Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008097.1 Hibiscus syriacus cultivar Beakdansim tig00110621_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: 3094402
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 5 of 12
Found at i:1123672 original size:22 final size:21
Alignment explanation
Indices: 1123638--1123678 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1123628 CGTATTTATG
1123638 CCTTCTTCCTTTCCTTTCTTTT
1 CCTTCTTCCTTT-CTTTCTTTT
**
1123660 CCTTCTTTGTTTCTTTCTT
1 CCTTCTTCCTTTCTTTCTT
1123679 CGAATTAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.00, C:0.32, G:0.02, T:0.66
Consensus pattern (21 bp):
CCTTCTTCCTTTCTTTCTTTT
Found at i:1123989 original size:43 final size:48
Alignment explanation
Indices: 1123932--1124045 Score: 139
Period size: 50 Copynumber: 2.4 Consensus size: 48
1123922 GTTTAAAGAC
* *
1123932 ACTAACAAATTAATTAATATTTTTT-T-T-ATAT-TTA-ATAACTTAA
1 ACTAACAAACTAATTAATATTTTTTATATAATATAATATATAACTTAA
*
1123975 ACTAAGAAACTAATTAACTAATTTTTTATATAATATAATATATAACTTAA
1 ACTAACAAACTAATTAA-T-ATTTTTTATATAATATAATATATAACTTAA
1124025 ACTAACAAACTAATATAATAT
1 ACTAACAAACTAAT-TAATAT
1124046 AACTTAAACT
Statistics
Matches: 59, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
43 15 0.25
44 1 0.02
45 7 0.12
46 1 0.02
47 1 0.02
48 4 0.07
49 4 0.07
50 23 0.39
51 3 0.05
ACGTcount: A:0.49, C:0.09, G:0.01, T:0.41
Consensus pattern (48 bp):
ACTAACAAACTAATTAATATTTTTTATATAATATAATATATAACTTAA
Found at i:1124045 original size:28 final size:30
Alignment explanation
Indices: 1124005--1124067 Score: 112
Period size: 28 Copynumber: 2.2 Consensus size: 30
1123995 ATTTTTTATA
1124005 TAATATAATATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
1124035 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
1124063 TAATA
1 TAATA
1124068 ATTTATACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 26 0.79
29 1 0.03
30 6 0.18
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:1124074 original size:28 final size:28
Alignment explanation
Indices: 1124009--1124074 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
1123999 TTTATATAAT
1124009 ATAATATATAACTTAAACTAACAAACTA
1 ATAATATATAACTTAAACTAACAAACTA
1124037 AT-ATAATATAACTTAAACTAACAAACTA
1 ATAAT-ATATAACTTAAACTAACAAACTA
*
1124065 ATAATTTATA
1 ATAATATATA
1124075 CTAACAAACT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
27 2 0.06
28 31 0.89
29 2 0.06
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (28 bp):
ATAATATATAACTTAAACTAACAAACTA
Found at i:1124077 original size:21 final size:21
Alignment explanation
Indices: 1124044--1124092 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1124034 CTAATATAAT
1124044 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
1124065 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
1124086 ATTAACT
1 A-TAACT
1124093 AGATTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:1124366 original size:21 final size:23
Alignment explanation
Indices: 1124342--1124390 Score: 66
Period size: 21 Copynumber: 2.2 Consensus size: 23
1124332 AATTTGTCTG
1124342 TTGAAGCAAATAA-TATT-AGCA
1 TTGAAGCAAATAACTATTGAGCA
* *
1124363 TTGAATCATATAACTATTGAGCA
1 TTGAAGCAAATAACTATTGAGCA
1124386 TTGAA
1 TTGAA
1124391 AGGCTACAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 11 0.46
22 4 0.17
23 9 0.38
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (23 bp):
TTGAAGCAAATAACTATTGAGCA
Found at i:1124515 original size:25 final size:25
Alignment explanation
Indices: 1124486--1124586 Score: 184
Period size: 25 Copynumber: 4.0 Consensus size: 25
1124476 GAATCTCCCA
*
1124486 GCTATGGATGCAACGCATGCATGAG
1 GCTATGGAGGCAACGCATGCATGAG
1124511 GCTATGGAGGCAACGCATGCATGAG
1 GCTATGGAGGCAACGCATGCATGAG
1124536 GCTATGGAGGCAACGCATGCATGAG
1 GCTATGGAGGCAACGCATGCATGAG
*
1124561 GCTATGGAGGCAACACATGCATGAG
1 GCTATGGAGGCAACGCATGCATGAG
1124586 G
1 G
1124587 GATGCACGAG
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 74 1.00
ACGTcount: A:0.29, C:0.20, G:0.35, T:0.17
Consensus pattern (25 bp):
GCTATGGAGGCAACGCATGCATGAG
Found at i:1124733 original size:29 final size:29
Alignment explanation
Indices: 1124700--1124763 Score: 119
Period size: 29 Copynumber: 2.2 Consensus size: 29
1124690 ACATGCATCA
*
1124700 CTCCTTGGTCGCCCGGATTGCATGGCGAC
1 CTCCTTGGTCGCCCGGAGTGCATGGCGAC
1124729 CTCCTTGGTCGCCCGGAGTGCATGGCGAC
1 CTCCTTGGTCGCCCGGAGTGCATGGCGAC
1124758 CTCCTT
1 CTCCTT
1124764 TTGTCACTGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.09, C:0.36, G:0.30, T:0.25
Consensus pattern (29 bp):
CTCCTTGGTCGCCCGGAGTGCATGGCGAC
Found at i:1130187 original size:51 final size:51
Alignment explanation
Indices: 1130117--1130239 Score: 174
Period size: 51 Copynumber: 2.4 Consensus size: 51
1130107 ATCAATGTTC
** **
1130117 TCTGATGAAGGACTGTCACTATTCCTTGATGAAGAAGACTCTTTACCATCA
1 TCTGATGAAGGACCATCACTATTCCCCGATGAAGAAGACTCTTTACCATCA
* * *
1130168 TCTGATGAAGGACCATCACTATTCCCCGATGAAGAAGATTCTTTACCGTCC
1 TCTGATGAAGGACCATCACTATTCCCCGATGAAGAAGACTCTTTACCATCA
*
1130219 TCTCATGAAGGACCATCACTA
1 TCTGATGAAGGACCATCACTA
1130240 CCCTCTAATA
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 64 1.00
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.28
Consensus pattern (51 bp):
TCTGATGAAGGACCATCACTATTCCCCGATGAAGAAGACTCTTTACCATCA
Found at i:1130254 original size:51 final size:50
Alignment explanation
Indices: 1130148--1130261 Score: 140
Period size: 51 Copynumber: 2.2 Consensus size: 50
1130138 TTCCTTGATG
* * * *
1130148 AAGAAGACTCTTTACCATCATCTGATGAAGGACCATCACTATTCCCCGATG
1 AAGAAGATTCTTTACCATCATCTCATGAAGGACCATCACTA-TCCCCAATA
* *
1130199 AAGAAGATTCTTTACCGTCCTCTCATGAAGGACCATCACTA-CCCTCTAATA
1 AAGAAGATTCTTTACCATCATCTCATGAAGGACCATCACTATCCC-C-AATA
1130250 AAGAAGATTCTT
1 AAGAAGATTCTT
1130262 CCCCTTCACC
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
49 3 0.05
50 1 0.02
51 51 0.93
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.27
Consensus pattern (50 bp):
AAGAAGATTCTTTACCATCATCTCATGAAGGACCATCACTATCCCCAATA
Found at i:1138969 original size:51 final size:51
Alignment explanation
Indices: 1138914--1139077 Score: 145
Period size: 51 Copynumber: 3.2 Consensus size: 51
1138904 ATGGTGAGGT
* **
1138914 TCCTTCATCAGATGG-TGCGGA-AGAATCTGCTTCACCAGAGGGTAGTGATAC
1 TCCTTCATCAGA-GGATG-GGATAGAATCTGCTTCAACAGAGGACAGTGATAC
* * * * *
1138965 TCCTTTATCAGAGGATGGTATAGAATCTTCTTCAATAGAGGACAGTGATAG
1 TCCTTCATCAGAGGATGGGATAGAATCTGCTTCAACAGAGGACAGTGATAC
* * * * * *
1139016 TCCTTCATCAGAAGATGGTAAAGAATCTTCTTCATCAG-GGAGCAGTGCTAC
1 TCCTTCATCAGAGGATGGGATAGAATCTGCTTCAACAGAGGA-CAGTGATAC
*
1139067 TCCTACATCAG
1 TCCTTCATCAG
1139078 GGGACGGTGA
Statistics
Matches: 94, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
50 7 0.07
51 87 0.93
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (51 bp):
TCCTTCATCAGAGGATGGGATAGAATCTGCTTCAACAGAGGACAGTGATAC
Found at i:1140597 original size:22 final size:22
Alignment explanation
Indices: 1140567--1140614 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
1140557 TGTTTTACTA
1140567 CTTTAGAATAGAAAAATAATAG
1 CTTTAGAATAGAAAAATAATAG
* *
1140589 CTTTCGAATAGGAAAATAATAG
1 CTTTAGAATAGAAAAATAATAG
1140611 CTTT
1 CTTT
1140615 TGAAAACATG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (22 bp):
CTTTAGAATAGAAAAATAATAG
Found at i:1146719 original size:43 final size:43
Alignment explanation
Indices: 1146667--1146768 Score: 105
Period size: 43 Copynumber: 2.4 Consensus size: 43
1146657 ATATATCTCG
* * * * *
1146667 ACCTTTTGCGCCGTTTGTCCCATAAACGCCGCTATATCTCTTC
1 ACCTATTGCGACGTTTATCCCAAAAACGCCACTATATCTCTTC
* * * * *
1146710 ACCTATTGCGACATTTATTCCAAAAATGTCATTATATCTCTTC
1 ACCTATTGCGACGTTTATCCCAAAAACGCCACTATATCTCTTC
*
1146753 ACCTATTGCGGCGTTT
1 ACCTATTGCGACGTTT
1146769 TTTGTTATTA
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.22, C:0.28, G:0.13, T:0.37
Consensus pattern (43 bp):
ACCTATTGCGACGTTTATCCCAAAAACGCCACTATATCTCTTC
Found at i:1148654 original size:30 final size:30
Alignment explanation
Indices: 1148612--1148670 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
1148602 GGTAACAAAA
1148612 TCAAACTTGAATTCTTTAATGGTAGTAAAT
1 TCAAACTTGAATTCTTTAATGGTAGTAAAT
* * *
1148642 TCAAA-TTCGAATTTTTTTATGGTTGTAAA
1 TCAAACTT-GAATTCTTTAATGGTAGTAAA
1148671 GTTGAACTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 2 0.08
30 23 0.92
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.44
Consensus pattern (30 bp):
TCAAACTTGAATTCTTTAATGGTAGTAAAT
Found at i:1153908 original size:31 final size:31
Alignment explanation
Indices: 1153873--1153947 Score: 141
Period size: 31 Copynumber: 2.4 Consensus size: 31
1153863 AGAATATGCA
1153873 GAGACTAGGGTTGTGAAAGTATATATACAAG
1 GAGACTAGGGTTGTGAAAGTATATATACAAG
*
1153904 GAGACGAGGGTTGTGAAAGTATATATACAAG
1 GAGACTAGGGTTGTGAAAGTATATATACAAG
1153935 GAGACTAGGGTTG
1 GAGACTAGGGTTG
1153948 CAGATTTGGC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.36, C:0.07, G:0.33, T:0.24
Consensus pattern (31 bp):
GAGACTAGGGTTGTGAAAGTATATATACAAG
Found at i:1159779 original size:17 final size:17
Alignment explanation
Indices: 1159750--1159797 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
1159740 ATTATATTTT
*
1159750 TTTATTAAAAATTATAA
1 TTTATTTAAAATTATAA
* *
1159767 -TTATTTTAAAATTTTTA
1 TTTA-TTTAAAATTATAA
1159784 TTTATTTAAAATTA
1 TTTATTTAAAATTA
1159798 AAATATAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 3 0.12
17 19 0.76
18 3 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTATTTAAAATTATAA
Found at i:1162232 original size:117 final size:117
Alignment explanation
Indices: 1162026--1162251 Score: 389
Period size: 117 Copynumber: 1.9 Consensus size: 117
1162016 TATTGGATCA
* * *
1162026 ACTGTCGAATCAAGTGGGGTTCACTCACAGCCATTGGTTGGTCATACTAATGACAGAGTAAATTG
1 ACTGTCGAATCAAGTGGGGTTCACCCACAGCCATGGGTTGGTCATACTAATGACAAAGTAAATTG
* *
1162091 TATCACTGTCACTGATGCTGATGCTCATACTTCCCCTACATGTGGAGGGTTT
66 TACCACCGTCACTGATGCTGATGCTCATACTTCCCCTACATGTGGAGGGTTT
*
1162143 ACTGTCGATTCAAGTGGGGTTCACCCACAGCCATGGGTTGGTCATACTAATGACAAAGTAAATTG
1 ACTGTCGAATCAAGTGGGGTTCACCCACAGCCATGGGTTGGTCATACTAATGACAAAGTAAATTG
*
1162208 TACCACCGTCACTGATGCTGATGCTTATACTTCCCCTACATGTG
66 TACCACCGTCACTGATGCTGATGCTCATACTTCCCCTACATGTG
1162252 TAGTCAATAC
Statistics
Matches: 102, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
117 102 1.00
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (117 bp):
ACTGTCGAATCAAGTGGGGTTCACCCACAGCCATGGGTTGGTCATACTAATGACAAAGTAAATTG
TACCACCGTCACTGATGCTGATGCTCATACTTCCCCTACATGTGGAGGGTTT
Found at i:1168783 original size:2 final size:2
Alignment explanation
Indices: 1168776--1168801 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1168766 TTTTGTTTAC
1168776 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1168802 GGTGTTACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1174898 original size:33 final size:33
Alignment explanation
Indices: 1174858--1174948 Score: 139
Period size: 33 Copynumber: 2.8 Consensus size: 33
1174848 CAAAGTTTGG
1174858 CCACCAACCAAGATGAAATTGT-CAATAAGTTAA
1 CCACCAACCAAGATGAAATT-TCCAATAAGTTAA
** *
1174891 CCACCAACCAAGAAAAAATTTCCAATAAGTTGA
1 CCACCAACCAAGATGAAATTTCCAATAAGTTAA
1174924 CCACCAACCAAGATGAAATTTCCAA
1 CCACCAACCAAGATGAAATTTCCAA
1174949 CTTGTCAACT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
32 1 0.02
33 51 0.98
ACGTcount: A:0.46, C:0.25, G:0.10, T:0.19
Consensus pattern (33 bp):
CCACCAACCAAGATGAAATTTCCAATAAGTTAA
Found at i:1178563 original size:21 final size:21
Alignment explanation
Indices: 1178529--1178568 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1178519 AGTTATATCT
*
1178529 AGCCGTTGGTGATG-TTTTGG
1 AGCCGTTGGGGATGATTTTGG
1178549 AGCCGTTTGGGGATGATTTT
1 AGCCG-TTGGGGATGATTTT
1178569 TCTGCAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 8 0.47
22 4 0.24
ACGTcount: A:0.12, C:0.10, G:0.38, T:0.40
Consensus pattern (21 bp):
AGCCGTTGGGGATGATTTTGG
Found at i:1185569 original size:59 final size:59
Alignment explanation
Indices: 1185506--1185628 Score: 131
Period size: 59 Copynumber: 2.1 Consensus size: 59
1185496 TAATAAGTTT
* *
1185506 AATTT-ATCCCTAAATTATAACTCTCGTTCTAAATTAATCCTTAAACTTTTAAACATTTC
1 AATTTCATACCTAAATTATAACTCTAGTTCTAAATTAATCC-TAAACTTTTAAACATTTC
** * * ** * * *
1185565 AATTTCATATTTAAATTATGACTTTAGTTCTAAATTGCTTCTAAACTTTTGAACATTTT
1 AATTTCATACCTAAATTATAACTCTAGTTCTAAATTAATCCTAAACTTTTAAACATTTC
1185624 AATTT
1 AATTT
1185629 TGTTCCAAAC
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
59 26 0.50
60 26 0.50
ACGTcount: A:0.34, C:0.15, G:0.04, T:0.46
Consensus pattern (59 bp):
AATTTCATACCTAAATTATAACTCTAGTTCTAAATTAATCCTAAACTTTTAAACATTTC
Found at i:1185595 original size:60 final size:59
Alignment explanation
Indices: 1185516--1185628 Score: 145
Period size: 60 Copynumber: 1.9 Consensus size: 59
1185506 AATTTATCCC
*
1185516 TAAATTATAACTCTCGTTCTAAATTAATCCTTAAACTTTTAAACATTTCAATTTCATATT
1 TAAATTATAACTCTAGTTCTAAATTAATCC-TAAACTTTTAAACATTTCAATTTCATATT
* * ** * * *
1185576 TAAATTATGACTTTAGTTCTAAATTGCTTCTAAACTTTTGAACATTTTAATTT
1 TAAATTATAACTCTAGTTCTAAATTAATCCTAAACTTTTAAACATTTCAATTT
1185629 TGTTCCAAAC
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
59 21 0.47
60 24 0.53
ACGTcount: A:0.35, C:0.14, G:0.04, T:0.47
Consensus pattern (59 bp):
TAAATTATAACTCTAGTTCTAAATTAATCCTAAACTTTTAAACATTTCAATTTCATATT
Found at i:1190959 original size:20 final size:20
Alignment explanation
Indices: 1190922--1190964 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1190912 ATTCCACCTC
* *
1190922 ATGCAACTATATGCTCCTAA
1 ATGCAACTAAATGATCCTAA
*
1190942 ATGCATCTAAATGATCCTAA
1 ATGCAACTAAATGATCCTAA
1190962 ATG
1 ATG
1190965 GGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGATCCTAA
Found at i:1195957 original size:27 final size:27
Alignment explanation
Indices: 1195927--1195979 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
1195917 GATCCAGGCA
*
1195927 GATTTCTCAGTCATGATTACAGATCCG
1 GATTTCTCAGTCATGATCACAGATCCG
* *
1195954 GATTTCTCGGTCATGATCAGAGATCC
1 GATTTCTCAGTCATGATCACAGATCC
1195980 CGTGAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.32
Consensus pattern (27 bp):
GATTTCTCAGTCATGATCACAGATCCG
Found at i:1196247 original size:20 final size:20
Alignment explanation
Indices: 1196210--1196252 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1196200 ATTCCACCTC
* *
1196210 ATGCAACTATATGCTCCTAA
1 ATGCAACTAAATGATCCTAA
*
1196230 ATGCATCTAAATGATCCTAA
1 ATGCAACTAAATGATCCTAA
1196250 ATG
1 ATG
1196253 GGCTCTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGATCCTAA
Found at i:1199607 original size:66 final size:66
Alignment explanation
Indices: 1199496--1199760 Score: 422
Period size: 66 Copynumber: 4.0 Consensus size: 66
1199486 GTCTTGGATA
* * * *
1199496 AAAGCTCTGATGGTCAGGTGAAAAATAAGAGCTCAGATGAAGTTTTTCCATCTGGTGCTCAGTCT
1 AAAGCTCTGATGGTCAAGTGAAAAAGAAGAGCTCAAATGAAGTTTTCCCATCTGGTGCTCAGTCT
1199561 G
66 G
* *
1199562 AAAGTTCTGACGGTCAAGTGAAAAAGAAGAGCTCAAATGAAGTTTTCCCATCTGGTGCTCAGTCT
1 AAAGCTCTGATGGTCAAGTGAAAAAGAAGAGCTCAAATGAAGTTTTCCCATCTGGTGCTCAGTCT
1199627 G
66 G
* * * *
1199628 AAAACTCTGATGGTCAAGCGAAAGAGAAGAGCTCAAATGAAGTTTTCCCATCTGGTGCTCAATCT
1 AAAGCTCTGATGGTCAAGTGAAAAAGAAGAGCTCAAATGAAGTTTTCCCATCTGGTGCTCAGTCT
1199693 G
66 G
* *
1199694 AAAGCTCTGATAGTCAAGTGGAAAAGAAGAGCTCAAATGAAGTTTTCCCATCTGGTGCTCAGTCT
1 AAAGCTCTGATGGTCAAGTGAAAAAGAAGAGCTCAAATGAAGTTTTCCCATCTGGTGCTCAGTCT
1199759 G
66 G
1199760 A
1 A
1199761 GCTTTTGAAG
Statistics
Matches: 181, Mismatches: 18, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
66 181 1.00
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (66 bp):
AAAGCTCTGATGGTCAAGTGAAAAAGAAGAGCTCAAATGAAGTTTTCCCATCTGGTGCTCAGTCT
G
Found at i:1211000 original size:223 final size:223
Alignment explanation
Indices: 1210605--1211050 Score: 842
Period size: 223 Copynumber: 2.0 Consensus size: 223
1210595 TGACTCTTAT
1210605 TCTAAATTTTCTTTAACCTTTTAACATTTCAATAACGTCCACCAAATCATTCAAAAGTTCAGAGA
1 TCTAAATTTTCTTTAACCTTTTAACATTTCAATAACGTCCACCAAATCATTCAAAAGTTCAGAGA
1210670 TGAAATGGGAACATTCATAGTTCGAGGTCTAATATAGAATGCATGTCACATTTTGGGGATGAATT
66 TGAAATGGGAACATTCATAGTTCGAGGTCTAATATAGAATGCATGTCACATTTTGGGGATGAATT
1210735 TGAAATTCTAAAAAAAATTAGAGACCAATTTAGAATGAGAGTCATAATTT-TGAATAAAACTGAA
131 TGAAATTCTAAAAAAAATTAGAGACCAATTTAGAATGAGAGTCATAATTTATGAATAAAACTGAA
*
1210799 ATATTCAAAAGTTTGGGGA-CAAATTAA
196 ATATTCAAAAGTTTAGGGACCAAATTAA
1210826 TCTAAATTGTTCTTTAACCTTTTAACATTTCAATAACGTCCACCAAATCATTCAAAAGTTCAGAG
1 TCTAAATT-TTCTTTAACCTTTTAACATTTCAATAACGTCCACCAAATCATTCAAAAGTTCAGAG
*
1210891 ATGAAATTGGAACATTCAATAGTTCGAGGTCTAATATAGAATGCATGTCACATTTTGGGGATGAA
65 ATGAAATGGGAACATTC-ATAGTTCGAGGTCTAATATAGAATGCATGTCACATTTTGGGGATGAA
1210956 TTTGAAATTCTAAAAAAAATTAGAGACCAATTTAGAATGAGAGTCATAATTTATGAATAAAACTG
129 TTTGAAATTCTAAAAAAAATTAGAGACCAATTTAGAATGAGAGTCATAATTTATGAATAAAACTG
1211021 AAATATTCAAAAGTTTAGGGACCAAATTAA
194 AAATATTCAAAAGTTTAGGGACCAAATTAA
1211051 AATAAGAGTC
Statistics
Matches: 219, Mismatches: 2, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
221 8 0.04
222 72 0.33
223 99 0.45
224 32 0.15
225 8 0.04
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.32
Consensus pattern (223 bp):
TCTAAATTTTCTTTAACCTTTTAACATTTCAATAACGTCCACCAAATCATTCAAAAGTTCAGAGA
TGAAATGGGAACATTCATAGTTCGAGGTCTAATATAGAATGCATGTCACATTTTGGGGATGAATT
TGAAATTCTAAAAAAAATTAGAGACCAATTTAGAATGAGAGTCATAATTTATGAATAAAACTGAA
ATATTCAAAAGTTTAGGGACCAAATTAA
Found at i:1214142 original size:15 final size:17
Alignment explanation
Indices: 1214122--1214153 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
1214112 TTTAAAAATT
1214122 ATATTAT-AA-TTATAA
1 ATATTATCAATTTATAA
1214137 ATATTATCAATTTATAA
1 ATATTATCAATTTATAA
1214154 TAAAATAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 2 0.13
17 6 0.40
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATTATCAATTTATAA
Found at i:1219211 original size:2 final size:2
Alignment explanation
Indices: 1219204--1219243 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1219194 CATGTATGTG
1219204 TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1219244 GAACTAAGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1219344 original size:20 final size:21
Alignment explanation
Indices: 1219316--1219355 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1219306 GATTATGAAA
1219316 TCATATGAA-AAGTGAAATGT
1 TCATATGAATAAGTGAAATGT
* *
1219336 TCATGTGAATATGTGAAATG
1 TCATATGAATAAGTGAAATG
1219356 ATATTTCCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.40, C:0.05, G:0.23, T:0.33
Consensus pattern (21 bp):
TCATATGAATAAGTGAAATGT
Found at i:1222952 original size:3 final size:3
Alignment explanation
Indices: 1222944--1222975 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1222934 AAATAAAGAA
1222944 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1222976 AACAAAGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1225058 original size:3 final size:3
Alignment explanation
Indices: 1225050--1225095 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
1225040 CTTACAATGG
1225050 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1225096 ATGATGATGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:1225474 original size:6 final size:6
Alignment explanation
Indices: 1225464--1225502 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
1225454 AATATATTTA
* * *
1225464 TATATG CATATG TATATG TATATG TATGTG TATGTG TAT
1 TATATG TATATG TATATG TATATG TATATG TATATG TAT
1225503 TAAGATATCC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.28, C:0.03, G:0.21, T:0.49
Consensus pattern (6 bp):
TATATG
Found at i:1235730 original size:3 final size:3
Alignment explanation
Indices: 1235724--1235764 Score: 64
Period size: 3 Copynumber: 13.3 Consensus size: 3
1235714 ATTATTAAAT
*
1235724 TTA TTA TAA ATTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1235765 ATAATTTGTC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 33 0.94
4 2 0.06
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:1238330 original size:18 final size:19
Alignment explanation
Indices: 1238304--1238339 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1238294 TTATATTACA
*
1238304 TAAATAAAT-TTATAAAAT
1 TAAAAAAATATTATAAAAT
1238322 TAAAAAAATATTATAAAA
1 TAAAAAAATATTATAAAA
1238340 ATTTAGATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAAAAAATATTATAAAAT
Found at i:1240628 original size:9 final size:9
Alignment explanation
Indices: 1240614--1240679 Score: 73
Period size: 9 Copynumber: 7.1 Consensus size: 9
1240604 CGAATTAAAT
1240614 TTTTAATAA
1 TTTTAATAA
1240623 TTTTAA-AA
1 TTTTAATAA
1240631 TTTTTAATAA
1 -TTTTAATAA
1240641 TTTTAATAA
1 TTTTAATAA
1240650 TTTTAATATAAA
1 TTTT-A-AT-AA
*
1240662 ATTTAATAA
1 TTTTAATAA
1240671 -TTTAATAA
1 TTTTAATAA
1240679 T
1 T
1240680 CAAAATGCAA
Statistics
Matches: 50, Mismatches: 1, Indels: 12
0.79 0.02 0.19
Matches are distributed among these distances:
8 10 0.20
9 27 0.54
10 5 0.10
11 3 0.06
12 5 0.10
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
TTTTAATAA
Found at i:1245170 original size:23 final size:22
Alignment explanation
Indices: 1245140--1245186 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
1245130 TATAATGTAA
1245140 GGGTGAATCTATAAAATTTTAG
1 GGGTGAATCTATAAAATTTTAG
**
1245162 GGGTCGAATCTATATTATTTTAG
1 GGGT-GAATCTATAAAATTTTAG
1245185 GG
1 GG
1245187 AATCGAAAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.30, C:0.06, G:0.26, T:0.38
Consensus pattern (22 bp):
GGGTGAATCTATAAAATTTTAG
Found at i:1246751 original size:21 final size:20
Alignment explanation
Indices: 1246665--1246822 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
1246655 AAATGACCAA
**
1246665 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
1246684 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
1246704 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
1246724 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
1246745 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1246766 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
1246786 CCAGAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1246807 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1246823 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 40 0.39
21 46 0.45
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1246815 original size:20 final size:20
Alignment explanation
Indices: 1246790--1246983 Score: 219
Period size: 20 Copynumber: 9.7 Consensus size: 20
1246780 GATTTTCCAG
** *
1246790 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATCCGTA
*
1246810 AATCGCAACGCGAA-CACATA
1 AATCGCAACGCGAATC-CGTA
*
1246830 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
* *
1246850 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGAATCCGTA
*
1246870 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
* *
1246890 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
*
1246910 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
** * *
1246930 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAATCCGT-A
*
1246951 AATCGCAACGAGAATCCGTA
1 AATCGCAACGCGAATCCGTA
1246971 AATCGCAACGCGA
1 AATCGCAACGCGA
1246984 TATTTAAAGC
Statistics
Matches: 152, Mismatches: 19, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
20 134 0.88
21 18 0.12
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.18
Consensus pattern (20 bp):
AATCGCAACGCGAATCCGTA
Found at i:1246873 original size:60 final size:60
Alignment explanation
Indices: 1246790--1246982 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
1246780 GATTTTCCAG
* ** *
1246790 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
* * * *
1246850 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATC-CGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACACATAAATCGCAACGCGTATCCGTA
** * * *
1246910 AATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGAGAATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT-AAATCGCAACGCGTATCCGTA
1246971 AATCGCAACGCG
1 AATCGCAACGCG
1246983 ATATTTAAAG
Statistics
Matches: 113, Mismatches: 17, Indels: 5
0.84 0.13 0.04
Matches are distributed among these distances:
59 1 0.01
60 80 0.71
61 32 0.28
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.18
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
Found at i:1247400 original size:33 final size:33
Alignment explanation
Indices: 1247361--1247431 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1247351 TTCACTTAGA
1247361 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
1247394 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1247427 TTTCA
1 TTTCA
1247432 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:1247555 original size:20 final size:20
Alignment explanation
Indices: 1247511--1247606 Score: 122
Period size: 21 Copynumber: 4.8 Consensus size: 20
1247501 TGCAGAAGAG
*
1247511 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
1247532 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
1247552 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
*
1247573 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
1247592 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
1247607 CGCAACGCGA
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
19 18 0.28
20 20 0.31
21 26 0.41
ACGTcount: A:0.46, C:0.18, G:0.24, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:1247568 original size:41 final size:40
Alignment explanation
Indices: 1247509--1247605 Score: 140
Period size: 41 Copynumber: 2.4 Consensus size: 40
1247499 TTTGCAGAAG
* *
1247509 AGTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGAC
1 AGTCGCAACGAGAGAAATGAAAATCGCAACGAGA-AATGAA
* *
1247550 TGTCGCAACGAGAGAAATGAAAATCGCAACGCGAAATGAA
1 AGTCGCAACGAGAGAAATGAAAATCGCAACGAGAAATGAA
*
1247590 AATCGCAACGAGAGAA
1 AGTCGCAACGAGAGAA
1247606 TCGCAACGCG
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
40 19 0.38
41 31 0.62
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.11
Consensus pattern (40 bp):
AGTCGCAACGAGAGAAATGAAAATCGCAACGAGAAATGAA
Found at i:1247681 original size:21 final size:21
Alignment explanation
Indices: 1247655--1247719 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
1247645 CGCGTTGCGA
1247655 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
1247676 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
1247696 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
1247717 TTC
1 TTC
1247720 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:1247716 original size:20 final size:20
Alignment explanation
Indices: 1247654--1247717 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
1247644 TCGCGTTGCG
1247654 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
***
1247674 ATTTCTCTCGTTGCGACAGTC
1 A-TTCTCTCGTTGCGATTTTC
1247695 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
1247715 ATT
1 ATT
1247718 TCAACCAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 20 0.54
21 17 0.46
ACGTcount: A:0.12, C:0.25, G:0.16, T:0.47
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:1249566 original size:93 final size:93
Alignment explanation
Indices: 1249407--1250059 Score: 1258
Period size: 93 Copynumber: 7.1 Consensus size: 93
1249397 TAGATTGCTT
*
1249407 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
1249472 TTTGTCTTTGTTTTATCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1249500 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1249565 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1249593 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1249658 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1249686 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1249751 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1249779 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
1249844 TTTGTC-TTGTTTTCTC-TTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1249870 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1249935 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1249963 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1250028 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1250055 AGTAA
1 AGTAA
1250060 TGCAATCCAT
Statistics
Matches: 554, Mismatches: 4, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
91 81 0.15
92 24 0.04
93 449 0.81
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1250144 original size:19 final size:19
Alignment explanation
Indices: 1250104--1250231 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
1250094 TAGTTTACTT
* *
1250104 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
1250124 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
1250143 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
1250162 TCGCAA--C-AAA--AGAA
1 TCGCAACGCGAAACCAAAA
1250176 TCGCAACGCGAAACC-AAA
1 TCGCAACGCGAAACCAAAA
1250194 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAACCAAAA
1250208 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
1250227 TCGCA
1 TCGCA
1250232 TTGCGATTTT
Statistics
Matches: 91, Mismatches: 6, Indels: 23
0.76 0.05 0.19
Matches are distributed among these distances:
13 1 0.01
14 19 0.21
16 8 0.09
17 4 0.04
18 9 0.10
19 37 0.41
20 13 0.14
ACGTcount: A:0.48, C:0.28, G:0.16, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:1250200 original size:32 final size:32
Alignment explanation
Indices: 1250139--1250231 Score: 125
Period size: 32 Copynumber: 2.8 Consensus size: 32
1250129 ACGCGAAACC
**
1250139 AAAATCGCAACGCGAAATGAAAATCGCAAC-AA
1 AAAATCGCAACGCGAAA-CCAAATCGCAACGAA
*
1250171 AAGAATCGCAACGCGAAACCAAATCGCAACGAC
1 AA-AATCGCAACGCGAAACCAAATCGCAACGAA
1250204 AAAATCGCAACGCGAAACCAAAATCGCA
1 AAAATCGCAACGCGAAACC-AAATCGCA
1250232 TTGCGATTTT
Statistics
Matches: 55, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
32 29 0.53
33 26 0.47
ACGTcount: A:0.49, C:0.27, G:0.16, T:0.08
Consensus pattern (32 bp):
AAAATCGCAACGCGAAACCAAATCGCAACGAA
Found at i:1250249 original size:19 final size:19
Alignment explanation
Indices: 1250227--1250399 Score: 168
Period size: 19 Copynumber: 9.6 Consensus size: 19
1250217 GAAACCAAAA
*
1250227 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1250246 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
1250262 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
1250279 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
1250295 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1250312 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
1250331 TCGCGTTGCGATTTTTGTT
1 TCGCGTTGCGATTTTCATT
* *
1250350 TCTCGTTGCGATTATCATT
1 TCGCGTTGCGATTTTCATT
*
1250369 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
1250389 TCGTGTTGCGA
1 TCGCGTTGCGA
1250400 AAGTAAACTA
Statistics
Matches: 127, Mismatches: 16, Indels: 21
0.77 0.10 0.13
Matches are distributed among these distances:
14 15 0.12
16 11 0.09
17 11 0.09
19 78 0.61
20 12 0.09
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1250268 original size:14 final size:14
Alignment explanation
Indices: 1250249--1250305 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1250239 TTTCATTTCG
1250249 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
1250263 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
1250280 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
1250296 CGTTGCGATT
1 CGTTGCGATT
1250306 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:1250357 original size:38 final size:38
Alignment explanation
Indices: 1250227--1250399 Score: 168
Period size: 33 Copynumber: 4.8 Consensus size: 38
1250217 GAAACCAAAA
*
1250227 TCGCATTGCGATTTTCATTTCGCGTTGCGA-T-TC-TT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
* *
1250262 T--CGTTGCGATTTTCATTTCGCATTGCGA-T-TC-TG
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
* **
1250295 T--CGTTGCGATTTTCATTTCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
** *
1250331 TCGCGTTGCGATTTTTGTTTCTCGTTGCGATTATCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
* *
1250369 TCGCGTTGCGATTTTAAGTTTCGTGTTGCGA
1 TCGCGTTGCGATTTTCA-TTTCGCGTTGCGA
1250400 AAGTAAACTA
Statistics
Matches: 116, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
33 56 0.48
34 1 0.01
35 2 0.02
36 2 0.02
38 44 0.38
39 11 0.09
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
Found at i:1252341 original size:14 final size:14
Alignment explanation
Indices: 1252322--1252357 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1252312 ATTGTTTAAT
1252322 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1252336 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1252350 TGATTTGT
1 TGATTTGT
1252358 GTAATGATGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1252477 original size:19 final size:19
Alignment explanation
Indices: 1252447--1252564 Score: 118
Period size: 19 Copynumber: 6.8 Consensus size: 19
1252437 GCATTATGTT
1252447 GAAATG-AAATCGCAATGC
1 GAAATGAAAATCGCAATGC
1252465 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAATGC
* *
1252482 G--A-GAGAATCGAAATGC
1 GAAATGAAAATCGCAATGC
1252498 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAATGC
1252515 G--A-G--AATCGCAATGC
1 GAAATGAAAATCGCAATGC
1252529 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
1252548 GGAAATGAAAATCGCAA
1 -GAAATGAAAATCGCAA
1252565 CGAGAGAATC
Statistics
Matches: 82, Mismatches: 4, Indels: 26
0.73 0.04 0.23
Matches are distributed among these distances:
12 8 0.10
14 12 0.15
15 2 0.02
16 3 0.04
17 5 0.06
18 7 0.09
19 29 0.35
20 16 0.20
ACGTcount: A:0.47, C:0.16, G:0.23, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAATGC
Found at i:1252522 original size:31 final size:32
Alignment explanation
Indices: 1252454--1252544 Score: 157
Period size: 31 Copynumber: 2.8 Consensus size: 32
1252444 GTTGAAATGA
1252454 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAAC-AGAG
*
1252487 AATCGAAATGCGAAATGAAAATCGCAAC-GAG
1 AATCGCAATGCGAAATGAAAATCGCAACAGAG
1252518 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
1252545 TGCGGAAATG
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
31 29 0.52
33 27 0.48
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (32 bp):
AATCGCAATGCGAAATGAAAATCGCAACAGAG
Found at i:1252636 original size:14 final size:14
Alignment explanation
Indices: 1252617--1252671 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1252607 TATTTCCGCA
1252617 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
1252631 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
1252648 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
1252664 TTGCGATT
1 TTGCGATT
1252672 TTCATTTCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:1252655 original size:33 final size:33
Alignment explanation
Indices: 1252597--1252809 Score: 193
Period size: 33 Copynumber: 6.2 Consensus size: 33
1252587 TCATTTCGCA
*
1252597 TTGCGATTTTTATTTCCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTT-CGCATTGCGATTCTCTCG
1252631 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
1252664 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG
* * * * *
1252701 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
*
1252736 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
* *
1252770 TTGGGA-TTTCATTTCGCATTGCGATTCTCTTG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1252802 TTGCGATT
1 TTGCGATT
1252810 GTAATTTCCG
Statistics
Matches: 147, Mismatches: 16, Indels: 33
0.75 0.08 0.17
Matches are distributed among these distances:
31 5 0.03
32 26 0.18
33 64 0.44
34 21 0.14
35 4 0.03
36 3 0.02
37 2 0.01
38 2 0.01
39 8 0.05
40 3 0.02
41 9 0.06
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:1252703 original size:53 final size:53
Alignment explanation
Indices: 1252631--1252795 Score: 282
Period size: 53 Copynumber: 3.2 Consensus size: 53
1252621 GATTCTCTCG
1252631 TTGCGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1252683 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
* *
1252736 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-GTTGGGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCCGCATTGCGATTCTC-TCGTTGCGATTTTCATTTCGCA
1252788 TTGCGATT
1 TTGCGATT
1252796 CTCTTGTTGC
Statistics
Matches: 109, Mismatches: 2, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
52 35 0.32
53 73 0.67
54 1 0.01
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (53 bp):
TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
Found at i:1252704 original size:86 final size:90
Alignment explanation
Indices: 1252579--1252809 Score: 331
Period size: 86 Copynumber: 2.7 Consensus size: 90
1252569 AGAATCGCAA
*
1252579 TGCGATTTTCATTTCGCATTGCGATTTTTATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1252644 TTCGCATTGCGA-TTC-TCT-CG-T
66 TTCGCATTGCGATTTCATCTCCGAT
1252665 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
*
1252730 TTCGCATTGCGATTTTCATTTCCGCAT
66 TTCGCATTGCGA-TTTCATCTCCG-AT
* *
1252757 TGCGATTTTCA--T-G--TTGGGA-TTTCATTT-CGCATTGCGATTCTCTTGTTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATT
1252810 GTAATTTCCG
Statistics
Matches: 135, Mismatches: 4, Indels: 13
0.89 0.03 0.09
Matches are distributed among these distances:
85 25 0.19
86 84 0.62
87 5 0.04
88 3 0.02
89 3 0.02
90 3 0.02
92 12 0.09
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (90 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
TTCGCATTGCGATTTCATCTCCGAT
Found at i:1252824 original size:52 final size:52
Alignment explanation
Indices: 1252631--1252824 Score: 166
Period size: 53 Copynumber: 3.7 Consensus size: 52
1252621 GATTCTCTCG
* * *
1252631 TTGCGATTTTCATTT-CGCATTGCGA-TTCTC-TCGTTGCGATTTTCATTTCGCA
1 TTGCGATTCTCATTTCCGCATTGCAATTTC-CAT-GTTGGGA-TTTCATTTCGCA
* * *
1252683 TTGCGATTTTCATTTCCGCATTGCGA-TTCTC-TCGTTGCGATTTTCATTTCGCA
1 TTGCGATTCTCATTTCCGCATTGCAATTTC-CAT-GTTGGGA-TTTCATTTCGCA
* * *
1252736 TTGCGATTTTCATTTCCGCATTGCGATTTTCATGTTGGGATTTCATTTCGCA
1 TTGCGATTCTCATTTCCGCATTGCAATTTCCATGTTGGGATTTCATTTCGCA
* * * *
1252788 TTGCGATTCTCTTGTTGCG-ATTGTAATTTCCGTGTTG
1 TTGCGATTCTCAT-TTCCGCATTGCAATTTCCATGTTG
1252825 CGCTAGTCAA
Statistics
Matches: 129, Mismatches: 9, Indels: 8
0.88 0.06 0.05
Matches are distributed among these distances:
52 52 0.40
53 74 0.57
54 3 0.02
ACGTcount: A:0.13, C:0.21, G:0.19, T:0.46
Consensus pattern (52 bp):
TTGCGATTCTCATTTCCGCATTGCAATTTCCATGTTGGGATTTCATTTCGCA
Found at i:1253511 original size:12 final size:12
Alignment explanation
Indices: 1253494--1253518 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1253484 TCTTCGGGGA
1253494 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1253506 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1253518 C
1 C
1253519 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1253727 original size:24 final size:24
Alignment explanation
Indices: 1253693--1253738 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
1253683 CTGAAACATC
1253693 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
1253717 ATCAAAGTCCGGATATTGACCA
1 ATCAAAATCCGGATATTGACCA
1253739 CGACCAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:1254460 original size:20 final size:20
Alignment explanation
Indices: 1254432--1254660 Score: 244
Period size: 20 Copynumber: 11.4 Consensus size: 20
1254422 AAATTTCAGT
* * *
1254432 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1254452 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
1254472 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1254492 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
1254512 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
1254532 ATTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
1254552 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
1254572 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
1254592 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
1254612 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
1254632 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
1254652 GTTGCGATT
1 GTTGCGATT
1254661 CTGGAAAATC
Statistics
Matches: 185, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
20 184 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:1256388 original size:19 final size:20
Alignment explanation
Indices: 1256346--1256388 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
1256336 AAAATATATT
*
1256346 GAAATATATTTTGAAGGTAA
1 GAAATATATTTTGAAAGTAA
*
1256366 -AAATATATTTT-AAATTAA
1 GAAATATATTTTGAAAGTAA
1256384 GAAAT
1 GAAAT
1256389 TAATATTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.51, C:0.00, G:0.12, T:0.37
Consensus pattern (20 bp):
GAAATATATTTTGAAAGTAA
Found at i:1270641 original size:14 final size:14
Alignment explanation
Indices: 1270624--1270652 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1270614 ACTGTAAGGG
1270624 TTCAGTTCAACCAA
1 TTCAGTTCAACCAA
1270638 TTCAGTTCAACCAA
1 TTCAGTTCAACCAA
1270652 T
1 T
1270653 AGATGAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.28, G:0.07, T:0.31
Consensus pattern (14 bp):
TTCAGTTCAACCAA
Found at i:1276108 original size:25 final size:25
Alignment explanation
Indices: 1276057--1276108 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
1276047 TAATTTAATG
* *
1276057 ATTTAATATTTTAACTAAATCTGAA
1 ATTTAATATTTTAACTAAAACTAAA
1276082 ATTTAA-ATTTTATACTAAAACTAAA
1 ATTTAATATTTTA-ACTAAAACTAAA
1276107 AT
1 AT
1276109 AATTTAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 6 0.25
25 18 0.75
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (25 bp):
ATTTAATATTTTAACTAAAACTAAA
Found at i:1278632 original size:19 final size:18
Alignment explanation
Indices: 1278595--1278634 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
1278585 AGGTAATCTC
* *
1278595 ATTATAGAATTTTAGATT
1 ATTATAGAATCTAAGATT
1278613 ATTATAGTAATCTAAGATT
1 ATTATAG-AATCTAAGATT
1278632 ATT
1 ATT
1278635 TGAATTAAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47
Consensus pattern (18 bp):
ATTATAGAATCTAAGATT
Found at i:1280108 original size:50 final size:50
Alignment explanation
Indices: 1280033--1280133 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
1280023 CTCCAACTTT
1280033 TCCATCTGGGAAACAGAAGAATTTCAATTAAGGATATATCTGACCATTGA
1 TCCATCTGGGAAACAGAAGAATTTCAATTAAGGATATATCTGACCATTGA
1280083 TCCATCTGGGAAACAGAAGAATTTCAATTAAGGATATATCTGACCATTGA
1 TCCATCTGGGAAACAGAAGAATTTCAATTAAGGATATATCTGACCATTGA
1280133 T
1 T
1280134 ACAAATTAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (50 bp):
TCCATCTGGGAAACAGAAGAATTTCAATTAAGGATATATCTGACCATTGA
Found at i:1287647 original size:16 final size:18
Alignment explanation
Indices: 1287626--1287666 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
1287616 ACGTTCATTA
*
1287626 AATATTTATTA-AAAAT-
1 AATATTTACTATAAAATC
1287642 AATATTT-CTATAAAATC
1 AATATTTACTATAAAATC
1287659 AATATTTA
1 AATATTTA
1287667 ATAGTGTGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 2 0.10
16 12 0.57
17 7 0.33
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (18 bp):
AATATTTACTATAAAATC
Found at i:1288862 original size:15 final size:15
Alignment explanation
Indices: 1288839--1288890 Score: 68
Period size: 15 Copynumber: 3.5 Consensus size: 15
1288829 TGAGACATTA
*
1288839 CCCGCCCCGCATTCG
1 CCCGCCCCGCATCCG
*
1288854 CCCGTCCCGCATCCG
1 CCCGCCCCGCATCCG
*
1288869 CCCGCCCCACATCCG
1 CCCGCCCCGCATCCG
*
1288884 CCTGCCC
1 CCCGCCC
1288891 AACTAAATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.08, C:0.63, G:0.17, T:0.12
Consensus pattern (15 bp):
CCCGCCCCGCATCCG
Found at i:1289902 original size:59 final size:59
Alignment explanation
Indices: 1289837--1289964 Score: 154
Period size: 59 Copynumber: 2.2 Consensus size: 59
1289827 TTAGGATGTT
*
1289837 TTTAAATTAT-ACTTTT-ATTTTAAATCGA-TTCTTAAATTTTAAAATATTTTATATCAATC
1 TTTAAATTATGA-TTTTCATTTT-AAT-GATTTCTTAAATTTTAAAACATTTTATATCAATC
* * **
1289896 TTTAAATTATGATTTTCATTTTAATTATTTCTTAAATTTTAAAACGTTTTATATTGATC
1 TTTAAATTATGATTTTCATTTTAATGATTTCTTAAATTTTAAAACATTTTATATCAATC
*
1289955 CTTAAATTAT
1 TTTAAATTAT
1289965 CAATATTATT
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
58 1 0.02
59 53 0.88
60 6 0.10
ACGTcount: A:0.35, C:0.08, G:0.03, T:0.54
Consensus pattern (59 bp):
TTTAAATTATGATTTTCATTTTAATGATTTCTTAAATTTTAAAACATTTTATATCAATC
Found at i:1291015 original size:7 final size:7
Alignment explanation
Indices: 1291000--1291031 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
1290990 AAGTGTCATA
*
1291000 TTTAAGG
1 TTTAGGG
1291007 TTTAGGG
1 TTTAGGG
1291014 TTTAGGG
1 TTTAGGG
1291021 TTTAGGG
1 TTTAGGG
1291028 TTTA
1 TTTA
1291032 TAGATTGAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.19, C:0.00, G:0.34, T:0.47
Consensus pattern (7 bp):
TTTAGGG
Found at i:1291022 original size:14 final size:14
Alignment explanation
Indices: 1291000--1291054 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
1290990 AAGTGTCATA
1291000 TTTAAGGTTTAGGG
1 TTTAAGGTTTAGGG
*
1291014 TTTAGGGTTTAGGG
1 TTTAAGGTTTAGGG
* * *
1291028 TTTATAGATTGA-GA
1 TTTA-AGGTTTAGGG
1291042 TTTAAGGTTTAGG
1 TTTAAGGTTTAGG
1291055 CTTATAGTTT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
13 5 0.16
14 23 0.72
15 4 0.12
ACGTcount: A:0.24, C:0.00, G:0.33, T:0.44
Consensus pattern (14 bp):
TTTAAGGTTTAGGG
Found at i:1295248 original size:15 final size:15
Alignment explanation
Indices: 1295223--1295264 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
1295213 TTATAAGTAT
1295223 TTATT-TAAAATAAA
1 TTATTATAAAATAAA
1295237 TTATTATAAAATAAA
1 TTATTATAAAATAAA
1295252 TTATTATAAAATA
1 TTATTATAAAATA
1295265 TGGATTGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 5 0.19
15 22 0.81
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TTATTATAAAATAAA
Found at i:1295324 original size:22 final size:22
Alignment explanation
Indices: 1295308--1295350 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1295298 AATTTATTAG
1295308 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
*
1295330 TATGGATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
1295351 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:1297447 original size:21 final size:22
Alignment explanation
Indices: 1297423--1297484 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 22
1297413 TTAGGTTAGG
* *
1297423 TAATAATTAATAA-AGAAATAT
1 TAATAATTAATAATAAAAATAC
1297444 TAAT-ATTAATAATAAAAATAC
1 TAATAATTAATAATAAAAATAC
* *
1297465 TAATAA-TAATATTTAAAATA
1 TAATAATTAATAATAAAAATA
1297485 TTTTTTTCGA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
20 8 0.23
21 26 0.74
22 1 0.03
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (22 bp):
TAATAATTAATAATAAAAATAC
Found at i:1297719 original size:18 final size:19
Alignment explanation
Indices: 1297690--1297731 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
1297680 AACATGTGAC
*
1297690 ATAAACAAAAATATATCTG
1 ATAAACAAAAATATATCCG
1297709 ATAAA-AAAAATATATCCG
1 ATAAACAAAAATATATCCG
1297727 ATAAA
1 ATAAA
1297732 TTTTACTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.62, C:0.10, G:0.05, T:0.24
Consensus pattern (19 bp):
ATAAACAAAAATATATCCG
Found at i:1298106 original size:18 final size:18
Alignment explanation
Indices: 1298085--1298133 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
1298075 TTAATTTTAC
1298085 AAATAAAAAAATCAGAAA
1 AAATAAAAAAATCAGAAA
* *
1298103 AAATTCAAAAAATCTGAAA
1 AAA-TAAAAAAATCAGAAA
*
1298122 AATTACAAAAAA
1 AAATA-AAAAAA
1298134 ATTAATATGA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 4 0.16
19 21 0.84
ACGTcount: A:0.71, C:0.08, G:0.04, T:0.16
Consensus pattern (18 bp):
AAATAAAAAAATCAGAAA
Found at i:1298114 original size:19 final size:19
Alignment explanation
Indices: 1298090--1298133 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
1298080 TTTACAAATA
1298090 AAAAAATCAGAAAAAATT-C
1 AAAAAATCAG-AAAAATTAC
*
1298109 AAAAAATCTGAAAAATTAC
1 AAAAAATCAGAAAAATTAC
1298128 AAAAAA
1 AAAAAA
1298134 ATTAATATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.70, C:0.09, G:0.05, T:0.16
Consensus pattern (19 bp):
AAAAAATCAGAAAAATTAC
Found at i:1298172 original size:25 final size:25
Alignment explanation
Indices: 1298144--1298196 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 25
1298134 ATTAATATGA
1298144 TTATTTATC-TAATTTAAATATATTT
1 TTATTTATCTTAATTT-AATATATTT
1298169 TTATTTATCTTATAATTTAATATATTT
1 TTATTTATC-T-TAATTTAATATATTT
1298196 T
1 T
1298197 AACTAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 9 0.36
27 10 0.40
28 6 0.24
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (25 bp):
TTATTTATCTTAATTTAATATATTT
Found at i:1299012 original size:20 final size:20
Alignment explanation
Indices: 1298987--1299024 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1298977 TTTGGTTCAC
1298987 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
1299007 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
1299025 GGAATAGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:1299451 original size:154 final size:156
Alignment explanation
Indices: 1299272--1299584 Score: 537
Period size: 154 Copynumber: 2.0 Consensus size: 156
1299262 TTAATAGTTG
*
1299272 TATAAGTTAAATAATAATTTTGATAGAATATAAATAAATTTTTAGTTTAATTAATGGTTAAATAT
1 TATAAGTTAAATAATAATTTCGATAGAATATAAATAAATTTTTAGTTTAATTAATGGTT-AATA-
*
1299337 TTTTTTGAAATG-TTCGGGATCAAATTGTATATCCACTAAAAACATTTAGTT-TTTAAGATA-TT
64 -TTTTTGAAATGTTTCGGGATCAAATTGTATATCCACTAAAAACATTTAGTTGATTAAGATATTT
*
1299399 AGTATAAATTAATTATAT-TTTTT-ATTA
128 AGTATAAACTAATTATATATTTTTGATTA
1299426 TATAAGTTAAATAATAATTTCGATAGAATATAAATAAATTTTTAGTTTAATTAATGGTTAATATT
1 TATAAGTTAAATAATAATTTCGATAGAATATAAATAAATTTTTAGTTTAATTAATGGTTAATATT
1299491 TTTGAAATGTTTCGGGATCAAATTGTATATCCACTAAAAACATTTAGTTGATTAAGATATTTAGT
66 TTTGAAATGTTTCGGGATCAAATTGTATATCCACTAAAAACATTTAGTTGATTAAGATATTTAGT
1299556 ATAAACTAATTATATATTTTTGATTA
131 ATAAACTAATTATATATTTTTGATTA
1299582 TAT
1 TAT
1299585 GCCTCACCAT
Statistics
Matches: 151, Mismatches: 3, Indels: 8
0.93 0.02 0.05
Matches are distributed among these distances:
151 11 0.07
152 39 0.26
153 12 0.08
154 77 0.51
155 5 0.03
156 7 0.05
ACGTcount: A:0.40, C:0.04, G:0.10, T:0.45
Consensus pattern (156 bp):
TATAAGTTAAATAATAATTTCGATAGAATATAAATAAATTTTTAGTTTAATTAATGGTTAATATT
TTTGAAATGTTTCGGGATCAAATTGTATATCCACTAAAAACATTTAGTTGATTAAGATATTTAGT
ATAAACTAATTATATATTTTTGATTA
Found at i:1303706 original size:8 final size:8
Alignment explanation
Indices: 1303693--1303733 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
1303683 CTCATTTTCA
1303693 GAGAATTT
1 GAGAATTT
1303701 GAGAATTT
1 GAGAATTT
*
1303709 -AGAGTTT
1 GAGAATTT
*
1303716 GGGAATTT
1 GAGAATTT
1303724 GAGAATTT
1 GAGAATTT
1303732 GA
1 GA
1303734 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:1304034 original size:128 final size:126
Alignment explanation
Indices: 1303806--1304289 Score: 893
Period size: 128 Copynumber: 3.8 Consensus size: 126
1303796 ATCGGAGTAC
1303806 ATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCAT
1 ATTCACATGAAGGCGCGTTCCC-GGGG-GCGCCTTCCATTATTTCGTCAGAGAATATGTTATCAT
1303871 TGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACT
64 TGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACT
1303934 ATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCAT
1 ATTCACATGAAGGCGCGTTCCC-GGGG-GCGCCTTCCATTATTTCGTCAGAGAATATGTTATCAT
1303999 TGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA-CTATTATTTCACT
64 TGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACT
1304061 ATTCACATGAAGGCGCGTTCCCGGGGGCG-CTTCCATTATTTCGTCAGAGAATATGTTATCATTG
1 ATTCACATGAAGGCGCGTTCCCGGGGGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTG
1304125 CCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACT
66 CCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACT
* *
1304186 ATTCACATGAAGACGCGTTCCCGGGGACGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTG
1 ATTCACATGAAGGCGCGTTCCCGGGGGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTG
1304251 -CCTATTATGTCACTCATGTCCCTCGGGGACACTAGATAT
66 CCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATAT
1304290 CAGTAAATAA
Statistics
Matches: 352, Mismatches: 2, Indels: 7
0.98 0.01 0.02
Matches are distributed among these distances:
124 82 0.23
125 82 0.23
126 39 0.11
127 35 0.10
128 114 0.32
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (126 bp):
ATTCACATGAAGGCGCGTTCCCGGGGGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTG
CCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACT
Found at i:1304725 original size:32 final size:34
Alignment explanation
Indices: 1304658--1304755 Score: 121
Period size: 33 Copynumber: 3.0 Consensus size: 34
1304648 AAATTTAATG
* *
1304658 TTAAATTTCGAATACTA-TAATTATATTTTAAAT
1 TTAAATTTCGAATAATATTATTTATATTTTAAAT
* *
1304691 TTAAATTT-GAATAATATTATTTTTATTTT-TAT
1 TTAAATTTCGAATAATATTATTTATATTTTAAAT
* *
1304723 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATTATTTATATTTTAAA
1304756 AACATTTATC
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
32 17 0.31
33 37 0.67
34 1 0.02
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.53
Consensus pattern (34 bp):
TTAAATTTCGAATAATATTATTTATATTTTAAAT
Found at i:1305332 original size:41 final size:42
Alignment explanation
Indices: 1305274--1305353 Score: 110
Period size: 41 Copynumber: 1.9 Consensus size: 42
1305264 ATAAAACCCT
* *
1305274 GCGGGCTAGGCATGTAA-CCTGGCGGGCTAGGCATGTAACATG
1 GCGGGCTAGGAATGTAACCCT-GCGGGCTAGGAATGTAACATG
*
1305316 GCGGG-TAGGAATGTAACCCTGCGGGCTCGGAATGTAAC
1 GCGGGCTAGGAATGTAACCCTGCGGGCTAGGAATGTAAC
1305354 CCTGTGGAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
41 26 0.76
42 8 0.24
ACGTcount: A:0.23, C:0.21, G:0.38, T:0.19
Consensus pattern (42 bp):
GCGGGCTAGGAATGTAACCCTGCGGGCTAGGAATGTAACATG
Found at i:1305355 original size:21 final size:21
Alignment explanation
Indices: 1305268--1305357 Score: 105
Period size: 21 Copynumber: 4.3 Consensus size: 21
1305258 TATGGTATAA
*
1305268 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
1305289 AA-CCTGGCGGGCTAGGCATGT
1 AACCCT-GCGGGCTAGGAATGT
*
1305310 AA-CATGGCGGG-TAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
1305330 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
1305351 AACCCTG
1 AACCCTG
1305358 TGGAGATGGC
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
20 18 0.29
21 44 0.71
ACGTcount: A:0.22, C:0.24, G:0.34, T:0.19
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:1306954 original size:17 final size:17
Alignment explanation
Indices: 1306909--1306962 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
1306899 TACATTATAA
* *
1306909 AAAATAAAAATTAATAT
1 AAAATAAAAATAAATTT
* * *
1306926 AAATTCATAATAAATTT
1 AAAATAAAAATAAATTT
1306943 AAAATAAAAATAAATTT
1 AAAATAAAAATAAATTT
1306960 AAA
1 AAA
1306963 TATTAACATT
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (17 bp):
AAAATAAAAATAAATTT
Found at i:1307174 original size:15 final size:15
Alignment explanation
Indices: 1307129--1307201 Score: 53
Period size: 15 Copynumber: 4.8 Consensus size: 15
1307119 AATATTATTT
1307129 TAATA-AAAAAATAA
1 TAATATAAAAAATAA
* *
1307143 T-ATTTACATAAAT-A
1 TAATATA-AAAAATAA
1307157 TAATATAAAAAATAA
1 TAATATAAAAAATAA
*
1307172 TAACTATTTAAAAAATAC
1 TAA-TA--TAAAAAATAA
*
1307190 TAACATAAAAAA
1 TAATATAAAAAA
1307202 AATTTCTTAC
Statistics
Matches: 46, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
13 2 0.04
14 9 0.20
15 20 0.43
16 2 0.04
17 1 0.02
18 12 0.26
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (15 bp):
TAATATAAAAAATAA
Found at i:1307184 original size:17 final size:16
Alignment explanation
Indices: 1307132--1307185 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 16
1307122 ATTATTTTAA
1307132 TAAAAA-AATAATATT
1 TAAAAATAATAATATT
1307147 TACATAAAT-ATAATA-T
1 TA-A-AAATAATAATATT
*
1307163 AAAAAATAATAACTATT
1 TAAAAATAATAA-TATT
1307180 TAAAAA
1 TAAAAA
1307186 ATACTAACAT
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
14 4 0.13
15 7 0.23
16 5 0.16
17 15 0.48
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (16 bp):
TAAAAATAATAATATT
Found at i:1307188 original size:32 final size:32
Alignment explanation
Indices: 1307133--1307204 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 32
1307123 TTATTTTAAT
* *
1307133 AAAAAAATAATATTTACATAAATA-TAATATA
1 AAAAAAATAATATTTACAAAAATACTAACATA
1307164 AAAAATAATAACTATTTA-AAAAATACTAACATA
1 AAAAA-AATAA-TATTTACAAAAATACTAACATA
1307197 AAAAAAAT
1 AAAAAAAT
1307205 TTCTTACCAC
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
31 5 0.14
32 14 0.39
33 17 0.47
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.28
Consensus pattern (32 bp):
AAAAAAATAATATTTACAAAAATACTAACATA
Found at i:1311740 original size:13 final size:13
Alignment explanation
Indices: 1311722--1311747 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1311712 GCTATTTTCT
1311722 AAATTCGTTGCGA
1 AAATTCGTTGCGA
1311735 AAATTCGTTGCGA
1 AAATTCGTTGCGA
1311748 TAGTTAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
AAATTCGTTGCGA
Found at i:1311840 original size:6 final size:6
Alignment explanation
Indices: 1311829--1311955 Score: 254
Period size: 6 Copynumber: 21.2 Consensus size: 6
1311819 GACACGTATT
1311829 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1311877 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1311925 ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG A
1311956 GACGAGACGA
Statistics
Matches: 121, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 121 1.00
ACGTcount: A:0.34, C:0.50, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1311962 original size:5 final size:5
Alignment explanation
Indices: 1311952--1311988 Score: 67
Period size: 5 Copynumber: 7.6 Consensus size: 5
1311942 GACCACGACC
1311952 ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG ACG-G ACG
1 ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG ACG
1311989 GCGGCGGCGG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.38, C:0.22, G:0.41, T:0.00
Consensus pattern (5 bp):
ACGAG
Found at i:1312496 original size:6 final size:6
Alignment explanation
Indices: 1312470--1312535 Score: 111
Period size: 6 Copynumber: 11.5 Consensus size: 6
1312460 TCTCGTCTCG
1312470 GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1312515 GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGT
1312536 AATGGTAATG
Statistics
Matches: 60, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 15 0.25
6 45 0.75
ACGTcount: A:0.00, C:0.17, G:0.53, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:1312541 original size:6 final size:6
Alignment explanation
Indices: 1312532--1312556 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1312522 GTCGTGGTCG
1312532 TGGTAA TGGTAA TGGTAA TGGTAA T
1 TGGTAA TGGTAA TGGTAA TGGTAA T
1312557 ACGTGTCTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (6 bp):
TGGTAA
Found at i:1312657 original size:19 final size:19
Alignment explanation
Indices: 1312633--1312702 Score: 77
Period size: 19 Copynumber: 3.5 Consensus size: 19
1312623 TTTTTTTACT
1312633 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
* * **
1312652 ATCGCAACGACAACTGTAGACT
1 ATCGCAACG--AA-TTTGGAAA
1312674 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
1312693 ATCGCAACGA
1 ATCGCAACGA
1312703 CATTGTAGAC
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 23 0.57
20 2 0.05
21 2 0.05
22 13 0.32
ACGTcount: A:0.40, C:0.21, G:0.20, T:0.19
Consensus pattern (19 bp):
ATCGCAACGAATTTGGAAA
Found at i:1312721 original size:40 final size:41
Alignment explanation
Indices: 1312630--1312722 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
1312620 CTTTTTTTTT
1312630 ACTATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAG
1 ACTATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAG
*
1312671 ACTATCGCAACGAATTTGGAAAATCGCAACGAC-ATTGTAG
1 ACTATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAG
1312711 ACTATCGCAACG
1 ACTATCGCAACG
1312723 CGAAATGAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
40 18 0.35
41 33 0.65
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (41 bp):
ACTATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAG
Found at i:1312735 original size:41 final size:41
Alignment explanation
Indices: 1312690--1312811 Score: 194
Period size: 41 Copynumber: 3.0 Consensus size: 41
1312680 ACGAATTTGG
1312690 AAAATCGCAACGAC-ATTGT-AGACTATCGCAACGCGAAATGA
1 AAAATCGCAACG-CGATTGTCA-ACTATCGCAACGCGAAATGA
*
1312731 AAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGA
1 AAAATCGCAACGCGATTGTCAACTATCGCAACGCGAAATGA
*
1312772 AAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATG
1 AAAATCGCAACGCGATTGTCAACTATCGCAACGCGAAATG
1312812 CAACGCGAAT
Statistics
Matches: 78, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
40 1 0.01
41 76 0.97
42 1 0.01
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (41 bp):
AAAATCGCAACGCGATTGTCAACTATCGCAACGCGAAATGA
Found at i:1312739 original size:20 final size:20
Alignment explanation
Indices: 1312714--1312786 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
1312704 ATTGTAGACT
1312714 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
** * **
1312734 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGA-AATGAAAA
1312755 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
1312775 ATCGCAACGCGA
1 ATCGCAACGCGA
1312787 TTTTCAACTA
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
20 27 0.64
21 15 0.36
ACGTcount: A:0.41, C:0.25, G:0.19, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAATGAAAA
Found at i:1312815 original size:21 final size:21
Alignment explanation
Indices: 1312711--1312815 Score: 106
Period size: 21 Copynumber: 5.1 Consensus size: 21
1312701 GACATTGTAG
1312711 ACTATCGCAACGCGAAATG-A
1 ACTATCGCAACGCGAAATGCA
** ** *
1312731 AAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
1312752 ACTATCGCAACGCGAAATG-A
1 ACTATCGCAACGCGAAATGCA
** ** *
1312772 AAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
1312793 ACTATCGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
1312814 AC
1 AC
1312816 GCGAATTTGC
Statistics
Matches: 63, Mismatches: 20, Indels: 3
0.73 0.23 0.03
Matches are distributed among these distances:
20 29 0.46
21 34 0.54
ACGTcount: A:0.39, C:0.26, G:0.17, T:0.18
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:1317371 original size:31 final size:31
Alignment explanation
Indices: 1317197--1317364 Score: 309
Period size: 31 Copynumber: 5.4 Consensus size: 31
1317187 GGATTTACTG
1317197 ATGTGAGATCTCATCTATGTTATATGTTCAT
1 ATGTGAGATCTCATCTATGTTATATGTTCAT
1317228 ATGTGAGATCTCATCTATGTTATATGTTCAT
1 ATGTGAGATCTCATCTATGTTATATGTTCAT
*
1317259 ATATGAGATCTCATCTATGTTATATGTTCAT
1 ATGTGAGATCTCATCTATGTTATATGTTCAT
1317290 ATGTGAGATCTCATCTATGTTATATGTTCAT
1 ATGTGAGATCTCATCTATGTTATATGTTCAT
*
1317321 ATGTGAGATCTCATCTATGTTATATGTTCAG
1 ATGTGAGATCTCATCTATGTTATATGTTCAT
*
1317352 ATGTAAGATCTCA
1 ATGTGAGATCTCA
1317365 GGTATGTCGT
Statistics
Matches: 133, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 133 1.00
ACGTcount: A:0.27, C:0.13, G:0.16, T:0.43
Consensus pattern (31 bp):
ATGTGAGATCTCATCTATGTTATATGTTCAT
Found at i:1318429 original size:20 final size:20
Alignment explanation
Indices: 1318406--1318469 Score: 53
Period size: 19 Copynumber: 3.2 Consensus size: 20
1318396 TAGTATTTAG
1318406 ATAAAT-TTATTAATAATTTT
1 ATAAATATT-TTAATAATTTT
* *
1318426 AT-AATCTTTTAATAAATTTA
1 ATAAATATTTTAAT-AATTTT
*
1318446 ATAAGTATTTT-ATAATTTT
1 ATAAATATTTTAATAATTTT
*
1318465 TTAAA
1 ATAAA
1318470 CTTTATTGAT
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
19 16 0.46
20 13 0.37
21 6 0.17
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (20 bp):
ATAAATATTTTAATAATTTT
Found at i:1318439 original size:19 final size:20
Alignment explanation
Indices: 1318415--1318464 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1318405 GATAAATTTA
*
1318415 TTAATAATTTTATAA-TCTT
1 TTAATAATTTTATAAGTATT
*
1318434 TTAATAAATTTAATAAGTATT
1 TTAAT-AATTTTATAAGTATT
1318455 TT-ATAATTTT
1 TTAATAATTTT
1318465 TTAAACTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 10 0.38
20 11 0.42
21 5 0.19
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TTAATAATTTTATAAGTATT
Found at i:1318467 original size:31 final size:30
Alignment explanation
Indices: 1318382--1318468 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
1318372 TTCGATAATA
* *
1318382 TAATAATTATTTTAT-AGTATTTAGATAAATT
1 TAATAA-TATTTTATAATTTTTTA-ATAAATT
* *
1318413 TATTAATAATTTTATAATCTTTTAATAAATT
1 TAATAAT-ATTTTATAATTTTTTAATAAATT
1318444 TAATAAGTATTTTATAATTTTTTAA
1 TAATAA-TATTTTATAATTTTTTAA
1318469 ACTTTATTGA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
30 1 0.02
31 40 0.85
32 6 0.13
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.54
Consensus pattern (30 bp):
TAATAATATTTTATAATTTTTTAATAAATT
Found at i:1318693 original size:31 final size:30
Alignment explanation
Indices: 1318651--1318737 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
1318641 TCAATAAAAT
1318651 TTAAAAAATTATAAAATACTTATTAAATTTA
1 TTAAAAAATTATAAAATA-TTATTAAATTTA
* *
1318682 TTAAAAGATTATAAAATTATTAATAAATTTA
1 TTAAAAAATTATAAAA-TATTATTAAATTTA
* *
1318713 TCT-AAATACTATAAAATAATTATTA
1 T-TAAAAAATTATAAAAT-ATTATTA
1318738 TATTATCGAA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
30 1 0.02
31 44 0.92
32 3 0.06
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (30 bp):
TTAAAAAATTATAAAATATTATTAAATTTA
Found at i:1330381 original size:14 final size:14
Alignment explanation
Indices: 1330362--1330397 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
1330352 TTTCTGTTAC
1330362 AGGCCCAACAATAA
1 AGGCCCAACAATAA
1330376 AGGCCCAACAATAA
1 AGGCCCAACAATAA
1330390 AGGCCCAA
1 AGGCCCAA
1330398 ATCCCAAGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.47, C:0.31, G:0.17, T:0.06
Consensus pattern (14 bp):
AGGCCCAACAATAA
Found at i:1331793 original size:13 final size:13
Alignment explanation
Indices: 1331775--1331800 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1331765 TTATTTTCTA
1331775 ATATATATAATAT
1 ATATATATAATAT
1331788 ATATATATAATAT
1 ATATATATAATAT
1331801 CGTATTTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATATATAATAT
Found at i:1332204 original size:10 final size:10
Alignment explanation
Indices: 1332189--1332213 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1332179 AGTATCTATT
1332189 TTTATTTTTC
1 TTTATTTTTC
1332199 TTTATTTTTC
1 TTTATTTTTC
1332209 TTTAT
1 TTTAT
1332214 CTTTGATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTATTTTTC
Found at i:1334713 original size:23 final size:23
Alignment explanation
Indices: 1334644--1334729 Score: 79
Period size: 23 Copynumber: 3.7 Consensus size: 23
1334634 TCATATAAAT
*
1334644 TTGCACCGTAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
* *
1334667 TTTTGTC-CCGAAG-GACGCGTAGAA
1 --TTG-CACCGAAGTGCCACGTAGAA
*
1334691 ATGCACCGAAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
1334714 TTGCACC-ATAGTGCCA
1 TTGCACCGA-AGTGCCA
1334730 TATAATATGT
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
21 1 0.02
22 9 0.18
23 22 0.44
24 9 0.18
25 8 0.16
26 1 0.02
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.21
Consensus pattern (23 bp):
TTGCACCGAAGTGCCACGTAGAA
Found at i:1346466 original size:105 final size:105
Alignment explanation
Indices: 1346284--1347091 Score: 1237
Period size: 105 Copynumber: 7.7 Consensus size: 105
1346274 GGTTTTACCC
* *
1346284 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGATTCGAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1346349 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTT
66 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTT
1346389 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1346454 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTT
66 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTT
* * *
1346494 CGAGCCAGTTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* * *
1346559 CGAAGGGACCGCTGGTTGTCAGCAAACAACTTCTCAAATTC
66 CGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAAATTT
*
1346600 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* *
1346665 CGAAGGGACCGCTGGTTGTCAATAAACATTTC-CCAATTT
66 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTT
* * *
1346704 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTTAACTTCACG
1 -AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
1346769 ACGAAGGGACCGCTGGTTGTCAATAAACATTTC-CCAATTT
65 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTT
1346809 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 -AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
1346874 ACGAAGGGA-CGCTGGTTGTCAACAAATAACTTCTC-AATTT
65 ACGAAGGGACCGCTGGTTGTCAACAAA-CATTTCTCAAATTT
*
1346914 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACG
1 -AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * * * * *
1346979 ACGAAGGGACCGCTGGTTGTCAATAAATAACTTCCCAACTTC
65 ACGAAGGGACCGCTGGTTGTCAACAAA-CATTTCTCAAATTT
* * * **** *
1347021 AGAGCCAATTTCAACTTCACAACGAAGGATTTTGGACTCAAGACAGTATAAGTTTAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1347086 CGAAGG
66 CGAAGG
1347092 AGCTATATAC
Statistics
Matches: 660, Mismatches: 37, Indels: 11
0.93 0.05 0.02
Matches are distributed among these distances:
104 21 0.03
105 450 0.68
106 186 0.28
107 3 0.00
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.23
Consensus pattern (105 bp):
AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTT
Found at i:1346856 original size:316 final size:315
Alignment explanation
Indices: 1346283--1347091 Score: 1352
Period size: 316 Copynumber: 2.6 Consensus size: 315
1346273 TGGTTTTACC
* *
1346283 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGATTCGAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
1346348 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTT-AGAGCCAATTTCAACTTCACAGC
66 ACGAAGGGACCGCTGGTTGTCAATAAACATTTC-CCAATTTCAGAGCCAATTTCAACTTCACAAC
* *
1346412 GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC
130 GAAGGATATTGGACTCCAGACAATGCAAGTTTAACTTCACGACGAAGGGACCGCTGGTTGTCAAC
*
1346477 AAACATTTCTCAAATTTCGAGCCAGTTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
195 AAACATTTCTCAAATTTCGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* *
1346542 TAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAGCAAACAACTTCTCAAATT
260 CAAGTTCAACTTCACGACGAAGGGA-CGCTGGTTGTCAACAAACAACTTCTCAAATT
*
1346599 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1346664 ACGAAGGGACCGCTGGTTGTCAATAAACATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACG
66 ACGAAGGGACCGCTGGTTGTCAATAAACATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACG
*
1346729 AAGGATATTGGACTCCAGACAATGCAAGTTTAACTTCACGACGAAGGGACCGCTGGTTGTCAATA
131 AAGGATATTGGACTCCAGACAATGCAAGTTTAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
*
1346794 AACATTTC-CCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
196 AACATTTCTCAAATTTC-GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* *
1346858 CAAGTTCAACTTCACGACGAAGGGACGCTGGTTGTCAACAAATAACTTCTCAATTT
260 CAAGTTCAACTTCACGACGAAGGGACGCTGGTTGTCAACAAACAACTTCTCAAATT
*
1346914 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
1346979 ACGAAGGGACCGCTGGTTGTCAATAAATAACTTCCCAACTTCAGAGCCAATTTCAACTTCACAAC
66 ACGAAGGGACCGCTGGTTGTCAATAAA-CATTTCCCAATTTCAGAGCCAATTTCAACTTCACAAC
* * * **
1347044 GAAGGATTTTGGACTCAAGACAGTATAAGTTTAACTTCACGACGAAGG
130 GAAGGATATTGGACTCCAGACAATGCAAGTTTAACTTCACGACGAAGG
1347092 AGCTATATAC
Statistics
Matches: 465, Mismatches: 25, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
315 131 0.28
316 334 0.72
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.23
Consensus pattern (315 bp):
CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAATAAACATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACG
AAGGATATTGGACTCCAGACAATGCAAGTTTAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
AACATTTCTCAAATTTCGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGC
AAGTTCAACTTCACGACGAAGGGACGCTGGTTGTCAACAAACAACTTCTCAAATT
Found at i:1347082 original size:421 final size:421
Alignment explanation
Indices: 1346283--1347091 Score: 1354
Period size: 421 Copynumber: 1.9 Consensus size: 421
1346273 TGGTTTTACC
* * *
1346283 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGATTCGAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1346348 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTTAGAGCCAATTTCAACTTCACAGCG
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTTAGAGCCAATTTCAACTTCACAGCG
1346413 AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
131 AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
* * * *
1346478 AACATTTCTCAAATTTCGAGCCAGTTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGT
196 AAAACTTCTCAAATTTCGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGC
* *
1346543 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAGCAAACAACTTCTCAAATTCAGAGCCAA
261 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAAATTCAGAGCCAA
* *
1346608 TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGA
326 TTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACGACGAAGGGA
1346673 CCGCTGGTTGTCAATAAACATTTCCCAATTT
391 CCGCTGGTTGTCAATAAACATTTCCCAATTT
* *
1346704 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTTAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
1346769 ACGAAGGGACCGCTGGTTGTCAATAAACATTTC-CCAATTTCAGAGCCAATTTCAACTTCACAGC
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTT-AGAGCCAATTTCAACTTCACAGC
1346833 GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGA-CGCTGGTTGTCAAC
130 GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC
1346897 AAATAACTTCTC-AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAA
195 AAA-AACTTCTCAAATTTC-GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAA
* * * *
1346961 TGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAATAACTTCCCAACTTCAGAGC
258 CGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAAATTCAGAGC
* ** * *
1347026 CAATTTCAACTTCACAACGAAGGATTTTGGACTCAAGACAGTATAAGTTTAACTTCACGACGAAG
323 CAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACGACGAAG
1347091 G
388 G
1347092 AGCTATATAC
Statistics
Matches: 361, Mismatches: 24, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
420 29 0.08
421 332 0.92
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.23
Consensus pattern (421 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTTAGAGCCAATTTCAACTTCACAGCG
AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
AAAACTTCTCAAATTTCGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGC
AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAAATTCAGAGCCAA
TTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACGACGAAGGGA
CCGCTGGTTGTCAATAAACATTTCCCAATTT
Found at i:1349319 original size:4 final size:4
Alignment explanation
Indices: 1349310--1349400 Score: 55
Period size: 4 Copynumber: 23.0 Consensus size: 4
1349300 TTTCCTCATC
* * *
1349310 TTAT TTAT TTAG TTAT CTAT TTAT TTA- TT-T TTCT TTA- TT-T TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
* * * **
1349354 CTTGAT TTAT TTAC TCAT ATTGT TTAT TTAT TTAT CCAT TTAT TTAT
1 -TT-AT TTAT TTAT TTAT -TTAT TTAT TTAT TTAT TTAT TTAT TTAT
1349401 GTATATTGTC
Statistics
Matches: 65, Mismatches: 15, Indels: 14
0.69 0.16 0.15
Matches are distributed among these distances:
3 8 0.12
4 49 0.75
5 6 0.09
6 2 0.03
ACGTcount: A:0.22, C:0.08, G:0.03, T:0.67
Consensus pattern (4 bp):
TTAT
Found at i:1366471 original size:2 final size:2
Alignment explanation
Indices: 1366464--1366507 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1366454 ATCATATACA
1366464 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1366506 AT
1 AT
1366508 TCATAATTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1367081 original size:3 final size:3
Alignment explanation
Indices: 1367068--1367105 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
1367058 TTAAGAACAC
1367068 TAA TCAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1367106 TTTATTAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1367680 original size:24 final size:24
Alignment explanation
Indices: 1367653--1367704 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
1367643 AGGGGAAGTA
1367653 AGGTAGTAGATGGTATCTAACGCC
1 AGGTAGTAGATGGTATCTAACGCC
1367677 AGGTAGTAGATGGTATCTAACGCC
1 AGGTAGTAGATGGTATCTAACGCC
1367701 AGGT
1 AGGT
1367705 TGAGAGTAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.29, C:0.15, G:0.31, T:0.25
Consensus pattern (24 bp):
AGGTAGTAGATGGTATCTAACGCC
Found at i:1370912 original size:15 final size:15
Alignment explanation
Indices: 1370894--1370949 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
1370884 TTTTGAATTT
1370894 TATTATTAATCATTA
1 TATTATTAATCATTA
** *
1370909 TATTATGCATAAATTA
1 TATTATTAAT-CATTA
1370925 TA-TATTTAATCATTA
1 TATTA-TTAATCATTA
1370940 TATTA-TAATC
1 TATTATTAATC
1370950 TGATTTATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
14 5 0.16
15 16 0.50
16 11 0.34
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.50
Consensus pattern (15 bp):
TATTATTAATCATTA
Found at i:1376629 original size:32 final size:32
Alignment explanation
Indices: 1376583--1376655 Score: 128
Period size: 32 Copynumber: 2.2 Consensus size: 32
1376573 ATCTCACCGA
1376583 TTGGATTTTTGTTCTCTTTTAGCAATCGGGTTG
1 TTGGA-TTTTGTTCTCTTTTAGCAATCGGGTTG
1376616 TTGGATTTTGTTCTCTTTTAGCAATCGGGTTG
1 TTGGATTTTGTTCTCTTTTAGCAATCGGGTTG
*
1376648 TTGTATTT
1 TTGGATTT
1376656 GTTTGTGAGA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
32 34 0.87
33 5 0.13
ACGTcount: A:0.12, C:0.11, G:0.23, T:0.53
Consensus pattern (32 bp):
TTGGATTTTGTTCTCTTTTAGCAATCGGGTTG
Found at i:1379942 original size:39 final size:39
Alignment explanation
Indices: 1379865--1379944 Score: 101
Period size: 40 Copynumber: 2.1 Consensus size: 39
1379855 TGTGCGTTTA
* * *
1379865 TTTAATAAATGAACGAACATGAACAAGATTTTGTGTTCG
1 TTTAATAAATGAACGAACATGAACAAGAGTCTGCGTTCG
1379904 TTTAATTAAATGAACGAACATGAACATAG-GTCT-CGTTCG
1 TTTAA-TAAATGAACGAACATGAACA-AGAGTCTGCGTTCG
1379943 TT
1 TT
1379945 CATTTACGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
39 12 0.33
40 22 0.61
41 2 0.06
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.34
Consensus pattern (39 bp):
TTTAATAAATGAACGAACATGAACAAGAGTCTGCGTTCG
Found at i:1379978 original size:24 final size:24
Alignment explanation
Indices: 1379951--1380006 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
1379941 CGTTCATTTA
1379951 CGTTC-GTGAACGTTCGGTTATGTT
1 CGTTCGGT-AACGTTCGGTTATGTT
* * *
1379975 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
1379999 CGTTCGGT
1 CGTTCGGT
1380007 TATGTTCATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 26 0.93
25 2 0.07
ACGTcount: A:0.09, C:0.16, G:0.29, T:0.46
Consensus pattern (24 bp):
CGTTCGGTAACGTTCGGTTATGTT
Done.