATACA
1 ATGTATCGATACA
1308214 CAAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1315448 original size:75 final size:75
Alignment explanation
Indices: 1315294--1315454 Score: 166
Period size: 74 Copynumber: 2.1 Consensus size: 75
1315284 CCTTTCAAGG
* * *
1315294 GGATACTCCAACCCCGCTCTTTGAAATTTGCCCAAATTGGAACCTTTCCTTTTTCAAAATCATTG
1 GGATACTCCAAACCCGCTCTTTCAAATTTGCCCAAATTGGAACCTTTCCTTTATCAAAATCATTG
* **
1315359 GTCATCTATG
66 GTCATCCAAA
* * * *
1315369 GGATACTCCAAACCCGCTC-TTCAAATTTG-TCAAGATTTGAACTTTTCCTTTATCAAAATTATC
1 GGATACTCCAAACCCGCTCTTTCAAATTTGCCCAA-ATTGGAACCTTTCCTTTATCAAAATCAT-
*
1315432 T-GTCCTCCACAA
64 TGGTCATCCA-AA
*
1315444 GGATACACCAA
1 GGATACTCCAA
1315455 CCCTATCCTT
Statistics
Matches: 71, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
73 3 0.04
74 39 0.55
75 29 0.41
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.33
Consensus pattern (75 bp):
GGATACTCCAAACCCGCTCTTTCAAATTTGCCCAAATTGGAACCTTTCCTTTATCAAAATCATTG
GTCATCCAAA
Found at i:1317389 original size:20 final size:20
Alignment explanation
Indices: 1317364--1317403 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1317354 ATTTTTTAAG
1317364 GTTTTTGGCTAAGGTGGCTA
1 GTTTTTGGCTAAGGTGGCTA
1317384 GTTTTTGGCTAAGGTGGCTA
1 GTTTTTGGCTAAGGTGGCTA
1317404 TCAAAAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.10, G:0.35, T:0.40
Consensus pattern (20 bp):
GTTTTTGGCTAAGGTGGCTA
Found at i:1319908 original size:13 final size:13
Alignment explanation
Indices: 1319890--1319915 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1319880 CAATTTTTTG
1319890 TGTATCGATACAT
1 TGTATCGATACAT
1319903 TGTATCGATACAT
1 TGTATCGATACAT
1319916 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1320655 original size:21 final size:21
Alignment explanation
Indices: 1320614--1320657 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1320604 CTCTCTTTTA
* *
1320614 TCTCCCCCATTTATTAATAAT
1 TCTCCCCCATTAATCAATAAT
1320635 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCATTAATCAA-TAAT
1320656 TC
1 TC
1320658 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.27, C:0.32, G:0.02, T:0.39
Consensus pattern (21 bp):
TCTCCCCCATTAATCAATAAT
Found at i:1322299 original size:21 final size:21
Alignment explanation
Indices: 1322275--1322321 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
1322265 TTTGATGCTG
1322275 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
1322295 -TATTTGAAGTGAAAAACAAGT
1 AT-TTTGAAGTGAAAAACAAGT
1322316 ATTTTG
1 ATTTTG
1322322 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 1 0.04
20 4 0.17
21 9 0.39
22 9 0.39
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:1322460 original size:13 final size:13
Alignment explanation
Indices: 1322442--1322480 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
1322432 ATAATCACCC
*
1322442 TGTATCGATACAG
1 TGTATCGATACAA
*
1322455 TGTATCGATATAA
1 TGTATCGATACAA
1322468 TGTATCGATACAA
1 TGTATCGATACAA
1322481 AGAAAAATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1322491 original size:20 final size:20
Alignment explanation
Indices: 1322466--1322544 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
1322456 GTATCGATAT
1322466 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
1322486 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
1322511 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
1322531 CATGTATCGATACA
1 AATGTATCGATACA
1322545 TTTTGGACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 32 0.64
25 18 0.36
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:1324570 original size:15 final size:15
Alignment explanation
Indices: 1324550--1324580 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1324540 ATTTCGTTTG
*
1324550 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1324565 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1324580 G
1 G
1324581 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1326413 original size:21 final size:21
Alignment explanation
Indices: 1326384--1326428 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1326374 AAGTTTTCAT
*
1326384 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1326404 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1326426 TTT
1 TTT
1326429 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1328665 original size:13 final size:13
Alignment explanation
Indices: 1328647--1328672 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1328637 CAATTTTTTG
1328647 TGTATCGATACAT
1 TGTATCGATACAT
1328660 TGTATCGATACAT
1 TGTATCGATACAT
1328673 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Done.