Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000002.1 Hibiscus syriacus cultivar Beakdansim tig00000003_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: 2131600
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 10
Found at i:1209176 original size:94 final size:93
Alignment explanation
Indices: 1208984--1209177 Score: 203
Period size: 94 Copynumber: 2.1 Consensus size: 93
1208974 ACATTGGAAT
** * ***
1208984 CCAGAAGGTAGAAATGATATCGATACTGAAAGGGAGTATTGGTACCATAGTATGGAAGTATTGGT
1 CCAGAAGGTAGAAATGATATCGATACTGAAAGGGAGTATCAGTACCATAGTATAGAAGTATCAAT
* * *
1209049 ACTAGGAGAAAAGTATCGATACCATGGAT
66 ACCAGGAG-AAAGTACCGATACCATGGAG
* *
1209078 CCAGAATGTAGAAATTG-TATCGATACTGAAAGGGAGTATCAGTACCGTAGTATAGAAGTATCAA
1 CCAGAAGGTAGAAA-TGATATCGATACTGAAAGGGAGTATCAGTACCATAGTATAGAAGTATCAA
** * *
1209142 TACCATGGTAG-GGGTACCGATACTATTGAG
65 TACCA-GG-AGAAAGTACCGATACCATGGAG
1209172 CCAGAA
1 CCAGAA
1209178 ATTTTAAGAT
Statistics
Matches: 82, Mismatches: 15, Indels: 6
0.80 0.15 0.06
Matches are distributed among these distances:
94 76 0.93
95 4 0.05
96 2 0.02
ACGTcount: A:0.37, C:0.13, G:0.26, T:0.24
Consensus pattern (93 bp):
CCAGAAGGTAGAAATGATATCGATACTGAAAGGGAGTATCAGTACCATAGTATAGAAGTATCAAT
ACCAGGAGAAAGTACCGATACCATGGAG
Found at i:1209841 original size:54 final size:54
Alignment explanation
Indices: 1209480--1209809 Score: 547
Period size: 54 Copynumber: 6.1 Consensus size: 54
1209470 CATTTACCCA
1209480 ATTGGCACTATGT-TG-AATCCTAAGAAATTCATAATAAGTTTATGAATTTTCGT
1 ATTGGCACTATGTGTGCAA-CCTAAGAAATTCATAATAAGTTTATGAATTTTCGT
*
1209533 ATTGGCACTATGTATGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGT
1 ATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGT
*
1209587 ATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGT
1 ATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGT
* ** * *
1209641 ATTGGCACTATGTGTGCAACCTAATAAATTCATAATAAGCGTATGAATTTCCAT
1 ATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGT
*
1209695 ATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGT
1 ATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGT
* *
1209749 ATTGGCACCATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTTCGT
1 ATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGT
1209803 ATTGGCA
1 ATTGGCA
1209810 TTAGATATGC
Statistics
Matches: 262, Mismatches: 13, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
53 13 0.05
54 247 0.94
55 2 0.01
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (54 bp):
ATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGT
Found at i:1210735 original size:28 final size:27
Alignment explanation
Indices: 1210704--1210759 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 27
1210694 AAATTCTCTC
*
1210704 TTTT-ATTTTATTTTTCAAGTTTTTATTT
1 TTTTCATTTCATTTTT-AAGTTTTT-TTT
1210732 TTTTCATTTCATTTTTAAGTTTTTTTT
1 TTTTCATTTCATTTTTAAGTTTTTTTT
1210759 T
1 T
1210760 AAATATGCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 4 0.15
28 12 0.46
29 10 0.38
ACGTcount: A:0.16, C:0.05, G:0.04, T:0.75
Consensus pattern (27 bp):
TTTTCATTTCATTTTTAAGTTTTTTTT
Found at i:1213321 original size:19 final size:20
Alignment explanation
Indices: 1213297--1213338 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1213287 AAACCCTAAC
* *
1213297 CCCCTA-TTATTACTATAAA
1 CCCCTATTTATAACCATAAA
1213316 CCCCTATTTATAACCATAAA
1 CCCCTATTTATAACCATAAA
1213336 CCC
1 CCC
1213339 ACTGGCTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.31
Consensus pattern (20 bp):
CCCCTATTTATAACCATAAA
Found at i:1216199 original size:21 final size:21
Alignment explanation
Indices: 1216150--1216211 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
1216140 TTTATTTTTT
* *
1216150 TAAAATTAATAATTAT-ATAA
1 TAAAAATAATATTTATAATAA
1216170 TAAAAAATAATATTTATAATAA
1 T-AAAAATAATATTTATAATAA
*
1216192 TAAAAATATTATTT-TAATAA
1 TAAAAATAATATTTATAATAA
1216212 AATTTGTCAC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 7 0.19
21 25 0.68
22 5 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAAAATAATATTTATAATAA
Found at i:1216784 original size:27 final size:28
Alignment explanation
Indices: 1216715--1216786 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 28
1216705 TATTTATATC
*
1216715 AATATTATTAAAATATTTACTAGAATACA
1 AATATTATTAAAATA-TTACTAGAACACA
* * *
1216744 AATATTA-T-ACATATTATTA-AACATA
1 AATATTATTAAAATATTACTAGAACACA
1216769 AATATTATTAAAATATTA
1 AATATTATTAAAATATTA
1216787 GTTACATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
25 11 0.31
26 6 0.17
27 11 0.31
28 1 0.03
29 7 0.19
ACGTcount: A:0.53, C:0.06, G:0.01, T:0.40
Consensus pattern (28 bp):
AATATTATTAAAATATTACTAGAACACA
Found at i:1218793 original size:18 final size:18
Alignment explanation
Indices: 1218770--1218807 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1218760 TTACCTGTTG
1218770 TCCTTAGCTTGCAACATT
1 TCCTTAGCTTGCAACATT
1218788 TCCTTAGCTTGCAACATT
1 TCCTTAGCTTGCAACATT
1218806 TC
1 TC
1218808 TTGGAATTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.29, G:0.11, T:0.39
Consensus pattern (18 bp):
TCCTTAGCTTGCAACATT
Found at i:1227703 original size:30 final size:26
Alignment explanation
Indices: 1227648--1227741 Score: 75
Period size: 27 Copynumber: 3.4 Consensus size: 26
1227638 AATTGTTTGA
*
1227648 AATATTTATTATTATGTTTCAATTTTCCCT
1 AATATTTATTATTATGCTT-AATTTT---T
1227678 AATATTTATTATTATGGGCTT-ATTTTT
1 AATATTTATTATTAT--GCTTAATTTTT
* *
1227705 AATATTTATTATTAGAAGCCT-ATTTTT
1 AATATTTATTATT--ATGCTTAATTTTT
1227732 AATATTTATT
1 AATATTTATT
1227742 TTTCTAATAT
Statistics
Matches: 57, Mismatches: 3, Indels: 11
0.80 0.04 0.15
Matches are distributed among these distances:
27 33 0.58
29 1 0.02
30 20 0.35
32 3 0.05
ACGTcount: A:0.30, C:0.07, G:0.06, T:0.56
Consensus pattern (26 bp):
AATATTTATTATTATGCTTAATTTTT
Found at i:1227707 original size:27 final size:27
Alignment explanation
Indices: 1227677--1227741 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
1227667 CAATTTTCCC
* *
1227677 TAATATTTATTATTATG-GGCTTATTTT
1 TAATATTTATTATTA-GAAGCCTATTTT
1227704 TAATATTTATTATTAGAAGCCTATTTT
1 TAATATTTATTATTAGAAGCCTATTTT
1227731 TAATATTTATT
1 TAATATTTATT
1227742 TTTCTAATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
26 1 0.03
27 34 0.97
ACGTcount: A:0.31, C:0.05, G:0.08, T:0.57
Consensus pattern (27 bp):
TAATATTTATTATTAGAAGCCTATTTT
Found at i:1227820 original size:29 final size:29
Alignment explanation
Indices: 1227739--1227821 Score: 80
Period size: 29 Copynumber: 2.7 Consensus size: 29
1227729 TTTAATATTT
* *
1227739 ATTTTTCTAATATTTG-TA-TAAATGTCTA
1 ATTTTTC-AATATTTGTTATTAAAGGTCCA
1227767 ATTTTTTGTCAATATTTTTGTTATTAAAGGTCCA
1 A--TTTT-TCAATA--TTTGTTATTAAAGGTCCA
1227801 ATTTTTCAATATTTGTTATTA
1 ATTTTTCAATATTTGTTATTA
1227822 GGTGCATACT
Statistics
Matches: 46, Mismatches: 2, Indels: 13
0.75 0.03 0.21
Matches are distributed among these distances:
28 1 0.02
29 10 0.22
30 8 0.17
31 8 0.17
32 8 0.17
33 2 0.04
34 9 0.20
ACGTcount: A:0.29, C:0.07, G:0.08, T:0.55
Consensus pattern (29 bp):
ATTTTTCAATATTTGTTATTAAAGGTCCA
Found at i:1227999 original size:72 final size:72
Alignment explanation
Indices: 1227909--1228043 Score: 175
Period size: 72 Copynumber: 1.9 Consensus size: 72
1227899 GGATTTTCAA
* * * * *
1227909 TTTTTAAATATTTGTTATTATG-AGCATACTCTTAAAATTTACATTTTTT-AATATTTATTATTA
1 TTTTTAAATACTTATTATTATGAAGC-TACCCTTAAAATTTA-ATTTTTTCAACACTTATTATTA
1227972 GAGACTCAT
64 GAGACTCAT
* *
1227981 TTTTTTAATACTTATTATTATGAAGCTACCCTTAAAATTTATTTTTTTCAACACTTATTATTA
1 TTTTTAAATACTTATTATTATGAAGCTACCCTTAAAATTTAATTTTTTCAACACTTATTATTA
1228044 TAAACTATTA
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
71 6 0.11
72 45 0.83
73 3 0.06
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.52
Consensus pattern (72 bp):
TTTTTAAATACTTATTATTATGAAGCTACCCTTAAAATTTAATTTTTTCAACACTTATTATTAGA
GACTCAT
Found at i:1228058 original size:43 final size:42
Alignment explanation
Indices: 1227979--1228059 Score: 101
Period size: 43 Copynumber: 1.9 Consensus size: 42
1227969 TTAGAGACTC
* * *
1227979 ATTTTTTTAATACTTATTATTATGAAGCTACCCTTAAAATTT
1 ATTTTTTTAACACTTATTATTATGAAACTACACTTAAAATTT
*
1228021 ATTTTTTTCAACACTTATTATTAT-AAACTATTACTTAAA
1 ATTTTTTT-AACACTTATTATTATGAAACTA-CACTTAAA
1228060 TAACGATATG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
42 13 0.39
43 20 0.61
ACGTcount: A:0.36, C:0.12, G:0.02, T:0.49
Consensus pattern (42 bp):
ATTTTTTTAACACTTATTATTATGAAACTACACTTAAAATTT
Found at i:1228448 original size:12 final size:12
Alignment explanation
Indices: 1228431--1228462 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1228421 GGACAAGTTT
*
1228431 AATTCTCTCCAA
1 AATTCTCCCCAA
1228443 AATTCTCCCCAA
1 AATTCTCCCCAA
1228455 AATTCTCC
1 AATTCTCC
1228463 TTATTTTCCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.31, C:0.38, G:0.00, T:0.31
Consensus pattern (12 bp):
AATTCTCCCCAA
Found at i:1235421 original size:20 final size:18
Alignment explanation
Indices: 1235375--1235424 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 18
1235365 ACTTCAATGC
1235375 TTAAAATTTTTGTTTAAT
1 TTAAAATTTTTGTTTAAT
1235393 TTAATAATTTCCTT-TTTAAGT
1 TTAA-AATTT--TTGTTTAA-T
1235414 TTAAAATTTTT
1 TTAAAATTTTT
1235425 TTCCTTAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
18 6 0.21
19 5 0.18
20 10 0.36
21 7 0.25
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (18 bp):
TTAAAATTTTTGTTTAAT
Found at i:1236054 original size:35 final size:35
Alignment explanation
Indices: 1236013--1236094 Score: 110
Period size: 35 Copynumber: 2.3 Consensus size: 35
1236003 TAAAAATATC
1236013 ATCTGATAAATAAAAATCATCTAATAACGGTAAAT
1 ATCTGATAAATAAAAATCATCTAATAACGGTAAAT
* * * * * *
1236048 ATCTGATAACTGAAAATCATTTGATAACTGTACAT
1 ATCTGATAAATAAAAATCATCTAATAACGGTAAAT
1236083 ATCTGATAAATA
1 ATCTGATAAATA
1236095 TGGAATGTCT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.32
Consensus pattern (35 bp):
ATCTGATAAATAAAAATCATCTAATAACGGTAAAT
Found at i:1236074 original size:18 final size:18
Alignment explanation
Indices: 1236010--1236091 Score: 78
Period size: 18 Copynumber: 4.7 Consensus size: 18
1236000 TCATAAAAAT
* *
1236010 ATCATCTGATAAATAAAA
1 ATCATCTGATAACTGAAA
* * *
1236028 ATCATCTAATAACGGTAA
1 ATCATCTGATAACTGAAA
1236046 AT-ATCTGATAACTGAAA
1 ATCATCTGATAACTGAAA
* * *
1236063 ATCATTTGATAACTGTAC
1 ATCATCTGATAACTGAAA
1236081 AT-ATCTGATAA
1 ATCATCTGATAA
1236092 ATATGGAATG
Statistics
Matches: 51, Mismatches: 12, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
17 22 0.43
18 29 0.57
ACGTcount: A:0.45, C:0.13, G:0.10, T:0.32
Consensus pattern (18 bp):
ATCATCTGATAACTGAAA
Found at i:1237033 original size:28 final size:27
Alignment explanation
Indices: 1237002--1237056 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 27
1236992 CTTAAATATA
1237002 AAATTCA-ATAAAAATAAATTCGATACTT
1 AAATTCATATAAAAATAAA-TCG-TACTT
* *
1237030 AAATTGATATAAAATTAAATCGTACTT
1 AAATTCATATAAAAATAAATCGTACTT
1237057 CCATCGTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 5 0.21
28 9 0.38
29 10 0.42
ACGTcount: A:0.51, C:0.09, G:0.05, T:0.35
Consensus pattern (27 bp):
AAATTCATATAAAAATAAATCGTACTT
Found at i:1238734 original size:30 final size:31
Alignment explanation
Indices: 1238700--1238785 Score: 83
Period size: 30 Copynumber: 2.8 Consensus size: 31
1238690 TAAAATCTAT
1238700 AACTTTTCAAAATTATATTTTTAGTCCCT-A
1 AACTTTTCAAAATTATATTTTTAGTCCCTAA
* *
1238730 AACTTTTACAAAATT-TATACTTTA-ACCCTAA
1 AACTTTT-CAAAATTATAT-TTTTAGTCCCTAA
*
1238761 AAC-TTTCAAAACTTACA-TTTTAGTC
1 AACTTTTCAAAA-TTATATTTTTAGTC
1238786 ACTAGTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
29 9 0.20
30 20 0.44
31 16 0.36
ACGTcount: A:0.37, C:0.19, G:0.02, T:0.42
Consensus pattern (31 bp):
AACTTTTCAAAATTATATTTTTAGTCCCTAA
Found at i:1258291 original size:31 final size:31
Alignment explanation
Indices: 1258253--1258362 Score: 193
Period size: 31 Copynumber: 3.5 Consensus size: 31
1258243 CTTAAAATTT
* *
1258253 CTTGTTTGTGTTCGTTCGTTAAGGAATGTAG
1 CTTGTTCGTGTTCGTTCGTTAAGGAATGTAA
*
1258284 CTTGTTTGTGTTCGTTCGTTAAGGAATGTAA
1 CTTGTTCGTGTTCGTTCGTTAAGGAATGTAA
1258315 CTTGTTCGTGTTCGTTCGTTAAGGAATGTAA
1 CTTGTTCGTGTTCGTTCGTTAAGGAATGTAA
1258346 CTTGTTCGTGTTCGTTC
1 CTTGTTCGTGTTCGTTC
1258363 ATTTAAATGA
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 77 1.00
ACGTcount: A:0.15, C:0.13, G:0.26, T:0.45
Consensus pattern (31 bp):
CTTGTTCGTGTTCGTTCGTTAAGGAATGTAA
Found at i:1258455 original size:23 final size:23
Alignment explanation
Indices: 1258411--1258500 Score: 108
Period size: 23 Copynumber: 3.9 Consensus size: 23
1258401 GGAACGGATG
** *
1258411 TAAACGAATATAAACGATCACAA
1 TAAACGAACGTAAACGAACACAA
* *
1258434 TCAACAAACGTAAACGAACACAAA
1 TAAACGAACGTAAACGAACAC-AA
*
1258458 TGAACGAACGTAAACGAACACAA
1 TAAACGAACGTAAACGAACACAA
*
1258481 TAAATGAACGTAAACGAACA
1 TAAACGAACGTAAACGAACA
1258501 TAAACGAAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
23 36 0.63
24 21 0.37
ACGTcount: A:0.56, C:0.20, G:0.12, T:0.12
Consensus pattern (23 bp):
TAAACGAACGTAAACGAACACAA
Found at i:1258472 original size:24 final size:24
Alignment explanation
Indices: 1258373--1258500 Score: 107
Period size: 24 Copynumber: 5.4 Consensus size: 24
1258363 ATTTAAATGA
* *
1258373 TAAACGAACACAAATGAACGAACA
1 TAAACGAACACAAATAAACGAACG
** ** ** **
1258397 TAAGGGAACGGATGTAAACGAATA
1 TAAACGAACACAAATAAACGAACG
* * *
1258421 TAAACGATCAC-AATCAACAAACG
1 TAAACGAACACAAATAAACGAACG
*
1258444 TAAACGAACACAAATGAACGAACG
1 TAAACGAACACAAATAAACGAACG
*
1258468 TAAACGAACAC-AATAAATGAACG
1 TAAACGAACACAAATAAACGAACG
1258491 TAAACGAACA
1 TAAACGAACA
1258501 TAAACGAAAA
Statistics
Matches: 79, Mismatches: 24, Indels: 3
0.75 0.23 0.03
Matches are distributed among these distances:
23 36 0.46
24 43 0.54
ACGTcount: A:0.54, C:0.19, G:0.16, T:0.12
Consensus pattern (24 bp):
TAAACGAACACAAATAAACGAACG
Found at i:1260835 original size:7 final size:7
Alignment explanation
Indices: 1260818--1260877 Score: 54
Period size: 7 Copynumber: 9.0 Consensus size: 7
1260808 TTTTATAATA
*
1260818 ATACATT
1 ATACATC
*
1260825 ATACCTC
1 ATACATC
1260832 ATACATC
1 ATACATC
1260839 A-ACATC
1 ATACATC
*
1260845 ATACTTC
1 ATACATC
*
1260852 ATACATA
1 ATACATC
*
1260859 ATA-GT-
1 ATACATC
1260864 ATACATC
1 ATACATC
1260871 ATACATC
1 ATACATC
1260878 CTGATGCTTT
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
5 3 0.07
6 8 0.19
7 31 0.74
ACGTcount: A:0.42, C:0.25, G:0.02, T:0.32
Consensus pattern (7 bp):
ATACATC
Found at i:1260848 original size:20 final size:20
Alignment explanation
Indices: 1260820--1260857 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1260810 TTATAATAAT
*
1260820 ACATTATACCTCATACATCA
1 ACATCATACCTCATACATCA
*
1260840 ACATCATACTTCATACAT
1 ACATCATACCTCATACAT
1260858 AATAGTATAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.29, G:0.00, T:0.32
Consensus pattern (20 bp):
ACATCATACCTCATACATCA
Found at i:1263597 original size:19 final size:20
Alignment explanation
Indices: 1263573--1263610 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1263563 TTTTTGACTT
1263573 GATTTGATT-AAAAAAAATA
1 GATTTGATTCAAAAAAAATA
*
1263592 GATTTGATTCGAAAAAAAT
1 GATTTGATTCAAAAAAAAT
1263611 TTAAGTCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.53, C:0.03, G:0.13, T:0.32
Consensus pattern (20 bp):
GATTTGATTCAAAAAAAATA
Found at i:1264417 original size:36 final size:36
Alignment explanation
Indices: 1264367--1264447 Score: 110
Period size: 36 Copynumber: 2.2 Consensus size: 36
1264357 TTTAAAATAA
*
1264367 TATATATA-TTTTTTTGAATAACTAAATTTAATAATTT
1 TATATATACTTTTTAT-AA-AACTAAATTTAATAATTT
* *
1264404 TTTATATACTTTTTATAAAATTAAATTTAATAATTT
1 TATATATACTTTTTATAAAACTAAATTTAATAATTT
1264440 TATATATA
1 TATATATA
1264448 TATATATATA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
36 24 0.62
37 9 0.23
38 6 0.15
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.54
Consensus pattern (36 bp):
TATATATACTTTTTATAAAACTAAATTTAATAATTT
Found at i:1264447 original size:2 final size:2
Alignment explanation
Indices: 1264440--1264471 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1264430 TTAATAATTT
1264440 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1264472 TTTAGGGGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1264877 original size:16 final size:16
Alignment explanation
Indices: 1264855--1264891 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
1264845 TTTTATATCA
1264855 CAAGTCATATTCAAAG
1 CAAGTCATATTCAAAG
*
1264871 TAAGTCATATTCAAAG
1 CAAGTCATATTCAAAG
1264887 CAAGT
1 CAAGT
1264892 TATAACATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.27
Consensus pattern (16 bp):
CAAGTCATATTCAAAG
Found at i:1271944 original size:13 final size:13
Alignment explanation
Indices: 1271926--1271950 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1271916 ATCCTCTATG
1271926 GCCAAAGGTAAGA
1 GCCAAAGGTAAGA
1271939 GCCAAAGGTAAG
1 GCCAAAGGTAAG
1271951 GCTTCAACTA
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:0.44, C:0.16, G:0.32, T:0.08
Consensus pattern (13 bp):
GCCAAAGGTAAGA
Found at i:1273102 original size:44 final size:44
Alignment explanation
Indices: 1273053--1273486 Score: 601
Period size: 44 Copynumber: 9.9 Consensus size: 44
1273043 TGTTACTGAA
1273053 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTTCC
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTTCC
*
1273097 ATAAATGAAAATGCATAAC-AGTGCATTATTGGCAGAAAGGTGCC
1 ATAAATGAAAATGCATAACGA-TGCATTATTGGCAGAAAGGTTCC
* * *
1273141 ATAAATGAAAATACATAACGGTGCATTATTGGCAG-AAGGATGCC
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGG-TTCC
*
1273185 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAATGTTCC
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTTCC
* * * *
1273229 ATAAATGAAAATGCATAATGGTGTATTATTGGCAGAAATGTGT-C
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGT-TCC
*
1273273 ATAAATGAAAATACATAAC-AGTGCATTATTGGCAGAAAGGTGT-C
1 ATAAATGAAAATGCATAACGA-TGCATTATTGGCAGAAAGGT-TCC
* * *
1273317 ATAAATGAAAATGCATAACAATGCATTATTGGCAGAAAAGTGCC
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTTCC
* *
1273361 ATAAATGAAAATGCATAACGGTGCATTATTGGCATAAAGGTTCC
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTTCC
* *
1273405 ATAAATGAAAATGCATAAC-AGTGCATTATTGGCATAAAGGTGCC
1 ATAAATGAAAATGCATAACGA-TGCATTATTGGCAGAAAGGTTCC
* *
1273449 ATAAATGAAAACGCATAACGGTGCATTATTGGCAGAAA
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAA
1273487 AGTACCACTG
Statistics
Matches: 352, Mismatches: 28, Indels: 20
0.88 0.07 0.05
Matches are distributed among these distances:
43 5 0.01
44 342 0.97
45 5 0.01
ACGTcount: A:0.41, C:0.13, G:0.21, T:0.25
Consensus pattern (44 bp):
ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTTCC
Found at i:1273290 original size:132 final size:131
Alignment explanation
Indices: 1273053--1273489 Score: 687
Period size: 132 Copynumber: 3.3 Consensus size: 131
1273043 TGTTACTGAA
* *
1273053 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTTCCATAAATGAAAATGCATAACAG
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAAGTTCCATAAATGAAAATGCATAACGG
* *
1273118 TGCATTATTGGCAGAAAGGTGCCATAAATGAAAATACATAACGGTGCATTATTGGCAGAAGGATG
66 TGCATTATTGGCAGAAAGGTGTCATAAATGAAAATACATAACAGTGCATTATTGGCAGAAGG-TG
1273183 CC
130 CC
* *
1273185 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAATGTTCCATAAATGAAAATGCATAATGG
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAAGTTCCATAAATGAAAATGCATAACGG
* *
1273250 TGTATTATTGGCAGAAATGTGTCATAAATGAAAATACATAACAGTGCATTATTGGCAGAAAGGTG
66 TGCATTATTGGCAGAAAGGTGTCATAAATGAAAATACATAACAGTGCATTATTGGCAG-AAGGTG
*
1273315 TC
130 CC
* *
1273317 ATAAATGAAAATGCATAACAATGCATTATTGGCAGAAAAGTGCCATAAATGAAAATGCATAACGG
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAAGTTCCATAAATGAAAATGCATAACGG
* * *
1273382 TGCATTATTGGCATAAAGGT-TCCATAAATGAAAATGCATAACAGTGCATTATTGGCATAAAGGT
66 TGCATTATTGGCAGAAAGGTGT-CATAAATGAAAATACATAACAGTGCATTATTGGCA-GAAGGT
1273446 GCC
129 GCC
* *
1273449 ATAAATGAAAACGCATAACGGTGCATTATTGGCAGAAAAGT
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAAGT
1273490 ACCACTGATG
Statistics
Matches: 281, Mismatches: 21, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
131 1 0.00
132 276 0.98
133 4 0.01
ACGTcount: A:0.41, C:0.13, G:0.21, T:0.25
Consensus pattern (131 bp):
ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAAGTTCCATAAATGAAAATGCATAACGG
TGCATTATTGGCAGAAAGGTGTCATAAATGAAAATACATAACAGTGCATTATTGGCAGAAGGTGC
C
Found at i:1273384 original size:25 final size:24
Alignment explanation
Indices: 1273356--1273472 Score: 65
Period size: 25 Copynumber: 5.2 Consensus size: 24
1273346 TGGCAGAAAA
1273356 GTGCCATAAATGAAAATGCATAACG
1 GTGCCATAAATGAAAA-GCATAACG
* * *
1273381 GTG-CATTATTG----GCATAAAG
1 GTGCCATAAATGAAAAGCATAACG
* *
1273400 GTTCCATAAATGAAAATGCATAACA
1 GTGCCATAAATGAAAA-GCATAACG
* * *
1273425 GTG-CATTATTG----GCATAAAG
1 GTGCCATAAATGAAAAGCATAACG
1273444 GTGCCATAAATGAAAACGCATAACG
1 GTGCCATAAATGAAAA-GCATAACG
1273469 GTGC
1 GTGC
1273473 ATTATTGGCA
Statistics
Matches: 64, Mismatches: 16, Indels: 24
0.62 0.15 0.23
Matches are distributed among these distances:
19 18 0.28
20 12 0.19
24 12 0.19
25 22 0.34
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.24
Consensus pattern (24 bp):
GTGCCATAAATGAAAAGCATAACG
Found at i:1276617 original size:11 final size:12
Alignment explanation
Indices: 1276601--1276633 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
1276591 CAAATACAAG
1276601 AAAATAAAAT-C
1 AAAATAAAATAC
1276612 AAAATAAAATAC
1 AAAATAAAATAC
1276624 ACAAATAAAA
1 A-AAATAAAA
1276634 AAATGTGCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.50
12 2 0.10
13 8 0.40
ACGTcount: A:0.76, C:0.09, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAATAAAATAC
Found at i:1281438 original size:20 final size:20
Alignment explanation
Indices: 1281403--1281452 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1281393 AAATGATTCT
* * *
1281403 ATTTTG-AAAGCAAAATTAG
1 ATTTTGAAAAACAAAATGAA
1281422 ATTTTGAAAAACAAAATGAA
1 ATTTTGAAAAACAAAATGAA
1281442 ATTTTGAAAAA
1 ATTTTGAAAAA
1281453 TAATTTTGAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 6 0.22
20 21 0.78
ACGTcount: A:0.54, C:0.04, G:0.12, T:0.30
Consensus pattern (20 bp):
ATTTTGAAAAACAAAATGAA
Found at i:1290786 original size:24 final size:23
Alignment explanation
Indices: 1290734--1290797 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
1290724 CTCATTGTTG
* *
1290734 CAAAAGCACACACTTCATCTGCTG
1 CAAAAGCACA-ACTTCATCGGCTA
*
1290758 TAAAAGCACAATCTTCATCGGCTA
1 CAAAAGCACAA-CTTCATCGGCTA
*
1290782 CAAAAGTACAAGCTTC
1 CAAAAGCACAA-CTTC
1290798 TGCAACTAAC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 1 0.03
24 32 0.97
ACGTcount: A:0.38, C:0.28, G:0.12, T:0.22
Consensus pattern (23 bp):
CAAAAGCACAACTTCATCGGCTA
Found at i:1298456 original size:38 final size:37
Alignment explanation
Indices: 1298412--1298577 Score: 151
Period size: 38 Copynumber: 4.4 Consensus size: 37
1298402 ACTAATATAG
*
1298412 TATAGTTTTTGAAAATATTTTTTTGAAAACATATAATA
1 TATAGTTTTTGAAAA-ATGTTTTTGAAAACATATAATA
* * *
1298450 TATAGTTTTT-AGAAAACGATTTTTGAAAGCATATAGTA
1 TATAGTTTTTGA-AAAATG-TTTTTGAAAACATATAATA
* *
1298488 TATAGTTTTTTAAAAATCGGTTTTTGAAAATATAT-ATA
1 TATAGTTTTTGAAAAAT--GTTTTTGAAAACATATAATA
* * **
1298526 -ATATGGTTTTGAAAACACGTTTTTGAAAATGTATAATA
1 TATA-GTTTTTGAAAA-ATGTTTTTGAAAACATATAATA
1298564 TATAG-TTTTGAAAA
1 TATAGTTTTTGAAAA
1298578 CGTATAATAT
Statistics
Matches: 107, Mismatches: 12, Indels: 19
0.78 0.09 0.14
Matches are distributed among these distances:
37 29 0.27
38 59 0.55
39 18 0.17
40 1 0.01
ACGTcount: A:0.40, C:0.04, G:0.13, T:0.43
Consensus pattern (37 bp):
TATAGTTTTTGAAAAATGTTTTTGAAAACATATAATA
Found at i:1298548 original size:37 final size:36
Alignment explanation
Indices: 1298453--1298577 Score: 117
Period size: 37 Copynumber: 3.3 Consensus size: 36
1298443 TATAATATAT
* ** *
1298453 AGTTTTTAGAAAACGATTTTTGAAAGCATATAGTATAT
1 AGTTTTGA-AAAACG-TTTTTGAAAATATATAATATAT
*
1298491 AGTTTTTTAAAAATCGGTTTTTGAAAATATAT-ATAATAT
1 AG-TTTTGAAAAA-C-GTTTTTGAAAATATATAAT-ATAT
* *
1298530 GGTTTTGAAAACACGTTTTTGAAAATGTATAATATAT
1 AGTTTTGAAAA-ACGTTTTTGAAAATATATAATATAT
1298567 AGTTTTGAAAA
1 AGTTTTGAAAA
1298578 CGTATAATAT
Statistics
Matches: 74, Mismatches: 7, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
37 29 0.39
38 18 0.24
39 26 0.35
40 1 0.01
ACGTcount: A:0.40, C:0.04, G:0.14, T:0.42
Consensus pattern (36 bp):
AGTTTTGAAAAACGTTTTTGAAAATATATAATATAT
Found at i:1298575 original size:23 final size:23
Alignment explanation
Indices: 1298546--1298590 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
1298536 GAAAACACGT
*
1298546 TTTTGAAAATGTATAATATATAG
1 TTTTGAAAACGTATAATATATAG
1298569 TTTTGAAAACGTATAATATATA
1 TTTTGAAAACGTATAATATATA
1298591 CAATTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.44, C:0.02, G:0.11, T:0.42
Consensus pattern (23 bp):
TTTTGAAAACGTATAATATATAG
Found at i:1298600 original size:23 final size:23
Alignment explanation
Indices: 1298547--1298601 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
1298537 AAAACACGTT
* **
1298547 TTTGAAAATGTATAATATATAGT
1 TTTGAAAACGTATAATATATAAA
1298570 TTTGAAAACGTATAATATATACAA
1 TTTGAAAACGTATAATATATA-AA
*
1298594 TTTAAAAA
1 TTTGAAAA
1298602 AATAATTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 20 0.74
24 7 0.26
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.38
Consensus pattern (23 bp):
TTTGAAAACGTATAATATATAAA
Found at i:1298632 original size:24 final size:25
Alignment explanation
Indices: 1298603--1298654 Score: 79
Period size: 24 Copynumber: 2.1 Consensus size: 25
1298593 ATTTAAAAAA
**
1298603 ATAATTTTTGAAAACATATATA-AT
1 ATAATTTTAAAAAACATATATATAT
1298627 ATAATTTTAAAAAACATATATATAT
1 ATAATTTTAAAAAACATATATATAT
1298652 ATA
1 ATA
1298655 TATATGTAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 20 0.80
25 5 0.20
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (25 bp):
ATAATTTTAAAAAACATATATATAT
Found at i:1298722 original size:22 final size:20
Alignment explanation
Indices: 1298696--1298743 Score: 69
Period size: 22 Copynumber: 2.3 Consensus size: 20
1298686 CATATATAAT
1298696 ATATATAATTTTTGGAAACATA
1 ATATATAATTTTT-GAAAC-TA
*
1298718 TTATATAATTTTTGAAACTA
1 ATATATAATTTTTGAAACTA
1298738 ATATAT
1 ATATAT
1298744 GTTATCTAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 7 0.29
21 5 0.21
22 12 0.50
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (20 bp):
ATATATAATTTTTGAAACTA
Found at i:1298783 original size:4 final size:4
Alignment explanation
Indices: 1298756--1298837 Score: 96
Period size: 4 Copynumber: 19.8 Consensus size: 4
1298746 TATCTAGTTT
*
1298756 TTTA TTATA TATTA ATTA TATTA TTTA TATTA -TTA TTT- TTTA TTTA
1 TTTA TT-TA T-TTA TTTA T-TTA TTTA T-TTA TTTA TTTA TTTA TTTA
1298802 TTTA TTTA TTTA TATTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTT
1298838 TTTTCATGTC
Statistics
Matches: 69, Mismatches: 2, Indels: 14
0.81 0.02 0.16
Matches are distributed among these distances:
3 6 0.09
4 46 0.67
5 16 0.23
6 1 0.01
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:1298837 original size:25 final size:25
Alignment explanation
Indices: 1298756--1298837 Score: 107
Period size: 25 Copynumber: 3.3 Consensus size: 25
1298746 TATCTAGTTT
*
1298756 TTTATTATATATTAATTATATTATTTA
1 TTTATT-TATATTATTTAT-TTATTTA
1298783 TATTA-TTAT-TT-TTTATTTATTTA
1 T-TTATTTATATTATTTATTTATTTA
1298806 TTTATTTATATTATTTATTTATTTA
1 TTTATTTATATTATTTATTTATTTA
1298831 TTTATTT
1 TTTATTT
1298838 TTTTCATGTC
Statistics
Matches: 50, Mismatches: 1, Indels: 10
0.82 0.02 0.16
Matches are distributed among these distances:
22 3 0.06
23 12 0.24
24 6 0.12
25 21 0.42
26 3 0.06
27 2 0.04
28 3 0.06
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (25 bp):
TTTATTTATATTATTTATTTATTTA
Found at i:1305251 original size:14 final size:14
Alignment explanation
Indices: 1305232--1305258 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1305222 ACCATACACT
1305232 CACTTGTACACCTC
1 CACTTGTACACCTC
1305246 CACTTGTACACCT
1 CACTTGTACACCT
1305259 GGTAAGGACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.41, G:0.07, T:0.30
Consensus pattern (14 bp):
CACTTGTACACCTC
Found at i:1307674 original size:29 final size:29
Alignment explanation
Indices: 1307631--1307695 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
1307621 ACAAGCCTTA
* * * *
1307631 GGAAAATTGGGGATCATTTTGTAAGTTTT
1 GGAAAATTGGAGATCAATTCGTAAATTTT
1307660 -GAAAAGTTGGAGATCAATTCGTAAATTTT
1 GGAAAA-TTGGAGATCAATTCGTAAATTTT
1307689 GGAAAAT
1 GGAAAAT
1307696 AGAGGGATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
28 5 0.17
29 20 0.67
30 5 0.17
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (29 bp):
GGAAAATTGGAGATCAATTCGTAAATTTT
Found at i:1308420 original size:59 final size:59
Alignment explanation
Indices: 1308321--1308457 Score: 195
Period size: 59 Copynumber: 2.3 Consensus size: 59
1308311 CAGCAGGCTG
** *
1308321 CATATTCGGGAATACACTAAAGGATACCTAGTGTATATGGTGGGCACGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGGCACGACCTTATGTGT
* ** *
1308380 CATATTCGGGACTGTACTTAAGGATACCTAGTACAGATGGTGGGCACGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGGCACGACCTTATGTGT
1308439 CATATTCGGG-ATAACACTA
1 CATATTCGGGAAT-ACACTA
1308458 CGATGCTTAT
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
58 1 0.02
59 65 0.98
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.28
Consensus pattern (59 bp):
CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGGCACGACCTTATGTGT
Found at i:1315281 original size:39 final size:37
Alignment explanation
Indices: 1315237--1315342 Score: 91
Period size: 33 Copynumber: 2.9 Consensus size: 37
1315227 ATTTTGCTCA
1315237 TTCGAACAAAAACTACTCTATCTGAATTTTTTTGCATGG
1 TTCGAAC-AAAACTACTCTATCTGAATTTTTTTGCAT-G
* *
1315276 TTCGAACCAAA-T--TGC-A-CTG-ATTTTTCTGC-TG
1 TTCGAACAAAACTACT-CTATCTGAATTTTTTTGCATG
* *
1315307 TTCGAACTAAAACTACACTGTCTGAATTTTTTTGCA
1 TTCGAAC-AAAACTACTCTATCTGAATTTTTTTGCA
1315343 CTGTATTTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 19
0.68 0.08 0.25
Matches are distributed among these distances:
31 8 0.15
32 4 0.08
33 10 0.19
34 4 0.08
35 2 0.04
36 4 0.08
37 10 0.19
38 3 0.06
39 7 0.13
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (37 bp):
TTCGAACAAAACTACTCTATCTGAATTTTTTTGCATG
Found at i:1318474 original size:11 final size:11
Alignment explanation
Indices: 1318458--1318494 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
1318448 AACAACGAAG
1318458 GAAAATTGAAA
1 GAAAATTGAAA
1318469 GAAAATTGAAA
1 GAAAATTGAAA
*
1318480 GAAAATTAAAA
1 GAAAATTGAAA
1318491 GAAA
1 GAAA
1318495 GGAATTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (11 bp):
GAAAATTGAAA
Found at i:1324109 original size:23 final size:24
Alignment explanation
Indices: 1324051--1324111 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 24
1324041 CTACTCATAT
* * *
1324051 AATTTGCACCGAAGTGTCGCGTAG
1 AATTTGTACCGAAGTGCCACGTAG
1324075 AATTTGTACCGAAGTGCCACGTAG
1 AATTTGTACCGAAGTGCCACGTAG
*
1324099 -ATTTGTCCCGAAG
1 AATTTGTACCGAAG
1324112 GACCGTGTAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
23 12 0.36
24 21 0.64
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (24 bp):
AATTTGTACCGAAGTGCCACGTAG
Found at i:1325673 original size:1 final size:1
Alignment explanation
Indices: 1325667--1325716 Score: 73
Period size: 1 Copynumber: 50.0 Consensus size: 1
1325657 AGACTTTTCC
* * *
1325667 TTTTTTTTTTTTTCTTTTTTTTTTTTTTTTCTTTTTTTCTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1325717 CTTTCTTTCT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (1 bp):
T
Found at i:1325684 original size:12 final size:12
Alignment explanation
Indices: 1325669--1325730 Score: 88
Period size: 12 Copynumber: 5.1 Consensus size: 12
1325659 ACTTTTCCTT
1325669 TTTTTTTTTTTC
1 TTTTTTTTTTTC
*
1325681 TTTTTTTTTTTT
1 TTTTTTTTTTTC
1325693 TTTTCTTTTTTTC
1 TTTT-TTTTTTTC
1325706 TTTTTTTTTTTC
1 TTTTTTTTTTTC
* *
1325718 TTTCTTTCTTTC
1 TTTTTTTTTTTC
1325730 T
1 T
1325731 ATCCCATTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
12 34 0.76
13 11 0.24
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (12 bp):
TTTTTTTTTTTC
Found at i:1325689 original size:17 final size:17
Alignment explanation
Indices: 1325667--1325714 Score: 87
Period size: 17 Copynumber: 2.8 Consensus size: 17
1325657 AGACTTTTCC
1325667 TTTTTTTTTTTTTCTTT
1 TTTTTTTTTTTTTCTTT
1325684 TTTTTTTTTTTTTCTTT
1 TTTTTTTTTTTTTCTTT
1325701 TTTTCTTTTTTTTT
1 TTTT-TTTTTTTTT
1325715 TTCTTTCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 21 0.70
18 9 0.30
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (17 bp):
TTTTTTTTTTTTTCTTT
Found at i:1325690 original size:20 final size:20
Alignment explanation
Indices: 1325661--1325728 Score: 95
Period size: 20 Copynumber: 3.5 Consensus size: 20
1325651 GCTTCCAGAC
*
1325661 TTTTCCTTTTTTTTTTT-TT
1 TTTTTCTTTTTTTTTTTCTT
1325680 CTTTTT-TTTTTTTTTTTCTT
1 -TTTTTCTTTTTTTTTTTCTT
1325700 TTTTTCTTTTTTTTTTTCTT
1 TTTTTCTTTTTTTTTTTCTT
*
1325720 TCTTTCTTT
1 TTTTTCTTT
1325729 CTATCCCATT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
19 16 0.36
20 28 0.64
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (20 bp):
TTTTTCTTTTTTTTTTTCTT
Found at i:1325695 original size:25 final size:25
Alignment explanation
Indices: 1325668--1325730 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 25
1325658 GACTTTTCCT
1325668 TTTTTTTTTTTTCTTTTTTT-TTTT
1 TTTTTTTTTTTTCTTTTTTTCTTTT
1325692 TTTTTCTTTTTTTCTTTTTTT-TTTT
1 TTTTT-TTTTTTTCTTTTTTTCTTTT
* * *
1325717 CTTTCTTTCTTTCT
1 TTTTTTTTTTTTCT
1325731 ATCCCATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
24 13 0.37
25 22 0.63
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (25 bp):
TTTTTTTTTTTTCTTTTTTTCTTTT
Found at i:1325721 original size:4 final size:4
Alignment explanation
Indices: 1325677--1325730 Score: 51
Period size: 4 Copynumber: 14.2 Consensus size: 4
1325667 TTTTTTTTTT
* * * *
1325677 TTTC TTT- TTT- TTT- TTTT TTTC TTTT TTTC TTTT TTTT TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
1325722 TTTC TTTC T
1 TTTC TTTC T
1325731 ATCCCATTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
3 9 0.20
4 35 0.80
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (4 bp):
TTTC
Found at i:1327076 original size:20 final size:21
Alignment explanation
Indices: 1327042--1327083 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1327032 AATTACATTC
* *
1327042 AAAATTAAAAGATAATTCCTA
1 AAAAATAAAAGATAAATCCTA
1327063 AAAAATAAAA-ATAAATCCTA
1 AAAAATAAAAGATAAATCCTA
1327083 A
1 A
1327084 TGAATTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.64, C:0.10, G:0.02, T:0.24
Consensus pattern (21 bp):
AAAAATAAAAGATAAATCCTA
Found at i:1327092 original size:21 final size:20
Alignment explanation
Indices: 1327042--1327095 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
1327032 AATTACATTC
*
1327042 AAAATTAAAAGATAATTCCTA
1 AAAATTAAAA-ATAAATCCTA
*
1327063 AAAAATAAAAATAAATCCTA
1 AAAATTAAAAATAAATCCTA
*
1327083 ATGAATTAAAAAT
1 A-AAATTAAAAAT
1327096 GTGGATGAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 10 0.36
21 18 0.64
ACGTcount: A:0.63, C:0.07, G:0.04, T:0.26
Consensus pattern (20 bp):
AAAATTAAAAATAAATCCTA
Found at i:1331588 original size:79 final size:79
Alignment explanation
Indices: 1331500--1331658 Score: 309
Period size: 79 Copynumber: 2.0 Consensus size: 79
1331490 GAGAGTTTTG
*
1331500 AATACGTGATTGTCTTTAAAGAAAGATGGTGCTTTGATTTTAGAATTTAAGTTAAAGCCTATGTT
1 AATACGTGATTGTCTTTAAAGAAAGATGGTGCTTTGATTGTAGAATTTAAGTTAAAGCCTATGTT
1331565 GTTAGATCGAGTAA
66 GTTAGATCGAGTAA
1331579 AATACGTGATTGTCTTTAAAGAAAGATGGTGCTTTGATTGTAGAATTTAAGTTAAAGCCTATGTT
1 AATACGTGATTGTCTTTAAAGAAAGATGGTGCTTTGATTGTAGAATTTAAGTTAAAGCCTATGTT
1331644 GTTAGATCGAGTAA
66 GTTAGATCGAGTAA
1331658 A
1 A
1331659 GGATCTTCAA
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.33, C:0.08, G:0.22, T:0.37
Consensus pattern (79 bp):
AATACGTGATTGTCTTTAAAGAAAGATGGTGCTTTGATTGTAGAATTTAAGTTAAAGCCTATGTT
GTTAGATCGAGTAA
Found at i:1332301 original size:20 final size:21
Alignment explanation
Indices: 1332276--1332317 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1332266 AAATTTTGGG
*
1332276 TAGTGACTAAAG-AAAAAGTT
1 TAGTGACCAAAGTAAAAAGTT
*
1332296 TAGTGACCAAAGTATAAAGTT
1 TAGTGACCAAAGTAAAAAGTT
1332317 T
1 T
1332318 GTAAAAGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.45, C:0.07, G:0.19, T:0.29
Consensus pattern (21 bp):
TAGTGACCAAAGTAAAAAGTT
Found at i:1337542 original size:87 final size:87
Alignment explanation
Indices: 1337396--1337569 Score: 285
Period size: 87 Copynumber: 2.0 Consensus size: 87
1337386 CAAAGGGTGA
* * * *
1337396 TGCATCACTCTTAATTTATAATACAAAGTGGGTAATTTAATGCCTTCTAGTATACTGCATGATAT
1 TGCATCACCCTTAATTTATAATACAAAGAGAGTAATTTAATGCCGTCTAGTATACTGCATGATAT
* *
1337461 TGTGTTTACTAGTAATAATACT
66 TATGTGTACTAGTAATAATACT
*
1337483 TGCATCACCCTTAATTTATAATACAAAGAGAGTCATTTAATGCCGTCTAGTATACTGCATGATAT
1 TGCATCACCCTTAATTTATAATACAAAGAGAGTAATTTAATGCCGTCTAGTATACTGCATGATAT
1337548 TATGTGTACTAGTAATAATACT
66 TATGTGTACTAGTAATAATACT
1337570 AATTTCATTA
Statistics
Matches: 80, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 80 1.00
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (87 bp):
TGCATCACCCTTAATTTATAATACAAAGAGAGTAATTTAATGCCGTCTAGTATACTGCATGATAT
TATGTGTACTAGTAATAATACT
Found at i:1337648 original size:82 final size:83
Alignment explanation
Indices: 1337529--1337695 Score: 318
Period size: 82 Copynumber: 2.0 Consensus size: 83
1337519 TTAATGCCGT
1337529 CTAGTATACTGCATGATATTATGTGTACTAGTAATAATACTAATTTCATTACTCATTACATACGA
1 CTAGTATACTGCATGA-ATTATGTGTACTAGTAATAATACTAATTTCATTACTCATTACATACGA
1337594 AGTTTGCTTTGAAGGGGTA
65 AGTTTGCTTTGAAGGGGTA
1337613 CTAGTATACTGCATG-ATTATGTGTACTAGTAATAATACTAATTTCATTACTCATTACATACGAA
1 CTAGTATACTGCATGAATTATGTGTACTAGTAATAATACTAATTTCATTACTCATTACATACGAA
1337677 GTTTGCTTTGAAGGGGTA
66 GTTTGCTTTGAAGGGGTA
1337695 C
1 C
1337696 ATATTGAACT
Statistics
Matches: 83, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
82 68 0.82
84 15 0.18
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.38
Consensus pattern (83 bp):
CTAGTATACTGCATGAATTATGTGTACTAGTAATAATACTAATTTCATTACTCATTACATACGAA
GTTTGCTTTGAAGGGGTA
Found at i:1337895 original size:85 final size:86
Alignment explanation
Indices: 1337750--1337921 Score: 283
Period size: 85 Copynumber: 2.0 Consensus size: 86
1337740 CAAAGGGTGA
* *
1337750 TGCATCACTCTTAATTTATAATACAAAGTGGGTAATTTAATGCCTTCTAGTATACTGCATGATAT
1 TGCATCACCCTTAATTTATAATACAAAG-GAGTAATTTAATGCCTTCTAGTATACTGCATGATAT
* *
1337815 TGTGTTTACTAGTAATAATACT
65 TATGTGTACTAGTAATAATACT
*
1337837 TGCATCACCCTTAATTTATAATACAAA-GAGTCATTTAATGCCTTCTAGTATACTGCATGATATT
1 TGCATCACCCTTAATTTATAATACAAAGGAGTAATTTAATGCCTTCTAGTATACTGCATGATATT
1337901 ATGTGTACTAGTAATAATACT
66 ATGTGTACTAGTAATAATACT
1337922 AATTTCATTA
Statistics
Matches: 80, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
85 54 0.68
87 26 0.32
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (86 bp):
TGCATCACCCTTAATTTATAATACAAAGGAGTAATTTAATGCCTTCTAGTATACTGCATGATATT
ATGTGTACTAGTAATAATACT
Found at i:1338187 original size:38 final size:38
Alignment explanation
Indices: 1338144--1338221 Score: 120
Period size: 38 Copynumber: 2.1 Consensus size: 38
1338134 TATCTCTAGC
* * *
1338144 TATCGATGGTTTCTCGGACTTCTTTAGTATCTCACGCT
1 TATCGACGGTTTCTCGGAATTCTTTAGTATCTCACACT
*
1338182 TATCGACGGTTTCTTGGAATTCTTTAGTATCTCACACT
1 TATCGACGGTTTCTCGGAATTCTTTAGTATCTCACACT
1338220 TA
1 TA
1338222 CTCATCTGGA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.19, C:0.22, G:0.17, T:0.42
Consensus pattern (38 bp):
TATCGACGGTTTCTCGGAATTCTTTAGTATCTCACACT
Found at i:1338861 original size:17 final size:18
Alignment explanation
Indices: 1338839--1338876 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
1338829 TGAATAAAGT
1338839 TAGTTCA-TTAATTAAAC
1 TAGTTCACTTAATTAAAC
*
1338856 TAGTTCACGTTTATTAAAC
1 TAGTTCAC-TTAATTAAAC
1338875 TA
1 TA
1338877 ACTCTTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
19 11 0.61
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (18 bp):
TAGTTCACTTAATTAAAC
Found at i:1341298 original size:19 final size:19
Alignment explanation
Indices: 1341257--1341300 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1341247 AATAAATTAT
** *
1341257 TGTTTATTCTAGTTTTCAT
1 TGTTTATTCTAGTTAACAA
1341276 TGTTTATTCTAGTTAACAA
1 TGTTTATTCTAGTTAACAA
1341295 TGTTTA
1 TGTTTA
1341301 ACTACATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.23, C:0.09, G:0.11, T:0.57
Consensus pattern (19 bp):
TGTTTATTCTAGTTAACAA
Found at i:1344209 original size:57 final size:57
Alignment explanation
Indices: 1344100--1344756 Score: 813
Period size: 57 Copynumber: 11.5 Consensus size: 57
1344090 GTGCAAAATA
* * * * * *
1344100 TAAGAAATCGTACTAAGTGTATGAAATTTTAGATAGAGTGTTTCATATGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATG-AATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* * *
1344158 TAATAAATCATACTAAGTGTATGACTTTCAGATAGGGCGTTTCGTACGCTAAAATTT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* *
1344215 TAAGAAGTCATACTAAGTGTATGAATTTCAGATAGGGCATTTCGTACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* * * * * *
1344272 TAAGAAATCATAGTAAGTGTATAAATTACAGATAGGGCTTTTCTTACGATAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* * * * *
1344329 TAAGAAAACATATTTAGTGTATGAATTTCAGATAGGGCATTTCGTACGGTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* * * * *
1344386 TAAGAAATCATACTAAGTGTATGAATTTTAGATAAGACATTTCGTACACTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* *
1344443 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGTGTTTCTTA-GCTAAAATG-
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* * * *
1344498 TAAGAAATCGTACTAAGTGTATGAATTTCAGACAGGGCATTTTGTACGCTAAAACT-T
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAA-TGT
* *
1344555 TAAGAAATCATACTAAGTGTTTGAATTTCTA-ATAGGGTGCTTT-GTACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTC-AGATAGGGCG-TTTCGTACGCTAAAATGT
*
1344612 TAAGAAATCATACTAAATGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* * * ** *
1344669 TAAGAAATCATATTAAGTGTATGACTTTCTAGATAGGGCACTTT-GTGTGCTAAAATGA
1 TAAGAAATCATACTAAGTGTATGAATTTC-AGATAGGGC-GTTTCGTACGCTAAAATGT
* *
1344727 TAATAAATTCATACTTAGTGTATGAATTTC
1 TAAGAAA-TCATACTAAGTGTATGAATTTC
1344757 TGTATTGGAC
Statistics
Matches: 519, Mismatches: 69, Indels: 21
0.85 0.11 0.03
Matches are distributed among these distances:
55 40 0.08
56 20 0.04
57 386 0.74
58 51 0.10
59 22 0.04
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.34
Consensus pattern (57 bp):
TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
Found at i:1345667 original size:45 final size:45
Alignment explanation
Indices: 1345420--1345660 Score: 374
Period size: 45 Copynumber: 5.4 Consensus size: 45
1345410 GCATAATTGT
* *
1345420 ATGAAAGGATGCCATAAATGAAATGTATAATAGTGTATCAAAGGT
1 ATGAAAGGATGCCATAAATGAAAGGTATAATAGTGTATCAAAGGC
** * *
1345465 ATGAAAGGATGTTATAAATGATATGTATAATAGTGTATCAAAGGC
1 ATGAAAGGATGCCATAAATGAAAGGTATAATAGTGTATCAAAGGC
1345510 ATGAAAGGATGCCATAAATGAAAGGTATAATAGTGTATCAAAGGC
1 ATGAAAGGATGCCATAAATGAAAGGTATAATAGTGTATCAAAGGC
*
1345555 ATGAAAGGATGCCATATATGAAAGGTATAATAGTGTATCAAAGGC
1 ATGAAAGGATGCCATAAATGAAAGGTATAATAGTGTATCAAAGGC
* * *
1345600 ATGAAAGGATGCCATATATGAAAGGTATAATAGTGTATAAAAGAC
1 ATGAAAGGATGCCATAAATGAAAGGTATAATAGTGTATCAAAGGC
* *
1345645 ATGTAAGGATGACATA
1 ATGAAAGGATGCCATA
1345661 TTTGAAATGC
Statistics
Matches: 183, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 183 1.00
ACGTcount: A:0.44, C:0.07, G:0.23, T:0.26
Consensus pattern (45 bp):
ATGAAAGGATGCCATAAATGAAAGGTATAATAGTGTATCAAAGGC
Found at i:1349402 original size:57 final size:57
Alignment explanation
Indices: 1349340--1349825 Score: 720
Period size: 57 Copynumber: 8.5 Consensus size: 57
1349330 GTACAAAATA
*
1349340 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCATTTCGTACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* * *
1349397 TAAGAACTCATACTAAGTGTATGAATTTCAGATAGGGCGTTTTGTAAGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
*
1349454 TAAGAAGTCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* * *
1349511 TAAGAAATCATACTACGTGTATGAGTTTCAGATAGGGTGTTTCGTACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* **
1349568 TAAGAAATCATACTAAGTGTTTGAATTTCAGATAGGATGTTTCGTACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* * *
1349625 TAAGAAATCATACTTAGTGTATTAATTTCAGATAGGGCGTTTCGTACGCTAAAATAT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
*
1349682 TAAGAAATCATACTAAGTGTATGAATTTCAGATAAGGCGTTTCGTACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* ** *** ** * *
1349739 TAATAAATCATACTAAGTGTATGGCTTTCCAGATAGGGTACTTCGTGTGCTAACATGA
1 TAAGAAATCATACTAAGTGTATGAATTT-CAGATAGGGCGTTTCGTACGCTAAAATGT
*
1349797 TAAGAAAATCATTCTAAGTGTATGAATTT
1 TAAG-AAATCATACTAAGTGTATGAATTT
1349826 TTGTATTAGA
Statistics
Matches: 387, Mismatches: 40, Indels: 2
0.90 0.09 0.00
Matches are distributed among these distances:
57 342 0.88
58 24 0.06
59 21 0.05
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (57 bp):
TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
Found at i:1350610 original size:45 final size:45
Alignment explanation
Indices: 1350489--1350630 Score: 196
Period size: 45 Copynumber: 3.2 Consensus size: 45
1350479 GCATAATTGT
* * * *
1350489 ATGAAGGGATGCCATCAATGAAATGTAGAATAGTGTATCAAAGGT
1 ATGAAAGGATGCCATAAATGAAATGTATAATAGTGTATCAAAGGC
** * *
1350534 ATGAAAGGAT-TTATAAATGAGATATATAATAGTGTATCAAAGGC
1 ATGAAAGGATGCCATAAATGAAATGTATAATAGTGTATCAAAGGC
*
1350578 ATGAAAGGATGCCATAAATGAAAGGTATAATAGTGTATCAAAGGC
1 ATGAAAGGATGCCATAAATGAAATGTATAATAGTGTATCAAAGGC
1350623 ATGAAAGG
1 ATGAAAGG
1350631 TATAATAATG
Statistics
Matches: 83, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
44 37 0.45
45 46 0.55
ACGTcount: A:0.44, C:0.07, G:0.25, T:0.25
Consensus pattern (45 bp):
ATGAAAGGATGCCATAAATGAAATGTATAATAGTGTATCAAAGGC
Found at i:1350627 original size:28 final size:28
Alignment explanation
Indices: 1350595--1350658 Score: 92
Period size: 28 Copynumber: 2.3 Consensus size: 28
1350585 GATGCCATAA
* * *
1350595 ATGAAAGGTATAATAGTGTATCAAAGGC
1 ATGAAAGGTATAATAATGTATAAAAGAC
1350623 ATGAAAGGTATAATAATGTATAAAAGAC
1 ATGAAAGGTATAATAATGTATAAAAGAC
*
1350651 ATGTAAGG
1 ATGAAAGG
1350659 ATGACATAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.47, C:0.05, G:0.23, T:0.25
Consensus pattern (28 bp):
ATGAAAGGTATAATAATGTATAAAAGAC
Found at i:1358792 original size:68 final size:69
Alignment explanation
Indices: 1358680--1358849 Score: 211
Period size: 68 Copynumber: 2.5 Consensus size: 69
1358670 ACGTGTGCCA
* * ** * * *
1358680 GGAAGCACCTACTCATATCTATTCTGGGTGACTAGCACGAGAGCCCCAAATGA-TAGAGTGACTC
1 GGAAGCATCTAATCATATCTATTCCAGGTGACTAGAACGAGAGCCCCAAAGGATTAGAGCGACTC
1358744 ATAC
66 ATAC
1358748 GGAAGCATCTAATCATATCTATTCCAGGTGACTAGAAC-AGGAGCCCCAAAGGATTAGAGCGACT
1 GGAAGCATCTAATCATATCTATTCCAGGTGACTAGAACGA-GAGCCCCAAAGGATTAGAGCGACT
1358812 CATAC
65 CATAC
* * *
1358817 GAAAACATCTAATCATATATA-TCTCAGGTGACT
1 GGAAGCATCTAATCATATCTATTC-CAGGTGACT
1358850 CGCACGTGAA
Statistics
Matches: 89, Mismatches: 10, Indels: 5
0.86 0.10 0.05
Matches are distributed among these distances:
67 1 0.01
68 47 0.53
69 41 0.46
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (69 bp):
GGAAGCATCTAATCATATCTATTCCAGGTGACTAGAACGAGAGCCCCAAAGGATTAGAGCGACTC
ATAC
Found at i:1358845 original size:69 final size:68
Alignment explanation
Indices: 1358692--1358849 Score: 194
Period size: 69 Copynumber: 2.3 Consensus size: 68
1358682 AAGCACCTAC
* ** * * * * *
1358692 TCATATCTATTCTGGGTGACTAGCACGAGAGCCCCAAATGATAGAGTGACTCATACGGAAGCATC
1 TCATATATATTCCAGGTGACTAGAACGAGAGCCCCAAAGGATAGAGCGACTCATACGAAAACATC
1358757 TAA
66 TAA
*
1358760 TCATATCTATTCCAGGTGACTAGAAC-AGGAGCCCCAAAGGATTAGAGCGACTCATACGAAAACA
1 TCATATATATTCCAGGTGACTAGAACGA-GAGCCCCAAAGGA-TAGAGCGACTCATACGAAAACA
1358824 TCTAA
64 TCTAA
1358829 TCATATATA-TCTCAGGTGACT
1 TCATATATATTC-CAGGTGACT
1358850 CGCACGTGAA
Statistics
Matches: 79, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
67 1 0.01
68 37 0.47
69 41 0.52
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (68 bp):
TCATATATATTCCAGGTGACTAGAACGAGAGCCCCAAAGGATAGAGCGACTCATACGAAAACATC
TAA
Found at i:1358869 original size:69 final size:69
Alignment explanation
Indices: 1358692--1358881 Score: 181
Period size: 69 Copynumber: 2.8 Consensus size: 69
1358682 AAGCACCTAC
* ** * * * * *
1358692 TCATATCTATTCTGGGTGACTAGCAC-GAGAGCCCCAAATGA-TAGAGTGACTCATACGGAAGCA
1 TCATATATATTCCAGGTGACTAGAACAG-GAACCCCAAAGGATTAGAGTGACTCATACGAAAACA
1358755 TCTAA
65 TCTAA
* * *
1358760 TCATATCTATTCCAGGTGACTAGAACAGGAGCCCCAAAGGATTAGAGCGACTCATACGAAAACAT
1 TCATATATATTCCAGGTGACTAGAACAGGAACCCCAAAGGATTAGAGTGACTCATACGAAAACAT
1358825 CTAA
66 CTAA
* * ***
1358829 TCATATATA-TCTCAGGTGACTCGCAC-GTGAACCTTGAAGGATTAGAGTGACTC
1 TCATATATATTC-CAGGTGACTAGAACAG-GAACCCCAAAGGATTAGAGTGACTC
1358882 GCACAAGAGC
Statistics
Matches: 103, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
68 38 0.37
69 65 0.63
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (69 bp):
TCATATATATTCCAGGTGACTAGAACAGGAACCCCAAAGGATTAGAGTGACTCATACGAAAACAT
CTAA
Found at i:1360470 original size:15 final size:15
Alignment explanation
Indices: 1360450--1360501 Score: 77
Period size: 15 Copynumber: 3.5 Consensus size: 15
1360440 GATATTTAGT
1360450 GGGCGGGCGGATATG
1 GGGCGGGCGGATATG
* **
1360465 GGGCGGACGGATGCG
1 GGGCGGGCGGATATG
1360480 GGGCGGGCGGATATG
1 GGGCGGGCGGATATG
1360495 GGGCGGG
1 GGGCGGG
1360502 TAAGGTCTCA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.12, C:0.15, G:0.63, T:0.10
Consensus pattern (15 bp):
GGGCGGGCGGATATG
Found at i:1363923 original size:23 final size:25
Alignment explanation
Indices: 1363896--1363955 Score: 63
Period size: 27 Copynumber: 2.4 Consensus size: 25
1363886 TTGTACTAAT
*
1363896 ATATACATG-TCAACATAAT-TAAA
1 ATATACATGCTCAAAATAATATAAA
1363919 ATATATCAACTGCTCAAAATAATATAAA
1 ATATA-C-A-TGCTCAAAATAATATAAA
1363947 AT-TACATGC
1 ATATACATGC
1363956 CACCAATCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
23 5 0.16
24 4 0.13
25 2 0.06
26 3 0.10
27 11 0.35
28 6 0.19
ACGTcount: A:0.50, C:0.15, G:0.05, T:0.30
Consensus pattern (25 bp):
ATATACATGCTCAAAATAATATAAA
Found at i:1366668 original size:25 final size:25
Alignment explanation
Indices: 1366610--1366732 Score: 111
Period size: 22 Copynumber: 5.3 Consensus size: 25
1366600 AATAATTACC
*
1366610 CCACTACCTAT-TAAAATAAT-AAA
1 CCACTACCTATAAAAAATAATCAAA
*
1366633 CTACTACCTATAAAAAATAATCAAA
1 CCACTACCTATAAAAAATAATCAAA
*
1366658 CCACTATCTATAAAAAATAATC-AA
1 CCACTACCTATAAAAAATAATCAAA
* * *
1366682 -CACTACATGT-TAAAATAAT-AAA
1 CCACTACCTATAAAAAATAATCAAA
* *
1366704 CC-CTACATAT-TAAAATAATC-AA
1 CCACTACCTATAAAAAATAATCAAA
1366726 CCACTAC
1 CCACTAC
1366733 TTATCAAATC
Statistics
Matches: 85, Mismatches: 9, Indels: 12
0.80 0.08 0.11
Matches are distributed among these distances:
22 30 0.35
23 22 0.26
24 10 0.12
25 23 0.27
ACGTcount: A:0.52, C:0.22, G:0.01, T:0.25
Consensus pattern (25 bp):
CCACTACCTATAAAAAATAATCAAA
Found at i:1366784 original size:17 final size:17
Alignment explanation
Indices: 1366762--1366854 Score: 67
Period size: 17 Copynumber: 5.8 Consensus size: 17
1366752 ATCAAAAAAA
1366762 AAATAT-ATATATATAAT
1 AAATATAATATA-ATAAT
1366779 AAATATAATATAATAAT
1 AAATATAATATAATAAT
1366796 AAATA-AA-A-AAT-AT
1 AAATATAATATAATAAT
* *
1366809 ATATGTAATAATAATAAT
1 AAATATAAT-ATAATAAT
*
1366827 AAACGA-AATATAA-AAT
1 AAA-TATAATATAATAAT
*
1366843 AAA-ATAAAATAA
1 AAATATAATATAA
1366855 AATTAAAATA
Statistics
Matches: 62, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
13 5 0.08
14 6 0.10
15 7 0.11
16 9 0.15
17 23 0.37
18 12 0.19
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.30
Consensus pattern (17 bp):
AAATATAATATAATAAT
Found at i:1366843 original size:25 final size:23
Alignment explanation
Indices: 1366761--1366864 Score: 72
Period size: 24 Copynumber: 4.3 Consensus size: 23
1366751 CATCAAAAAA
*
1366761 AAAAT-ATATATATATAATAAATAT
1 AAAATAATA-ATA-ATAAAAAATAT
*
1366785 AATATAATAATAAATAAAAAATAT
1 AAAATAATAAT-AATAAAAAATAT
1366809 ATATGTAATAATAATAATAAACGAAATAT
1 A-A---AATAATAATAATAAA--AAATAT
1366838 AAAATAA-AATAA-AATAAAAT-T
1 AAAATAATAATAATAA-AAAATAT
1366859 AAAATA
1 AAAATA
1366865 TGAACTGAAG
Statistics
Matches: 68, Mismatches: 3, Indels: 21
0.74 0.03 0.23
Matches are distributed among these distances:
21 7 0.10
22 4 0.06
23 2 0.03
24 23 0.34
25 10 0.15
27 6 0.09
28 9 0.13
29 7 0.10
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.30
Consensus pattern (23 bp):
AAAATAATAATAATAAAAAATAT
Found at i:1366863 original size:11 final size:11
Alignment explanation
Indices: 1366832--1366864 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
1366822 ATAATAAACG
1366832 AAATATAAAATA
1 AAAT-TAAAATA
1366844 AAA-TAAAATA
1 AAATTAAAATA
1366854 AAATTAAAATA
1 AAATTAAAATA
1366865 TGAACTGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.50
11 7 0.35
12 3 0.15
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AAATTAAAATA
Found at i:1368644 original size:106 final size:105
Alignment explanation
Indices: 1368433--1368644 Score: 318
Period size: 106 Copynumber: 2.0 Consensus size: 105
1368423 TTGCGTTGTT
*
1368433 TCGAGGCCAATATCCTTCGCCGTGAAGTTGAAATTGACTCTGAAACTGGACAGTGTTTGTTGAGA
1 TCGAGGCCAATATCCTTCGCCGTGAAGTTGAAATTGACTCTGAAACTGGACAGTGTTTGTTGACA
* *
1368498 ACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTC
66 ACCAGCGGCCCCTTCGTTGTGAAGTCGAACTTGTGCTGTC
* * * * *
1368538 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGACATTGGGA-AGTTGTTTGTTGA
1 TCGAGGCCAATATCCTTCGCCGTGAAGTTGAAATTGACTCTGAAACT-GGACAG-TGTTTGTTGA
*
1368602 CAGCCAGCGGCCCCTTCGTTGTGAAGTCGAACTTGTGCTGTC
64 CAACCAGCGGCCCCTTCGTTGTGAAGTCGAACTTGTGCTGTC
1368644 T
1 T
1368645 TAAACTGGGA
Statistics
Matches: 96, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
105 44 0.46
106 52 0.54
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.32
Consensus pattern (105 bp):
TCGAGGCCAATATCCTTCGCCGTGAAGTTGAAATTGACTCTGAAACTGGACAGTGTTTGTTGACA
ACCAGCGGCCCCTTCGTTGTGAAGTCGAACTTGTGCTGTC
Found at i:1368673 original size:64 final size:64
Alignment explanation
Indices: 1368594--1368773 Score: 333
Period size: 64 Copynumber: 2.8 Consensus size: 64
1368584 TGGGAAGTTG
* *
1368594 TTTGTTGACAGCCAGCGGCCCCTTCGTTGTGAAGTCGAACTTGTGCTGTCTTAAACTGGGAAAT
1 TTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTTAAACTGGGAAAT
1368658 TTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTTAAACTGGGAAAT
1 TTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTTAAACTGGGAAAT
*
1368722 TTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
1 TTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTT
1368774 GAGTGGAACG
Statistics
Matches: 113, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 113 1.00
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.34
Consensus pattern (64 bp):
TTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTTAAACTGGGAAAT
Found at i:1369870 original size:1 final size:1
Alignment explanation
Indices: 1369866--1369906 Score: 64
Period size: 1 Copynumber: 41.0 Consensus size: 1
1369856 TTTTCTTTCA
* *
1369866 TTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1369907 CTTTGTCTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.00, C:0.00, G:0.05, T:0.95
Consensus pattern (1 bp):
T
Found at i:1369882 original size:13 final size:13
Alignment explanation
Indices: 1369866--1369917 Score: 72
Period size: 12 Copynumber: 4.1 Consensus size: 13
1369856 TTTTCTTTCA
1369866 TTTTTTTTG-TTT
1 TTTTTTTTGTTTT
1369878 TTTTTTTT-TTTT
1 TTTTTTTTGTTTT
1369890 TTTTTTTTGTTTT
1 TTTTTTTTGTTTT
*
1369903 TTTTCTTTGTCTTT
1 TTTTTTTTGT-TTT
1369917 T
1 T
1369918 CGACTTAGGA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
12 19 0.53
13 13 0.36
14 4 0.11
ACGTcount: A:0.00, C:0.04, G:0.06, T:0.90
Consensus pattern (13 bp):
TTTTTTTTGTTTT
Found at i:1369882 original size:24 final size:23
Alignment explanation
Indices: 1369855--1369910 Score: 76
Period size: 24 Copynumber: 2.4 Consensus size: 23
1369845 CGTCCTTTGC
1369855 TTTTTCTTTCATTTTTTTTGTTTT
1 TTTTTCTTTCATTTTTTTTG-TTT
* **
1369879 TTTTTTTTTTTTTTTTTTTGTTT
1 TTTTTCTTTCATTTTTTTTGTTT
1369902 TTTTTCTTT
1 TTTTTCTTT
1369911 GTCTTTTCGA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 11 0.39
24 17 0.61
ACGTcount: A:0.02, C:0.05, G:0.04, T:0.89
Consensus pattern (23 bp):
TTTTTCTTTCATTTTTTTTGTTT
Found at i:1380981 original size:23 final size:22
Alignment explanation
Indices: 1380954--1381074 Score: 116
Period size: 23 Copynumber: 5.3 Consensus size: 22
1380944 ATAATTACCC
1380954 CACTACCTATTAAAATAATAAA
1 CACTACCTATTAAAATAATAAA
*
1380976 CTACTACCTATAAAAATAATCAAA
1 C-ACTACCTATTAAAATAAT-AAA
* * *
1381000 CCACTATCTATAAAAAATAATCAA
1 -CACTACCTAT-TAAAATAATAAA
* *
1381024 CACTACATGTTAAAATAATAAA
1 CACTACCTATTAAAATAATAAA
* * *
1381046 CCCTACATATTAAAATAATCAAC
1 CACTACCTATTAAAATAAT-AAA
1381069 CACTAC
1 CACTAC
1381075 TTATCAAATC
Statistics
Matches: 82, Mismatches: 12, Indels: 9
0.80 0.12 0.09
Matches are distributed among these distances:
22 28 0.34
23 31 0.38
24 13 0.16
25 10 0.12
ACGTcount: A:0.52, C:0.21, G:0.01, T:0.26
Consensus pattern (22 bp):
CACTACCTATTAAAATAATAAA
Found at i:1380995 original size:47 final size:46
Alignment explanation
Indices: 1380942--1381074 Score: 135
Period size: 47 Copynumber: 2.9 Consensus size: 46
1380932 CAAAACAACT
** * *
1380942 AAATAATTACCCCACTACCTATTAAAATAATAAACTACTACCTATAA
1 AAATAATTAAACCACTACCTATTAAAATAATCAAC-ACTACATATAA
* * * * *
1380989 AAATAATCAAACCACTATCTATAAAAAATAATCAACACTACATGTTA
1 AAATAATTAAACCACTACCTAT-TAAAATAATCAACACTACATATAA
*
1381036 AAATAA-TAAACC-CTACATATTAAAATAATCAACCACTAC
1 AAATAATTAAACCACTACCTATTAAAATAATCAA-CACTAC
1381075 TTATCAAATC
Statistics
Matches: 71, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
44 11 0.15
45 12 0.17
46 5 0.07
47 32 0.45
48 11 0.15
ACGTcount: A:0.52, C:0.22, G:0.01, T:0.26
Consensus pattern (46 bp):
AAATAATTAAACCACTACCTATTAAAATAATCAACACTACATATAA
Found at i:1381021 original size:25 final size:24
Alignment explanation
Indices: 1380953--1381074 Score: 121
Period size: 22 Copynumber: 5.3 Consensus size: 24
1380943 AATAATTACC
*
1380953 CCACTACCTATTAAAATAAT-AAA
1 CCACTACCTATAAAAATAATCAAA
*
1380976 CTACTACCTATAAAAATAATCAAA
1 CCACTACCTATAAAAATAATCAAA
*
1381000 CCACTATCTATAAAAAATAATC-AA
1 CCACTACCTAT-AAAAATAATCAAA
* * *
1381024 -CACTACATGTTAAAATAAT-AAA
1 CCACTACCTATAAAAATAATCAAA
* *
1381046 CC-CTACATATTAAAATAATC-AA
1 CCACTACCTATAAAAATAATCAAA
1381068 CCACTAC
1 CCACTAC
1381075 TTATCAAATC
Statistics
Matches: 84, Mismatches: 9, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
22 30 0.36
23 30 0.36
24 14 0.17
25 10 0.12
ACGTcount: A:0.52, C:0.22, G:0.01, T:0.25
Consensus pattern (24 bp):
CCACTACCTATAAAAATAATCAAA
Found at i:1381106 original size:2 final size:2
Alignment explanation
Indices: 1381099--1381132 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1381089 CTACCATCAA
*
1381099 AT AT AT AT AT AT AT AT AT AT AA AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1381133 ATAATAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1381136 original size:8 final size:9
Alignment explanation
Indices: 1381101--1381138 Score: 53
Period size: 8 Copynumber: 4.3 Consensus size: 9
1381091 ACCATCAAAT
1381101 ATATATATA
1 ATATATATA
1381110 TATATATATA
1 -ATATATATA
1381120 A-ATATATA
1 ATATATATA
1381128 ATATA-ATA
1 ATATATATA
1381136 ATA
1 ATA
1381139 AATAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 14 0.52
9 4 0.15
10 9 0.33
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
ATATATATA
Found at i:1381198 original size:16 final size:17
Alignment explanation
Indices: 1381174--1381206 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1381164 ATAATAAACG
1381174 AAATATAAAATAAAATA
1 AAATATAAAATAAAATA
*
1381191 AAAT-TAAATTAAAATA
1 AAATATAAAATAAAATA
1381207 TGAACTGAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AAATATAAAATAAAATA
Found at i:1382505 original size:2 final size:2
Alignment explanation
Indices: 1382500--1382530 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1382490 TTCCTTGTGT
1382500 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 T
1382531 TTAAAATATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1387107 original size:2 final size:2
Alignment explanation
Indices: 1387102--1387132 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1387092 CCTTATATTC
1387102 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 T
1387133 TTGTTTGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1390312 original size:45 final size:47
Alignment explanation
Indices: 1390262--1390365 Score: 160
Period size: 46 Copynumber: 2.3 Consensus size: 47
1390252 AATCCAAGAT
* *
1390262 TTTTGATTATTGGT-TTGTCAAAAGT-AAAATCAAAGGATTAGTTCC
1 TTTTGATTATTGGTGTTGCCAAAAGTAAAAACCAAAGGATTAGTTCC
1390307 TTTTGATTATT-GTGTTGCCAAAAGTAAAAACCAAAGGATTAGTTCC
1 TTTTGATTATTGGTGTTGCCAAAAGTAAAAACCAAAGGATTAGTTCC
*
1390353 TTTCGATTATTGG
1 TTTTGATTATTGG
1390366 GTTACGAAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
44 2 0.04
45 21 0.40
46 29 0.55
47 1 0.02
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (47 bp):
TTTTGATTATTGGTGTTGCCAAAAGTAAAAACCAAAGGATTAGTTCC
Found at i:1390401 original size:39 final size:39
Alignment explanation
Indices: 1390333--1390407 Score: 105
Period size: 39 Copynumber: 1.9 Consensus size: 39
1390323 GCCAAAAGTA
*
1390333 AAAACCAAAGGATTAGTTCCTTTCGATTATTGGGTTACG
1 AAAACCAAAGGATTAGTTCATTTCGATTATTGGGTTACG
* * **
1390372 AAAATCAAATGATTAGTTCATTTTTATTATTGGGTT
1 AAAACCAAAGGATTAGTTCATTTCGATTATTGGGTT
1390408 GCTAAACCTG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 31 1.00
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (39 bp):
AAAACCAAAGGATTAGTTCATTTCGATTATTGGGTTACG
Found at i:1390719 original size:58 final size:58
Alignment explanation
Indices: 1390581--1390781 Score: 280
Period size: 58 Copynumber: 3.5 Consensus size: 58
1390571 ATTCTTGCGT
* *
1390581 TGATTCTAACTTTGTAAGGGAAATAAATTGTTGAATTT-TTTGCTTTAGAATCTTA-AA
1 TGATTCTAACTTTGTAAGGGAAATAAATTGTTGAATTTATTTCCTTGAGAATC-TAGAA
* * *
1390638 TGATTCTAACTTTGTAAGGGAAATAAACTGTTGAATTTATTTTCTTGATAATCTAGAA
1 TGATTCTAACTTTGTAAGGGAAATAAATTGTTGAATTTATTTCCTTGAGAATCTAGAA
* * *
1390696 TGATTCTAACTTTGTTAGGGAAATAAATTGTTGAATTTATTTCCTTGAGAATTTTGAA
1 TGATTCTAACTTTGTAAGGGAAATAAATTGTTGAATTTATTTCCTTGAGAATCTAGAA
* **
1390754 TGATTTTAACTTTGTAAGAAAAATAAAT
1 TGATTCTAACTTTGTAAGGGAAATAAAT
1390782 CCTTTAGAAT
Statistics
Matches: 128, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
57 39 0.30
58 89 0.70
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (58 bp):
TGATTCTAACTTTGTAAGGGAAATAAATTGTTGAATTTATTTCCTTGAGAATCTAGAA
Found at i:1391743 original size:26 final size:25
Alignment explanation
Indices: 1391714--1391780 Score: 63
Period size: 24 Copynumber: 2.8 Consensus size: 25
1391704 TAAAATCATC
1391714 TCATATTCTTTTCATTCATACATATT
1 TCATATTCTTTTCATTCATACAT-TT
*
1391740 TCATA-AC-TTTCA-T-AT-CATTT
1 TCATATTCTTTTCATTCATACATTT
* *
1391760 CCATATTCTTTTCTTTCATAC
1 TCATATTCTTTTCATTCATAC
1391781 TCATCATAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 11
0.68 0.09 0.23
Matches are distributed among these distances:
20 6 0.19
21 4 0.12
22 6 0.19
23 2 0.06
24 7 0.22
25 2 0.06
26 5 0.16
ACGTcount: A:0.25, C:0.22, G:0.00, T:0.52
Consensus pattern (25 bp):
TCATATTCTTTTCATTCATACATTT
Found at i:1391795 original size:18 final size:18
Alignment explanation
Indices: 1391772--1391817 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
1391762 ATATTCTTTT
1391772 CTTTCATACTCATCATAA
1 CTTTCATACTCATCATAA
*
1391790 CTTTCATACTCGTCATAA
1 CTTTCATACTCATCATAA
1391808 CTTTCATACT
1 CTTTCATACT
1391818 TACCTTTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.28, C:0.28, G:0.02, T:0.41
Consensus pattern (18 bp):
CTTTCATACTCATCATAA
Found at i:1393850 original size:3 final size:3
Alignment explanation
Indices: 1393842--1393875 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1393832 GCAACGGCTG
1393842 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1393876 CTGAAATTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1394704 original size:39 final size:39
Alignment explanation
Indices: 1394650--1394800 Score: 188
Period size: 38 Copynumber: 4.0 Consensus size: 39
1394640 AATTCTGATA
*
1394650 TGTAGAATGAAATAAATCGTTGGATTTATTTTCTTATTT
1 TGTAGAATGAAATAAATCGTTGGATTTATTTTCCTATTT
* *
1394689 TGTAGAATGAAATAAATTGTTGGACTTATTTT-CTATTT
1 TGTAGAATGAAATAAATCGTTGGATTTATTTTCCTATTT
* * * *
1394727 TGTAAAAAGAAATAACTTGTTGGATTTATTTTCCTA-TT
1 TGTAGAATGAAATAAATCGTTGGATTTATTTTCCTATTT
*
1394765 T-TAG---GAAATAAATCGTTGAATTTATTTTCCTATTT
1 TGTAGAATGAAATAAATCGTTGGATTTATTTTCCTATTT
1394800 T
1 T
1394801 ATAAAAATCA
Statistics
Matches: 99, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
34 25 0.25
35 3 0.03
37 2 0.02
38 36 0.36
39 33 0.33
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.48
Consensus pattern (39 bp):
TGTAGAATGAAATAAATCGTTGGATTTATTTTCCTATTT
Found at i:1394815 original size:31 final size:33
Alignment explanation
Indices: 1394750--1394823 Score: 107
Period size: 31 Copynumber: 2.3 Consensus size: 33
1394740 AACTTGTTGG
*
1394750 ATTTATTTTCCTATTTTAGGAAATAAATCGTTGA
1 ATTTATTTTCCTATTTTA-GAAATAAATCATTGA
*
1394784 ATTTATTTTCCTATTTTA-TAA-AAATCATTGA
1 ATTTATTTTCCTATTTTAGAAATAAATCATTGA
1394815 ATTTATTTT
1 ATTTATTTT
1394824 TTTAGAATCT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
31 18 0.47
32 2 0.05
34 18 0.47
ACGTcount: A:0.32, C:0.08, G:0.07, T:0.53
Consensus pattern (33 bp):
ATTTATTTTCCTATTTTAGAAATAAATCATTGA
Found at i:1397016 original size:54 final size:56
Alignment explanation
Indices: 1396929--1397079 Score: 146
Period size: 54 Copynumber: 2.7 Consensus size: 56
1396919 AAGCTCGATA
* *
1396929 TCTATCTTGAGCTTCCCTTTCGGACACTCGCACCAATGTCTTGGCAAGCCCAATAC
1 TCTATCTTGAGCTTCCCTTTCAGACACTCGCACCAATGTCTTGGCAAACCCAATAC
* * * *
1396985 TCTATCTTGA-C-T-CCTTGTCAGACACTTGCACCGATGTCTTTGCAAACCCAATCC
1 TCTATCTTGAGCTTCCCTT-TCAGACACTCGCACCAATGTCTTGGCAAACCCAATAC
* * * * * * * *
1397039 TCTGTCTTAAACTTTCCTATCGGACACTTGCACCAGTGTCT
1 TCTATCTTGAGCTTCCCTTTCAGACACTCGCACCAATGTCT
1397080 CGGACCCAAG
Statistics
Matches: 79, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
53 4 0.05
54 40 0.51
55 2 0.03
56 30 0.38
57 3 0.04
ACGTcount: A:0.21, C:0.32, G:0.15, T:0.32
Consensus pattern (56 bp):
TCTATCTTGAGCTTCCCTTTCAGACACTCGCACCAATGTCTTGGCAAACCCAATAC
Found at i:1412376 original size:130 final size:129
Alignment explanation
Indices: 1412240--1412487 Score: 424
Period size: 130 Copynumber: 1.9 Consensus size: 129
1412230 TATTTATATA
*
1412240 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* *
1412305 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTTTACCACCTAATTATTATATATGCT
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATG-TCACCACCTAATTATTATATATGCT
1412370 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* * * *
1412435 TTAACACATGATCATGATATGTGTTATTGGTGACACATGTCACCTCCTAATTA
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTA
1412488 GAAGAAAATT
Statistics
Matches: 111, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
129 12 0.11
130 99 0.89
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.37
Consensus pattern (129 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTATATATGCT
Found at i:1412967 original size:16 final size:18
Alignment explanation
Indices: 1412946--1412979 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1412936 ATTTCTTATT
1412946 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
1412962 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
1412980 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:1413120 original size:21 final size:21
Alignment explanation
Indices: 1413096--1413138 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1413086 TATTACCTTA
1413096 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
1413117 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
1413138 A
1 A
1413139 GGGTTTAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.47
Consensus pattern (21 bp):
AATTGAAGTATTTTAGAATTT
Found at i:1413156 original size:35 final size:35
Alignment explanation
Indices: 1413107--1413192 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
1413097 ATTGAAGTAT
** * *
1413107 TTTAGAATTTAATTGAAGTATTTTAGAATTTAGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
* * *
1413142 TTTAGAATAAAATTGAATTACTTTGGAAATTGGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
*
1413177 TTTAGAATGAAATTGA
1 TTTAGAATAAAATTGA
1413193 TGACTGTTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.37, C:0.01, G:0.21, T:0.41
Consensus pattern (35 bp):
TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
Found at i:1414170 original size:128 final size:129
Alignment explanation
Indices: 1413810--1414436 Score: 518
Period size: 128 Copynumber: 4.9 Consensus size: 129
1413800 GATCTGATCA
* ** ** ** *
1413810 GGTGATGACACGGTTCCTATGTGATGACCACGGTTGGTTATCTGGGTTGACACAGCTCATACATA
1 GGTGATAACACGGTTCCTACATGATGAGGACGACTGGTTATCTGGGTTGACACAGCTCCTACATA
* * * * * * * * ** * *
1413875 ATGAAGAGATCTGGTCGGGTGATGACACGG-TTCCTACGTGGTGAAGACGACTGGTAATCCAAT
66 ATGAGGAGATCTAGTCGGGTGATGACACGGCTTCATACGCGATGAAGATGGCAGGCCATCTAAG
* * * * *
1413938 GGTGATAACACGTTTCTTACGTGATGAGGACGACTGGTTATCTGGGGTTGACACAGTTCATACAT
1 GGTGATAACACGGTTCCTACATGATGAGGACGACTGGTTATCT-GGGTTGACACAGCTCCTACAT
* * * * *
1414003 GATGAGGAAATC-AGGTCGGGTGATGACAC-GTTTCCTACGCGATGAGGATGGCAGGCCATCTAA
65 AATGAGGAGATCTA-GTCGGGTGATGACACGGCTTCATACGCGATGAAGATGGCAGGCCATCTAA
1414066 G
129 G
* ** *
1414067 GGTGATATCACGGTTCCTAGGTGATAAGGACGACTGGTTATCTGGGTTGACACAGCTCCTACATA
1 GGTGATAACACGGTTCCTACATGATGAGGACGACTGGTTATCTGGGTTGACACAGCTCCTACATA
* * ** *
1414132 ATGAGGAGATCTAGTTGGGTGATGACATGGCTT-ATACGCGATGAAGA-GTTATGGCCATCTAAA
66 ATGAGGAGATCTAGTCGGGTGATGACACGGCTTCATACGCGATGAAGATGGCA-GGCCATCTAAG
* * * ** * *
1414195 GGTGATAATATGGTTCCTACATGATGAGGATGGTTGGTTATC-GAGGTTGACACAACTCCTATAT
1 GGTGATAACACGGTTCCTACATGATGAGGACGACTGGTTATCTG-GGTTGACACAGCTCCTACAT
* * * ** * * **
1414259 AATGAAGAGATCTGGTCAGGTGATGACACGG-TTCCTATGTGTGATGAGGATGGTC-GGTTATCT
65 AATGAGGAGATCTAGTCGGGTGATGACACGGCTT-C-ATACGCGATGAAGATGG-CAGGCCATCT
1414322 AAG
127 AAG
* * *** * * *
1414325 GGTGATAACATGGTTCCTACATGATGAGAACGACTGGTTAAAAGGGTTGATATAACTCCTACATA
1 GGTGATAACACGGTTCCTACATGATGAGGACGACTGGTTATCTGGGTTGACACAGCTCCTACATA
* * *
1414390 ATGAGGAGATCTATTC-GGTGGATGACACAGC-TCATACGTGATGAAGA
66 ATGAGGAGATCTAGTCGGGT-GATGACACGGCTTCATACGCGATGAAGA
1414437 ATTATGGCCA
Statistics
Matches: 402, Mismatches: 82, Indels: 30
0.78 0.16 0.06
Matches are distributed among these distances:
127 5 0.01
128 188 0.47
129 113 0.28
130 94 0.23
131 2 0.00
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.27
Consensus pattern (129 bp):
GGTGATAACACGGTTCCTACATGATGAGGACGACTGGTTATCTGGGTTGACACAGCTCCTACATA
ATGAGGAGATCTAGTCGGGTGATGACACGGCTTCATACGCGATGAAGATGGCAGGCCATCTAAG
Found at i:1414941 original size:24 final size:22
Alignment explanation
Indices: 1414914--1414971 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 22
1414904 TTTCAAGATA
*
1414914 TGAAAATATTAATTAGAAGAGTTT
1 TGAAAATATTAATCA-AA-AGTTT
*
1414938 TGAAAAATGTTTAATCAAAAGTTT
1 TG-AAAAT-ATTAATCAAAAGTTT
1414962 TGAAAATATT
1 TGAAAATATT
1414972 GCCCCTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
22 2 0.07
23 5 0.17
24 9 0.31
25 7 0.24
26 6 0.21
ACGTcount: A:0.47, C:0.02, G:0.14, T:0.38
Consensus pattern (22 bp):
TGAAAATATTAATCAAAAGTTT
Found at i:1416961 original size:13 final size:13
Alignment explanation
Indices: 1416916--1416962 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
1416906 CTTAAAAATG
* *
1416916 AAATGCATATGTA
1 AAATGCAGATGCA
1416929 AAATGCAAAGATGC-
1 AAATGC--AGATGCA
1416943 AAATGCAGATGCA
1 AAATGCAGATGCA
1416956 AAATGCA
1 AAATGCA
1416963 AAGATGTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 6 0.21
13 13 0.45
14 6 0.21
15 4 0.14
ACGTcount: A:0.49, C:0.13, G:0.19, T:0.19
Consensus pattern (13 bp):
AAATGCAGATGCA
Found at i:1416985 original size:27 final size:27
Alignment explanation
Indices: 1416916--1416985 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 27
1416906 CTTAAAAATG
*
1416916 AAATGCATATGTAAAATGCAAAGATGC
1 AAATGCAGATGTAAAATGCAAAGATGC
* *
1416943 AAATGCAGATGCAAAATGCAAAGATGT
1 AAATGCAGATGTAAAATGCAAAGATGC
* *
1416970 TAATGCAGATTTAAAA
1 AAATGCAGATGTAAAA
1416986 AATGTTTATC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.49, C:0.10, G:0.19, T:0.23
Consensus pattern (27 bp):
AAATGCAGATGTAAAATGCAAAGATGC
Found at i:1417786 original size:32 final size:32
Alignment explanation
Indices: 1417713--1417787 Score: 98
Period size: 32 Copynumber: 2.3 Consensus size: 32
1417703 TGATACAATC
*
1417713 AAAAGAAA-TAAGTTAGTGTACATAAACAAAAG
1 AAAAGAAATTAA-TTAGTGTACACAAACAAAAG
* *
1417745 GAAAGAAATTAATTAGTGTACACAAACAAATG
1 AAAAGAAATTAATTAGTGTACACAAACAAAAG
*
1417777 AAAATAAATTA
1 AAAAGAAATTA
1417788 GTTAATACAG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 34 0.92
33 3 0.08
ACGTcount: A:0.59, C:0.07, G:0.13, T:0.21
Consensus pattern (32 bp):
AAAAGAAATTAATTAGTGTACACAAACAAAAG
Found at i:1420755 original size:20 final size:22
Alignment explanation
Indices: 1420710--1420761 Score: 76
Period size: 20 Copynumber: 2.5 Consensus size: 22
1420700 TAATTCAATC
1420710 GGTATCGATACCGAAGGGGTAA
1 GGTATCGATACCGAAGGGGTAA
1420732 --TATCGATACCGAA-GGG-AA
1 GGTATCGATACCGAAGGGGTAA
1420750 GGTATCGATACC
1 GGTATCGATACC
1420762 AATTCAAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 2 0.07
19 3 0.11
20 23 0.82
ACGTcount: A:0.33, C:0.17, G:0.31, T:0.19
Consensus pattern (22 bp):
GGTATCGATACCGAAGGGGTAA
Found at i:1421318 original size:46 final size:46
Alignment explanation
Indices: 1421262--1421517 Score: 352
Period size: 46 Copynumber: 5.4 Consensus size: 46
1421252 GAATAAAAGA
* *
1421262 AAAATACATGAAAGGATGCATTTTGGCATGAAAGGATGCCATAAAT
1 AAAATGCATGAAAGGATGCATTATGGCATGAAAGGATGCCATAAAT
* * *
1421308 AAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGTCATAAAT
1 AAAATGCATGAAAGGATGCATTATGGCATGAAAGGATGCCATAAAT
*
1421354 AAAATGCATGAAAGGATGCCATAAATAAAAT-GCATGAAAGGATACCATAAAT
1 AAAATGCATGAAAGGATG-CAT---T---ATGGCATGAAAGGATGCCATAAAT
* *
1421406 AAAATTCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAAT
1 AAAATGCATGAAAGGATGCATTATGGCATGAAAGGATGCCATAAAT
*
1421452 AAAATGCATGAAATGATGCATTATTGGCATGAAAGGATGCCATAAAT
1 AAAATGCATGAAAGGATGCATTA-TGGCATGAAAGGATGCCATAAAT
1421499 AAAATGCATGAAAGGATGC
1 AAAATGCATGAAAGGATGC
1421518 CATAAATAAA
Statistics
Matches: 185, Mismatches: 16, Indels: 17
0.85 0.07 0.08
Matches are distributed among these distances:
45 1 0.01
46 99 0.54
47 43 0.23
48 1 0.01
50 1 0.01
51 3 0.02
52 36 0.19
53 1 0.01
ACGTcount: A:0.46, C:0.11, G:0.21, T:0.22
Consensus pattern (46 bp):
AAAATGCATGAAAGGATGCATTATGGCATGAAAGGATGCCATAAAT
Found at i:1421325 original size:26 final size:26
Alignment explanation
Indices: 1421287--1421762 Score: 400
Period size: 26 Copynumber: 20.0 Consensus size: 26
1421277 ATGCATTTTG
1421287 GCATGAAAGGATGCCATAAATAAAAT
1 GCATGAAAGGATGCCATAAATAAAAT
* *
1421313 GCATGAAATGATG-CAT---T--AAG
1 GCATGAAAGGATGCCATAAATAAAAT
*
1421333 GCATGAAAGGATGTCATAAATAAAAT
1 GCATGAAAGGATGCCATAAATAAAAT
1421359 GCATGAAAGGATGCCATAAATAAAAT
1 GCATGAAAGGATGCCATAAATAAAAT
*
1421385 GCATGAAAGGATACCATAAATAAAAT
1 GCATGAAAGGATGCCATAAATAAAAT
* *
1421411 TCATGAAAGGATG-CAT---T--AAG
1 GCATGAAAGGATGCCATAAATAAAAT
1421431 GCATGAAAGGATGCCATAAATAAAAT
1 GCATGAAAGGATGCCATAAATAAAAT
* *
1421457 GCATGAAATGATG-CAT---T--ATT
1 GCATGAAAGGATGCCATAAATAAAAT
1421477 GGCATGAAAGGATGCCATAAATAAAAT
1 -GCATGAAAGGATGCCATAAATAAAAT
1421504 GCATGAAAGGATGCCATAAATAAAAT
1 GCATGAAAGGATGCCATAAATAAAAT
*
1421530 GCATGAAAGGATG-CAT---T--ATT
1 GCATGAAAGGATGCCATAAATAAAAT
*
1421550 GGCATGAAAGGATGTCATAAATAAAAT
1 -GCATGAAAGGATGCCATAAATAAAAT
*
1421577 GCATGAAAGGATG-CAT---T--AAG
1 GCATGAAAGGATGCCATAAATAAAAT
*
1421597 GCATGAAAAGATGCCATAAATAAAAT
1 GCATGAAAGGATGCCATAAATAAAAT
* * *
1421623 GCATG-AA--ATG--ATGAAT-TATT
1 GCATGAAAGGATGCCATAAATAAAAT
*
1421643 GGCATGAAAAGATGCCATAAATAAAAT
1 -GCATGAAAGGATGCCATAAATAAAAT
* *
1421670 GCATGAAATGATG-CAT---T--AAG
1 GCATGAAAGGATGCCATAAATAAAAT
1421690 GCATGAAAGGATGCCATAAATAAAAT
1 GCATGAAAGGATGCCATAAATAAAAT
* *
1421716 GCATCAAAGGATG-CAT---T-AAGT
1 GCATGAAAGGATGCCATAAATAAAAT
*
1421737 -CATGAAAAGATGCCATAAATAAAAT
1 GCATGAAAGGATGCCATAAATAAAAT
1421762 G
1 G
1421763 AAATTTAACA
Statistics
Matches: 364, Mismatches: 35, Indels: 102
0.73 0.07 0.20
Matches are distributed among these distances:
20 72 0.20
21 53 0.15
22 15 0.04
23 3 0.01
24 8 0.02
25 28 0.08
26 179 0.49
27 6 0.02
ACGTcount: A:0.47, C:0.11, G:0.21, T:0.22
Consensus pattern (26 bp):
GCATGAAAGGATGCCATAAATAAAAT
Found at i:1421505 original size:119 final size:119
Alignment explanation
Indices: 1421359--1421630 Score: 465
Period size: 119 Copynumber: 2.3 Consensus size: 119
1421349 TAAATAAAAT
*
1421359 GCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATACCATAAATAAAATTCATGAAAGGATG
1 GCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATACCATAAATAAAATGCATGAAAGGATG
* *
1421424 CATTA-AGGCATGAAAGGATGCCATAAATAAAATGCATGAAATGATGCATTATTG
66 CATTATAGGCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATGCATTA-AG
*
1421478 GCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATG
1 GCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATACCATAAATAAAATGCATGAAAGGATG
* *
1421543 CATTATTGGCATGAAAGGATGTCATAAATAAAATGCATGAAAGGATGCATTAAG
66 CATTATAGGCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATGCATTAAG
*
1421597 GCATGAAAAGATGCCATAAATAAAATGCATGAAA
1 GCATGAAAGGATGCCATAAATAAAATGCATGAAA
1421631 TGATGAATTA
Statistics
Matches: 145, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
119 102 0.70
120 43 0.30
ACGTcount: A:0.47, C:0.11, G:0.21, T:0.22
Consensus pattern (119 bp):
GCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATACCATAAATAAAATGCATGAAAGGATG
CATTATAGGCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATGCATTAAG
Found at i:1421592 original size:166 final size:168
Alignment explanation
Indices: 1421333--1421727 Score: 565
Period size: 166 Copynumber: 2.4 Consensus size: 168
1421323 ATGCATTAAG
*
1421333 GCATGAAAGGATGTCATAAATAAAATGCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATA
1 GCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATGCCAT--AT-AAATGCATGAAAGGATA
* *
1421398 CCATAAATAAAATTCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAATAAAATGCATGA
63 CCATAAATAAAATGCATGAAAGGATGCATTAAGGCATGAAAAGATGCCATAAATAAAATGCATGA
* *
1421463 AATGATGCATTATTGGCATGAAAGGATGCCATAAATAAAAT
128 AATGATGAATTATTGGCATGAAAAGATGCCATAAATAAAAT
* **
1421504 GCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATG-CAT-T-ATTGGCATGAAAGGATGTC
1 GCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATGCCATATAAAT-GCATGAAAGGATACC
1421566 ATAAATAAAATGCATGAAAGGATGCATTAAGGCATGAAAAGATGCCATAAATAAAATGCATGAAA
65 ATAAATAAAATGCATGAAAGGATGCATTAAGGCATGAAAAGATGCCATAAATAAAATGCATGAAA
1421631 TGATGAATTATTGGCATGAAAAGATGCCATAAATAAAAT
130 TGATGAATTATTGGCATGAAAAGATGCCATAAATAAAAT
* * *
1421670 GCATGAAATGATG-CAT---T--AAGGCATGAAAGGATGCCATAAATAAAATGCATCAAAGGAT
1 GCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATGCCAT--AT-AAATGCATGAAAGGAT
1421728 GCATTAAGTC
Statistics
Matches: 205, Mismatches: 12, Indels: 20
0.86 0.05 0.08
Matches are distributed among these distances:
160 15 0.07
161 3 0.01
162 1 0.00
164 1 0.00
165 16 0.08
166 127 0.62
167 1 0.00
170 3 0.01
171 38 0.19
ACGTcount: A:0.47, C:0.10, G:0.21, T:0.22
Consensus pattern (168 bp):
GCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATGCCATATAAATGCATGAAAGGATACCA
TAAATAAAATGCATGAAAGGATGCATTAAGGCATGAAAAGATGCCATAAATAAAATGCATGAAAT
GATGAATTATTGGCATGAAAAGATGCCATAAATAAAAT
Found at i:1421617 original size:46 final size:46
Alignment explanation
Indices: 1421504--1421762 Score: 401
Period size: 46 Copynumber: 5.6 Consensus size: 46
1421494 TAAATAAAAT
* *
1421504 GCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATGCATTATTG
1 GCATGAAAAGATGCCATAAATAAAATGCATGAAAGGATGCATTA-AG
* *
1421551 GCATGAAAGGATGTCATAAATAAAATGCATGAAAGGATGCATTAAG
1 GCATGAAAAGATGCCATAAATAAAATGCATGAAAGGATGCATTAAG
* * *
1421597 GCATGAAAAGATGCCATAAATAAAATGCATGAAATGATGAATTATTG
1 GCATGAAAAGATGCCATAAATAAAATGCATGAAAGGATGCATTA-AG
*
1421644 GCATGAAAAGATGCCATAAATAAAATGCATGAAATGATGCATTAAG
1 GCATGAAAAGATGCCATAAATAAAATGCATGAAAGGATGCATTAAG
* *
1421690 GCATGAAAGGATGCCATAAATAAAATGCATCAAAGGATGCATTAAG
1 GCATGAAAAGATGCCATAAATAAAATGCATGAAAGGATGCATTAAG
*
1421736 TCATGAAAAGATGCCATAAATAAAATG
1 GCATGAAAAGATGCCATAAATAAAATG
1421763 AAATTTAACA
Statistics
Matches: 197, Mismatches: 14, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
46 110 0.56
47 87 0.44
ACGTcount: A:0.46, C:0.10, G:0.21, T:0.22
Consensus pattern (46 bp):
GCATGAAAAGATGCCATAAATAAAATGCATGAAAGGATGCATTAAG
Found at i:1421625 original size:93 final size:93
Alignment explanation
Indices: 1421504--1421762 Score: 430
Period size: 93 Copynumber: 2.8 Consensus size: 93
1421494 TAAATAAAAT
* *
1421504 GCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATGCATTATTGGCATGAAAGGATGTCATA
1 GCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATGCATTATTGGCATGAAAAGATGCCATA
1421569 AATAAAATGCATGAAAGGATGCATTAAG
66 AATAAAATGCATGAAAGGATGCATTAAG
* * *
1421597 GCATGAAAAGATGCCATAAATAAAATGCATGAAATGATGAATTATTGGCATGAAAAGATGCCATA
1 GCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATGCATTATTGGCATGAAAAGATGCCATA
*
1421662 AATAAAATGCATGAAATGATGCATTAAG
66 AATAAAATGCATGAAAGGATGCATTAAG
* * *
1421690 GCATGAAAGGATGCCATAAATAAAATGCATCAAAGGATGCATTA-AGTCATGAAAAGATGCCATA
1 GCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATGCATTATTGGCATGAAAAGATGCCATA
1421754 AATAAAATG
66 AATAAAATG
1421763 AAATTTAACA
Statistics
Matches: 154, Mismatches: 12, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
92 27 0.18
93 127 0.82
ACGTcount: A:0.46, C:0.10, G:0.21, T:0.22
Consensus pattern (93 bp):
GCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATGCATTATTGGCATGAAAAGATGCCATA
AATAAAATGCATGAAAGGATGCATTAAG
Found at i:1437186 original size:3 final size:3
Alignment explanation
Indices: 1437180--1437240 Score: 90
Period size: 3 Copynumber: 20.7 Consensus size: 3
1437170 TTCATTTGAA
*
1437180 TAT TAT T-T ATAT TAT TAT TAT TAT TAT TAT TAT AAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1437225 TAT TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TA
1437241 ATAAATATTT
Statistics
Matches: 53, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
2 3 0.06
3 49 0.92
4 1 0.02
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1437560 original size:18 final size:19
Alignment explanation
Indices: 1437525--1437560 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1437515 CCATTCTTTC
*
1437525 GTGAGTCACCACAAGTTTG
1 GTGACTCACCACAAGTTTG
1437544 GTGACTCACCA-AAGTTT
1 GTGACTCACCACAAGTTT
1437561 ACTCCTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (19 bp):
GTGACTCACCACAAGTTTG
Found at i:1438556 original size:12 final size:12
Alignment explanation
Indices: 1438539--1438567 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
1438529 TGTTTACTTT
1438539 TTATTATTACTA
1 TTATTATTACTA
1438551 TTATTATTACTA
1 TTATTATTACTA
1438563 TTATT
1 TTATT
1438568 TAACCATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (12 bp):
TTATTATTACTA
Found at i:1441142 original size:14 final size:14
Alignment explanation
Indices: 1441123--1441160 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
1441113 ATTTTAAATA
1441123 ATTTACATTTACAT
1 ATTTACATTTACAT
*
1441137 ATTTACATTCACAT
1 ATTTACATTTACAT
1441151 ATTTACATTT
1 ATTTACATTT
1441161 GCCTTTGGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.34, C:0.16, G:0.00, T:0.50
Consensus pattern (14 bp):
ATTTACATTTACAT
Done.