Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007847.1 Hibiscus syriacus cultivar Beakdansim tig00110204_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1444154
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 6
Found at i:1240491 original size:99 final size:99
Alignment explanation
Indices: 1240335--1240532 Score: 297
Period size: 99 Copynumber: 2.0 Consensus size: 99
1240325 TTGTAGATTG
* ** **
1240335 GAAGGTAGTGGTGATTCATGTGAAGTAATTGAAAGGACTCGTCACCTGTCCTGTGTCCAAGAAAA
1 GAAGGTAGTGGTGATTCATGTGAAATAACCGAAAGGACTCGTCACCTGTCCAATGTCCAAGAAAA
*
1240400 ATATGATGTGCCAAAGAAATTCGAGGCTTTACCT
66 ATATGATGTGCCAAAGAAATTCGAGACTTTACCT
* ** *
1240434 GAAGGTAGTGGTGGTTCATGTGAAATAACCGAAAGGACTCGTCATTTGTCCAATGTCCAAGAAGA
1 GAAGGTAGTGGTGATTCATGTGAAATAACCGAAAGGACTCGTCACCTGTCCAATGTCCAAGAAAA
*
1240499 ATATGATGTGCGAAAGAAATTCGAGACTTTACCT
66 ATATGATGTGCCAAAGAAATTCGAGACTTTACCT
1240533 AAAGCAAAAG
Statistics
Matches: 88, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
99 88 1.00
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (99 bp):
GAAGGTAGTGGTGATTCATGTGAAATAACCGAAAGGACTCGTCACCTGTCCAATGTCCAAGAAAA
ATATGATGTGCCAAAGAAATTCGAGACTTTACCT
Found at i:1247957 original size:22 final size:22
Alignment explanation
Indices: 1247932--1247973 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1247922 TGGAACATAT
*
1247932 GAAATAAGAAAG-GTTACTAAAG
1 GAAATAACAAAGTGTT-CTAAAG
1247954 GAAATAACAAAGTGTTCTAA
1 GAAATAACAAAGTGTTCTAA
1247974 TAAAAGTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.52, C:0.07, G:0.19, T:0.21
Consensus pattern (22 bp):
GAAATAACAAAGTGTTCTAAAG
Found at i:1250678 original size:125 final size:126
Alignment explanation
Indices: 1250454--1250705 Score: 488
Period size: 125 Copynumber: 2.0 Consensus size: 126
1250444 AACACCGTTC
1250454 ACGTTCCTAACTGAATATGTATACTCCACAAAAGGAATTCTGCAGACAAGAACATAAAGTAAATT
1 ACGTTCCTAACTGAATA-GTATACTCCACAAAAGGAATTCTGCAGACAAGAACATAAAGTAAATT
1250519 AATCACAATTAGCACATGATAATATAACCATACAAAAATAACAATAATACTATGGAAAATGT
65 AATCACAATTAGCACATGATAATATAACCATACAAAAATAACAATAATACTATGGAAAATGT
1250581 ACGTTCCTAACTGAATA-TATACTCCACAAAAGGAATTCTGCAGACAAGAACATAAAGTAAATTA
1 ACGTTCCTAACTGAATAGTATACTCCACAAAAGGAATTCTGCAGACAAGAACATAAAGTAAATTA
1250645 ATCACAATTAGCACATGATAATATAACCATACAAAAATAACAATAATACTATGGAAAATGT
66 ATCACAATTAGCACATGATAATATAACCATACAAAAATAACAATAATACTATGGAAAATGT
1250706 CCAAAGAAAC
Statistics
Matches: 125, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
125 108 0.86
127 17 0.14
ACGTcount: A:0.48, C:0.17, G:0.11, T:0.24
Consensus pattern (126 bp):
ACGTTCCTAACTGAATAGTATACTCCACAAAAGGAATTCTGCAGACAAGAACATAAAGTAAATTA
ATCACAATTAGCACATGATAATATAACCATACAAAAATAACAATAATACTATGGAAAATGT
Found at i:1261613 original size:3 final size:3
Alignment explanation
Indices: 1261591--1261635 Score: 54
Period size: 3 Copynumber: 14.3 Consensus size: 3
1261581 TAAATTATAC
* *
1261591 TTA TAA TTA TTTA GTTA TTA TTA TTA TTA TTA TTA TTA TTT TTA T
1 TTA TTA TTA -TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1261636 CAATGATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
3 30 0.83
4 6 0.17
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1261899 original size:30 final size:32
Alignment explanation
Indices: 1261865--1261931 Score: 77
Period size: 30 Copynumber: 2.2 Consensus size: 32
1261855 TATTTTCTTA
*
1261865 ATTTTAAT-TTATTTAAACAAA-TTAAAAATT
1 ATTTTAATAATATTTAAACAAATTTAAAAATT
* * *
1261895 ATTTT-ATAATATTTTAATAAATTTAATAATT
1 ATTTTAATAATATTTAAACAAATTTAAAAATT
1261926 ATTTTA
1 ATTTTA
1261932 TAACATTAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
29 2 0.07
30 15 0.50
31 13 0.43
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (32 bp):
ATTTTAATAATATTTAAACAAATTTAAAAATT
Found at i:1263353 original size:160 final size:163
Alignment explanation
Indices: 1263081--1263401 Score: 621
Period size: 160 Copynumber: 2.0 Consensus size: 163
1263071 TGACATAGTT
1263081 GAAATTATTTTTATGAGATGTTGCTTAATGTTTTAGGGAATTGTGTTCAATGGAGTAATGCGTCA
1 GAAATTATTTTTATGAGATGTTGCTTAATGTTTTAGGGAATTGTGTTCAATGGAGTAATGCGTCA
1263146 GTCCCATGTTATTATGACTCCTCATTTTCATGAAATATTTGTGCTTGGCACATTCAAACAC-GTA
66 GTCCCATGTTATTATGACTCCTCATTTTCATGAAATATTTGTGCTTGGCACATTCAAACACGGTA
1263210 TTGGACAAGTTCCTTC-AATATATGGAAAAAAA
131 TTGGACAAGTTCCTTCAAATATATGGAAAAAAA
1263242 GAAATTA-TTTTATGAGATGTTGCTTAATGTTTTAGGGAATTGTGTTCAATGGAGTAATGCGTCA
1 GAAATTATTTTTATGAGATGTTGCTTAATGTTTTAGGGAATTGTGTTCAATGGAGTAATGCGTCA
1263306 GTCCCATGTTATTATGACTCCTCATTTTCATGAAATATTTGTGCTTGGCACATTCAAACACGGTA
66 GTCCCATGTTATTATGACTCCTCATTTTCATGAAATATTTGTGCTTGGCACATTCAAACACGGTA
1263371 TTGGACAAGTTCCTTCAAATATATGGAAAAA
131 TTGGACAAGTTCCTTCAAATATATGGAAAAA
1263402 CTAAAAAATT
Statistics
Matches: 158, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
160 118 0.75
161 26 0.16
162 14 0.09
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (163 bp):
GAAATTATTTTTATGAGATGTTGCTTAATGTTTTAGGGAATTGTGTTCAATGGAGTAATGCGTCA
GTCCCATGTTATTATGACTCCTCATTTTCATGAAATATTTGTGCTTGGCACATTCAAACACGGTA
TTGGACAAGTTCCTTCAAATATATGGAAAAAAA
Found at i:1273131 original size:118 final size:117
Alignment explanation
Indices: 1272953--1273186 Score: 405
Period size: 118 Copynumber: 2.0 Consensus size: 117
1272943 TACGGGTACG
1272953 AGTCCAACAGGGATGGGTTCAATTTTTTTTTAATAATTTTTCATGTATATGGAGGATCTTTAGAA
1 AGTCCAACAGGGATGGGTTCAATTTTTTTTTAATAATTTTTCATGTATATGGAGGATCTTTAGAA
* * * *
1273018 GATCGCATCTCCATATTCGTGTCCAGATATGATTTGGAAACGGATGTTGGGT
66 GATCACATCTCCATACTCGTGTCCAAATATGATTTGGAAACGGATCTTGGGT
*
1273070 AGTCCAACAGGGATGGGTTCAATTCTTTTTTTAATAATTTTTCATGTATTTGGAGGATCTTTAGA
1 AGTCCAACAGGGATGGGTTCAATT-TTTTTTTAATAATTTTTCATGTATATGGAGGATCTTTAGA
*
1273135 AGATCATATCTCCATACTCGTGTCCAAATATGATTTGGAAACGGATCTTGGG
65 AGATCACATCTCCATACTCGTGTCCAAATATGATTTGGAAACGGATCTTGGG
1273187 AATGGATAAT
Statistics
Matches: 110, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
117 24 0.22
118 86 0.78
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.38
Consensus pattern (117 bp):
AGTCCAACAGGGATGGGTTCAATTTTTTTTTAATAATTTTTCATGTATATGGAGGATCTTTAGAA
GATCACATCTCCATACTCGTGTCCAAATATGATTTGGAAACGGATCTTGGGT
Found at i:1280760 original size:15 final size:17
Alignment explanation
Indices: 1280724--1280762 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
1280714 TAAAAATCAT
1280724 AATTTAAACTAAATTTC
1 AATTTAAACTAAATTTC
1280741 -A-TTAAA-T-AATTTC
1 AATTTAAACTAAATTTC
1280754 AATTTAAAC
1 AATTTAAAC
1280763 GTTATCTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 7
0.73 0.00 0.27
Matches are distributed among these distances:
13 6 0.32
14 2 0.11
15 10 0.53
16 1 0.05
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (17 bp):
AATTTAAACTAAATTTC
Found at i:1297565 original size:18 final size:17
Alignment explanation
Indices: 1297531--1297565 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1297521 TCCCTTAGGT
*
1297531 ACTAAACATGTAGTTTA
1 ACTAAACATGAAGTTTA
1297548 ACTAAACATGAAAGTTTA
1 ACTAAACATG-AAGTTTA
1297566 GATACTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.31
Consensus pattern (17 bp):
ACTAAACATGAAGTTTA
Found at i:1298030 original size:14 final size:14
Alignment explanation
Indices: 1298011--1298066 Score: 55
Period size: 14 Copynumber: 4.1 Consensus size: 14
1298001 AAATAAATTA
1298011 AATATTAATTTTTT
1 AATATTAATTTTTT
* *
1298025 AATATT-ATATTAT
1 AATATTAATTTTTT
*
1298038 AGATATTAA--GTTT
1 A-ATATTAATTTTTT
1298051 AATATTAATTTTTT
1 AATATTAATTTTTT
1298065 AA
1 AA
1298067 ATAAATTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
12 7 0.21
13 9 0.27
14 16 0.48
15 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (14 bp):
AATATTAATTTTTT
Found at i:1305080 original size:37 final size:36
Alignment explanation
Indices: 1305005--1305080 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
1304995 TTTTTATATT
*
1305005 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
1305041 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
1305078 TTT
1 TTT
1305081 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:1307927 original size:20 final size:20
Alignment explanation
Indices: 1307902--1308091 Score: 114
Period size: 20 Copynumber: 9.4 Consensus size: 20
1307892 TTCCATAATA
1307902 GCAACGCGAATATGAAAATC
1 GCAACGCGAATATGAAAATC
*
1307922 GCAACGCGAACAT-ATAAATC
1 GCAACGCGAATATGA-AAATC
* * **
1307942 GCAACGCGATTCTGACTATC
1 GCAACGCGAATATGAAAATC
* * *
1307962 GCAACGCGTATCTGTAAATC
1 GCAACGCGAATATGAAAATC
* * *
1307982 GCAACGAGAATACGTAAATC
1 GCAACGCGAATATGAAAATC
* * ** *
1308002 GCAATGCGTATCCGTAAATC
1 GCAACGCGAATATGAAAATC
* * ** *
1308022 GCAATGCGTATCCGTAAATC
1 GCAACGCGAATATGAAAATC
* * *
1308042 GCAATGCAAATACGTAAAATC
1 GCAACGCGAATATG-AAAATC
*
1308063 GCAACGCGTAT-TCGAAAATC
1 GCAACGCGAATAT-GAAAATC
1308083 GCAACGCGA
1 GCAACGCGA
1308092 TTTTTAAAGC
Statistics
Matches: 138, Mismatches: 28, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
19 1 0.01
20 122 0.88
21 15 0.11
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.19
Consensus pattern (20 bp):
GCAACGCGAATATGAAAATC
Found at i:1307981 original size:60 final size:57
Alignment explanation
Indices: 1307902--1308090 Score: 166
Period size: 60 Copynumber: 3.1 Consensus size: 57
1307892 TTCCATAATA
* * * *
1307902 GCAACGCGAATATGAAAATCGCAACGCGAACATATAAATCGCAACGCGATTCTGACTATC
1 GCAACGCGTATCTGTAAATCGCAACGCGAA-ATATAAATCGCAACGCGATTC-GA-AATC
* * *
1307962 GCAACGCGTATCTGTAAATCGCAACGAG-AATACGTAAATCGCAATGCGTATCCGTAAATC
1 GCAACGCGTATCTGTAAATCGCAACGCGAAATA--TAAATCGCAACGCG-ATTCG-AAATC
* * *
1308022 GCAATGCGTATCCGTAAATCGCAATGC-AAATACGTAAAATCGCAACGCGTATTCGAAAATC
1 GCAACGCGTATCTGTAAATCGCAACGCGAAATA--T-AAATCGCAACGCG-ATTCG-AAATC
1308083 GCAACGCG
1 GCAACGCG
1308091 ATTTTTAAAG
Statistics
Matches: 108, Mismatches: 15, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
58 3 0.03
59 1 0.01
60 71 0.66
61 33 0.31
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.20
Consensus pattern (57 bp):
GCAACGCGTATCTGTAAATCGCAACGCGAAATATAAATCGCAACGCGATTCGAAATC
Found at i:1308675 original size:20 final size:20
Alignment explanation
Indices: 1308650--1308721 Score: 76
Period size: 20 Copynumber: 3.6 Consensus size: 20
1308640 GTTTCTAAAC
*
1308650 TTAAAATCGCAACATGAAAA
1 TTAAAATCGCAACACGAAAA
1308670 TTAAAATCGCAACACG-AAA
1 TTAAAATCGCAACACGAAAA
** *
1308689 TTGACTATCGCAACGC-AAAA
1 TT-AAAATCGCAACACGAAAA
*
1308709 TGAAAATCGCAAC
1 TTAAAATCGCAAC
1308722 GAGAGAATCG
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
19 14 0.33
20 29 0.67
ACGTcount: A:0.49, C:0.21, G:0.12, T:0.18
Consensus pattern (20 bp):
TTAAAATCGCAACACGAAAA
Found at i:1308837 original size:20 final size:19
Alignment explanation
Indices: 1308748--1308860 Score: 110
Period size: 20 Copynumber: 6.1 Consensus size: 19
1308738 GAAACCAAAA
*
1308748 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1308767 TCGCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
1308786 TCGCGTTGC--TATTC---
1 TCGCGTTGCGATTTTCATT
* **
1308800 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
1308819 TCCGCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
*
1308839 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1308859 TC
1 TC
1308861 AACCAAAAGA
Statistics
Matches: 77, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
14 8 0.10
16 4 0.05
17 3 0.04
19 29 0.38
20 32 0.42
21 1 0.01
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1310859 original size:19 final size:20
Alignment explanation
Indices: 1310824--1310871 Score: 80
Period size: 19 Copynumber: 2.5 Consensus size: 20
1310814 AAAACAGACT
1310824 ATCGCAACGCGGAAATGAAA
1 ATCGCAACGCGGAAATGAAA
*
1310844 ATCGCAATGC-GAAATGAAA
1 ATCGCAACGCGGAAATGAAA
1310863 ATCGCAACG
1 ATCGCAACG
1310872 AGTGAATCGC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGAAA
Found at i:1310922 original size:20 final size:19
Alignment explanation
Indices: 1310896--1310964 Score: 85
Period size: 20 Copynumber: 3.8 Consensus size: 19
1310886 CGAAAATAAA
1310896 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
1310915 ATTTTCGCATTGCGA--TTC
1 A-TTTCGCATTGCGATTTTC
*
1310933 A-CTCG--TTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
1310949 ATTTCGCATTGCGATT
1 ATTTCGCATTGCGATT
1310965 CTCTCCTTGC
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
14 6 0.14
16 7 0.17
17 3 0.07
18 4 0.10
19 9 0.21
20 13 0.31
ACGTcount: A:0.16, C:0.22, G:0.17, T:0.45
Consensus pattern (19 bp):
ATTTCGCATTGCGATTTTC
Found at i:1310959 original size:33 final size:34
Alignment explanation
Indices: 1310904--1310977 Score: 123
Period size: 33 Copynumber: 2.2 Consensus size: 34
1310894 AAATTTCGCA
*
1310904 TTGCGATTTTCATTTTCGCATTGCGATTCACTCG
1 TTGCGATTTTCATTTTCGCATTGCGATTCACTCC
*
1310938 TTGCGATTTTCA-TTTCGCATTGCGATTCTCTCC
1 TTGCGATTTTCATTTTCGCATTGCGATTCACTCC
1310971 TTGCGAT
1 TTGCGAT
1310978 AGTAATTTCC
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 26 0.68
34 12 0.32
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.45
Consensus pattern (34 bp):
TTGCGATTTTCATTTTCGCATTGCGATTCACTCC
Found at i:1310986 original size:33 final size:33
Alignment explanation
Indices: 1310917--1310997 Score: 99
Period size: 33 Copynumber: 2.4 Consensus size: 33
1310907 CGATTTTCAT
* ** *
1310917 TTTCGCATTGCGATTCACTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTCACTCCTTGCGATAGTAA
*
1310950 TTTCGCATTGCGATTCTCTCCTTGCGATAGTAA
1 TTTCGCATTGCGATTCACTCCTTGCGATAGTAA
*
1310983 TTTCCGCGTTGCGAT
1 TTT-CGCATTGCGAT
1310998 AGTCAATTCC
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
33 31 0.76
34 10 0.24
ACGTcount: A:0.15, C:0.25, G:0.20, T:0.41
Consensus pattern (33 bp):
TTTCGCATTGCGATTCACTCCTTGCGATAGTAA
Found at i:1310996 original size:20 final size:20
Alignment explanation
Indices: 1310971--1311023 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
1310961 GATTCTCTCC
*
1310971 TTGCGATAGT-AATTTCCGCG
1 TTGCGATAGTCAA-TTCCGCA
1310991 TTGCGATAGTCAATTCCGCA
1 TTGCGATAGTCAATTCCGCA
1311011 TTGCGATAGTCAA
1 TTGCGATAGTCAA
1311024 ATGAATGTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 29 0.94
21 2 0.06
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.32
Consensus pattern (20 bp):
TTGCGATAGTCAATTCCGCA
Found at i:1313454 original size:24 final size:24
Alignment explanation
Indices: 1313420--1313469 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
1313410 CTGAAAAATC
1313420 ATCAAAATCC-GAGTATTGACCAAG
1 ATCAAAATCCGGA-TATTGACCAAG
*
1313444 ATCAAAGTCCGGATATTGACCAAG
1 ATCAAAATCCGGATATTGACCAAG
1313468 AT
1 AT
1313470 TAAATTTCGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 22 0.92
25 2 0.08
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAG
Found at i:1313487 original size:24 final size:24
Alignment explanation
Indices: 1313420--1313487 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
1313410 CTGAAAAATC
* * *
1313420 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
1313444 ATCAAAGTCCGGATATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* * *
1313468 ATTAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
1313488 TAGTACTCAC
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.25
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:1314345 original size:20 final size:19
Alignment explanation
Indices: 1314324--1314562 Score: 160
Period size: 20 Copynumber: 11.9 Consensus size: 19
1314314 GCGATTGTCA
*
1314324 GAATCTCGTTGCGATTTAC
1 GAATCGCGTTGCGATTTAC
* *
1314343 AGATTCGCATTGCGATTTAC
1 -GAATCGCGTTGCGATTTAC
* *
1314363 GTATTCGCATTGCGATTTAC
1 G-AATCGCGTTGCGATTTAC
* *
1314383 GTATTCGCATTGCGATTTAC
1 G-AATCGCGTTGCGATTTAC
* *
1314403 GGATACGCATTGCGA-TTAC
1 GAAT-CGCGTTGCGATTTAC
* *
1314422 GTATTCTCGTTGCGATTTAC
1 G-AATCGCGTTGCGATTTAC
1314442 -AGATACGCGTTGCGATTTAC
1 GA-AT-CGCGTTGCGATTTAC
*
1314462 GGATACGCGTTGCGATTTTAC
1 GAAT-CGCGTTGCGA-TTTAC
* *
1314483 GTATTGTCGTTGCGATTTAC
1 GAATCG-CGTTGCGATTTAC
*
1314503 GGATACGCGTTGCGATTTTAC
1 GAAT-CGCGTTGCGA-TTTAC
* * *
1314524 GGATACTCGTTGCGATAGT-C
1 GAAT-CGCGTTGCGAT-TTAC
1314544 AGAATCGCGTTGCGATTTA
1 -GAATCGCGTTGCGATTTA
1314563 TATGTTCGCG
Statistics
Matches: 184, Mismatches: 21, Indels: 28
0.79 0.09 0.12
Matches are distributed among these distances:
18 1 0.01
19 17 0.09
20 126 0.68
21 40 0.22
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (19 bp):
GAATCGCGTTGCGATTTAC
Found at i:1314494 original size:41 final size:39
Alignment explanation
Indices: 1314330--1314600 Score: 231
Period size: 40 Copynumber: 6.8 Consensus size: 39
1314320 GTCAGAATCT
* * *
1314330 CGTTGCGATTTACAGATTCGCATTGCGATTTACGTATTCG
1 CGTTGCGATTTACGGATTCGCGTTGCGATTTACGGA-TCG
* * *
1314370 CATTGCGATTTACGTATTCGCATTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATTCGCGTTGCGATTTACGGAT-CG
* * * *
1314410 CATTGCGA-TTACGTATTCTCGTTGCGATTTACAGATACG
1 CGTTGCGATTTACGGATTCGCGTTGCGATTTACGGAT-CG
* * *
1314449 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTG
1 CGTTGCGATTTACGGATTCGCGTTGCGA-TTTACGGATCG
* *
1314489 TCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACT
1 -CGTTGCGATTTACGGATTCGCGTTGCGA-TTTACGGAT-CG
* * * ** *
1314531 CGTTGCGATAGT-CAGAATCGCGTTGCGATTTATATGTTCG
1 CGTTGCGAT-TTACGGATTCGCGTTGCGATTTA-CGGATCG
* **
1314571 CGTTGCGATTTTCATATTCGCGTTGCGATT
1 CGTTGCGATTTACGGATTCGCGTTGCGATT
1314601 ATGGAAAATC
Statistics
Matches: 195, Mismatches: 28, Indels: 16
0.82 0.12 0.07
Matches are distributed among these distances:
39 37 0.19
40 89 0.46
41 68 0.35
42 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (39 bp):
CGTTGCGATTTACGGATTCGCGTTGCGATTTACGGATCG
Found at i:1314555 original size:61 final size:58
Alignment explanation
Indices: 1314330--1314562 Score: 234
Period size: 59 Copynumber: 3.9 Consensus size: 58
1314320 GTCAGAATCT
* * * * * * *
1314330 CGTTGCGATTTACAGATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCG
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTACG-AATCGCGTTGCGATTTACGGATACG
* * * * *
1314390 CATTGCGATTTACGGATACGCATTGCGATTACGTATTCTCGTTGCGATTTACAGATACG
1 CGTTGCGATTTACGGATACGCGTTGCGATTACG-AATCGCGTTGCGATTTACGGATACG
* *
1314449 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACGCGTTGCGA--TTACGAATCG-CGTTGCGATTTACGGATACG
*
1314510 CGTTGCGATTTTACGGATACTCGTTGCGA-TAGTCAGAATCGCGTTGCGATTTA
1 CGTTGCGA-TTTACGGATACGCGTTGCGATTA--C-GAATCGCGTTGCGATTTA
1314563 TATGTTCGCG
Statistics
Matches: 148, Mismatches: 18, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
59 54 0.36
60 26 0.18
61 45 0.30
62 23 0.16
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (58 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTACGAATCGCGTTGCGATTTACGGATACG
Found at i:1314571 original size:20 final size:20
Alignment explanation
Indices: 1314548--1314600 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
1314538 ATAGTCAGAA
*
1314548 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
1314568 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
1314588 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1314601 ATGGAAAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.13, C:0.19, G:0.25, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:1314573 original size:61 final size:61
Alignment explanation
Indices: 1314330--1314599 Score: 195
Period size: 61 Copynumber: 4.5 Consensus size: 61
1314320 GTCAGAATCT
* * * * * * * *
1314330 CGTTGCGA-TTTACAGATTCGCATTGCGAT-TTACGTATTCG-CATTGCGATTTACGTATTCG
1 CGTTGCGATTTTACGGATACGCGTTGCGATGTCACG-AATCGTCGTTGCGATTTAAG-ATACG
* * *
1314390 CATTGCGA-TTTACGGATACGCATTGCGAT-T-ACGTATTC-TCGTTGCGATTTACAGATACG
1 CGTTGCGATTTTACGGATACGCGTTGCGATGTCACG-AATCGTCGTTGCGATTTA-AGATACG
* * * * *
1314449 CGTTGCGA-TTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACG
1 CGTTGCGATTTTACGGATACGCGTTGCGATGTCACGAATCGTCGTTGCGATTTA-AGATACG
* *
1314510 CGTTGCGATTTTACGGATACTCGTTGCGATAGTCA-GAATCG-CGTTGCGATTTATATG-TTCG
1 CGTTGCGATTTTACGGATACGCGTTGCGAT-GTCACGAATCGTCGTTGCGATTTA-A-GATACG
** *
1314571 CGTTGCGATTTT-CATATTCGCGTTGCGAT
1 CGTTGCGATTTTACGGATACGCGTTGCGAT
1314600 TATGGAAAAT
Statistics
Matches: 178, Mismatches: 24, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
59 50 0.28
60 43 0.24
61 58 0.33
62 25 0.14
63 2 0.01
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (61 bp):
CGTTGCGATTTTACGGATACGCGTTGCGATGTCACGAATCGTCGTTGCGATTTAAGATACG
Found at i:1314698 original size:20 final size:19
Alignment explanation
Indices: 1314650--1314700 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
1314640 ATTCTTCATA
*
1314650 ATCGCGTTGCGATTCTGGG
1 ATCGCTTTGCGATTCTGGG
* *
1314669 AACTGATTTGCGATTCTGGAG
1 ATC-GCTTTGCGATTCTGG-G
1314690 ATCGCTTTGCG
1 ATCGCTTTGCG
1314701 GTTTTTATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 2 0.08
20 20 0.80
21 3 0.12
ACGTcount: A:0.16, C:0.20, G:0.31, T:0.33
Consensus pattern (19 bp):
ATCGCTTTGCGATTCTGGG
Found at i:1324975 original size:5 final size:5
Alignment explanation
Indices: 1324965--1324989 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1324955 AACAAGGATG
1324965 AATAA AATAA AATAA AATAA AATAA
1 AATAA AATAA AATAA AATAA AATAA
1324990 GATACGATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:1328366 original size:55 final size:54
Alignment explanation
Indices: 1328264--1328371 Score: 180
Period size: 55 Copynumber: 2.0 Consensus size: 54
1328254 TAAAAGCAGT
*
1328264 CTACTATCTTACCTCCCCTTACCCATTACATAAGAGAACAAGGGACAACCATTC
1 CTACTATCTTACCTCCCCTTACCCATTACATAAGAGAACAAGAGACAACCATTC
* *
1328318 CTACTATCTTACCTCTCCTTACCCCATTACATATGAGAACAAGAGACAACCATT
1 CTACTATCTTACCTCCCCTTA-CCCATTACATAAGAGAACAAGAGACAACCATT
1328372 TTTCTATAAG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
54 20 0.40
55 30 0.60
ACGTcount: A:0.33, C:0.32, G:0.08, T:0.26
Consensus pattern (54 bp):
CTACTATCTTACCTCCCCTTACCCATTACATAAGAGAACAAGAGACAACCATTC
Found at i:1328715 original size:54 final size:53
Alignment explanation
Indices: 1328647--1328758 Score: 127
Period size: 54 Copynumber: 2.1 Consensus size: 53
1328637 ACTTCCGGTG
*
1328647 TTCACATCCCTTCCGAACAA-CACATATCACCGGAGATAACCACTACTGAAGCTA
1 TTCACATCCCTTCCGAACAAGCA-AT-TCACCGGAGAAAACCACTACTGAAGCTA
* * * * * *
1328701 TTCACGTCGCTTCCGTACAAGTCAATTCACTGGAGAAAACCGCTACTGAAGCTG
1 TTCACATCCCTTCCGAACAAG-CAATTCACCGGAGAAAACCACTACTGAAGCTA
1328755 TTCA
1 TTCA
1328759 AGGCAAATCC
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
54 45 0.92
55 2 0.04
56 2 0.04
ACGTcount: A:0.31, C:0.30, G:0.15, T:0.23
Consensus pattern (53 bp):
TTCACATCCCTTCCGAACAAGCAATTCACCGGAGAAAACCACTACTGAAGCTA
Found at i:1328842 original size:54 final size:54
Alignment explanation
Indices: 1328754--1329387 Score: 822
Period size: 54 Copynumber: 11.7 Consensus size: 54
1328744 TACTGAAGCT
* *
1328754 GTTCAAGGCAAATCCTCGGAGAAAGCCGCAACTGAAGCTGTTCACGTCACTTCC
1 GTTCAAGGCAAATCCTCGGAGAAAGCCGCCACTGAAGCTGTTCACGTCGCTTCC
** *
1328808 GTTCAAGGCAAATCCTCGGAGAAAGAAGCCACTGAAGCTGTTCATGTCGCTTCC
1 GTTCAAGGCAAATCCTCGGAGAAAGCCGCCACTGAAGCTGTTCACGTCGCTTCC
* * *
1328862 GTTCAAGGCAAATCCGCGAAGAAAGCCGCCACTGAAGCTGTTCACATCGCTTCC
1 GTTCAAGGCAAATCCTCGGAGAAAGCCGCCACTGAAGCTGTTCACGTCGCTTCC
* *
1328916 GTTCAAGGCAAATCGTCGGAAAAAGCCGCCACTGAAGCTGTTCACGTCGCTTCC
1 GTTCAAGGCAAATCCTCGGAGAAAGCCGCCACTGAAGCTGTTCACGTCGCTTCC
* * *
1328970 TTTCAAGGCAAATCCTCGGGGAAAGCCGCTACTGAAGCTGTTCACGTCGCTTCC
1 GTTCAAGGCAAATCCTCGGAGAAAGCCGCCACTGAAGCTGTTCACGTCGCTTCC
* *
1329024 GTTCTAGGCAAATCCTCGGAGAAAGTCGCCACTGAAGCTGTTCACGTCGCTTCC
1 GTTCAAGGCAAATCCTCGGAGAAAGCCGCCACTGAAGCTGTTCACGTCGCTTCC
* * * *
1329078 GTTCTAGGCAAATTCTCGGAGAAAGCCGCCACTGAAGATGTTCATGTCGCTTCC
1 GTTCAAGGCAAATCCTCGGAGAAAGCCGCCACTGAAGCTGTTCACGTCGCTTCC
* *
1329132 GTTCAAGGCAAATCATCGGGGAAAGCCGCCACTGAAGCTGTTCACGTCGCTTCC
1 GTTCAAGGCAAATCCTCGGAGAAAGCCGCCACTGAAGCTGTTCACGTCGCTTCC
* * **
1329186 GTTCAAGGCAAATCATCGGGGAAAGCCGTTACTGAAGCTGTTCACGTCGCTTCC
1 GTTCAAGGCAAATCCTCGGAGAAAGCCGCCACTGAAGCTGTTCACGTCGCTTCC
* * * * *
1329240 GTACAAGGCAAATCCTCGGGGAAAGCCGCAACTGAAGCTGTTCATGCCGCTTCC
1 GTTCAAGGCAAATCCTCGGAGAAAGCCGCCACTGAAGCTGTTCACGTCGCTTCC
** * * * * *** *
1329294 GCACAACGCAAATCATTGCAGAAAAG-CGCTGTTGAAGCTGTTCACGCCGCTTCC
1 GTTCAAGGCAAATCCTCGGAG-AAAGCCGCCACTGAAGCTGTTCACGTCGCTTCC
* * * * * *
1329348 GTGCAACGG-AATTCATCGCAGAAAACCGTCACTGAAGCTG
1 GTTCAA-GGCAAATCCTCGGAGAAAGCCGCCACTGAAGCTG
1329388 CTGACGCCGC
Statistics
Matches: 513, Mismatches: 64, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
53 3 0.01
54 505 0.98
55 5 0.01
ACGTcount: A:0.26, C:0.29, G:0.24, T:0.21
Consensus pattern (54 bp):
GTTCAAGGCAAATCCTCGGAGAAAGCCGCCACTGAAGCTGTTCACGTCGCTTCC
Found at i:1340623 original size:24 final size:24
Alignment explanation
Indices: 1340596--1340641 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
1340586 TTTATTAATA
1340596 TTTATAATAAT-ATAATATAATATT
1 TTTATAATAATAAT-ATATAATATT
**
1340620 TTTATTTTAATAATATATAATA
1 TTTATAATAATAATATATAATA
1340642 AATTATTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 17 0.89
25 2 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
TTTATAATAATAATATATAATATT
Found at i:1340720 original size:19 final size:19
Alignment explanation
Indices: 1340684--1340764 Score: 62
Period size: 19 Copynumber: 4.3 Consensus size: 19
1340674 TTCATAGAAA
*
1340684 TAAT-ATTATTAA-ATTAT
1 TAATAATTAATAATATTAT
*
1340701 TAATAATGAATAATATTATT
1 TAATAATTAATAATATTA-T
* *
1340721 TATATATTTAATAATAATA-
1 TA-ATAATTAATAATATTAT
*
1340740 TAATAATCTAATTATATT-T
1 TAATAAT-TAATAATATTAT
1340759 TAATAA
1 TAATAA
1340765 AGATATTTAA
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
17 4 0.08
18 10 0.20
19 20 0.40
20 3 0.06
21 13 0.26
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (19 bp):
TAATAATTAATAATATTAT
Found at i:1340728 original size:27 final size:26
Alignment explanation
Indices: 1340681--1340764 Score: 78
Period size: 28 Copynumber: 3.0 Consensus size: 26
1340671 AATTTCATAG
*
1340681 AAATAATATTATTAAATTATTAATAAT
1 AAATAATATTATTATA-TATTAATAAT
*
1340708 GAATAATATTATTTATATATTTAATAAT
1 AAATAATATTA-TTATATA-TTAATAAT
*
1340736 AATATAATAATCTAATTATATTTTAATAA
1 AA-ATAAT-AT-T-ATTATATATTAATAA
1340765 AGATATTTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
27 12 0.26
28 13 0.28
29 5 0.11
30 9 0.19
31 7 0.15
32 1 0.02
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (26 bp):
AAATAATATTATTATATATTAATAAT
Found at i:1340785 original size:23 final size:24
Alignment explanation
Indices: 1340759--1340804 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
1340749 AATTATATTT
1340759 TAATAAAGA-TATTTAAAATATAC
1 TAATAAAGATTATTTAAAATATAC
* * *
1340782 TAATTAATATTTTTTAAAATATA
1 TAATAAAGATTATTTAAAATATA
1340805 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (24 bp):
TAATAAAGATTATTTAAAATATAC
Found at i:1342167 original size:35 final size:35
Alignment explanation
Indices: 1342121--1342197 Score: 127
Period size: 35 Copynumber: 2.2 Consensus size: 35
1342111 TAAAACAGTC
* *
1342121 TTCAATTTCATTCTAAACCCCAATTTCCAAAGTAA
1 TTCAATTTCATTCTAAACCCCAAATTCCAAAATAA
*
1342156 TTCAATTTCATTCTAAACCCTAAATTCCAAAATAA
1 TTCAATTTCATTCTAAACCCCAAATTCCAAAATAA
1342191 TTCAATT
1 TTCAATT
1342198 AAATTCAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.39, C:0.23, G:0.01, T:0.36
Consensus pattern (35 bp):
TTCAATTTCATTCTAAACCCCAAATTCCAAAATAA
Found at i:1345196 original size:21 final size:21
Alignment explanation
Indices: 1345170--1345209 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1345160 CAGAACCCCA
*
1345170 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
1345191 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
1345210 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:1345244 original size:20 final size:21
Alignment explanation
Indices: 1345190--1345252 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
1345180 GATTCCCCTG
1345190 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
1345214 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
1345234 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
1345253 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:1349102 original size:22 final size:21
Alignment explanation
Indices: 1349060--1349099 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1349050 GAGTTTGTTT
*
1349060 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1349081 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1349100 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1351773 original size:130 final size:130
Alignment explanation
Indices: 1351627--1351874 Score: 415
Period size: 130 Copynumber: 1.9 Consensus size: 130
1351617 TATTTATATA
* **
1351627 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * *
1351692 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCGCCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
1351757 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * *
1351822 TTAACACATGATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTA
1351875 GAAGAAAATT
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.35
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:1351905 original size:130 final size:129
Alignment explanation
Indices: 1351641--1351905 Score: 300
Period size: 130 Copynumber: 2.0 Consensus size: 129
1351631 ATTTGGTCCT
* ** *
1351641 AAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* * *** * * **** *
1351706 TGACACGTGTCATTGGTGACACATGTCGCCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAAAAGT-CA
1351771 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* * * *
1351836 TGATATATGTTATTGGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAAAAAAGT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAAAAGT
1351900 -A
128 CA
1351901 AAATT
1 AAATT
1351906 TGGGTCTTGG
Statistics
Matches: 112, Mismatches: 20, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
130 99 0.88
132 8 0.07
133 5 0.04
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.34
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAAAAGTCA
Found at i:1352364 original size:16 final size:18
Alignment explanation
Indices: 1352343--1352376 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1352333 ATTTCTTATT
1352343 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
1352359 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
1352377 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:1354242 original size:20 final size:20
Alignment explanation
Indices: 1354217--1354270 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
1354207 TGGTTGTGAG
*
1354217 TTTTTTTTAAAGGAGTTGATT
1 TTTTTTTTAAAGGAGCTGA-T
1354238 TTTTTTTGTAAAAGGAGCTGA-
1 TTTTTTT-T-AAAGGAGCTGAT
1354259 TTTTTTTTAAAG
1 TTTTTTTTAAAG
1354271 ATTTAGAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
19 4 0.13
20 1 0.03
21 14 0.47
22 1 0.03
23 10 0.33
ACGTcount: A:0.26, C:0.02, G:0.19, T:0.54
Consensus pattern (20 bp):
TTTTTTTTAAAGGAGCTGAT
Found at i:1354242 original size:22 final size:23
Alignment explanation
Indices: 1354217--1354266 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
1354207 TGGTTGTGAG
*
1354217 TTTTTTT-T-AAAGGAGTTGATT
1 TTTTTTTGTAAAAGGAGCTGATT
1354238 TTTTTTTGTAAAAGGAGCTGATT
1 TTTTTTTGTAAAAGGAGCTGATT
1354261 TTTTTT
1 TTTTTT
1354267 AAAGATTTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 7 0.27
22 1 0.04
23 18 0.69
ACGTcount: A:0.22, C:0.02, G:0.18, T:0.58
Consensus pattern (23 bp):
TTTTTTTGTAAAAGGAGCTGATT
Found at i:1357540 original size:48 final size:48
Alignment explanation
Indices: 1357474--1357565 Score: 148
Period size: 48 Copynumber: 1.9 Consensus size: 48
1357464 TTTAAAATTT
* *
1357474 TCGGTAAAGTGTCTAATAATAACAAAATCAGTAGAAAGAATAATAAAA
1 TCGGTAAAGTGCCCAATAATAACAAAATCAGTAGAAAGAATAATAAAA
* *
1357522 TCGGTAAAGTGCCCAATAATAACAAAATCGGTAGAAATAATAAT
1 TCGGTAAAGTGCCCAATAATAACAAAATCAGTAGAAAGAATAAT
1357566 GTTTTTGGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.51, C:0.11, G:0.15, T:0.23
Consensus pattern (48 bp):
TCGGTAAAGTGCCCAATAATAACAAAATCAGTAGAAAGAATAATAAAA
Found at i:1357560 original size:21 final size:21
Alignment explanation
Indices: 1357488--1357564 Score: 64
Period size: 21 Copynumber: 3.4 Consensus size: 21
1357478 TAAAGTGTCT
*
1357488 AATAATAACAAAATCAGTAGA
1 AATAATAACAAAATCGGTAGA
* * *
1357509 AAGAATAATAAAATCGGTAAAGTGCCC
1 AATAATAACAAAATCGGT--A--G--A
1357536 AATAATAACAAAATCGGTAGA
1 AATAATAACAAAATCGGTAGA
1357557 AATAATAA
1 AATAATAA
1357565 TGTTTTTGGT
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
21 23 0.53
23 2 0.05
25 2 0.05
27 16 0.37
ACGTcount: A:0.57, C:0.10, G:0.13, T:0.19
Consensus pattern (21 bp):
AATAATAACAAAATCGGTAGA
Found at i:1357576 original size:48 final size:48
Alignment explanation
Indices: 1357470--1357576 Score: 133
Period size: 48 Copynumber: 2.2 Consensus size: 48
1357460 ATTTTTTAAA
* *
1357470 ATTTTCGGTAAAGTGTCTAATAATAACAAAATCAGTAGAAAGAATAAT
1 ATTTTCGGTAAAGTGCCCAATAATAACAAAATCAGTAGAAAGAATAAT
*** * *
1357518 AAAATCGGTAAAGTGCCCAATAATAACAAAATCGGTAGAAATAATAAT
1 ATTTTCGGTAAAGTGCCCAATAATAACAAAATCAGTAGAAAGAATAAT
* *
1357566 GTTTTTGGTAA
1 ATTTTCGGTAA
1357577 TTTTTTATCG
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.47, C:0.09, G:0.16, T:0.28
Consensus pattern (48 bp):
ATTTTCGGTAAAGTGCCCAATAATAACAAAATCAGTAGAAAGAATAAT
Found at i:1367147 original size:162 final size:160
Alignment explanation
Indices: 1366959--1367835 Score: 659
Period size: 156 Copynumber: 5.8 Consensus size: 160
1366949 CCGCCTTCTT
* * * * *
1366959 CAGCTCGGAACGTGAATCAACCAGAAAAAGATA-AGCAAGCCATCAATGGAGTAATTCCTTCAAA
1 CAGCTCGGAACGTGGAGCAACCAGAAAAAGATAGA-CAACCCATCGATGGAGTAACTCCTTCAAA
* *
1367023 GCATGATCATCAACGTAAACAGCCCCGTCCGATGGAGGACCCTCCTTCAAAAGATCGAAAGAACC
65 -CACGATCATCAACGTAAACAGCACCGTCCGATGGAGGACCCTCCTTCAAAAGATCGAAAGAACC
*
1367088 ATAACCAAAACCAGCCACCTCCACCTCCAGCTC
129 AGAACCAAAACCAGCCACCTCCACCTCCA-CTC
* * *
1367121 CAGCTCGGACCGTGGAGCAACCAGAAAATGATAGACAACCCTTCGATGGAGTAACTCCTTCGAAA
1 CAGCTCGGAACGTGGAGCAACCAGAAAAAGATAGACAACCCATCGATGGAGTAACTCCTTC-AAA
* * *
1367186 CACGATCATCAACATAAACAGCACCGTTCGATGGAGGACACTCCTTCAAAAGATCG---G---CA
65 CACGATCATCAACGTAAACAGCACCGTCCGATGGAGGACCCTCCTTCAAAAGATCGAAAGAACCA
* * *
1367245 GAA-CAAGAACCAGCCGCCGCCGCCTCCA---
130 GAACCAA-AACCAGCCACCTCCACCTCCACTC
* *
1367273 C--CTCGGAAAGTGGATCAACCAGAAAAAGATAG-------A-C-A---A-T--CTCCTTCAAAA
1 CAGCTCGGAACGTGGAGCAACCAGAAAAAGATAGACAACCCATCGATGGAGTAACTCCTTC-AAA
* * * *
1367321 CACGATCATCAACGTAAACAGCAACGTCCGATTGAGGACTCTCCTTCAAAAGATAGAAAGAACCA
65 CACGATCATCAACGTAAACAGCACCGTCCGATGGAGGACCCTCCTTCAAAAGATCGAAAGAACCA
1367386 GAACCAAAACCAGCCACCTCCA----C-CTC
130 GAACCAAAACCAGCCACCTCCACCTCCACTC
* * *
1367412 CAGCTCGGACCGTGGAGCAACCAGAAAATGATAGACAACCCTTCGATGGAGTAACTCCTTCCAAA
1 CAGCTCGGAACGTGGAGCAACCAGAAAAAGATAGACAACCCATCGATGGAGTAACTCCTT-CAAA
* * * * * *
1367477 CACGATGATCAACGTGAACAGCACCATTCGATTGAGGAGCCTCCTTCAAAAGATC----G-A-CA
65 CACGATCATCAACGTAAACAGCACCGTCCGATGGAGGACCCTCCTTCAAAAGATCGAAAGAACCA
* * *
1367536 GAATCAGAACCAG------CCGCCT-C-CTC
130 GAACCAAAACCAGCCACCTCCACCTCCACTC
* * * * *
1367559 CAGCTCGGAATGCGGAGCAACCAGAAAATGATAGACAA-CC-TC----------CTAC--AAAAC
1 CAGCTCGGAACGTGGAGCAACCAGAAAAAGATAGACAACCCATCGATGGAGTAACTCCTTCAAAC
* * * *
1367610 ACAATCATCAATC-TAAACAGTACCGTCCGATGGAGGACCCTCCTTTAAAAGATCTAAAGAACCA
66 ACGATCATCAA-CGTAAACAGCACCGTCCGATGGAGGACCCTCCTTCAAAAGATCGAAAGAACCA
*
1367674 GAACCAAAACCAGCCA-C-CC-CC-AC-CTC
130 GAACCAAAACCAGCCACCTCCACCTCCACTC
* ** * * *
1367700 CAGCTCGGACCGTGGAGCAACCAGAAAACTATAGACAACCCTTCAATGGAGTAACTCCTCCAAAA
1 CAGCTCGGAACGTGGAGCAACCAGAAAAAGATAGACAACCCATCGATGGAGTAACTCCTTC-AAA
* * * * * *
1367765 CACGATCATCTAAC-TAAACAGTACCTTCCGATGGAGGATCTTCCTTCAAAAGAACTG-AAGAAG
65 CACGATCATC-AACGTAAACAGCACCGTCCGATGGAGGACCCTCCTTCAAAAGATC-GAAAGAAC
1367828 CAGAACCA
128 CAGAACCA
1367836 GCCGCCGGCG
Statistics
Matches: 573, Mismatches: 79, Indels: 132
0.73 0.10 0.17
Matches are distributed among these distances:
132 47 0.08
133 1 0.00
135 63 0.11
136 1 0.00
137 3 0.01
138 15 0.03
139 1 0.00
141 84 0.15
142 8 0.01
143 2 0.00
144 2 0.00
145 2 0.00
146 2 0.00
147 39 0.07
149 1 0.00
150 41 0.07
151 1 0.00
152 2 0.00
153 4 0.01
154 1 0.00
155 3 0.01
156 140 0.24
157 3 0.01
159 1 0.00
162 102 0.18
163 4 0.01
ACGTcount: A:0.37, C:0.30, G:0.18, T:0.16
Consensus pattern (160 bp):
CAGCTCGGAACGTGGAGCAACCAGAAAAAGATAGACAACCCATCGATGGAGTAACTCCTTCAAAC
ACGATCATCAACGTAAACAGCACCGTCCGATGGAGGACCCTCCTTCAAAAGATCGAAAGAACCAG
AACCAAAACCAGCCACCTCCACCTCCACTC
Found at i:1367547 original size:291 final size:287
Alignment explanation
Indices: 1367014--1367847 Score: 1142
Period size: 288 Copynumber: 2.9 Consensus size: 287
1367004 ATGGAGTAAT
* * *
1367014 TCCTTCAAAGCATGATCATCAACGTAAACAGCCCCGTCCGATGGAGGACCCTCCTTCAAAAGATC
1 TCCTTCAAAACACGATCATCAACGTAAACAGCACCGTCCGATGGAGGACCCTCCTTCAAAAGATC
*
1367079 GAAAGAACCATAACCAAAACCAGCCACCTCCACCTCCAGCTCCAGCTCGGACCGTGGAGCAACCA
66 GAAAGAACCAGAACCAAAACCAGCCACCTCCA----C--CTCCAGCTCGGACCGTGGAGCAACCA
*
1367144 GAAAATGATAGACAACCCTTCGATGGAGTAACTCCTTCGAAACACGATCATCAACATAAACAGCA
125 GAAAATGATAGACAACCCTTCGATGGAGTAACTCCTTCCAAACACGATCATCAAC-TAAACAGCA
*
1367209 CCGTTCGATGGAGGACACTCCTTCAAAAGATCGGCAGAACAAGAACCAGCCGCCGCCGCCTCCAC
189 CC-TTCGATGGAGGAC-CTCCTTCAAAAGATCGACAGAAC-AGAACCAGCCGCCGCCGCCTCCAC
* * *
1367274 CTCGGAAAGTGGATCAACCAGAAAAAGATAGACAATC
251 CTCGGAAAGCGGAGCAACCAGAAAAAGATAGACAACC
* * * *
1367311 TCCTTCAAAACACGATCATCAACGTAAACAGCAACGTCCGATTGAGGACTCTCCTTCAAAAGATA
1 TCCTTCAAAACACGATCATCAACGTAAACAGCACCGTCCGATGGAGGACCCTCCTTCAAAAGATC
1367376 GAAAGAACCAGAACCAAAACCAGCCACCTCCACCTCCAGCTCGGACCGTGGAGCAACCAGAAAAT
66 GAAAGAACCAGAACCAAAACCAGCCACCTCCACCTCCAGCTCGGACCGTGGAGCAACCAGAAAAT
* *
1367441 GATAGACAACCCTTCGATGGAGTAACTCCTTCCAAACACGATGATCAACGTGAACAGCACCATTC
131 GATAGACAACCCTTCGATGGAGTAACTCCTTCCAAACACGATCATCAAC-TAAACAGCACC-TTC
* * *
1367506 GATTGAGGAGCCTCCTTCAAAAGATCGACAGAATCAGAACCA---GCCGCCTCCTCCAGCTCGGA
194 GATGGAGGA-CCTCCTTCAAAAGATCGACAGAA-CAGAACCAGCCGCCGCCGCCTCCACCTCGGA
* *
1367568 ATGCGGAGCAACCAGAAAATGATAGACAACC
257 AAGCGGAGCAACCAGAAAAAGATAGACAACC
* * * *
1367599 TCCTACAAAACACAATCATCAATC-TAAACAGTACCGTCCGATGGAGGACCCTCCTTTAAAAGAT
1 TCCTTCAAAACACGATCATCAA-CGTAAACAGCACCGTCCGATGGAGGACCCTCCTTCAAAAGAT
* *
1367663 CTAAAGAACCAGAACCAAAACCAGCCACCCCCACCTCCAGCTCGGACCGTGGAGCAACCAGAAAA
65 CGAAAGAACCAGAACCAAAACCAGCCACCTCCACCTCCAGCTCGGACCGTGGAGCAACCAGAAAA
* *
1367728 CT-ATAGACAACCCTTCAATGGAGTAACTCC-TCCAAAACACGATCATCTAACTAAACAGTACCT
130 -TGATAGACAACCCTTCGATGGAGTAACTCCTTCC-AAACACGATCATC-AACTAAACAGCACCT
* * *
1367791 TCCGATGGAGGATCTTCCTTCAAAAGAACTGA-AGAAGCAGAACCAGCCGCCGGCGCC
192 T-CGATGGAGGA-CCTCCTTCAAAAGATC-GACAGAA-CAGAACCAGCCGCCGCCGCC
1367848 GCCGCAGCAG
Statistics
Matches: 483, Mismatches: 43, Indels: 28
0.87 0.08 0.05
Matches are distributed among these distances:
287 5 0.01
288 244 0.51
289 7 0.01
291 135 0.28
292 2 0.00
293 1 0.00
297 89 0.18
ACGTcount: A:0.36, C:0.31, G:0.18, T:0.15
Consensus pattern (287 bp):
TCCTTCAAAACACGATCATCAACGTAAACAGCACCGTCCGATGGAGGACCCTCCTTCAAAAGATC
GAAAGAACCAGAACCAAAACCAGCCACCTCCACCTCCAGCTCGGACCGTGGAGCAACCAGAAAAT
GATAGACAACCCTTCGATGGAGTAACTCCTTCCAAACACGATCATCAACTAAACAGCACCTTCGA
TGGAGGACCTCCTTCAAAAGATCGACAGAACAGAACCAGCCGCCGCCGCCTCCACCTCGGAAAGC
GGAGCAACCAGAAAAAGATAGACAACC
Found at i:1369470 original size:93 final size:92
Alignment explanation
Indices: 1369370--1369691 Score: 324
Period size: 93 Copynumber: 3.4 Consensus size: 92
1369360 AATAGTGGTG
* ** * *
1369370 ACAATCAAAGCAGTCATAAAAACTCCCGCCACCACCACCACCAACAAAAACAAGCATCTCCTGCG
1 ACAATCAAAGCAGTCATAAAAACTCCCACCACCACCACCACCAACAGCAGCAAGCATCTCCGGCG
* * * *
1369435 -GGGATTATTCCAGAAAACGACAATCTTC
66 ACGG-TTCTTCCAGAAAACGAAAATC-TA
* * * * * * *
1369463 ACAATCAAAGTAGTCATGAAAATTCCTACCATCATCATCACCAGCAGCAGCAGCAAGCATCTCCG
1 ACAATCAAAGCAGTCATAAAAACTCCCACCA-C--CACCACCACCAACAGCAGCAAGCATCTCCG
* *
1369528 GCGACTGTTCTTCCAGAAAACGAAAATCCTG
63 GCGACGGTTCTTCCAGAAAACGAAAAT-CTA
** * ** * *
1369559 ATGATCAAAGCAGTCATAAAAACTCCCACCATCACCACCACCCCCAGCAGCAAACATCTCCGGTG
1 ACAATCAAAGCAGTCATAAAAACTCCCACCACCACCACCACCAACAGCAGCAAGCATCTCCGGCG
*
1369624 ACGGTTCTTCCAGGAAAC-AATAATACTA
66 ACGGTTCTTCCAGAAAACGAA-AAT-CTA
1369652 ACAATCAAAGCAGTCATAAAAACTCCCACCACCACCACCA
1 ACAATCAAAGCAGTCATAAAAACTCCCACCACCACCACCA
1369692 TAACCAGTAC
Statistics
Matches: 186, Mismatches: 37, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
92 2 0.01
93 111 0.60
94 1 0.01
96 70 0.38
97 2 0.01
ACGTcount: A:0.38, C:0.33, G:0.12, T:0.16
Consensus pattern (92 bp):
ACAATCAAAGCAGTCATAAAAACTCCCACCACCACCACCACCAACAGCAGCAAGCATCTCCGGCG
ACGGTTCTTCCAGAAAACGAAAATCTA
Found at i:1378306 original size:25 final size:26
Alignment explanation
Indices: 1378248--1378321 Score: 123
Period size: 25 Copynumber: 2.9 Consensus size: 26
1378238 ATTCCCCATC
* *
1378248 TTCTTTTTCTTCACTTTTCTTCTTCT
1 TTCTTTCTCTTCACTTTTCTTCTACT
1378274 TTCTTTCTCTTCACTTTTCTT-TACT
1 TTCTTTCTCTTCACTTTTCTTCTACT
1378299 TTCTTTCTCTTCACTTTTCTTCT
1 TTCTTTCTCTTCACTTTTCTTCT
1378322 TTTCCTCTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
25 24 0.53
26 21 0.47
ACGTcount: A:0.05, C:0.28, G:0.00, T:0.66
Consensus pattern (26 bp):
TTCTTTCTCTTCACTTTTCTTCTACT
Found at i:1379657 original size:26 final size:26
Alignment explanation
Indices: 1379622--1379671 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
1379612 TTCGATGCGA
*
1379622 AAGAAGAAAAGTGAAGAGAAAGAAAG
1 AAGAAGAAAAGTGAAGAAAAAGAAAG
1379648 AAGAAGAAAAGTGAAGAAAAAGAA
1 AAGAAGAAAAGTGAAGAAAAAGAA
1379672 GATGGGGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.68, C:0.00, G:0.28, T:0.04
Consensus pattern (26 bp):
AAGAAGAAAAGTGAAGAAAAAGAAAG
Found at i:1383624 original size:30 final size:31
Alignment explanation
Indices: 1383567--1383626 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
1383557 TCAGATGAGT
*
1383567 TTAATTGATTTTTCTAAAAAGTTTTGAAGAC
1 TTAATTGATTTTTCTAAAAAGTGTTGAAGAC
*
1383598 TTAATTGA-TTTTCTTTAAAA-TGTTGAAGA
1 TTAATTGATTTTTC-TAAAAAGTGTTGAAGA
1383627 TTTATTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 13 0.50
31 13 0.50
ACGTcount: A:0.35, C:0.05, G:0.13, T:0.47
Consensus pattern (31 bp):
TTAATTGATTTTTCTAAAAAGTGTTGAAGAC
Found at i:1384481 original size:59 final size:60
Alignment explanation
Indices: 1384385--1384502 Score: 141
Period size: 59 Copynumber: 2.0 Consensus size: 60
1384375 TGAATCGTCG
* * * * *
1384385 GGTGATTATTTTATAACTTTTAATAGTCAGAGAACACAA-CAAGCAACACTCTATAATCA
1 GGTGATCATCTTATAACTTTCAATAGTAAGAGAACACAATCAAACAACACTCTATAATCA
* * *
1384444 GGTGATCATCTTATAACTTTCAATAGTAA-AGGTACACAATGAAACATCACTCTATAATC
1 GGTGATCATCTTATAACTTTCAATAGTAAGA-GAACACAATCAAACAACACTCTATAATC
1384503 TGGAGAGTAT
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
58 1 0.02
59 32 0.65
60 16 0.33
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.31
Consensus pattern (60 bp):
GGTGATCATCTTATAACTTTCAATAGTAAGAGAACACAATCAAACAACACTCTATAATCA
Found at i:1392878 original size:26 final size:27
Alignment explanation
Indices: 1392841--1392892 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
1392831 TTGTTTGGCT
*
1392841 CTGAATGGTTCC-TTCAGCATTCAGCG
1 CTGAATGATTCCATTCAGCATTCAGCG
1392867 CTGAATGATTCCATTCAGCATTCAGC
1 CTGAATGATTCCATTCAGCATTCAGC
1392893 ACGTTTGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 11 0.46
27 13 0.54
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.31
Consensus pattern (27 bp):
CTGAATGATTCCATTCAGCATTCAGCG
Found at i:1400848 original size:15 final size:15
Alignment explanation
Indices: 1400828--1400858 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1400818 GTTGTTATCC
1400828 GTTGAGAGAGACTGA
1 GTTGAGAGAGACTGA
1400843 GTTGAGAGAGACTGA
1 GTTGAGAGAGACTGA
1400858 G
1 G
1400859 AGAGTGCAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.42, T:0.19
Consensus pattern (15 bp):
GTTGAGAGAGACTGA
Found at i:1405876 original size:22 final size:23
Alignment explanation
Indices: 1405851--1405894 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
1405841 CAACAATACT
1405851 AAATATTATTAAATAAT-TTAAA
1 AAATATTATTAAATAATCTTAAA
* *
1405873 AAATATTTTTTAATAATCTTAA
1 AAATATTATTAAATAATCTTAA
1405895 GTAATTGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (23 bp):
AAATATTATTAAATAATCTTAAA
Found at i:1407739 original size:21 final size:21
Alignment explanation
Indices: 1407709--1407758 Score: 82
Period size: 21 Copynumber: 2.3 Consensus size: 21
1407699 GAAATTTAAA
1407709 TGCATAAATGACTAATGAAGAT
1 TGCAT-AATGACTAATGAAGAT
*
1407731 TGGATAATGACTAATGAAGAT
1 TGCATAATGACTAATGAAGAT
1407752 TGCATAA
1 TGCATAA
1407759 ATAATCCTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.44, C:0.08, G:0.20, T:0.28
Consensus pattern (21 bp):
TGCATAATGACTAATGAAGAT
Found at i:1407773 original size:24 final size:21
Alignment explanation
Indices: 1407709--1407775 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 21
1407699 GAAATTTAAA
*
1407709 TGCATAAATGACTAATGAAGAT
1 TGCAT-AATAACTAATGAAGAT
* *
1407731 TGGATAATGACTAATGAAGAT
1 TGCATAATAACTAATGAAGAT
1407752 TGCATAAATAATCCTAATGAAGAT
1 TGCAT-AATAA--CTAATGAAGAT
1407776 AGATTGTGCT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
21 20 0.51
22 8 0.21
24 11 0.28
ACGTcount: A:0.45, C:0.09, G:0.18, T:0.28
Consensus pattern (21 bp):
TGCATAATAACTAATGAAGAT
Found at i:1413390 original size:38 final size:38
Alignment explanation
Indices: 1413339--1413464 Score: 189
Period size: 38 Copynumber: 3.3 Consensus size: 38
1413329 GTTCATGTCG
*
1413339 AATATGGGTATTTTATATTCAAGTTCGAGTATGTGTAA
1 AATATGGGTATTTTATATTCAAGTTCGAGTATGTGTAC
* * *
1413377 AATATAGGTATTTTATATTCAAGTTAGAGTATGTGTTC
1 AATATGGGTATTTTATATTCAAGTTCGAGTATGTGTAC
* * *
1413415 AATATGGGTGTTTTATATTTAAGTTCGAGTATGTGTCC
1 AATATGGGTATTTTATATTCAAGTTCGAGTATGTGTAC
1413453 AATATGGGTATT
1 AATATGGGTATT
1413465 GGAGATACAA
Statistics
Matches: 78, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 78 1.00
ACGTcount: A:0.29, C:0.06, G:0.21, T:0.44
Consensus pattern (38 bp):
AATATGGGTATTTTATATTCAAGTTCGAGTATGTGTAC
Found at i:1417061 original size:23 final size:23
Alignment explanation
Indices: 1417035--1417103 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
1417025 CACCACAGCT
*
1417035 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
1417058 CGTAGAATTTCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
* *
1417081 CATAGAAATGCACCGGAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
1417104 TATAAAATGT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.32, C:0.26, G:0.25, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:1419600 original size:29 final size:29
Alignment explanation
Indices: 1419560--1419632 Score: 94
Period size: 29 Copynumber: 2.6 Consensus size: 29
1419550 TTATTTAAAA
* * *
1419560 TAAAAAA-ATAAAATTATTATTATTTTTT
1 TAAAAAACTTAAAATTATTAATATATTTT
*
1419588 TAAAATACTTAAAATTATTAATATATTTT
1 TAAAAAACTTAAAATTATTAATATATTTT
*
1419617 TAAAAAACTCAAAATT
1 TAAAAAACTTAAAATT
1419633 TTGAACATCT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
28 6 0.16
29 32 0.84
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (29 bp):
TAAAAAACTTAAAATTATTAATATATTTT
Found at i:1422460 original size:143 final size:143
Alignment explanation
Indices: 1422202--1422483 Score: 564
Period size: 143 Copynumber: 2.0 Consensus size: 143
1422192 CTCACGGCAA
1422202 GTTCTTCTCCAACGGCTATGATCTCGCCTGGGCAGGCTCTTCACCCGAAAAGATCCGTTTGTTGT
1 GTTCTTCTCCAACGGCTATGATCTCGCCTGGGCAGGCTCTTCACCCGAAAAGATCCGTTTGTTGT
1422267 CTTCCAAGCTCCGAGATCTCGTCGCTGACCTAATTTCCTTTCCTATGCCTACGTCGCCGCCATCA
66 CTTCCAAGCTCCGAGATCTCGTCGCTGACCTAATTTCCTTTCCTATGCCTACGTCGCCGCCATCA
1422332 CTGGCCAGGCCTG
131 CTGGCCAGGCCTG
1422345 GTTCTTCTCCAACGGCTATGATCTCGCCTGGGCAGGCTCTTCACCCGAAAAGATCCGTTTGTTGT
1 GTTCTTCTCCAACGGCTATGATCTCGCCTGGGCAGGCTCTTCACCCGAAAAGATCCGTTTGTTGT
1422410 CTTCCAAGCTCCGAGATCTCGTCGCTGACCTAATTTCCTTTCCTATGCCTACGTCGCCGCCATCA
66 CTTCCAAGCTCCGAGATCTCGTCGCTGACCTAATTTCCTTTCCTATGCCTACGTCGCCGCCATCA
1422475 CTGGCCAGG
131 CTGGCCAGG
1422484 TCTGCGCGGC
Statistics
Matches: 139, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
143 139 1.00
ACGTcount: A:0.16, C:0.34, G:0.21, T:0.29
Consensus pattern (143 bp):
GTTCTTCTCCAACGGCTATGATCTCGCCTGGGCAGGCTCTTCACCCGAAAAGATCCGTTTGTTGT
CTTCCAAGCTCCGAGATCTCGTCGCTGACCTAATTTCCTTTCCTATGCCTACGTCGCCGCCATCA
CTGGCCAGGCCTG
Found at i:1424165 original size:32 final size:33
Alignment explanation
Indices: 1424103--1424165 Score: 76
Period size: 32 Copynumber: 1.9 Consensus size: 33
1424093 CAATAATTCG
* *
1424103 ATTATCATAAAATATAAAATTATTTGAAATTTT
1 ATTATCATAAAATATAAAATCATTTAAAATTTT
*
1424136 ATTATC-TAATAAT-TAAAATCCTTTAAAATT
1 ATTATCATAA-AATATAAAATCATTTAAAATT
1424166 GATACCATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
32 17 0.65
33 9 0.35
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (33 bp):
ATTATCATAAAATATAAAATCATTTAAAATTTT
Found at i:1435978 original size:3 final size:3
Alignment explanation
Indices: 1435970--1435998 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1435960 TTCATTTTTC
1435970 TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1435999 ATTTATATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:1437404 original size:26 final size:27
Alignment explanation
Indices: 1437360--1437410 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
1437350 TTAATTTTTG
1437360 TGAATGTAAAATATAAATAA-AATAAA
1 TGAATGTAAAATATAAATAATAATAAA
*
1437386 TGAATGTAAAACTGT-AATAATAATA
1 TGAATGTAAAA-TATAAATAATAATA
1437411 TTAACTGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.59, C:0.02, G:0.10, T:0.29
Consensus pattern (27 bp):
TGAATGTAAAATATAAATAATAATAAA
Found at i:1437733 original size:21 final size:21
Alignment explanation
Indices: 1437700--1437762 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
1437690 TTTTTTTATC
* *
1437700 AAAAATATTCATTTTAAATAAC
1 AAAAATA-ACATTTTAAATAAA
* * *
1437722 GAAATTAACATTTTCAATAAA
1 AAAAATAACATTTTAAATAAA
1437743 AAAAATAACATTTTAAATAA
1 AAAAATAACATTTTAAATAA
1437763 TATTCTACCA
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
21 28 0.85
22 5 0.15
ACGTcount: A:0.57, C:0.08, G:0.02, T:0.33
Consensus pattern (21 bp):
AAAAATAACATTTTAAATAAA
Done.