Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold373
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: 3053563
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 20
Found at i:1067562 original size:158 final size:158
Alignment explanation
Indices: 1067274--1067562 Score: 411
Period size: 158 Copynumber: 1.8 Consensus size: 158
1067264 TAGAGATAAA
*
1067274 AATAGGGTTGGAGTATCCCCGATGATGAAAAATTAGTATTTTAAAAATAAAATCAGGGTTGGAGT
1 AATAGGGTTGGAGTATCCCCGATGATGAAAAATTAGTATTTTAAAAATAAAACCAGGGTTGGAGT
*** * **
1067339 ATCCCCTTGGAAATAACAAGATTGGAGTATCCTTGATGGTGAAAAATTGGTGTTTTGAAAATAAA
66 ATCCCCTCAAAAATAACAAGATTGGAGTATCCTCGATGGTGAAAAATCAGTGTTTTGAAAATAAA
1067404 ATCGAGGTTGGAGTATCCCCTCGAAAAT
131 ATCGAGGTTGGAGTATCCCCTCGAAAAT
* * * *
1067432 AATAGGGTTGGAGTATCCGCGATTATGAAAAATTGGTATTTTAGAAATAAAACC-GAGGTTGGAG
1 AATAGGGTTGGAGTATCCCCGATGATGAAAAATTAGTATTTTAAAAATAAAACCAG-GGTTGGAG
** * *
1067496 TATCCCCTCAAAAATAACGGGGTTGGAGTATCCTCGATTGTGAAAAATCAGTGTTTT-AGAAATA
65 TATCCCCTCAAAAATAACAAGATTGGAGTATCCTCGATGGTGAAAAATCAGTGTTTTGA-AAATA
1067560 AAA
129 AAA
1067563 ACATCAATAA
Statistics
Matches: 114, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
157 2 0.02
158 112 0.98
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (158 bp):
AATAGGGTTGGAGTATCCCCGATGATGAAAAATTAGTATTTTAAAAATAAAACCAGGGTTGGAGT
ATCCCCTCAAAAATAACAAGATTGGAGTATCCTCGATGGTGAAAAATCAGTGTTTTGAAAATAAA
ATCGAGGTTGGAGTATCCCCTCGAAAAT
Found at i:1069900 original size:50 final size:50
Alignment explanation
Indices: 1069846--1069961 Score: 153
Period size: 50 Copynumber: 2.3 Consensus size: 50
1069836 AAAAATGCTT
* * * *
1069846 GAATGTATTGATAC-ATTAAGAAATGTATCAATATATCTGGGTAAAACCTA
1 GAATGTATCGATACAATGAAG-AATGTATCAATACATCTAGGTAAAACCTA
* *
1069896 GAATGTATCGATACAATGAAGAATGTATCGATACATCTAGTTAAAACCTA
1 GAATGTATCGATACAATGAAGAATGTATCAATACATCTAGGTAAAACCTA
*
1069946 GAATGTATCGGTACAA
1 GAATGTATCGATACAA
1069962 ATAGTGAAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
50 53 0.91
51 5 0.09
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.29
Consensus pattern (50 bp):
GAATGTATCGATACAATGAAGAATGTATCAATACATCTAGGTAAAACCTA
Found at i:1070595 original size:61 final size:61
Alignment explanation
Indices: 1070490--1070992 Score: 571
Period size: 61 Copynumber: 8.3 Consensus size: 61
1070480 CATCCTACCT
* * * * * *
1070490 TTTGAGGACTAGAAGGTGTCACCAGCTTGTGTGGGCTTTGAAAGGAGAAGGCGTCCTGCTC
1 TTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGACGTCCTGCTC
* *
1070551 TTTGGGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGACGTCCTACTC
1 TTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGACGTCCTGCTC
* * *
1070612 TTTGAGGACTGAAAGGTGCCACCGACTTGTGTGGGCTTTAAAAGGAAAAGATGTCCTGCTC
1 TTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGACGTCCTGCTC
** * * * **
1070673 TTTGAGGACTGGAAAATGCTACCAACTTGTGTGGGCTTTAAAAGGACAAGATGTCCTATTC
1 TTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGACGTCCTGCTC
* * ** *
1070734 TTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTATAAAAAGAAAAGGTGTCTTGCTC
1 TTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGACGTCCTGCTC
* * * * * *
1070795 TTTGAGGATTGGAAGGTCCCACCAACTTGTGTGGGCTTTGAAAGG-AAAG-TGCCCTGCTT
1 TTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGACGTCCTGCTC
* * * * * *
1070854 TTTGAGGACTGAAAAGTGCCACCAACTTATGTGGGCTTTAAAAGGAAAAAAACATCCTACTC
1 TTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGG-AAAAGACGTCCTGCTC
* * * * * * *
1070916 TTTGAGGATTGAAAGGTGCTACCAACTTGTATGGACTTTAAAAGGAAAA-AGCATTCTGCTC
1 TTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGA-CGTCCTGCTC
* *
1070977 TTTGAAGACTGAAAGG
1 TTTGAGGACTGGAAGG
1070993 ATAAAAGGTT
Statistics
Matches: 377, Mismatches: 61, Indels: 8
0.85 0.14 0.02
Matches are distributed among these distances:
59 46 0.12
60 5 0.01
61 282 0.75
62 44 0.12
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.27
Consensus pattern (61 bp):
TTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGACGTCCTGCTC
Found at i:1071557 original size:13 final size:13
Alignment explanation
Indices: 1071539--1071564 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1071529 ACATAAGTTT
1071539 TGTATCGATACAA
1 TGTATCGATACAA
1071552 TGTATCGATACAA
1 TGTATCGATACAA
1071565 AACTACCCTG
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:1072214 original size:10 final size:10
Alignment explanation
Indices: 1072199--1072223 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1072189 CTTCCCATAA
1072199 AAACACCTTC
1 AAACACCTTC
1072209 AAACACCTTC
1 AAACACCTTC
1072219 AAACA
1 AAACA
1072224 TTGATTGATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.36, G:0.00, T:0.16
Consensus pattern (10 bp):
AAACACCTTC
Found at i:1082689 original size:13 final size:13
Alignment explanation
Indices: 1082671--1082696 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1082661 CAATTTTTTG
1082671 TGTATCGATACAT
1 TGTATCGATACAT
1082684 TGTATCGATACAT
1 TGTATCGATACAT
1082697 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:1082781 original size:20 final size:20
Alignment explanation
Indices: 1082756--1082828 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1082746 CAACTTTTTT
1082756 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
1082776 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
1082797 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1082817 ATGTATCGATAC
1 ATGTATCGATAC
1082829 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:1082794 original size:41 final size:41
Alignment explanation
Indices: 1082735--1082828 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
1082725 CTGCCAAGAA
*
1082735 ATGTATCGATACAACTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
*
1082776 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
1082817 ATGTATCGATAC
1 ATGTATCGATAC
1082829 TTTGAATTGT
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:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
Found at i:1082810 original size:21 final size:21
Alignment explanation
Indices: 1082735--1082810 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
1082725 CTGCCAAGAA
* *
1082735 ATGTATCGATACAACTTTTTT
1 ATGTATCGATACATCTTTTTC
****
1082756 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
1082776 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
1082797 ATGTATCGATACAT
1 ATGTATCGATACAT
1082811 TGCAACATGT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:1085275 original size:13 final size:13
Alignment explanation
Indices: 1085257--1085321 Score: 112
Period size: 13 Copynumber: 5.0 Consensus size: 13
1085247 ATAATCACCC
*
1085257 TGTATCGATACAG
1 TGTATCGATACAA
1085270 TGTATCGATACAA
1 TGTATCGATACAA
*
1085283 TGTATCGATACAG
1 TGTATCGATACAA
1085296 TGTATCGATACAA
1 TGTATCGATACAA
1085309 TGTATCGATACAA
1 TGTATCGATACAA
1085322 AGAAAAATGT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 49 1.00
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1085286 original size:26 final size:26
Alignment explanation
Indices: 1085257--1085320 Score: 128
Period size: 26 Copynumber: 2.5 Consensus size: 26
1085247 ATAATCACCC
1085257 TGTATCGATACAGTGTATCGATACAA
1 TGTATCGATACAGTGTATCGATACAA
1085283 TGTATCGATACAGTGTATCGATACAA
1 TGTATCGATACAGTGTATCGATACAA
1085309 TGTATCGATACA
1 TGTATCGATACA
1085321 AAGAAAAATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (26 bp):
TGTATCGATACAGTGTATCGATACAA
Found at i:1085332 original size:20 final size:20
Alignment explanation
Indices: 1085307--1085385 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
1085297 GTATCGATAC
1085307 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
1085327 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
*
1085352 GATGTATCGATACACAA-AAA
1 AATGTATCGATACA-AAGAAA
*
1085372 CATGTATCGATACA
1 AATGTATCGATACA
1085386 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:1087421 original size:15 final size:15
Alignment explanation
Indices: 1087401--1087431 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1087391 ATTTCGTTTG
*
1087401 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1087416 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1087431 G
1 G
1087432 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:1091572 original size:20 final size:20
Alignment explanation
Indices: 1091547--1091619 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1091537 CAACTTTTTT
1091547 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
1091567 ATGTATCGATACATATTTTTC
1 ATGTATCGATACAT-TGCAAC
1091588 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1091608 ATGTATCGATAC
1 ATGTATCGATAC
1091620 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:0.33, C:0.18, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:1091586 original size:41 final size:41
Alignment explanation
Indices: 1091526--1091619 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 41
1091516 CTGCCAAGAA
*
1091526 ATGTATCGATACAACTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
1091567 ATGTATCGATACATA-TTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACA-ACTTTTTCATGTATCGATACATTGCAAC
1091608 ATGTATCGATAC
1 ATGTATCGATAC
1091620 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
41 50 0.98
42 1 0.02
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
Found at i:1091592 original size:21 final size:21
Alignment explanation
Indices: 1091526--1091601 Score: 84
Period size: 21 Copynumber: 3.7 Consensus size: 21
1091516 CTGCCAAGAA
*
1091526 ATGTATCGATACA-ACTTTTTT
1 ATGTATCGATACATA-TTTTTC
****
1091547 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATATTTTTC
1091567 ATGTATCGATACATATTTTTC
1 ATGTATCGATACATATTTTTC
1091588 ATGTATCGATACAT
1 ATGTATCGATACAT
1091602 TGCAACATGT
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATATTTTTC
Found at i:1093247 original size:165 final size:164
Alignment explanation
Indices: 1092941--1093257 Score: 370
Period size: 165 Copynumber: 1.9 Consensus size: 164
1092931 TCAGTGTTTT
* ** * * * ** **
1092941 ACAATGTGCCAGTGTGCAGATTCAAGGCTTGTAATATTGGTCTTAAAGATGTGAAGAATGTTAAA
1 ACAATGTGCCAATGTGCAGATTCAAGGCCAGCAACATTGGACTTAAAGATAAGAAGAATAATAAA
** * * * *
1093006 GGTGCCAATATGCTGGTTCACGGCCAGCGATATCAGGCTTAACAATGAAAAAGGTGCCAATATGT
66 GGTGCCAATATGCTAATTCAAGGCCAGCAATATCAGGCTTAACAATGAAAAAGATGCCAATATGC
** * *
1093071 TGGTTCACGGCCAGCGATATCAAGCTTACCGATG
131 TAATCCACGGCCAGCGACATCAAGCTTACCGATG
*
1093105 ACAATAGTGCCAATGTGCTA-ATTCAAGGCCAGCAACATTGGACTTGAAGATAAGAAGAATAATA
1 ACAAT-GTGCCAATGTGC-AGATTCAAGGCCAGCAACATTGGACTTAAAGATAAGAAGAATAATA
*
1093169 AAGGTGCCAATATGCTAATTCAAGGCCAGCAATATTAGGCTTAA-AGATGCAAAAA-ATGCCAAT
64 AAGGTGCCAATATGCTAATTCAAGGCCAGCAATATCAGGCTTAACA-ATG-AAAAAGATGCCAAT
*
1093232 GTGCTAATCCACGGCCAGCGACATCA
127 ATGCTAATCCACGGCCAGCGACATCA
1093258 GACTCGAAGA
Statistics
Matches: 126, Mismatches: 23, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
164 6 0.05
165 114 0.90
166 6 0.05
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.24
Consensus pattern (164 bp):
ACAATGTGCCAATGTGCAGATTCAAGGCCAGCAACATTGGACTTAAAGATAAGAAGAATAATAAA
GGTGCCAATATGCTAATTCAAGGCCAGCAATATCAGGCTTAACAATGAAAAAGATGCCAATATGC
TAATCCACGGCCAGCGACATCAAGCTTACCGATG
Found at i:1093442 original size:43 final size:45
Alignment explanation
Indices: 1093340--1093447 Score: 139
Period size: 43 Copynumber: 2.4 Consensus size: 45
1093330 ACCAATAGGT
*
1093340 TGATTCAAGGCCAGCGATATTAGACTTAAGAAAAAAGTGCTAATGTGC
1 TGATTCAAGGCCAGCGATATTAGACTT---AAAAAAGTGCCAATGTGC
* * *
1093388 TGATTCAAGGCCAGCGATATTGGAC-T-CAAAGGTGCCAATGTGC
1 TGATTCAAGGCCAGCGATATTAGACTTAAAAAAGTGCCAATGTGC
1093431 TGATTCAAGGCCAGCGA
1 TGATTCAAGGCCAGCGA
1093448 CAATGGGCTT
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
43 31 0.55
47 1 0.02
48 24 0.43
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.23
Consensus pattern (45 bp):
TGATTCAAGGCCAGCGATATTAGACTTAAAAAAGTGCCAATGTGC
Found at i:1093614 original size:95 final size:95
Alignment explanation
Indices: 1093451--1093722 Score: 298
Period size: 95 Copynumber: 2.9 Consensus size: 95
1093441 CCAGCGACAA
* * * * * * * ** *
1093451 TGGGCTTAGAAGGAGATGCCACCAAGTTGTGTGGGGTTTTTAA-AGGGTTATCACCGACTTGTGT
1 TGGGCTTTGAAGGGGTTGCCACTAACTTGTGTGGGCTTTTGAAGA-GGTTGCCACCAACTTGTGT
* * *
1093515 GGGCTTT-AAGAAGGGTTACCACTAGCTTTTG
65 GGGCTTTGAAGAA-GGTTACCACCAACTTATG
*
1093546 TGGGCTTTGAAGGGGTTGCCACTAACTTGTGTGGGCTTTTGAAGAGGTTGCCACCAACTTGTTTG
1 TGGGCTTTGAAGGGGTTGCCACTAACTTGTGTGGGCTTTTGAAGAGGTTGCCACCAACTTGTGTG
*
1093611 GGCTTTGAAGAAGGTTGCCACCAACTTATG
66 GGCTTTGAAGAAGGTTACCACCAACTTATG
* * * **
1093641 TGGGCTTTGAAGAAGGTTGCCACTAGCTTGTGTGGGC-TTTGGAGAAGGTTGCTGCCAACTTGTG
1 TGGGCTTTGAAG-GGGTTGCCACTAACTTGTGTGGGCTTTTGAAG-AGGTTGCCACCAACTTGTG
*
1093705 TGGGCTTTGGAGAAGGTT
64 TGGGCTTTGAAGAAGGTT
1093723 TCTCCACTAG
Statistics
Matches: 151, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
95 90 0.60
96 61 0.40
ACGTcount: A:0.20, C:0.15, G:0.33, T:0.32
Consensus pattern (95 bp):
TGGGCTTTGAAGGGGTTGCCACTAACTTGTGTGGGCTTTTGAAGAGGTTGCCACCAACTTGTGTG
GGCTTTGAAGAAGGTTACCACCAACTTATG
Found at i:1093676 original size:96 final size:95
Alignment explanation
Indices: 1093502--1093722 Score: 293
Period size: 96 Copynumber: 2.3 Consensus size: 95
1093492 AAAGGGTTAT
* * * * *
1093502 CACCGACTTGTGTGGGCTTT-AAGAAGGGTTACCACTAGCTTTTGTGGGCTTTGAAGGGGTTGCC
1 CACCAACTTGTGTGGGCTTTGAAGAA-GGTTACCACCAACTTATGTGGGCTTTGAAGAGGTTGCC
1093566 ACTAACTTGTGTGGGCTTTTGAAG-AGGTTGC
65 ACTAACTTGTGTGGGC-TTTGAAGAAGGTTGC
* *
1093597 CACCAACTTGTTTGGGCTTTGAAGAAGGTTGCCACCAACTTATGTGGGCTTTGAAGAAGGTTGCC
1 CACCAACTTGTGTGGGCTTTGAAGAAGGTTACCACCAACTTATGTGGGCTTTGAAG-AGGTTGCC
* *
1093662 ACTAGCTTGTGTGGGCTTTGGAGAAGGTTGC
65 ACTAACTTGTGTGGGCTTTGAAGAAGGTTGC
** *
1093693 TGCCAACTTGTGTGGGCTTTGGAGAAGGTT
1 CACCAACTTGTGTGGGCTTTGAAGAAGGTT
1093723 TCTCCACTAG
Statistics
Matches: 110, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
95 50 0.45
96 60 0.55
ACGTcount: A:0.19, C:0.17, G:0.33, T:0.32
Consensus pattern (95 bp):
CACCAACTTGTGTGGGCTTTGAAGAAGGTTACCACCAACTTATGTGGGCTTTGAAGAGGTTGCCA
CTAACTTGTGTGGGCTTTGAAGAAGGTTGC
Found at i:1093713 original size:32 final size:32
Alignment explanation
Indices: 1093467--1093722 Score: 241
Period size: 32 Copynumber: 8.0 Consensus size: 32
1093457 TAGAAGGAGA
* * **
1093467 TGCCACCAAGTTGTGTGGGGTTTTTA-AAGGGT
1 TGCCACCAACTTGTGTGGGCTTTGGAGAA-GGT
** * *
1093499 TATCACCGACTTGTGTGGGCTTT-AAGAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTGGAGAA-GGT
* * * * * *
1093531 TACCACTAGCTTTTGTGGGCTTTGAAG-GGGT
1 TGCCACCAACTTGTGTGGGCTTTGGAGAAGGT
* *
1093562 TGCCACTAACTTGTGTGGGCTTTTGA-AGAGGT
1 TGCCACCAACTTGTGTGGGCTTTGGAGA-AGGT
* *
1093594 TGCCACCAACTTGTTTGGGCTTTGAAGAAGGT
1 TGCCACCAACTTGTGTGGGCTTTGGAGAAGGT
* *
1093626 TGCCACCAACTTATGTGGGCTTTGAAGAAGGT
1 TGCCACCAACTTGTGTGGGCTTTGGAGAAGGT
* *
1093658 TGCCACTAGCTTGTGTGGGCTTTGGAGAAGGT
1 TGCCACCAACTTGTGTGGGCTTTGGAGAAGGT
**
1093690 TGCTGCCAACTTGTGTGGGCTTTGGAGAAGGT
1 TGCCACCAACTTGTGTGGGCTTTGGAGAAGGT
1093722 T
1 T
1093723 TCTCCACTAG
Statistics
Matches: 187, Mismatches: 32, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
31 25 0.13
32 158 0.84
33 4 0.02
ACGTcount: A:0.19, C:0.16, G:0.32, T:0.32
Consensus pattern (32 bp):
TGCCACCAACTTGTGTGGGCTTTGGAGAAGGT
Found at i:1093713 original size:64 final size:64
Alignment explanation
Indices: 1093502--1093722 Score: 286
Period size: 64 Copynumber: 3.5 Consensus size: 64
1093492 AAAGGGTTAT
* * * *
1093502 CACCGACTTGTGTGGGCTTT-AAGAAGGGTTACCACTAGCTTTTGTGGGCTTTGAAG-GGGTTGC
1 CACCAACTTGTGTGGGCTTTGAAGAA-GGTTGCCACTAGCTTGTGTGGGCTTTGAAGAAGGTTGC
* * * *
1093565 CACTAACTTGTGTGGGCTTTTGAAG-AGGTTGCCACCAACTTGTTTGGGCTTTGAAGAAGGTTGC
1 CACCAACTTGTGTGGGC-TTTGAAGAAGGTTGCCACTAGCTTGTGTGGGCTTTGAAGAAGGTTGC
* *
1093629 CACCAACTTATGTGGGCTTTGAAGAAGGTTGCCACTAGCTTGTGTGGGCTTTGGAGAAGGTTGC
1 CACCAACTTGTGTGGGCTTTGAAGAAGGTTGCCACTAGCTTGTGTGGGCTTTGAAGAAGGTTGC
** *
1093693 TGCCAACTTGTGTGGGCTTTGGAGAAGGTT
1 CACCAACTTGTGTGGGCTTTGAAGAAGGTT
1093723 TCTCCACTAG
Statistics
Matches: 136, Mismatches: 18, Indels: 7
0.84 0.11 0.04
Matches are distributed among these distances:
63 47 0.35
64 86 0.63
65 3 0.02
ACGTcount: A:0.19, C:0.17, G:0.33, T:0.32
Consensus pattern (64 bp):
CACCAACTTGTGTGGGCTTTGAAGAAGGTTGCCACTAGCTTGTGTGGGCTTTGAAGAAGGTTGC
Found at i:1093974 original size:28 final size:28
Alignment explanation
Indices: 1093904--1093993 Score: 135
Period size: 28 Copynumber: 3.2 Consensus size: 28
1093894 GTGTCATTGA
* ** *
1093904 TTGTGGACTTCGAAAAAATGCCACTAAC
1 TTGTGGACTTCGAAGAGGTGCCACTGAC
1093932 TTGTGGACTTCGAAGAGGTGCCACTGAC
1 TTGTGGACTTCGAAGAGGTGCCACTGAC
1093960 TTGTGGACTTCGAAGAGGTGCCACTGAC
1 TTGTGGACTTCGAAGAGGTGCCACTGAC
*
1093988 TAGTGG
1 TTGTGG
1093994 GCTTTGTGAA
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 57 1.00
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.26
Consensus pattern (28 bp):
TTGTGGACTTCGAAGAGGTGCCACTGAC
Found at i:1094075 original size:15 final size:14
Alignment explanation
Indices: 1094037--1094066 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1094027 CTTAATGAAG
1094037 TTTC-TGACAAAAA
1 TTTCTTGACAAAAA
1094050 TTTCTTGACAAAAA
1 TTTCTTGACAAAAA
1094064 TTT
1 TTT
1094067 TGTTGACAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (14 bp):
TTTCTTGACAAAAA
Found at i:1111221 original size:32 final size:31
Alignment explanation
Indices: 1111175--1111430 Score: 221
Period size: 32 Copynumber: 8.0 Consensus size: 31
1111165 CCAGTGGAGA
*
1111175 AACCTTCTCCAAAACCCACACAAGTTGGTGGC
1 AACCTTCT-TAAAACCCACACAAGTTGGTGGC
*
1111207 AACCTTCTCTAAAACCCACACAAGCTGGTGGC
1 AACCTTCT-TAAAACCCACACAAGTTGGTGGC
* *
1111239 AATCTTCTTCAAAGCCCACACAAGTTGGTGGC
1 AACCTTCTT-AAAACCCACACAAGTTGGTGGC
* * *
1111271 AATCTTCTTCAAAGCCCACACAAGTTAGTGGC
1 AACCTTCTT-AAAACCCACACAAGTTGGTGGC
* * *
1111303 AACC-TCTTTAAAAGCCCACACAAGTCGATGGT
1 AACCTTC-TTAAAA-CCCACACAAGTTGGTGGC
* * * *
1111335 AACC-CCTTCAAAGCCCACACAAGCTGGTGGT
1 AACCTTCTT-AAAACCCACACAAGTTGGTGGC
* * * *
1111366 AACCCTTCATAAAGCCCACACAAGTCGGTGGT
1 AA-CCTTCTTAAAACCCACACAAGTTGGTGGC
* *
1111398 AACCTT-TTCAAAAGCTCACACAAATTGGTGGC
1 AACCTTCTT-AAAA-CCCACACAAGTTGGTGGC
1111430 A
1 A
1111431 TCTTCTTCTA
Statistics
Matches: 189, Mismatches: 27, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
30 1 0.01
31 32 0.17
32 154 0.81
33 2 0.01
ACGTcount: A:0.32, C:0.30, G:0.17, T:0.21
Consensus pattern (31 bp):
AACCTTCTTAAAACCCACACAAGTTGGTGGC
Found at i:1111289 original size:64 final size:65
Alignment explanation
Indices: 1111178--1111446 Score: 268
Period size: 64 Copynumber: 4.2 Consensus size: 65
1111168 GTGGAGAAAC
* * *
1111178 CTTCTCCAAAACCCACACAAGTTGGTGGCAACCTTC-TCTAAAA-CCCACACAAGCTGGTGGCAA
1 CTTCTTCAAAGCCCACACAAGTCGGTGGCAACCTTCTTC-AAAAGCCCACACAAGCTGGTGGCAA
1111241 T
65 T
* * * *
1111242 CTTCTTCAAAGCCCACACAAGTTGGTGGCAATCTTCTTC-AAAGCCCACACAAGTTAGTGGCAA-
1 CTTCTTCAAAGCCCACACAAGTCGGTGGCAACCTTCTTCAAAAGCCCACACAAGCTGGTGGCAAT
* * * * * *
1111305 CCTCTTTAAAAGCCCACACAAGTCGATGGTAACC-CCTTC-AAAGCCCACACAAGCTGGTGGTAA
1 CTTC-TTCAAAGCCCACACAAGTCGGTGGCAACCTTCTTCAAAAGCCCACACAAGCTGGTGGCAA
*
1111368 CC
65 -T
* * * **
1111370 CTTCAT-AAAGCCCACACAAGTCGGTGGTAACCTT-TTCAAAAGCTCACACAAATTGGTGGC-AT
1 CTTCTTCAAAGCCCACACAAGTCGGTGGCAACCTTCTTCAAAAGCCCACACAAGCTGGTGGCAAT
*
1111432 CTTCTTCTAAGCCCA
1 CTTCTTCAAAGCCCA
1111447 ATGTTGCTGG
Statistics
Matches: 171, Mismatches: 26, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
62 5 0.03
63 67 0.39
64 94 0.55
65 5 0.03
ACGTcount: A:0.30, C:0.31, G:0.16, T:0.22
Consensus pattern (65 bp):
CTTCTTCAAAGCCCACACAAGTCGGTGGCAACCTTCTTCAAAAGCCCACACAAGCTGGTGGCAAT
Found at i:1111444 original size:95 final size:95
Alignment explanation
Indices: 1111175--1111446 Score: 300
Period size: 95 Copynumber: 2.9 Consensus size: 95
1111165 CCAGTGGAGA
* * *
1111175 AACCTTC-TCCAAAACCCACACAAGTTGGTGGCAACCTTCTCTAAAA-CCCACACAAGCTGGTGG
1 AACCTTCAT-CAAAGCCCACACAAGTTGGTGGCAACCTTTTC-AAAAGCCCACACAAGTTGGTGG
*
1111238 CAATCTTCTTCAAAGCCCACACAAGTTGGTGGC
64 C-ATCTTCTTCAAAGCCCACACAAGCTGGTGGC
* * * * * *
1111271 AATCTTCTTCAAAGCCCACACAAGTTAGTGGCAACCTCTTT-AAAAGCCCACACAAGTCGATGGT
1 AACCTTCATCAAAGCCCACACAAGTTGGTGGCAACCT-TTTCAAAAGCCCACACAAGTTGGTGGC
* ** *
1111335 AACCCCTTCAAAGCCCACACAAGCTGGTGGT
65 ATCTTCTTCAAAGCCCACACAAGCTGGTGGC
* * * *
1111366 AACCCTTCAT-AAAGCCCACACAAGTCGGTGGTAACCTTTTCAAAAGCTCACACAAATTGGTGGC
1 AA-CCTTCATCAAAGCCCACACAAGTTGGTGGCAACCTTTTCAAAAGCCCACACAAGTTGGTGGC
*
1111430 ATCTTCTTCTAAGCCCA
65 ATCTTCTTCAAAGCCCA
1111447 ATGTTGCTGG
Statistics
Matches: 144, Mismatches: 27, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
94 3 0.02
95 87 0.60
96 51 0.35
97 3 0.02
ACGTcount: A:0.31, C:0.31, G:0.16, T:0.22
Consensus pattern (95 bp):
AACCTTCATCAAAGCCCACACAAGTTGGTGGCAACCTTTTCAAAAGCCCACACAAGTTGGTGGCA
TCTTCTTCAAAGCCCACACAAGCTGGTGGC
Found at i:1111506 original size:43 final size:44
Alignment explanation
Indices: 1111452--1111567 Score: 144
Period size: 48 Copynumber: 2.6 Consensus size: 44
1111442 GCCCAATGTT
* * *
1111452 GCTGGCTTTGAATCAGCACATTGGCACC-GTTAAGTCCAATATC
1 GCTGGCTTTGAATCAGCATATTGGCACCTCTTAAGTCCAACATC
* *
1111495 GTTGGCCTTGAATCAGCATATTGGCACCTTTTTCTTAAGTCCAACATC
1 GCTGGCTTTGAATCAGCATATTGGCACC----TCTTAAGTCCAACATC
1111543 GCTGGCTTTGAATCAGCATATTGGC
1 GCTGGCTTTGAATCAGCATATTGGC
1111568 GCCTTTGTCA
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
43 25 0.41
48 36 0.59
ACGTcount: A:0.23, C:0.24, G:0.21, T:0.32
Consensus pattern (44 bp):
GCTGGCTTTGAATCAGCATATTGGCACCTCTTAAGTCCAACATC
Found at i:1111615 original size:52 final size:48
Alignment explanation
Indices: 1111481--1111617 Score: 168
Period size: 48 Copynumber: 2.8 Consensus size: 48
1111471 ATTGGCACCG
*
1111481 TTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTTTTC
1 TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTTC
* * *
1111529 TTAAGTCCAACATCGCTGGCTTTGAATCAGCATATTGGCGCCTTTGTCATC
1 TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTT-T--TC
* *
1111580 TTTATGTCTAATATCGCTGGCCTT-ATATCAGCATATTG
1 -TTAAGTCCAATATCGCTGGCCTTGA-ATCAGCATATTG
1111618 ACAGTTTTCT
Statistics
Matches: 76, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
48 41 0.54
49 1 0.01
51 3 0.04
52 31 0.41
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.37
Consensus pattern (48 bp):
TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTTC
Found at i:1111766 original size:61 final size:61
Alignment explanation
Indices: 1111671--1111789 Score: 175
Period size: 61 Copynumber: 2.0 Consensus size: 61
1111661 AGACATTAGC
* * *
1111671 ATTCTTCGCATCTTTAAGCCCAATATTGCTGGCCTTGAATCAACATATTGGCACCTTTATT
1 ATTCTTCGCATCTTCAAGCCCAATATTGCTGGCCTTAAATCAACACATTGGCACCTTTATT
** * *
1111732 ATTCTTCTTATCTTCAAGTCCAATGTTGCTGGCCTTAAATCAACACATTGGCACCTTT
1 ATTCTTCGCATCTTCAAGCCCAATATTGCTGGCCTTAAATCAACACATTGGCACCTTT
1111790 GTCATCGTTA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 51 1.00
ACGTcount: A:0.24, C:0.25, G:0.13, T:0.38
Consensus pattern (61 bp):
ATTCTTCGCATCTTCAAGCCCAATATTGCTGGCCTTAAATCAACACATTGGCACCTTTATT
Found at i:1111880 original size:113 final size:113
Alignment explanation
Indices: 1111679--1111885 Score: 252
Period size: 113 Copynumber: 1.8 Consensus size: 113
1111669 GCATTCTTCG
* * * * * **
1111679 CATCTTTAAGCCCAATATTGCTGGCCTTGAATCAACATATTGGCACCTTTATTATTCTTCTTATC
1 CATCGTTAAGCCCAATATCGCTGGCCATGAACCAACATATTGGCACCTTTATCATTCTTCACATC
* * * **
1111744 TTCAAGTCCAATGTTGCTGGCCTTAAATCAACACATTGGCACCTTTGT
66 TTCAAGACCAATATTACAAGCCTTAAATCAACACATTGGCACCTTTGT
** **
1111792 CATCGTTAAGCCTGATATCGCTGGCCATGAACCAGTATATTGGCACCTTTATCATTCTTCACATC
1 CATCGTTAAGCCCAATATCGCTGGCCATGAACCAACATATTGGCACCTTTATCATTCTTCACATC
* *
1111857 TTTAAGACCAATATTACAAGCCTTGAATC
66 TTCAAGACCAATATTACAAGCCTTAAATC
1111886 TGCATACTGG
Statistics
Matches: 76, Mismatches: 18, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
113 76 1.00
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.35
Consensus pattern (113 bp):
CATCGTTAAGCCCAATATCGCTGGCCATGAACCAACATATTGGCACCTTTATCATTCTTCACATC
TTCAAGACCAATATTACAAGCCTTAAATCAACACATTGGCACCTTTGT
Found at i:1116526 original size:12 final size:12
Alignment explanation
Indices: 1116505--1116539 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
1116495 CTTAAGCAGG
1116505 TTCTTTTTTTTC
1 TTCTTTTTTTTC
1116517 -TCTATTTTTTTC
1 TTCT-TTTTTTTC
1116529 TTCTTTTTTTT
1 TTCTTTTTTTT
1116540 TTGAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 3 0.14
12 15 0.71
13 3 0.14
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (12 bp):
TTCTTTTTTTTC
Found at i:1116526 original size:13 final size:13
Alignment explanation
Indices: 1116508--1116540 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1116498 AAGCAGGTTC
1116508 TTTTTTTTC-TCT
1 TTTTTTTTCTTCT
*
1116520 ATTTTTTTCTTCT
1 TTTTTTTTCTTCT
1116533 TTTTTTTT
1 TTTTTTTT
1116541 TGAAAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 8 0.44
13 10 0.56
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTTTTCTTCT
Found at i:1127002 original size:16 final size:17
Alignment explanation
Indices: 1126983--1127014 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1126973 TTTATTTGAA
1126983 TGATTTTGTG-TTTTTG
1 TGATTTTGTGATTTTTG
1126999 TGATTTTGTGATTTTT
1 TGATTTTGTGATTTTT
1127015 TTATGATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.09, C:0.00, G:0.22, T:0.69
Consensus pattern (17 bp):
TGATTTTGTGATTTTTG
Found at i:1128927 original size:22 final size:22
Alignment explanation
Indices: 1128902--1128951 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
1128892 AGGGGAGTGT
**
1128902 TTAAAGA-GAGATTAATTTTGTA
1 TTAAAGATGAGAAAAATTTT-TA
1128924 TTAAAGATGAGAAAAATTTTTA
1 TTAAAGATGAGAAAAATTTTTA
1128946 TTAAAG
1 TTAAAG
1128952 GGGAGTTACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 15 0.60
23 10 0.40
ACGTcount: A:0.46, C:0.00, G:0.16, T:0.38
Consensus pattern (22 bp):
TTAAAGATGAGAAAAATTTTTA
Found at i:1129500 original size:22 final size:22
Alignment explanation
Indices: 1129475--1129524 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
1129465 AGGGGAGTGT
**
1129475 TTAAAGA-GAGATTAATTTTGTA
1 TTAAAGATGAGAAAAATTTT-TA
1129497 TTAAAGATGAGAAAAATTTTTA
1 TTAAAGATGAGAAAAATTTTTA
1129519 TTAAAG
1 TTAAAG
1129525 GGGAGTTACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 15 0.60
23 10 0.40
ACGTcount: A:0.46, C:0.00, G:0.16, T:0.38
Consensus pattern (22 bp):
TTAAAGATGAGAAAAATTTTTA
Found at i:1130264 original size:13 final size:13
Alignment explanation
Indices: 1130246--1130276 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1130236 CAATACATGG
1130246 TACATTGTATCGA
1 TACATTGTATCGA
*
1130259 TACATTGTATTGA
1 TACATTGTATCGA
1130272 TACAT
1 TACAT
1130277 AGTAAAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:1137265 original size:15 final size:16
Alignment explanation
Indices: 1137234--1137266 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1137224 TTTTTCCAAA
*
1137234 AAGGGCGATAGATAAC
1 AAGGGCGACAGATAAC
1137250 AAGGGCGACA-ATAAC
1 AAGGGCGACAGATAAC
1137265 AA
1 AA
1137267 TTTGACAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.48, C:0.15, G:0.27, T:0.09
Consensus pattern (16 bp):
AAGGGCGACAGATAAC
Found at i:1138662 original size:22 final size:22
Alignment explanation
Indices: 1138637--1138679 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1138627 GTACCTCGTC
1138637 CATCTTCTAAAGACATCAAATT
1 CATCTTCTAAAGACATCAAATT
*
1138659 CATCTTCTAAAGCCATCAAAT
1 CATCTTCTAAAGACATCAAAT
1138680 CAATCCAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.26, G:0.05, T:0.30
Consensus pattern (22 bp):
CATCTTCTAAAGACATCAAATT
Found at i:1148817 original size:34 final size:35
Alignment explanation
Indices: 1148779--1148844 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
1148769 CCTTATAACA
1148779 CTATCTTTT-C-AAGGGCTAAAATAGAACCTCTTCC
1 CTATCTTTTACAAAGGG-TAAAATAGAACCTCTTCC
*
1148813 CTATCTTTTACAAAGGGTAAGATAGAACCTCT
1 CTATCTTTTACAAAGGGTAAAATAGAACCTCT
1148845 CAATCATTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
34 9 0.31
35 15 0.52
36 5 0.17
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.32
Consensus pattern (35 bp):
CTATCTTTTACAAAGGGTAAAATAGAACCTCTTCC
Found at i:1149311 original size:52 final size:52
Alignment explanation
Indices: 1149233--1149341 Score: 164
Period size: 52 Copynumber: 2.1 Consensus size: 52
1149223 AATGCATTTG
* * *
1149233 AAATTCTAGCCGTTGGACTCAATGTATCGATACAATTTATAATGTATCGATA
1 AAATTATAGCCATTGGACTCAATGTATCGATACAATTTACAATGTATCGATA
* *
1149285 AAATTATAGCCATTGGGCTCAATGTATCGATACAATTTACCATGTATCGATA
1 AAATTATAGCCATTGGACTCAATGTATCGATACAATTTACAATGTATCGATA
*
1149337 CAATT
1 AAATT
1149342 CACTTAAGGT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.34
Consensus pattern (52 bp):
AAATTATAGCCATTGGACTCAATGTATCGATACAATTTACAATGTATCGATA
Found at i:1151628 original size:10 final size:10
Alignment explanation
Indices: 1151605--1151647 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
1151595 TATCATAATG
1151605 AAAATCAACA
1 AAAATCAACA
1151615 AAAATACAACA
1 AAAAT-CAACA
1151626 AAAATCAA-A
1 AAAATCAACA
* *
1151635 TATATCAACA
1 AAAATCAACA
1151645 AAA
1 AAA
1151648 TCTATAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
9 7 0.26
10 10 0.37
11 10 0.37
ACGTcount: A:0.70, C:0.16, G:0.00, T:0.14
Consensus pattern (10 bp):
AAAATCAACA
Found at i:1154154 original size:69 final size:69
Alignment explanation
Indices: 1154025--1154155 Score: 174
Period size: 69 Copynumber: 1.9 Consensus size: 69
1154015 AGTATCCTCG
* **
1154025 TGACCCTAAAAAACTCTAAAAATAATCAATATATCTCTAAATATACCTTTGACATAAAAGTACAT
1 TGACCCTAAAAAACTCTAAAAATAATCAAAATATCTCTAAATATACCTTCAACATAAAAGTACAT
1154090 CAAA
66 CAAA
* * * * *
1154094 TGACCCTAAAAGACTCTAAAAATGA-CTAAAATATCTCTAAGTATACCTTCAATATGAAAGTA
1 TGACCCTAAAAAACTCTAAAAATAATC-AAAATATCTCTAAATATACCTTCAACATAAAAGTA
1154156 TCCAATAATC
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
68 1 0.02
69 52 0.98
ACGTcount: A:0.47, C:0.18, G:0.07, T:0.27
Consensus pattern (69 bp):
TGACCCTAAAAAACTCTAAAAATAATCAAAATATCTCTAAATATACCTTCAACATAAAAGTACAT
CAAA
Found at i:1154796 original size:19 final size:18
Alignment explanation
Indices: 1154772--1154832 Score: 69
Period size: 19 Copynumber: 3.6 Consensus size: 18
1154762 CAAGTAACTG
1154772 TATCGATACATAAGTGTT
1 TATCGATACATAAGTGTT
1154790 ATATCGATAC--AA-TG--
1 -TATCGATACATAAGTGTT
1154804 TATCGATACATAAGTGTT
1 TATCGATACATAAGTGTT
1154822 GTATCGATACA
1 -TATCGATACA
1154833 ATGTATCGCT
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
13 9 0.25
15 2 0.06
16 4 0.11
17 2 0.06
19 19 0.53
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.34
Consensus pattern (18 bp):
TATCGATACATAAGTGTT
Found at i:1154811 original size:32 final size:32
Alignment explanation
Indices: 1154770--1154840 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
1154760 AACAAGTAAC
1154770 TGTATCGATACATAAGTGTTATATCGATACAA
1 TGTATCGATACATAAGTGTTATATCGATACAA
*
1154802 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTATATCGATACAA
1154834 TGTATCG
1 TGTATCG
1154841 CTATGAAGCT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTATATCGATACAA
Found at i:1154903 original size:13 final size:13
Alignment explanation
Indices: 1154885--1154912 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1154875 ATTACTCAAA
1154885 TGTATCGATACAT
1 TGTATCGATACAT
1154898 TGTATCGATACAT
1 TGTATCGATACAT
1154911 TG
1 TG
1154913 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1161993 original size:21 final size:22
Alignment explanation
Indices: 1161967--1162008 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
1161957 TAAAACCCAA
1161967 TAATGTATCGATACAT-TTCAT
1 TAATGTATCGATACATCTTCAT
1161988 TAATGTATCGATACATCTTCA
1 TAATGTATCGATACATCTTCA
1162009 CGGATTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (22 bp):
TAATGTATCGATACATCTTCAT
Found at i:1167225 original size:11 final size:11
Alignment explanation
Indices: 1167207--1167236 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1167197 TGATGCGATG
1167207 AATTTTAAATT
1 AATTTTAAATT
*
1167218 AGTTTTAAATT
1 AATTTTAAATT
1167229 AATTTTAA
1 AATTTTAA
1167237 CATCGTACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (11 bp):
AATTTTAAATT
Found at i:1167627 original size:18 final size:17
Alignment explanation
Indices: 1167581--1167629 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
1167571 ATATGTGTAT
1167581 TTTTTAAATTTTATTTAAA
1 TTTTTAAA--TTATTTAAA
*
1167600 TTTTT-GATTAGTTTAAA
1 TTTTTAAATTA-TTTAAA
1167617 TTTTTAAATTATT
1 TTTTTAAATTATT
1167630 ATTAAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
16 3 0.12
17 13 0.50
18 5 0.19
19 5 0.19
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (17 bp):
TTTTTAAATTATTTAAA
Found at i:1168220 original size:16 final size:16
Alignment explanation
Indices: 1168201--1168253 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
1168191 CCCGAATCTG
1168201 AAATAATCTGAACTCA
1 AAATAATCTGAACTCA
* *
1168217 AAATGATTTGAA-TCCA
1 AAATAATCTGAACT-CA
*
1168233 AAACAATCTGAACTCGA
1 AAATAATCTGAACTC-A
1168250 AAAT
1 AAAT
1168254 GACCTAAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 5
0.72 0.15 0.13
Matches are distributed among these distances:
15 1 0.04
16 22 0.79
17 5 0.18
ACGTcount: A:0.49, C:0.17, G:0.09, T:0.25
Consensus pattern (16 bp):
AAATAATCTGAACTCA
Found at i:1173342 original size:13 final size:13
Alignment explanation
Indices: 1173324--1173380 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
1173314 CATAAAGTGT
1173324 TGTATCGATACAA
1 TGTATCGATACAA
1173337 TGTATCGATACATAA
1 TGTATCGATAC--AA
1173352 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
1173369 TGTATCGATACA
1 TGTATCGATACA
1173381 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1173359 original size:32 final size:32
Alignment explanation
Indices: 1173304--1173404 Score: 175
Period size: 32 Copynumber: 3.1 Consensus size: 32
1173294 TTCAATGATT
1173304 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
1173337 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
* *
1173369 TGTATCGATACATAAGTTTTGTATTGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1173401 TGTA
1 TGTA
1173405 AGCTACTGCC
Statistics
Matches: 66, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
32 53 0.80
33 13 0.20
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:1173361 original size:19 final size:18
Alignment explanation
Indices: 1173302--1173399 Score: 81
Period size: 19 Copynumber: 5.8 Consensus size: 18
1173292 ATTTCAATGA
1173302 TTTGTATCGATACATAAAG
1 TTTGTATCGATACAT-AAG
1173321 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
1173337 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
1173353 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
1173369 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
*
1173385 TTTTGTATTGATACA
1 -TTTGTATCGATACA
1173400 ATGTAAGCTA
Statistics
Matches: 65, Mismatches: 1, Indels: 26
0.71 0.01 0.28
Matches are distributed among these distances:
13 22 0.34
15 4 0.06
17 4 0.06
19 23 0.35
20 12 0.18
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:1173515 original size:52 final size:52
Alignment explanation
Indices: 1173475--1173591 Score: 180
Period size: 52 Copynumber: 2.2 Consensus size: 52
1173465 TACTGATCTT
* ** *
1173475 TGTATCGATGCATGTAGGCAAATCTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATACAGGCAAATCTACCCAGATGTATCGATACACTATAAAA
* *
1173527 TGTATCGATACATACAGGCAAATTTACCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATACAGGCAAATCTACCCAGATGTATCGATACACTATAAAA
1173579 TGTATCGATACAT
1 TGTATCGATACAT
1173592 GCAGATAAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 59 1.00
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATACAGGCAAATCTACCCAGATGTATCGATACACTATAAAA
Found at i:1173602 original size:52 final size:52
Alignment explanation
Indices: 1173501--1173603 Score: 170
Period size: 52 Copynumber: 2.0 Consensus size: 52
1173491 GGCAAATCTG
*
1173501 CCCAGATGTATCGATACACTATAAAATGTATCGATACATACAGGCAAATTTA
1 CCCAGATGTATCGATACACTATAAAATGTATCGATACATACAGACAAATTTA
* * *
1173553 CCCAGATGTATCGATACACTATGAAATGTATCGATACATGCAGATAAATTT
1 CCCAGATGTATCGATACACTATAAAATGTATCGATACATACAGACAAATTT
1173604 TCATATTTCG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.28
Consensus pattern (52 bp):
CCCAGATGTATCGATACACTATAAAATGTATCGATACATACAGACAAATTTA
Found at i:1177802 original size:22 final size:22
Alignment explanation
Indices: 1177772--1177815 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1177762 CATAATTCCC
1177772 ATAAAGAAATTTATTATGCCAT
1 ATAAAGAAATTTATTATGCCAT
*
1177794 ATAAGGAAATTTATTATGCCAT
1 ATAAAGAAATTTATTATGCCAT
1177816 GAGAGAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.36
Consensus pattern (22 bp):
ATAAAGAAATTTATTATGCCAT
Found at i:1180002 original size:20 final size:20
Alignment explanation
Indices: 1179974--1180019 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
1179964 TTGTTGTTTT
*
1179974 ATTGGTGTTTATTTGTTGGA
1 ATTGATGTTTATTTGTTGGA
1179994 ATTGATGTTTATTTGTTGGA
1 ATTGATGTTTATTTGTTGGA
1180014 ATTGAT
1 ATTGAT
1180020 TGTTGCTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.20, C:0.00, G:0.26, T:0.54
Consensus pattern (20 bp):
ATTGATGTTTATTTGTTGGA
Found at i:1180447 original size:3 final size:3
Alignment explanation
Indices: 1180435--1180495 Score: 63
Period size: 3 Copynumber: 20.3 Consensus size: 3
1180425 TAATTGATAC
* *
1180435 TAT T-T TAT TAT TAT TTT TAT TATT TAT TAT TAT TTT TAT TATT TAT
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TA-T TAT
*
1180481 TAT T-T TTT TAT TAT T
1 TAT TAT TAT TAT TAT T
1180496 CATGTTAAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
2 4 0.08
3 39 0.80
4 6 0.12
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (3 bp):
TAT
Found at i:1180462 original size:19 final size:19
Alignment explanation
Indices: 1180438--1180495 Score: 109
Period size: 19 Copynumber: 3.1 Consensus size: 19
1180428 TTGATACTAT
1180438 TTTATTATTATTTTTATTA
1 TTTATTATTATTTTTATTA
1180457 TTTATTATTATTTTTATTA
1 TTTATTATTATTTTTATTA
1180476 TTTATTATT-TTTTTATTA
1 TTTATTATTATTTTTATTA
1180494 TT
1 TT
1180496 CATGTTAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
18 11 0.28
19 28 0.72
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTATTATTATTTTTATTA
Found at i:1184026 original size:52 final size:52
Alignment explanation
Indices: 1183878--1184006 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
1183868 CAAAATATGA
*
1183878 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGAGC
*
1183930 AAATTTGCCTGTATGTATCGATACATTTCATAGTGTATCGATACATCTGAGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGAGC
1183982 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1184007 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGAGC
Found at i:1184033 original size:13 final size:13
Alignment explanation
Indices: 1184015--1184039 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1184005 CAAAGATCAG
1184015 TGTATCGATACAA
1 TGTATCGATACAA
1184028 TGTATCGATACA
1 TGTATCGATACA
1184040 TTTGAGTAAT
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):
TGTATCGATACAA
Found at i:1184937 original size:101 final size:99
Alignment explanation
Indices: 1184784--1185691 Score: 1034
Period size: 101 Copynumber: 9.3 Consensus size: 99
1184774 AAAGATAATG
* * * * * * **
1184784 TGCTGACTCATGGCCAGCGACATTTAGACTTGAAGA--AAAATGCCAATGTGCTGAGGCAAGGCC
1 TGCTGATTCAAGGCCAGCGATA-TTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCC
* * * * *
1184847 AGTGACATTGGGCTTAGGAATGTTAAAGATGCCAATA
65 AGCGACATTGGACTTA--AATGATGAAGGTGCCAATA
** * * * *
1184884 CACTGATTCAAGGCCAACGATATTGGACTTAAGGATGAAGGTGCCAATATGCTGATTCAAGGACC
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGG-CC
* * * *
1184949 AGTGATATTGGACTTAAA-GATGAAGATGCCAATG
65 AGCGACATTGGACTTAAATGATGAAGGTGCCAATA
*
1184983 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCA
1185048 GCGACATTGGACTTAAAGATGATGAAGGTGCCAATA
66 GCGACATTGGACTT-AA-ATGATGAAGGTGCCAATA
*
1185084 TGCTGATTTAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTC-AGGCCA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCA
*
1185148 GCGACATTGGACTTCAAGATGACGAAGGTGCCAATA
66 GCGACATTGGACTT-AA-ATGATGAAGGTGCCAATA
**
1185184 TGCTGATTCAAGGCCAGCGATACCGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCA
*
1185249 GCGACATTGGACTTAAAGATGACGAAGGTGCCAATA
66 GCGACATTGGACTT-AA-ATGATGAAGGTGCCAATA
*
1185285 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCTA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCA
* * *
1185350 GCGACATTGGTCTTAAA-GA-CAAGGTGTCAATA
66 GCGACATTGGACTTAAATGATGAAGGTGCCAATA
1185382 TGCTGATTCAAGGCCAGCGATATTGGACTT-AA-A-G--G-TGCCAATGTGCTGATTCAAGGCCA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCA
* *
1185441 GCGACATTGGTCTTAAA-GATGACAAAGGAGCCAATA
66 GCGACATTGGACTTAAATGATG---AAGGTGCCAATA
* * *
1185477 TGCTAATTCAAGGCCAGCGATATTGGGC-T-----T----ATGCTAATGTGCTGATTCAAGGCCA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCA
* *
1185532 GCGACATTGGTCTTAAA-GA-CAAGGTGCCAATA
66 GCGACATTGGACTTAAATGATGAAGGTGCCAATA
* *
1185564 TGCTAATTCAAGGCCAGCGATATTGGACTT-AA-A-G--G-TGCCAATGTGTTGATTCAAGGCCA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCA
* * *
1185623 GCGACATTGGTCTTAAA-GATCACAAAGGCGCCAATA
66 GCGACATTGGACTTAAATGAT---GAAGGTGCCAATA
*
1185659 TGCTGATTCAAGGCCAGCGATATTGGGCTTAAA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAA
1185692 AGAAGACGCC
Statistics
Matches: 724, Mismatches: 60, Indels: 52
0.87 0.07 0.06
Matches are distributed among these distances:
87 38 0.05
88 1 0.00
91 125 0.17
92 1 0.00
94 2 0.00
95 76 0.10
96 4 0.01
97 41 0.06
98 17 0.02
99 81 0.11
100 116 0.16
101 206 0.28
102 16 0.02
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (99 bp):
TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCA
GCGACATTGGACTTAAATGATGAAGGTGCCAATA
Found at i:1184939 original size:49 final size:49
Alignment explanation
Indices: 1184876--1185691 Score: 890
Period size: 49 Copynumber: 16.8 Consensus size: 49
1184866 ATGTTAAAGA
** * *
1184876 TGCCAATACACTGATTCAAGGCCAACGATATTGGACTTAAGGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* *
1184925 TGCCAATATGCTGATTCAAGGACCAGTGATATTGGACTTAAAGATGAAGA
1 TGCCAATATGCTGATTCAAGG-CCAGCGATATTGGACTTAAAGATGAAGG
* * *
1184975 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* *
1185024 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AA-A-GATGAAGG
* *
1185076 TGCCAATATGCTGATTTAAGGCCAGCGATATTGGACTTAAAGATGAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* * *
1185125 TGCCAATGTGCTGATTC-AGGCCAGCGACATTGGACTTCAAGATGACGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AA-A-GATGAAGG
** *
1185176 TGCCAATATGCTGATTCAAGGCCAGCGATACCGGACTTAAAGATGAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* *
1185225 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT---GAAGG
*
1185277 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* * * * *
1185326 TGCCAATGTGCTGATTCAAGGCTAGCGACATTGGTCTTAAAGA-CAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
*
1185374 TGTCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* * *
1185417 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGACAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG---AAGG
* * *
1185469 AGCCAATATGCTAATTCAAGGCCAGCGATATTGGGC-T-----T--A--
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* * * * *
1185508 TGCTAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGA-CAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
*
1185556 TGCCAATATGCTAATTCAAGGCCAGCGATATTGGACTT----A--AAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* * * * *
1185599 TGCCAATGTGTTGATTCAAGGCCAGCGACATTGGTCTTAAAGATCACAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT---GAAGG
* *
1185651 CGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
1185692 AGAAGACGCC
Statistics
Matches: 654, Mismatches: 74, Indels: 75
0.81 0.09 0.09
Matches are distributed among these distances:
39 30 0.05
40 1 0.00
41 1 0.00
43 75 0.11
44 2 0.00
46 2 0.00
47 2 0.00
48 88 0.13
49 196 0.30
50 49 0.07
51 28 0.04
52 180 0.28
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (49 bp):
TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
Found at i:1185431 original size:43 final size:44
Alignment explanation
Indices: 1185273--1185693 Score: 334
Period size: 52 Copynumber: 9.1 Consensus size: 44
1185263 AAAGATGACG
* *
1185273 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAA
* *
1185317 AGATGAAGATGCCAATGTGCTGATTCAAGGCTAGCGACATTGGTCTTAAAGA
1 A-A-G--G-TGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTT--A-A
* * *
1185369 CAAGGTGTCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-A
1 -AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAA
*
1185413 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGACA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTC-T-----T-A-A
* * * *
1185465 AAGGAGCCAATATGCTAATTCAAGGCCAGCGATATTGGGCTT--
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAA
* *
1185507 -A--TGCTAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTT--A-A
* * *
1185551 CAAGGTGCCAATATGCTAATTCAAGGCCAGCGATATTGGACTT-A
1 -AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAA
* *
1185595 AAGGTGCCAATGTGTTGATTCAAGGCCAGCGACATTGGTCTTAAAGATCACA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTC-T-----T-A-A
* * *
1185647 AAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAA
1185691 AAG
1 AAG
1185694 AAGACGCCAC
Statistics
Matches: 302, Mismatches: 39, Indels: 72
0.73 0.09 0.17
Matches are distributed among these distances:
39 32 0.11
41 1 0.00
43 71 0.24
44 9 0.03
45 2 0.01
46 4 0.01
48 67 0.22
49 37 0.12
51 4 0.01
52 74 0.25
53 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.25
Consensus pattern (44 bp):
AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAA
Found at i:1185516 original size:91 final size:89
Alignment explanation
Indices: 1185326--1185690 Score: 518
Period size: 91 Copynumber: 4.0 Consensus size: 89
1185316 AAGATGAAGA
* * *
1185326 TGCCAATGTGCTGATTCAAGGCTAGCGACATTGGTCTTAAAGACAAGGTGTCAATATGCTGATTC
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTAATTC
1185391 AAGGCCAGCGATATTGGACTTAAAGG
66 AAGGCCAGCGATATTGGACTT-AA-G
*
1185417 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGACAAAGGAGCCAATATGCTA
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT-AA-A-GAC-AAGGTGCCAATATGCTA
*
1185482 ATTCAAGGCCAGCGATATTGGGCTT-A-
62 ATTCAAGGCCAGCGATATTGGACTTAAG
*
1185508 TGCTAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTAATTC
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTAATTC
1185573 AAGGCCAGCGATATTGGACTTAAAGG
66 AAGGCCAGCGATATTGGACTT-AA-G
* * *
1185599 TGCCAATGTGTTGATTCAAGGCCAGCGACATTGGTCTTAAAGATCACAAAGGCGCCAATATGCTG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAG---AC-AAGGTGCCAATATGCTA
*
1185664 ATTCAAGGCCAGCGATATTGGGCTTAA
62 ATTCAAGGCCAGCGATATTGGACTTAA
1185691 AAGAAGACGC
Statistics
Matches: 249, Mismatches: 13, Indels: 21
0.88 0.05 0.07
Matches are distributed among these distances:
87 40 0.16
88 3 0.01
89 2 0.01
90 2 0.01
91 114 0.46
92 2 0.01
93 2 0.01
94 7 0.03
95 77 0.31
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.25
Consensus pattern (89 bp):
TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTAATTC
AAGGCCAGCGATATTGGACTTAAG
Found at i:1185637 original size:182 final size:182
Alignment explanation
Indices: 1185325--1185689 Score: 658
Period size: 182 Copynumber: 2.0 Consensus size: 182
1185315 AAAGATGAAG
* * *
1185325 ATGCCAATGTGCTGATTCAAGGCTAGCGACATTGGTCTTAAAGACAAGGTGTCAATATGCTGATT
1 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTAATT
1185390 CAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT
66 CAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT
*
1185455 AAAGATGACAAAGGAGCCAATATGCTAATTCAAGGCCAGCGATATTGGGCTT
131 AAAGATCACAAAGGAGCCAATATGCTAATTCAAGGCCAGCGATATTGGGCTT
*
1185507 ATGCTAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTAATT
1 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTAATT
*
1185572 CAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGTTGATTCAAGGCCAGCGACATTGGTCTT
66 CAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT
* *
1185637 AAAGATCACAAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT
131 AAAGATCACAAAGGAGCCAATATGCTAATTCAAGGCCAGCGATATTGGGCTT
1185689 A
1 A
1185690 AAAGAAGACG
Statistics
Matches: 175, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
182 175 1.00
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.25
Consensus pattern (182 bp):
ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTAATT
CAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT
AAAGATCACAAAGGAGCCAATATGCTAATTCAAGGCCAGCGATATTGGGCTT
Found at i:1185811 original size:33 final size:33
Alignment explanation
Indices: 1185774--1186013 Score: 171
Period size: 33 Copynumber: 7.3 Consensus size: 33
1185764 AACTTATGGG
*
1185774 CTTAAAAAGAGAAAGATGCCACGAAGTTGTGGA
1 CTTAAAAAGAGAAAGGTGCCACGAAGTTGTGGA
* * *
1185807 CTTAAAAGGA-ACAAGGTGCCACGGAGTTGTGGG
1 CTTAAAAAGAGA-AAGGTGCCACGAAGTTGTGGA
* * *
1185840 CTTTAAAAGGGAAAAGGGTGCCAC-AGAGTCGTGGA
1 CTTAAAAAGAG-AAA-GGTGCCACGA-AGTTGTGGA
* *
1185875 CTTAAAAAGAAAAAGAG-GCCACGGAGTTGTGGA
1 CTTAAAAAGAGAAAG-GTGCCACGAAGTTGTGGA
*
1185908 CTT--AAA-AG---GGTACCAC-AGAGTTGTGGA
1 CTTAAAAAGAGAAAGGTGCCACGA-AGTTGTGGA
* * *
1185935 CTTAAAAGGA-ACAAGGTGCCACGGAGTTGTGGG
1 CTTAAAAAGAGA-AAGGTGCCACGAAGTTGTGGA
*
1185968 CTTTAAAAGAGAAAAAGGTGCCACTG-AGTTGTGGA
1 C-TTAAAA-AGAGAAAGGTGCCAC-GAAGTTGTGGA
1186003 CTTTAAAAAGA
1 C-TTAAAAAGA
1186014 TATTGCAACT
Statistics
Matches: 162, Mismatches: 24, Indels: 41
0.71 0.11 0.18
Matches are distributed among these distances:
26 1 0.01
27 17 0.10
29 2 0.01
30 2 0.01
31 3 0.02
32 1 0.01
33 67 0.41
34 15 0.09
35 52 0.32
36 2 0.01
ACGTcount: A:0.37, C:0.13, G:0.31, T:0.19
Consensus pattern (33 bp):
CTTAAAAAGAGAAAGGTGCCACGAAGTTGTGGA
Found at i:1185881 original size:68 final size:67
Alignment explanation
Indices: 1185790--1186010 Score: 271
Period size: 68 Copynumber: 3.4 Consensus size: 67
1185780 AAGAGAAAGA
1185790 TGCCAC-GAAGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGGAAA
1 TGCCACAG-AGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAGTTGTGGGCTTTAAAA-GGAAA
1185854 AGGG
64 AGGG
* * * *
1185858 TGCCACAGAGTCGTGGACTTAAAAAGAAAAAGAG-GCCACGGAGTTGTGGAC-TT------AAAA
1 TGCCACAGAGTTGTGGACTTAAAAGGAACAAG-GTGCCACGGAGTTGTGGGCTTTAAAAGGAAAA
1185915 GGG
65 GGG
*
1185918 TACCACAGAGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAGTTGTGGGCTTTAAAAGAGAAAA
1 TGCCACAGAGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAGTTGTGGGCTTTAAAAG-GAAAA
*
1185983 AGG
65 GGG
*
1185986 TGCCACTGAGTTGTGGACTTTAAAA
1 TGCCACAGAGTTGTGGAC-TTAAAA
1186011 AGATATTGCA
Statistics
Matches: 129, Mismatches: 12, Indels: 23
0.79 0.07 0.14
Matches are distributed among these distances:
59 1 0.01
60 51 0.40
61 2 0.02
67 2 0.02
68 65 0.50
69 8 0.06
ACGTcount: A:0.34, C:0.14, G:0.32, T:0.20
Consensus pattern (67 bp):
TGCCACAGAGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAG
GG
Found at i:1185914 original size:26 final size:26
Alignment explanation
Indices: 1185885--1185943 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 26
1185875 CTTAAAAAGA
*
1185885 AAAAGAGG-CCACGGAGTTGTGGACTT
1 AAAAG-GGACCACAGAGTTGTGGACTT
1185911 AAAAGGGTACCACAGAGTTGTGGACTT
1 AAAAGGG-ACCACAGAGTTGTGGACTT
1185938 AAAAGG
1 AAAAGG
1185944 AACAAGGTGC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 2 0.07
26 5 0.17
27 23 0.77
ACGTcount: A:0.36, C:0.14, G:0.32, T:0.19
Consensus pattern (26 bp):
AAAAGGGACCACAGAGTTGTGGACTT
Found at i:1185956 original size:60 final size:61
Alignment explanation
Indices: 1185851--1185976 Score: 184
Period size: 60 Copynumber: 2.1 Consensus size: 61
1185841 TTTAAAAGGG
*
1185851 AAAAGGGTGCCACAGAGTCGTGGACTTAAAAAGAAAAAGAGGCCACGGAGTTGTGGAC-TT
1 AAAAGGGTACCACAGAGTCGTGGACTTAAAAAGAAAAAGAGGCCACGGAGTTGTGGACTTT
* * * *
1185911 AAAAGGGTACCACAGAGTTGTGGACTTAAAAGGAACAAG-GTGCCACGGAGTTGTGGGCTTT
1 AAAAGGGTACCACAGAGTCGTGGACTTAAAAAGAAAAAGAG-GCCACGGAGTTGTGGACTTT
1185972 AAAAG
1 AAAAG
1185977 AGAAAAAGGT
Statistics
Matches: 59, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
59 1 0.02
60 51 0.86
61 7 0.12
ACGTcount: A:0.36, C:0.14, G:0.32, T:0.18
Consensus pattern (61 bp):
AAAAGGGTACCACAGAGTCGTGGACTTAAAAAGAAAAAGAGGCCACGGAGTTGTGGACTTT
Found at i:1186033 original size:31 final size:31
Alignment explanation
Indices: 1185990--1186048 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
1185980 AAAAGGTGCC
*
1185990 ACTGAGTTGTGGACTTTAAAAAGATATTGCA
1 ACTGAGTCGTGGACTTTAAAAAGATATTGCA
*
1186021 ACTGAGTCGTGGACTTTAAAAAGGTATT
1 ACTGAGTCGTGGACTTTAAAAAGATATT
1186049 TGAAGAATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.32
Consensus pattern (31 bp):
ACTGAGTCGTGGACTTTAAAAAGATATTGCA
Found at i:1187292 original size:22 final size:22
Alignment explanation
Indices: 1187265--1187306 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1187255 TTTGCACTTT
*
1187265 TTTTGTGTGTGTTTTTTTTTTG
1 TTTTGTGTGTGTTTATTTTTTG
*
1187287 TTTTGTTTGTGTTTATTTTT
1 TTTTGTGTGTGTTTATTTTT
1187307 GGCTTTTTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.02, C:0.00, G:0.19, T:0.79
Consensus pattern (22 bp):
TTTTGTGTGTGTTTATTTTTTG
Found at i:1194385 original size:52 final size:52
Alignment explanation
Indices: 1194237--1194365 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
1194227 CGAAATATGA
1194237 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
* * *
1194289 AAATTTGCCTGTATGAATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
1194341 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1194366 AAGATCAGTG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
Found at i:1194475 original size:19 final size:19
Alignment explanation
Indices: 1194451--1194532 Score: 113
Period size: 19 Copynumber: 4.6 Consensus size: 19
1194441 AGCGATACAT
*
1194451 TGTATCGATACAAAACTTA
1 TGTATCGATACAACACTTA
1194470 TGTATCGAT---ACA---A
1 TGTATCGATACAACACTTA
1194483 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
1194502 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
1194521 TGTATCGATACA
1 TGTATCGATACA
1194533 TTGTATCGAT
Statistics
Matches: 56, Mismatches: 1, Indels: 12
0.81 0.01 0.17
Matches are distributed among these distances:
13 10 0.18
16 5 0.09
19 41 0.73
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:1194487 original size:32 final size:32
Alignment explanation
Indices: 1194438--1194514 Score: 127
Period size: 32 Copynumber: 2.4 Consensus size: 32
1194428 GCAGTAGCTT
* *
1194438 TGTAGCGATACATTGTATCGATACAAAACTTA
1 TGTATCGATACAATGTATCGATACAAAACTTA
*
1194470 TGTATCGATACAATGTATCGATACAACACTTA
1 TGTATCGATACAATGTATCGATACAAAACTTA
1194502 TGTATCGATACAA
1 TGTATCGATACAA
1194515 CACTTATGTA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (32 bp):
TGTATCGATACAATGTATCGATACAAAACTTA
Found at i:1194495 original size:13 final size:13
Alignment explanation
Indices: 1194469--1194495 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1194459 TACAAAACTT
1194469 ATGTATCGATACA
1 ATGTATCGATACA
1194482 ATGTATCGATACA
1 ATGTATCGATACA
1194495 A
1 A
1194496 CACTTATGTA
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:1194539 original size:13 final size:13
Alignment explanation
Indices: 1194521--1194545 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1194511 ACAACACTTA
1194521 TGTATCGATACAT
1 TGTATCGATACAT
1194534 TGTATCGATACA
1 TGTATCGATACA
1194546 AATCGTTGAA
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:1197888 original size:13 final size:13
Alignment explanation
Indices: 1197870--1197900 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1197860 TCTCATATTT
1197870 TTTTAAAATAATA
1 TTTTAAAATAATA
*
1197883 TTTTAAAATAATT
1 TTTTAAAATAATA
1197896 TTTTA
1 TTTTA
1197901 TAATTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TTTTAAAATAATA
Found at i:1204235 original size:3 final size:3
Alignment explanation
Indices: 1204227--1204252 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1204217 TACATTCCTT
1204227 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
1204253 TTTCTGGCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1204958 original size:16 final size:16
Alignment explanation
Indices: 1204906--1204958 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
1204896 ATAAAAATAT
* *
1204906 TATATATTAAAATTTA
1 TATAAATTAAATTTTA
* *
1204922 TTTAAAATAAATTATTA
1 TATAAATTAAATT-TTA
1204939 -ATAAATTAAATTTTA
1 TATAAATTAAATTTTA
1204954 TATAA
1 TATAA
1204959 TATTTTATTA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
15 3 0.10
16 23 0.79
17 3 0.10
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATAAATTAAATTTTA
Found at i:1205022 original size:22 final size:23
Alignment explanation
Indices: 1204983--1205031 Score: 82
Period size: 22 Copynumber: 2.2 Consensus size: 23
1204973 TATAAAAAAT
*
1204983 AAAATAAAATATTATTTTTTAAA
1 AAAATAAAATAATATTTTTTAAA
1205006 AAAATAAAATAAT-TTTTTTAAA
1 AAAATAAAATAATATTTTTTAAA
1205028 AAAA
1 AAAA
1205032 AATTCTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 13 0.52
23 12 0.48
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
AAAATAAAATAATATTTTTTAAA
Found at i:1205032 original size:23 final size:23
Alignment explanation
Indices: 1204978--1205032 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 23
1204968 ATAAATATAA
1204978 AAAATAAAATAAAATATTATTTTT
1 AAAA-AAAATAAAATATTATTTTT
*
1205002 TAAAAAAATAAAATAATT-TTTTT
1 AAAAAAAATAAAAT-ATTATTTTT
1205025 AAAAAAAA
1 AAAAAAAA
1205033 ATTCTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 22 0.79
24 6 0.21
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (23 bp):
AAAAAAAATAAAATATTATTTTT
Found at i:1205525 original size:2 final size:2
Alignment explanation
Indices: 1205518--1205544 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1205508 ATCTGAAATT
1205518 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1205545 TGTATTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1205614 original size:14 final size:13
Alignment explanation
Indices: 1205591--1205633 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
1205581 TCTAAAATTT
1205591 TATATA-TAAATAA
1 TATATATTAAAT-A
1205604 TATATATTAAATA
1 TATATATTAAATA
*
1205617 TATTATATTAATTA
1 TA-TATATTAAATA
1205631 TAT
1 TAT
1205634 TTAATCATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 10 0.37
14 17 0.63
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
TATATATTAAATA
Found at i:1205618 original size:24 final size:23
Alignment explanation
Indices: 1205591--1205653 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
1205581 TCTAAAATTT
1205591 TATATATAAATAATATATATTAAA
1 TATAT-TAAATAATATATATTAAA
* *
1205615 TATATTATATTAAT-TATATTTAA
1 TATATTA-AATAATATATATTAAA
*
1205638 TCATATTAAATTATAT
1 T-ATATTAAATAATAT
1205654 TTTTATAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
23 15 0.47
24 17 0.53
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
TATATTAAATAATATATATTAAA
Found at i:1205643 original size:10 final size:10
Alignment explanation
Indices: 1205618--1205655 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
1205608 TATTAAATAT
1205618 ATTATA-TTA
1 ATTATATTTA
1205627 ATTATATTTA
1 ATTATATTTA
* *
1205637 ATCATATTAA
1 ATTATATTTA
1205647 ATTATATTT
1 ATTATATTT
1205656 TTATAATAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
9 6 0.25
10 18 0.75
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (10 bp):
ATTATATTTA
Found at i:1205690 original size:18 final size:20
Alignment explanation
Indices: 1205648--1205694 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 20
1205638 TCATATTAAA
*
1205648 TTATATTT-TTATAATAATT
1 TTATATTTATTATAATAATC
1205667 TTATATTTATTA-AAT-ATC
1 TTATATTTATTATAATAATC
1205685 TTATATTTAT
1 TTATATTTAT
1205695 AATATATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 12 0.46
19 11 0.42
20 3 0.12
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATATTTATTATAATAATC
Found at i:1205701 original size:18 final size:18
Alignment explanation
Indices: 1205655--1205701 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
1205645 AAATTATATT
*
1205655 TTTATAATA-ATTTTATA
1 TTTATAATATATCTTATA
1205672 TTTATTAA-ATATCTTATA
1 TTTA-TAATATATCTTATA
1205690 TTTATAATATAT
1 TTTATAATATAT
1205702 TATTGTTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 8 0.31
18 18 0.69
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTATAATATATCTTATA
Found at i:1206474 original size:15 final size:15
Alignment explanation
Indices: 1206454--1206503 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
1206444 TTTATTGTTG
*
1206454 AATAAAATTATAAAA
1 AATAAAAATATAAAA
1206469 AATAAAAATATCATAAA
1 AATAAAAATAT-A-AAA
* *
1206486 AAGAAAAATATTAAA
1 AATAAAAATATAAAA
1206501 AAT
1 AAT
1206504 TGATTAATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 15 0.52
16 1 0.03
17 13 0.45
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (15 bp):
AATAAAAATATAAAA
Found at i:1206512 original size:17 final size:18
Alignment explanation
Indices: 1206492--1206541 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
1206482 TAAAAAGAAA
*
1206492 AATATTAAAAATTGA-TT
1 AATATTAAAAATTAATTT
*
1206509 AATAAATAAAAA-TAATTT
1 AAT-ATTAAAAATTAATTT
*
1206527 AAAATTAAAAATTAA
1 AATATTAAAAATTAA
1206542 AAATTTATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (18 bp):
AATATTAAAAATTAATTT
Found at i:1206554 original size:10 final size:10
Alignment explanation
Indices: 1206539--1206596 Score: 71
Period size: 10 Copynumber: 5.7 Consensus size: 10
1206529 AATTAAAAAT
*
1206539 TAAAAATTTA
1 TAAAAATTAA
1206549 TAAAAATTAA
1 TAAAAATTAA
*
1206559 TATAAATTAA
1 TAAAAATTAA
1206569 TAAAAATTAA
1 TAAAAATTAA
* *
1206579 TACAAATCAA
1 TAAAAATTAA
1206589 TTAAAAAT
1 -TAAAAAT
1206597 AGGAAGGATA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
10 35 0.85
11 6 0.15
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (10 bp):
TAAAAATTAA
Found at i:1206629 original size:3 final size:3
Alignment explanation
Indices: 1206621--1206645 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1206611 AGTACTACCC
1206621 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
1206646 TTTAAACTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1217436 original size:35 final size:35
Alignment explanation
Indices: 1217382--1217455 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 35
1217372 ATAGAAGTAG
*
1217382 TTATAGGAGATTACTTGTAAATT-AGTAGATCATAA
1 TTATAGGAGATTACGTGTAAATTAAG-AGATCATAA
* * *
1217417 TTATAGGAGGTTAGGTGTAAATTAAGAGATCATAG
1 TTATAGGAGATTACGTGTAAATTAAGAGATCATAA
1217452 TTAT
1 TTAT
1217456 GTTTCAGAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 32 0.94
36 2 0.06
ACGTcount: A:0.38, C:0.04, G:0.22, T:0.36
Consensus pattern (35 bp):
TTATAGGAGATTACGTGTAAATTAAGAGATCATAA
Found at i:1219311 original size:26 final size:26
Alignment explanation
Indices: 1219281--1219332 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
1219271 CTAAAGAAAG
*
1219281 ACAAGATATTTATTAGGAGGGAAACT
1 ACAAGATATTTACTAGGAGGGAAACT
*
1219307 ACAAGATATTTGCTAGGAGGGAAACT
1 ACAAGATATTTACTAGGAGGGAAACT
1219333 TCCAGTCCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.40, C:0.10, G:0.25, T:0.25
Consensus pattern (26 bp):
ACAAGATATTTACTAGGAGGGAAACT
Found at i:1219430 original size:2 final size:2
Alignment explanation
Indices: 1219423--1219459 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1219413 TATGTGCGTG
1219423 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1219460 GGAATAAACC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1224014 original size:11 final size:11
Alignment explanation
Indices: 1223991--1224023 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1223981 TATTCACTCT
1223991 AAAAATTCA-A
1 AAAAATTCATA
*
1224001 AAAAATTTATA
1 AAAAATTCATA
1224012 AAAAATTCATA
1 AAAAATTCATA
1224023 A
1 A
1224024 TGGCATTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 8 0.40
11 12 0.60
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (11 bp):
AAAAATTCATA
Found at i:1225174 original size:20 final size:20
Alignment explanation
Indices: 1225149--1225228 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 20
1225139 GTTACAAGCA
1225149 ATGTATCGATACAATTCATC
1 ATGTATCGATACAATTCATC
1225169 ATGTATCGATACAATGTATCGATAC
1 ATGTATCGATACAA--T-TC-AT-C
* *
1225194 AATGTATCGATAC-ATTGTACC
1 -ATGTATCGATACAATT-CATC
1225215 ATGTATCGATACAA
1 ATGTATCGATACAA
1225229 ACAGTGGTAA
Statistics
Matches: 50, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
20 26 0.52
21 2 0.04
22 3 0.06
23 3 0.06
24 2 0.04
25 2 0.04
26 12 0.24
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACAATTCATC
Found at i:1225187 original size:13 final size:13
Alignment explanation
Indices: 1225147--1225212 Score: 81
Period size: 13 Copynumber: 5.5 Consensus size: 13
1225137 CCGTTACAAG
1225147 CAATGTATCGATA
1 CAATGTATCGATA
1225160 CAA--T-TC-AT-
1 CAATGTATCGATA
1225168 C-ATGTATCGATA
1 CAATGTATCGATA
1225180 CAATGTATCGATA
1 CAATGTATCGATA
1225193 CAATGTATCGATA
1 CAATGTATCGATA
*
1225206 CATTGTA
1 CAATGTA
1225213 CCATGTATCG
Statistics
Matches: 46, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
7 1 0.02
8 1 0.02
9 3 0.07
10 4 0.09
11 3 0.07
12 1 0.02
13 33 0.72
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1225301 original size:19 final size:20
Alignment explanation
Indices: 1225257--1225311 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
1225247 CTGCCAATCT
**
1225257 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGAA
1225277 CATGTATCGATACAATT-AA
1 CATGTATCGATACAATTGAA
1225296 CATGTATCGATACAAT
1 CATGTATCGATACAAT
1225312 GTATCGATAC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:1225315 original size:13 final size:13
Alignment explanation
Indices: 1225297--1225323 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1225287 TACAATTAAC
1225297 ATGTATCGATACA
1 ATGTATCGATACA
1225310 ATGTATCGATACA
1 ATGTATCGATACA
1225323 A
1 A
1225324 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:1225900 original size:21 final size:22
Alignment explanation
Indices: 1225868--1225939 Score: 85
Period size: 22 Copynumber: 3.3 Consensus size: 22
1225858 AGTTTTCGTT
1225868 TTTCTCCTCCTTAATTAAAGAA
1 TTTCTCCTCCTTAATTAAAGAA
*
1225890 TTTCT-CTCCTTTAA-TAAAAAA
1 TTTCTCCTCC-TTAATTAAAGAA
* * *
1225911 TTTCTCCCCCTTAATCAAAGCA
1 TTTCTCCTCCTTAATTAAAGAA
1225933 TTTCTCC
1 TTTCTCC
1225940 CGCTTTGTCA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
21 19 0.45
22 23 0.55
ACGTcount: A:0.29, C:0.28, G:0.03, T:0.40
Consensus pattern (22 bp):
TTTCTCCTCCTTAATTAAAGAA
Found at i:1226778 original size:33 final size:33
Alignment explanation
Indices: 1226741--1226805 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1226731 TACAAGCCAA
1226741 TGTATCGATATAAT-TTTTTGTGTATCGATACAT
1 TGTATCGATA-AATGTTTTTGTGTATCGATACAT
*
1226774 TGTATCGATACATGTTTTTGTGTATCGATACA
1 TGTATCGATAAATGTTTTTGTGTATCGATACA
1226806 AGTTTGGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 2 0.07
33 28 0.93
ACGTcount: A:0.26, C:0.11, G:0.17, T:0.46
Consensus pattern (33 bp):
TGTATCGATAAATGTTTTTGTGTATCGATACAT
Found at i:1226779 original size:13 final size:13
Alignment explanation
Indices: 1226761--1226786 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1226751 TAATTTTTTG
1226761 TGTATCGATACAT
1 TGTATCGATACAT
1226774 TGTATCGATACAT
1 TGTATCGATACAT
1226787 GTTTTTGTGT
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:1227548 original size:21 final size:21
Alignment explanation
Indices: 1227507--1227550 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1227497 CTCCCCTTTA
* *
1227507 TCTCCCCCATTTATTAATAAT
1 TCTCCCCCATTAATCAATAAT
1227528 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCATTAATCAA-TAAT
1227549 TC
1 TC
1227551 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:1229363 original size:13 final size:13
Alignment explanation
Indices: 1229345--1229369 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1229335 ATAATCCCCC
1229345 TGTATCGATACAG
1 TGTATCGATACAG
1229358 TGTATCGATACA
1 TGTATCGATACA
1229370 AAGAAAAATG
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:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1231468 original size:15 final size:15
Alignment explanation
Indices: 1231448--1231479 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1231438 ATTTCGTTTG
*
1231448 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1231463 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1231478 GA
1 GA
1231480 ACACTTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.22, G:0.16, T:0.47
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1240056 original size:19 final size:20
Alignment explanation
Indices: 1240012--1240065 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 20
1240002 CTGCCAATCT
**
1240012 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGAA
1240032 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
1240051 CATGTATCGATACAA
1 CATGTATCGATACAA
1240066 AGCATAATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:1244027 original size:13 final size:13
Alignment explanation
Indices: 1243990--1244027 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1243980 AGCTCACTCA
*
1243990 GTATCGATACAGT
1 GTATCGATACATT
1244003 GTATCGATACATT
1 GTATCGATACATT
1244016 GTATCGATACAT
1 GTATCGATACAT
1244028 GGTCAAATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1245055 original size:20 final size:21
Alignment explanation
Indices: 1245011--1245064 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
1245001 ATTCAACAAT
* *
1245011 TGTATCAATATATTAGGGTAA
1 TGTATCAATACATAAGGGTAA
*
1245032 TGTATCAATACATAAGTG-AA
1 TGTATCAATACATAAGGGTAA
1245052 TGTATCAATACAT
1 TGTATCAATACAT
1245065 GTCTGAAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 15 0.50
21 15 0.50
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (21 bp):
TGTATCAATACATAAGGGTAA
Found at i:1245071 original size:20 final size:21
Alignment explanation
Indices: 1245030--1245084 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
1245020 ATATTAGGGT
*
1245030 AATGTATCAATACATAAGTG-
1 AATGTATCAATACATAACTGA
**
1245050 AATGTATCAATACATGTCTGA
1 AATGTATCAATACATAACTGA
*
1245071 AATGTATCGATACA
1 AATGTATCAATACA
1245085 AGCCCATGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.31
Consensus pattern (21 bp):
AATGTATCAATACATAACTGA
Found at i:1245498 original size:14 final size:14
Alignment explanation
Indices: 1245479--1245533 Score: 80
Period size: 14 Copynumber: 4.1 Consensus size: 14
1245469 AATTAATATT
1245479 TAAAATATATTTAA
1 TAAAATATATTTAA
1245493 TAAAATATA-TT--
1 TAAAATATATTTAA
*
1245504 TAAAATACATTTAA
1 TAAAATATATTTAA
1245518 TAAAATATATTTAA
1 TAAAATATATTTAA
1245532 TA
1 TA
1245534 CCAAAAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
11 8 0.22
12 2 0.06
13 2 0.06
14 24 0.67
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (14 bp):
TAAAATATATTTAA
Found at i:1245503 original size:25 final size:25
Alignment explanation
Indices: 1245474--1245531 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
1245464 AACCGAATTA
*
1245474 ATATTTAAAATATATTTAATAAAAT
1 ATATTTAAAATACATTTAATAAAAT
1245499 ATATTTAAAATACATTTAATAAAAT
1 ATATTTAAAATACATTTAATAAAAT
1245524 ATATTTAA
1 ATATTTAA
1245532 TACCAAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (25 bp):
ATATTTAAAATACATTTAATAAAAT
Found at i:1250203 original size:10 final size:10
Alignment explanation
Indices: 1250173--1250197 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1250163 CTAGCCTAGC
1250173 TTTTCTATTT
1 TTTTCTATTT
1250183 TTTTCTATTT
1 TTTTCTATTT
1250193 TTTTC
1 TTTTC
1250198 CTTTTTCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTCTATTT
Found at i:1251734 original size:18 final size:18
Alignment explanation
Indices: 1251700--1251733 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1251690 ATAAAATGCT
1251700 AATAGATTTTTTCTTTTG
1 AATAGATTTTTTCTTTTG
*
1251718 AATA-ATTTTTTATTTT
1 AATAGATTTTTTCTTTT
1251734 TTTGGGTATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
AATAGATTTTTTCTTTTG
Found at i:1256046 original size:21 final size:20
Alignment explanation
Indices: 1256021--1256060 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1256011 AATTTATATT
1256021 GATACAAACAATGAATGTATC
1 GATACAAA-AATGAATGTATC
* *
1256042 GATACATAAGTGAATGTAT
1 GATACAAAAATGAATGTAT
1256061 TGATTCATGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.45, C:0.10, G:0.17, T:0.28
Consensus pattern (20 bp):
GATACAAAAATGAATGTATC
Found at i:1256168 original size:19 final size:19
Alignment explanation
Indices: 1256130--1256168 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1256120 AAAGAAAATA
*
1256130 TATCGATATATTTTTATTT
1 TATCGATATATTTTGATTT
*
1256149 TATCGATATATTTTGGTTT
1 TATCGATATATTTTGATTT
1256168 T
1 T
1256169 TAACCTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.23, C:0.05, G:0.10, T:0.62
Consensus pattern (19 bp):
TATCGATATATTTTGATTT
Found at i:1256262 original size:52 final size:52
Alignment explanation
Indices: 1256149--1256262 Score: 122
Period size: 52 Copynumber: 2.2 Consensus size: 52
1256139 ATTTTTATTT
* * * * * * * * *
1256149 TATCGATATATT-TTGGTTTTTAACCTAAATGTGTTGATACATTTTTCATTG
1 TATCGATACATTCTGGGTTTTTAACCCAAACGTATCGATACATTCTTAAATG
*
1256200 TATTGATACATTCTGGGTTTTTAACCCAAACGTATCGATACATTCTTAAATG
1 TATCGATACATTCTGGGTTTTTAACCCAAACGTATCGATACATTCTTAAATG
*
1256252 TATCGTTACAT
1 TATCGATACAT
1256263 GCAGGCTATT
Statistics
Matches: 50, Mismatches: 12, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
51 10 0.20
52 40 0.80
ACGTcount: A:0.28, C:0.14, G:0.13, T:0.45
Consensus pattern (52 bp):
TATCGATACATTCTGGGTTTTTAACCCAAACGTATCGATACATTCTTAAATG
Found at i:1258871 original size:28 final size:28
Alignment explanation
Indices: 1258831--1258902 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
1258821 GAAATAAAGC
** *
1258831 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
1258859 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
1258887 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
1258903 TCGATTGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:1259003 original size:50 final size:50
Alignment explanation
Indices: 1258896--1259004 Score: 130
Period size: 50 Copynumber: 2.2 Consensus size: 50
1258886 ACGAGGTTGG
* * *
1258896 AGTATCCTCGATTGTGAGAAATTAGTGTTTTGGAAATAAAATCAGAGTTGA
1 AGTATCC-CGATTATGAGAAATTAGTGTTTTAGAAATAAAATCAGAGTTCA
* * * *
1258947 AATATCCCGATTATG-GAGAATTGGTGTTTTAGAAATAAAATCGGGGTTCA
1 AGTATCCCGATTATGAGA-AATTAGTGTTTTAGAAATAAAATCAGAGTTCA
1258997 AGTATCCC
1 AGTATCCC
1259005 CTCGAGAATA
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
49 2 0.04
50 41 0.84
51 6 0.12
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (50 bp):
AGTATCCCGATTATGAGAAATTAGTGTTTTAGAAATAAAATCAGAGTTCA
Found at i:1259112 original size:80 final size:78
Alignment explanation
Indices: 1258950--1259143 Score: 226
Period size: 80 Copynumber: 2.4 Consensus size: 78
1258940 GAGTTGAAAT
* * * * * *
1258950 ATCCCGATTATGGAGAATTGGTGTTTTAGAAATAAAATCGGGGTTCAAGTATCCCCTCGAGAATA
1 ATCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTCAAGTATCCCCTCAAAAATA
* * *
1259015 ATGGGGTTGGAGT
66 ACGAGGTTGGAGA
**
1259028 ATCCCTGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGGTTGGAGTATCCCCTCAAAAA
1 ATCCC-GATTATGAAAAATTGATGTTTTAGAAATAAAACC-GGGGTTCAAGTATCCCCTCAAAAA
1259093 TAACGAGGTTGGAGA
64 TAACGAGGTTGGAGA
* * * *
1259108 ATCCCCAATTGTGAAAAATCGATGATTTAGAAATAA
1 AT-CCCGATTATGAAAAATTGATGTTTTAGAAATAA
1259144 GATAAGGGTT
Statistics
Matches: 98, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
78 5 0.05
79 30 0.31
80 60 0.61
81 3 0.03
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (78 bp):
ATCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTCAAGTATCCCCTCAAAAATA
ACGAGGTTGGAGA
Done.