Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008087.1 Hibiscus syriacus cultivar Beakdansim tig00110597_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: 8279816
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 37
Found at i:3174396 original size:18 final size:18
Alignment explanation
Indices: 3174373--3174407 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3174363 AGCAAATGGC
3174373 AATCAAAATCGCAATCAA
1 AATCAAAATCGCAATCAA
*
3174391 AATCAAAATCTCAATCA
1 AATCAAAATCGCAATCA
3174408 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.23, G:0.03, T:0.20
Consensus pattern (18 bp):
AATCAAAATCGCAATCAA
Found at i:3174717 original size:140 final size:140
Alignment explanation
Indices: 3174465--3174747 Score: 530
Period size: 140 Copynumber: 2.0 Consensus size: 140
3174455 GCAAACGTTG
*
3174465 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAATAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAATAACTTGAGT
*
3174530 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
*
3174595 CGAATTTGAC
131 CGAATATGAC
*
3174605 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAATAACTTGAGT
3174670 TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
3174735 CGAATATGAC
131 CGAATATGAC
3174745 TAT
1 TAT
3174748 CGCAACGCAA
Statistics
Matches: 139, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 139 1.00
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.43
Consensus pattern (140 bp):
TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAATAACTTGAGT
TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
CGAATATGAC
Found at i:3174750 original size:20 final size:20
Alignment explanation
Indices: 3174718--3174888 Score: 210
Period size: 20 Copynumber: 8.8 Consensus size: 20
3174708 TTACACATTC
*
3174718 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
3174738 ATATGACTATCGCAACGC-A
1 ATTTGACTATCGCAACGCGA
* *
3174757 A----A-AATTGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
3174772 ATTTGATTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
3174792 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
3174812 ATTTGACTATCGTAACGCGA
1 ATTTGACTATCGCAACGCGA
*
3174832 ATTTGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
* * *
3174852 ATTTGATTATCGCAATGGGA
1 ATTTGACTATCGCAACGCGA
3174872 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
3174889 AGAAAATTGC
Statistics
Matches: 130, Mismatches: 15, Indels: 12
0.83 0.10 0.08
Matches are distributed among these distances:
14 9 0.07
15 3 0.02
19 3 0.02
20 115 0.88
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:3174956 original size:20 final size:20
Alignment explanation
Indices: 3174931--3174988 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 20
3174921 CGCGAATTGA
*
3174931 CTTTCGCGTTGCGATTTTGG
1 CTTTCGCATTGCGATTTTGG
*
3174951 CTTTCGCATT-CGATTTTGA
1 CTTTCGCATTGCGATTTTGG
* *
3174970 CTTTTGCATTGTGATTTTG
1 CTTTCGCATTGCGATTTTG
3174989 AGTTTAGCGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.10, C:0.17, G:0.22, T:0.50
Consensus pattern (20 bp):
CTTTCGCATTGCGATTTTGG
Found at i:3174989 original size:20 final size:20
Alignment explanation
Indices: 3174927--3175003 Score: 84
Period size: 20 Copynumber: 3.9 Consensus size: 20
3174917 GCAACGCGAA
*
3174927 TTGACTTTCGCGTTGCGATT
1 TTGACTTTCGCATTGCGATT
*
3174947 TTGGCTTTCGCATT-CGATT
1 TTGACTTTCGCATTGCGATT
* *
3174966 TTGACTTTTGCATTGTGATT
1 TTGACTTTCGCATTGCGATT
* * *
3174986 TTGAGTTTAGCGTTGCGA
1 TTGACTTTCGCATTGCGA
3175004 AAGTGTACCT
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
19 17 0.36
20 30 0.64
ACGTcount: A:0.13, C:0.16, G:0.25, T:0.47
Consensus pattern (20 bp):
TTGACTTTCGCATTGCGATT
Found at i:3176595 original size:42 final size:42
Alignment explanation
Indices: 3176541--3176648 Score: 112
Period size: 42 Copynumber: 2.6 Consensus size: 42
3176531 TTGAATGGTG
* *
3176541 GGAGA-GACCTCTTCAACGATGACAAGGGCCTCTTGAAC-AGTG
1 GGAGAGGA-CTCTTGAACGATGACAAGGGCCTCTTGAACGA-TA
* ** * *
3176583 GGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGATA
1 GGAGAGGACTCTTGAACGATGACAAGGGCCTCTTGAACGATA
*
3176625 GGAGAGGCCTCTTGAACGATGACA
1 GGAGAGGACTCTTGAACGATGACA
3176649 GGTGAGTCGG
Statistics
Matches: 52, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
42 49 0.94
43 3 0.06
ACGTcount: A:0.27, C:0.19, G:0.34, T:0.19
Consensus pattern (42 bp):
GGAGAGGACTCTTGAACGATGACAAGGGCCTCTTGAACGATA
Found at i:3177152 original size:20 final size:20
Alignment explanation
Indices: 3177127--3177170 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
3177117 AATAGTTTCT
3177127 GAAACTTAAAATCGCAACAC
1 GAAACTTAAAATCGCAACAC
*
3177147 GAAACTTAAAATCGCAACGC
1 GAAACTTAAAATCGCAACAC
3177167 GAAA
1 GAAA
3177171 ATGACTATCG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.50, C:0.23, G:0.14, T:0.14
Consensus pattern (20 bp):
GAAACTTAAAATCGCAACAC
Found at i:3177258 original size:20 final size:19
Alignment explanation
Indices: 3177229--3177337 Score: 66
Period size: 20 Copynumber: 5.8 Consensus size: 19
3177219 CGAAACTAAA
*
3177229 TTCGCGTTGCGATTTTCATT
1 TTCGCATTGCGATTTTCA-T
*
3177249 TTCGCATTGCAATTTTCA-
1 TTCGCATTGCGATTTTCAT
*
3177267 --CG--TTGCGATTTTTAT
1 TTCGCATTGCGATTTTCAT
** *
3177282 TTCGCATTGCGATAGTCAAA
1 TTCGCATTGCGATTTTC-AT
* * **
3177302 TCCGCGTTGCGATAGTCATT
1 TTCGCATTGCGATTTTCA-T
3177322 TTCGCATTGCGATTTT
1 TTCGCATTGCGATTTT
3177338 AAGTTTCGTG
Statistics
Matches: 67, Mismatches: 15, Indels: 14
0.70 0.16 0.15
Matches are distributed among these distances:
14 10 0.15
16 2 0.03
17 2 0.03
19 9 0.13
20 44 0.66
ACGTcount: A:0.17, C:0.20, G:0.19, T:0.43
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:3179269 original size:20 final size:20
Alignment explanation
Indices: 3179246--3179286 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
3179236 TCTGAAACTT
3179246 AAAATCCCAACACGAAAATG
1 AAAATCCCAACACGAAAATG
*
3179266 AAAATCGCAACACGAAAATG
1 AAAATCCCAACACGAAAATG
3179286 A
1 A
3179287 CTATCGCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.56, C:0.22, G:0.12, T:0.10
Consensus pattern (20 bp):
AAAATCCCAACACGAAAATG
Found at i:3179292 original size:20 final size:20
Alignment explanation
Indices: 3179253--3179316 Score: 83
Period size: 20 Copynumber: 3.2 Consensus size: 20
3179243 CTTAAAATCC
**
3179253 CAACACGAAAATGAAAATCG
1 CAACACGAAAATGACTATCG
3179273 CAACACGAAAATGACTATCG
1 CAACACGAAAATGACTATCG
* **
3179293 CAACGCGAATTTGACTATCG
1 CAACACGAAAATGACTATCG
3179313 CAAC
1 CAAC
3179317 GAGATAATCG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.44, C:0.25, G:0.16, T:0.16
Consensus pattern (20 bp):
CAACACGAAAATGACTATCG
Found at i:3179769 original size:22 final size:22
Alignment explanation
Indices: 3179742--3179783 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
3179732 AGATAGACGA
3179742 ATTTCGCCGGAGATGGGGACAG
1 ATTTCGCCGGAGATGGGGACAG
*
3179764 ATTTCGGCGGAGATGGGGAC
1 ATTTCGCCGGAGATGGGGAC
3179784 GGATGTTGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.17, G:0.43, T:0.19
Consensus pattern (22 bp):
ATTTCGCCGGAGATGGGGACAG
Found at i:3179985 original size:20 final size:20
Alignment explanation
Indices: 3179962--3180026 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
3179952 TTATCGTAAC
*
3179962 GCGATAGTCAGAATCGCGTT
1 GCGATAGTCAAAATCGCGTT
*
3179982 GCGATTA-T-ATATTATCGCGTT
1 GCGA-TAGTCA-A-AATCGCGTT
*
3180003 GCGATAGTCAAAACCGCGTT
1 GCGATAGTCAAAATCGCGTT
3180023 GCGA
1 GCGA
3180027 ATCTGGAAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
19 1 0.03
20 18 0.50
21 16 0.44
22 1 0.03
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (20 bp):
GCGATAGTCAAAATCGCGTT
Found at i:3179995 original size:41 final size:41
Alignment explanation
Indices: 3179930--3180026 Score: 113
Period size: 41 Copynumber: 2.4 Consensus size: 41
3179920 TGGCGCTTTG
* * * *
3179930 AAAATCGCATTGCGATTTTGTATTATCGTAACGCGATAGTC
1 AAAATCGCGTTGCGATTATATATTATCGCAACGCGATAGTC
* ***
3179971 AGAATCGCGTTGCGATTATATATTATCGCGTTGCGATAGTC
1 AAAATCGCGTTGCGATTATATATTATCGCAACGCGATAGTC
*
3180012 AAAACCGCGTTGCGA
1 AAAATCGCGTTGCGA
3180027 ATCTGGAAAC
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.31
Consensus pattern (41 bp):
AAAATCGCGTTGCGATTATATATTATCGCAACGCGATAGTC
Found at i:3182981 original size:53 final size:53
Alignment explanation
Indices: 3182918--3183028 Score: 213
Period size: 53 Copynumber: 2.1 Consensus size: 53
3182908 ATGACATGGC
*
3182918 TATTTCAGTGTTTTATGAGCAAGAGAAGAAAGTTCATCTACTTCTTAATTTAA
1 TATTTCAGTGTTTTATGAGCAAGAGAAGAAAGTTCATCTACGTCTTAATTTAA
3182971 TATTTCAGTGTTTTATGAGCAAGAGAAGAAAGTTCATCTACGTCTTAATTTAA
1 TATTTCAGTGTTTTATGAGCAAGAGAAGAAAGTTCATCTACGTCTTAATTTAA
3183024 TATTT
1 TATTT
3183029 TCCCTTTTCT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 57 1.00
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (53 bp):
TATTTCAGTGTTTTATGAGCAAGAGAAGAAAGTTCATCTACGTCTTAATTTAA
Found at i:3192860 original size:20 final size:18
Alignment explanation
Indices: 3192794--3192862 Score: 65
Period size: 18 Copynumber: 3.9 Consensus size: 18
3192784 AAAATACAAC
3192794 ATTCCC-AGTAATC--TT
1 ATTCCCTAGTAATCTTTT
3192809 ATTCCCT-GATAATCTTTT
1 ATTCCCTAG-TAATCTTTT
* *
3192827 ATTTCCTGGTAATCTTTT
1 ATTCCCTAGTAATCTTTT
3192845 ATTACCACTAGTAATCTT
1 ATT-CC-CTAGTAATCTT
3192863 ACATTTCGTG
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
15 7 0.16
16 5 0.11
18 20 0.45
19 2 0.05
20 10 0.23
ACGTcount: A:0.25, C:0.22, G:0.07, T:0.46
Consensus pattern (18 bp):
ATTCCCTAGTAATCTTTT
Found at i:3193668 original size:2 final size:2
Alignment explanation
Indices: 3193650--3193724 Score: 132
Period size: 2 Copynumber: 37.5 Consensus size: 2
3193640 TCCTAACTTT
* *
3193650 TA TA TT TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3193692 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3193725 TAATTCTAAA
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3195158 original size:12 final size:12
Alignment explanation
Indices: 3195141--3195171 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
3195131 AAGATAAGAA
3195141 GGTTAACCATCC
1 GGTTAACCATCC
3195153 GGTTAACCATCC
1 GGTTAACCATCC
3195165 GGTTAAC
1 GGTTAAC
3195172 ACTAATTCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (12 bp):
GGTTAACCATCC
Found at i:3201798 original size:25 final size:24
Alignment explanation
Indices: 3201746--3201805 Score: 102
Period size: 24 Copynumber: 2.5 Consensus size: 24
3201736 ATTATAAAAC
*
3201746 AAAAACTATCAAGTTTTATTGGTG
1 AAAAACTATCAAGTTTTATTGGGG
3201770 AAAAACTATCAAGTTTTATTGGGG
1 AAAAACTATCAAGTTTTATTGGGG
*
3201794 AAAAACTTTCAA
1 AAAAACTATCAA
3201806 ATAATTGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (24 bp):
AAAAACTATCAAGTTTTATTGGGG
Found at i:3207507 original size:23 final size:23
Alignment explanation
Indices: 3207479--3207529 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
3207469 TTGGTATAGA
3207479 TCTTCTGCATATCTACCGTCCCT
1 TCTTCTGCATATCTACCGTCCCT
*
3207502 TCTTCTGCATATCTATCGTCCCT
1 TCTTCTGCATATCTACCGTCCCT
3207525 TCTTC
1 TCTTC
3207530 CACCTTTTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.12, C:0.37, G:0.08, T:0.43
Consensus pattern (23 bp):
TCTTCTGCATATCTACCGTCCCT
Found at i:3210426 original size:120 final size:112
Alignment explanation
Indices: 3210267--3210515 Score: 295
Period size: 113 Copynumber: 2.2 Consensus size: 112
3210257 ACCATCCGAA
* *** *
3210267 TCAAATCTTTTTTT-TTTCCTCATCAACTAATCTTGCAAAAGATGGCAATATGGAAGAAGAAGAA
1 TCAAATCTTTTTTTCTTTCCTCATCAACTAATCTTACAAAAGACAACAACAT-G-A-AAGAAG-A
3210331 AAATGGATTGGGAAAATAAGTTGAAAAAGAACTTAGTTAAGGAAGGT-AGAGGGT
62 AAA--GATTGGG-AAATAAGTTGAAAAAGAACTTAGTTAAGGAAGGTGA-AGGGT
* *
3210385 TCAAATCTTCTTTTTCTTTCCTTATCAACTAATCTTACAAAAGACAACAACATGAAAGAAGAAGA
1 TCAAATCTT-TTTTTCTTTCCTCATCAACTAATCTTACAAAAGACAACAACATGAAAGAAGAAAA
* ** *
3210450 GATTTGGAAATGGGTTGAAGAAGAACTTAGTTAAGGAAGGTGAAGGGT
65 GATTGGGAAATAAGTTGAAAAAGAACTTAGTTAAGGAAGGTGAAGGGT
3210498 TCAAATCTTTTTCTTCTT
1 TCAAATCTTTTT-TTCTT
3210516 CTTTTGATAT
Statistics
Matches: 116, Mismatches: 11, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
112 3 0.03
113 50 0.43
114 7 0.06
116 3 0.03
117 6 0.05
118 10 0.09
119 6 0.05
120 31 0.27
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.31
Consensus pattern (112 bp):
TCAAATCTTTTTTTCTTTCCTCATCAACTAATCTTACAAAAGACAACAACATGAAAGAAGAAAAG
ATTGGGAAATAAGTTGAAAAAGAACTTAGTTAAGGAAGGTGAAGGGT
Found at i:3212981 original size:22 final size:23
Alignment explanation
Indices: 3212941--3212983 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
3212931 TATAATAAAA
3212941 TAATATTATTTATTATAAAAACT
1 TAATATTATTTATTATAAAAACT
*
3212964 TAATATTA-TTATTTTAAAAA
1 TAATATTATTTATTATAAAAA
3212984 TATTAGAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
TAATATTATTTATTATAAAAACT
Found at i:3213144 original size:21 final size:23
Alignment explanation
Indices: 3213119--3213165 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
3213109 TCTATAAAAA
*
3213119 TAAAAATATT-AT-ATTATATTT
1 TAAAAATATTAATAAATATATTT
3213140 TAAAAATATTAATAAATATATTT
1 TAAAAATATTAATAAATATATTT
3213163 TAA
1 TAA
3213166 GGAATTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 10 0.43
22 2 0.09
23 11 0.48
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TAAAAATATTAATAAATATATTT
Found at i:3213163 original size:23 final size:21
Alignment explanation
Indices: 3213119--3213180 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 21
3213109 TCTATAAAAA
*
3213119 TAAAAATATTATATTATATTT
1 TAAAAATATTATAATATATTT
3213140 TAAAAATATTAATAAATATATTT
1 TAAAAATATT-AT-AATATATTT
* *
3213163 TAAGGAATTTTATAATAT
1 TAA-AAATATTATAATAT
3213181 TATTAGACTA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 10 0.29
22 7 0.20
23 13 0.37
24 5 0.14
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (21 bp):
TAAAAATATTATAATATATTT
Found at i:3213341 original size:26 final size:26
Alignment explanation
Indices: 3213312--3213371 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
3213302 TATTAAAATA
3213312 ATAATATAA-T-AGTATCATATATTATT
1 ATAATATAATTGAGTAT-AT-TATTATT
3213338 ATAATATAATTGAGTATATTATTATT
1 ATAATATAATTGAGTATATTATTATT
*
3213364 ATATTATA
1 ATAATATA
3213372 TTATTAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 23 0.74
27 3 0.10
28 5 0.16
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (26 bp):
ATAATATAATTGAGTATATTATTATT
Found at i:3213410 original size:23 final size:23
Alignment explanation
Indices: 3213368--3213424 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
3213358 ATTATTATAT
3213368 TATATTATTAAAAATATTAATAAA
1 TATATT-TTAAAAATATTAATAAA
* * *
3213392 TATATTTTAAATATGTTAATAAT
1 TATATTTTAAAAATATTAATAAA
3213415 TAATATTTTA
1 T-ATATTTTA
3213425 TTAAAATGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 15 0.52
24 14 0.48
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
TATATTTTAAAAATATTAATAAA
Found at i:3224835 original size:17 final size:16
Alignment explanation
Indices: 3224788--3224824 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
3224778 ATTTAGAACT
3224788 AAATAAAA-A-AAT-C
1 AAATAAAATATAATAC
3224801 AAATAAAATATAATAC
1 AAATAAAATATAATAC
3224817 AAATAAAA
1 AAATAAAA
3224825 ATAGATGACA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 8 0.38
14 1 0.05
15 3 0.14
16 9 0.43
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.19
Consensus pattern (16 bp):
AAATAAAATATAATAC
Found at i:3231698 original size:51 final size:51
Alignment explanation
Indices: 3231634--3231739 Score: 185
Period size: 51 Copynumber: 2.1 Consensus size: 51
3231624 TTACTCTAAG
* *
3231634 TATGTAATCCATGGAGTCTTTGAGTAAACACAAACCCAATGGAAACAATGA
1 TATGAAATCCATGGAATCTTTGAGTAAACACAAACCCAATGGAAACAATGA
*
3231685 TATGAAATCCATGGAATCTTTGAGTAAACACAAACCCAATGGTAACAATGA
1 TATGAAATCCATGGAATCTTTGAGTAAACACAAACCCAATGGAAACAATGA
3231736 TATG
1 TATG
3231740 TGTATGATTA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.25
Consensus pattern (51 bp):
TATGAAATCCATGGAATCTTTGAGTAAACACAAACCCAATGGAAACAATGA
Found at i:3231849 original size:5 final size:5
Alignment explanation
Indices: 3231839--3231869 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
3231829 ATAATTCCCG
3231839 CCAAA CCAAA CCAAA CCAAA CCAAA CCAAA C
1 CCAAA CCAAA CCAAA CCAAA CCAAA CCAAA C
3231870 GTGTTCATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.58, C:0.42, G:0.00, T:0.00
Consensus pattern (5 bp):
CCAAA
Found at i:3235668 original size:21 final size:21
Alignment explanation
Indices: 3235623--3235668 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
3235613 TTATAAGTAG
3235623 TAAA-CAAATAAATTAATTAT
1 TAAATCAAATAAATTAATTAT
*
3235643 CAAATCAAATATAATTAA-TAT
1 TAAATCAAATA-AATTAATTAT
3235664 TAAAT
1 TAAAT
3235669 TGTTTACTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 3 0.14
21 13 0.59
22 6 0.27
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAATCAAATAAATTAATTAT
Found at i:3235988 original size:27 final size:27
Alignment explanation
Indices: 3235950--3236010 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
3235940 GTAGTCCTCT
*
3235950 TATCATTTAAAATCGTTGAAATTAAAC
1 TATCATTTAAAATCGTTGAAATCAAAC
*
3235977 TATCATTTAAAATCGTTGAAATCAAAT
1 TATCATTTAAAATCGTTGAAATCAAAC
3236004 TATCATT
1 TATCATT
3236011 CTATTCATCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.39
Consensus pattern (27 bp):
TATCATTTAAAATCGTTGAAATCAAAC
Found at i:3240791 original size:18 final size:19
Alignment explanation
Indices: 3240756--3240792 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
3240746 CACGGAATGT
3240756 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
3240776 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
3240793 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:3241369 original size:11 final size:11
Alignment explanation
Indices: 3241353--3241380 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
3241343 TGGGATTCCC
3241353 ATCCCATGGGA
1 ATCCCATGGGA
3241364 ATCCCATGGGA
1 ATCCCATGGGA
3241375 ATCCCA
1 ATCCCA
3241381 CATTCCTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.29, C:0.32, G:0.21, T:0.18
Consensus pattern (11 bp):
ATCCCATGGGA
Found at i:3248638 original size:50 final size:51
Alignment explanation
Indices: 3248565--3248660 Score: 140
Period size: 50 Copynumber: 1.9 Consensus size: 51
3248555 GTGTTATTAG
** *
3248565 AACTCGTCATGTCGAGGTGACGAGTTCTAATAAAAAAT-ATTTTTTATTCA
1 AACTCGTCACCTCGAGGTAACGAGTTCTAATAAAAAATAATTTTTTATTCA
* *
3248615 AACTCGTCACCTCGAGTTAACGAGTTCTAATAAAATATAATTTTTT
1 AACTCGTCACCTCGAGGTAACGAGTTCTAATAAAAAATAATTTTTT
3248661 TATTAAAATC
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
50 33 0.82
51 7 0.17
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (51 bp):
AACTCGTCACCTCGAGGTAACGAGTTCTAATAAAAAATAATTTTTTATTCA
Found at i:3255189 original size:25 final size:27
Alignment explanation
Indices: 3255158--3255222 Score: 71
Period size: 30 Copynumber: 2.4 Consensus size: 27
3255148 AAATACTCAA
3255158 AATAATATTATTTTA-TA-AATTTAAT
1 AATAATATTATTTTAGTACAATTTAAT
*
3255183 AATAATATGATATTTTAGTATCATTTTAAT
1 AATAATAT--TATTTTAGTA-CAATTTAAT
*
3255213 AAAAATATTA
1 AATAATATTA
3255223 ATTATTAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
25 8 0.24
27 7 0.21
28 4 0.12
30 14 0.42
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.48
Consensus pattern (27 bp):
AATAATATTATTTTAGTACAATTTAAT
Found at i:3255254 original size:23 final size:24
Alignment explanation
Indices: 3255214--3255262 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
3255204 CATTTTAATA
3255214 AAAATATTAATTATTAAT-TTATTT
1 AAAATATTAATTATTAATATT-TTT
*
3255238 AAAATA-TATTTATTAATATTTTT
1 AAAATATTAATTATTAATATTTTT
3255261 AA
1 AA
3255263 TAACGTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
AAAATATTAATTATTAATATTTTT
Found at i:3256142 original size:2 final size:2
Alignment explanation
Indices: 3256135--3256197 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
3256125 GAATTTCATG
3256135 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3256177 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
3256198 TAAGATTCAC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3258955 original size:3 final size:3
Alignment explanation
Indices: 3258947--3258972 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3258937 GGGCTCATAT
3258947 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
3258973 TTATTATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3258977 original size:3 final size:3
Alignment explanation
Indices: 3258971--3259004 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
3258961 ATAATAATAA
3258971 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3259005 TAGAATCAAA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:3261836 original size:19 final size:18
Alignment explanation
Indices: 3261776--3261863 Score: 55
Period size: 17 Copynumber: 5.1 Consensus size: 18
3261766 TTTATGTTAT
3261776 TATTTTT-TTAAATAGTTA
1 TATTTTTATTAAATA-TTA
3261794 T-TATTTT-TT--ATATTAA
1 TAT-TTTTATTAAATATT-A
*
3261810 TATATTTATGTAAATATTA
1 TATTTTTAT-TAAATATTA
*
3261829 TATTTTTATTAAA-ATAA
1 TATTTTTATTAAATATTA
* *
3261846 TATTTATA-TAATTATTA
1 TATTTTTATTAAATATTA
3261863 T
1 T
3261864 TTATTTAGAA
Statistics
Matches: 56, Mismatches: 6, Indels: 17
0.71 0.08 0.22
Matches are distributed among these distances:
15 2 0.04
16 11 0.20
17 17 0.30
18 12 0.21
19 9 0.16
20 5 0.09
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (18 bp):
TATTTTTATTAAATATTA
Found at i:3261869 original size:36 final size:33
Alignment explanation
Indices: 3261782--3261870 Score: 85
Period size: 34 Copynumber: 2.7 Consensus size: 33
3261772 TTATTATTTT
* *
3261782 TTTAAATAGTTATTATTT-TTTATATTAATATA
1 TTTATATAATTATTATTTATTTATATTAATATA
* * *
3261814 TTTATGTAAATATTATATT-TTTAT-TAAAATAATA
1 TTTATATAATTATTAT-TTATTTATAT-TAAT-ATA
3261848 TTTATATAATTATTATTTATTTA
1 TTTATATAATTATTATTTATTTA
3261871 GAATTTTTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
32 13 0.28
33 12 0.26
34 21 0.46
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.58
Consensus pattern (33 bp):
TTTATATAATTATTATTTATTTATATTAATATA
Found at i:3262026 original size:17 final size:17
Alignment explanation
Indices: 3262004--3262057 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
3261994 AATGTTAATA
3262004 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
3262021 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
3262038 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
3262055 TTT
1 TTT
3262058 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:3263618 original size:21 final size:21
Alignment explanation
Indices: 3263588--3263635 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
3263578 GTAGGGGTAC
* *
3263588 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
3263609 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
3263630 ATGCCA
1 ATGCCA
3263636 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:3263665 original size:21 final size:21
Alignment explanation
Indices: 3263639--3263732 Score: 145
Period size: 21 Copynumber: 4.5 Consensus size: 21
3263629 TATGCCATCT
3263639 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
3263660 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
*
3263681 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCGAGC
* *
3263702 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCGAGC
3263723 CCGCAGGGTT
1 CCGCAGGGTT
3263733 TTATACCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 2 0.03
21 65 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.34, G:0.28, T:0.20
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCGAGC
Found at i:3264313 original size:33 final size:34
Alignment explanation
Indices: 3264254--3264350 Score: 124
Period size: 33 Copynumber: 2.9 Consensus size: 34
3264244 AAATGTTTTT
*
3264254 AAAATACAAATTATATTATTCAAAATTTAAAATA
1 AAAATAAAAATTATATTATTCAAAATTTAAAATA
* * *
3264288 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAATTATATTATTCAAAATTTAAAATA
* * *
3264321 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCAAAATTTAA
3264351 CATTAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCAAAATTTAAAATA
Found at i:3264357 original size:34 final size:32
Alignment explanation
Indices: 3264252--3264357 Score: 122
Period size: 34 Copynumber: 3.2 Consensus size: 32
3264242 ATAAATGTTT
*
3264252 TTAAAATACAAATTATATTATTCAAAATTTAAAA
1 TTAAAATAAAAATTATATTATTC-AAATTT-AAA
* *
3264286 TAAAAATAAAAATAATATTATTCAAATTTAAA
1 TTAAAATAAAAATTATATTATTCAAATTTAAA
* *
3264318 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATAAAAATTATATTATTC-AAATTTAA-A
3264353 TTAAA
1 TTAAA
3264358 TTTCAACTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 3 0.05
33 25 0.40
34 33 0.53
35 1 0.02
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.38
Consensus pattern (32 bp):
TTAAAATAAAAATTATATTATTCAAATTTAAA
Found at i:3264916 original size:128 final size:128
Alignment explanation
Indices: 3264754--3265248 Score: 857
Period size: 128 Copynumber: 3.9 Consensus size: 128
3264744 CTGATTTACA
* *
3264754 GATATATCTAGTGTCCCCGAGGGACGTGAGTGACATAATAGGGCAATGATAACATATTCTATGAC
1 GATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAC
* *** *
3264819 AAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCT-GAGAAATAATAGGTACT
66 GAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGGTACT
* *
3264882 GATTTATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAT
1 GATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAC
* *
3264947 GAAATAATGGAAGGTGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAAT
66 GAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACT
*
3265010 GATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAT
1 GATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAC
3265075 GAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACT
66 GAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACT
*
3265138 GATATATCTAGTGTCCCCGAGGGACATGCGTGACATAATAGGGCAATGATAACATATTCTCTGAC
1 GATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAC
3265203 GAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATA
66 GAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATA
3265249 ATACTCCGAT
Statistics
Matches: 350, Mismatches: 16, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
127 1 0.00
128 349 1.00
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.23
Consensus pattern (128 bp):
GATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAC
GAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACT
Found at i:3265334 original size:8 final size:8
Alignment explanation
Indices: 3265321--3265361 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
3265311 TCACAATCTT
3265321 TCAAATTC
1 TCAAATTC
3265329 TCAAATTC
1 TCAAATTC
* *
3265337 CCAAACTC
1 TCAAATTC
3265345 T-AAATTC
1 TCAAATTC
3265352 TCAAATTC
1 TCAAATTC
3265360 TC
1 TC
3265362 TGAAAATGAG
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:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:3270176 original size:14 final size:15
Alignment explanation
Indices: 3270159--3270195 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
3270149 GAGATAGAAT
3270159 TTAAAATTTT-AATA
1 TTAAAATTTTAAATA
*
3270173 TT-AAATTTTAAATT
1 TTAAAATTTTAAATA
3270187 TTAAAATTT
1 TTAAAATTT
3270196 AGATTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 7 0.35
14 7 0.35
15 6 0.30
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TTAAAATTTTAAATA
Found at i:3270183 original size:7 final size:7
Alignment explanation
Indices: 3270156--3270203 Score: 53
Period size: 7 Copynumber: 7.0 Consensus size: 7
3270146 TTAGAGATAG
*
3270156 AATTTAA
1 AATTTTA
3270163 AATTTT-
1 AATTTTA
*
3270169 AATATTA
1 AATTTTA
3270176 AATTTTA
1 AATTTTA
3270183 AATTTTA
1 AATTTTA
*
3270190 AAATTTA
1 AATTTTA
*
3270197 GATTTTA
1 AATTTTA
3270204 TTATTATAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
6 5 0.15
7 29 0.85
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (7 bp):
AATTTTA
Found at i:3270203 original size:21 final size:20
Alignment explanation
Indices: 3270156--3270194 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3270146 TTAGAGATAG
* *
3270156 AATTTAAAATTTTAATATTA
1 AATTTTAAATTTTAAAATTA
3270176 AATTTTAAATTTTAAAATT
1 AATTTTAAATTTTAAAATT
3270195 TAGATTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AATTTTAAATTTTAAAATTA
Found at i:3271935 original size:25 final size:24
Alignment explanation
Indices: 3271875--3271935 Score: 81
Period size: 26 Copynumber: 2.5 Consensus size: 24
3271865 TTTACAAAAA
3271875 TATTTTATTA-TATTATATATTTT
1 TATTTTATTATTATTATATATTTT
3271898 T-TTATTAATTATTATTAATATATTTT
1 TATT-TT-ATTATTATT-ATATATTTT
3271924 TATTTTATTATT
1 TATTTTATTATT
3271936 TTTGCAAACC
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
22 2 0.06
23 3 0.09
24 4 0.12
25 10 0.30
26 12 0.36
27 2 0.06
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (24 bp):
TATTTTATTATTATTATATATTTT
Found at i:3272432 original size:14 final size:14
Alignment explanation
Indices: 3272413--3272459 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
3272403 TATATATATA
*
3272413 TTTATTTATTTATT
1 TTTATTAATTTATT
3272427 TTTATTAATATTA-T
1 TTTATTAAT-TTATT
*
3272441 TATATTAATTT-TT
1 TTTATTAATTTATT
3272454 TTTATT
1 TTTATT
3272460 TTCTCATGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 8 0.29
14 17 0.61
15 3 0.11
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTATTAATTTATT
Found at i:3273692 original size:14 final size:15
Alignment explanation
Indices: 3273673--3273712 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
3273663 AATGGGAAGT
3273673 AATCCCTGC-TAATA
1 AATCCCTGCATAATA
3273687 AATCCCTGCATAAT-
1 AATCCCTGCATAATA
*
3273701 AATCTCTGCATA
1 AATCCCTGCATA
3273713 TAGACAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 20 0.83
15 4 0.17
ACGTcount: A:0.35, C:0.28, G:0.07, T:0.30
Consensus pattern (15 bp):
AATCCCTGCATAATA
Found at i:3283825 original size:112 final size:110
Alignment explanation
Indices: 3283585--3283915 Score: 459
Period size: 112 Copynumber: 3.0 Consensus size: 110
3283575 CGTTGTAGTT
* * *
3283585 TAGTTGGTTAGGATATTCGGCTCTCACCC-GAGATCCGGGATCAAGTCCCGGCAACGGAAAATGT
1 TAGTTGGTTAGGATACTCGGCTCTCACCCAGAGACCCGGGTTCAAGTCCCGGCAACGGAAAATGT
** ** *
3283649 TTTATGTAATTGTT-TTCCCTCCTTTTTTCCTCCTCATTGATGGTC
66 TTTATGTGGTTGTTGGGCCAT-CTTTTTTCCTCCTCATTGATGGTC
* *
3283694 TAGTTGGTTAGGATACTCGGCTCTCACCCAAGAGACCCGAGTTCAAGTCCCGGCATCGGAAAATG
1 TAGTTGGTTAGGATACTCGGCTCTCACCC-AGAGACCCGGGTTCAAGTCCCGGCAACGGAAAATG
** * *
3283759 TTTTACATGGTTGTTGGGCCATCTTTTAATCCTCCTCATTAATGGTC
65 TTTTATGTGGTTGTTGGGCCATCTTTT-TTCCTCCTCATTGATGGTC
* *
3283806 TAGTTGGTTAGGATACTCGGCTCTCACCCGAGAGACCTGGGTTCAAGTCCCGGCAACGGAAAATA
1 TAGTTGGTTAGGATACTCGGCTCTCACCC-AGAGACCCGGGTTCAAGTCCCGGCAACGGAAAATG
*
3283871 TTTTATGTGGTTGTTGGGCCATTTTTTTTCCTCCTCATTGATGGT
65 TTTTATGTGGTTGTTGGGCCATCTTTTTTCCTCCTCATTGATGGT
3283916 ACCCTACTGG
Statistics
Matches: 194, Mismatches: 24, Indels: 6
0.87 0.11 0.03
Matches are distributed among these distances:
109 28 0.14
111 62 0.32
112 104 0.54
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.34
Consensus pattern (110 bp):
TAGTTGGTTAGGATACTCGGCTCTCACCCAGAGACCCGGGTTCAAGTCCCGGCAACGGAAAATGT
TTTATGTGGTTGTTGGGCCATCTTTTTTCCTCCTCATTGATGGTC
Found at i:3285034 original size:21 final size:21
Alignment explanation
Indices: 3285004--3285138 Score: 152
Period size: 21 Copynumber: 6.4 Consensus size: 21
3284994 GATTTACATA
*
3285004 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
3285025 TTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
3285046 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
3285069 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
3285088 TTCGCGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA--TAGTCCAAG
*
3285111 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
3285130 TTCGCGTTG
1 TTCGCGTTG
3285139 TGATTTATTC
Statistics
Matches: 96, Mismatches: 10, Indels: 16
0.79 0.08 0.13
Matches are distributed among these distances:
19 18 0.19
21 60 0.62
23 18 0.19
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.34
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:3285056 original size:42 final size:41
Alignment explanation
Indices: 3285004--3285227 Score: 247
Period size: 42 Copynumber: 5.3 Consensus size: 41
3284994 GATTTACATA
* *
3285004 TTCGCATTGCGA-TAGTCCAAGTTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATTATTCCAAGTT--CGTTGCGATAGTCGAAG
* *
3285046 TTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAG
1 TTCGCGTTGCGA-TTATTCCAAGTTCGTTGCGATAGTCGAAG
3285088 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGA-TTATTCCAAGTTCGTTGCGATAGTCGAAG
* * * * *
3285130 TTCGCGTTGTGATTTATTCCAAATTCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA-TTATTCCAAGTTCGTTGCGA--TAGTCGAAG
* *
3285174 TT--CATTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGA-TTATTCCAAGTTCGTTGCGATAGTCGAAG
*
3285214 TTTGCGTTGCGATT
1 TTCGCGTTGCGATT
3285228 TTTTTCAAAT
Statistics
Matches: 159, Mismatches: 17, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
40 8 0.05
41 2 0.01
42 132 0.83
44 17 0.11
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (41 bp):
TTCGCGTTGCGATTATTCCAAGTTCGTTGCGATAGTCGAAG
Found at i:3285158 original size:21 final size:21
Alignment explanation
Indices: 3285050--3285205 Score: 176
Period size: 21 Copynumber: 7.4 Consensus size: 21
3285040 TCGAAGTTCG
3285050 CGTTGCGATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAATT
* *
3285071 CGTTGCGA--TAGTCCAAGTT
1 CGTTGCGATTTATTCCAAATT
*
3285090 CGCGTTGCGATTTATTCCAAGTT
1 --CGTTGCGATTTATTCCAAATT
* * *
3285113 CGTTGCGA--TAGTCGAAGTT
1 CGTTGCGATTTATTCCAAATT
*
3285132 CGCGTTGTGATTTATTCCAAATT
1 --CGTTGCGATTTATTCCAAATT
3285155 CGTTGCGATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAATT
*
3285176 CATTGCGATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAATT
3285197 CGTTGCGAT
1 CGTTGCGAT
3285206 AGTCGAAGTT
Statistics
Matches: 115, Mismatches: 12, Indels: 16
0.80 0.08 0.11
Matches are distributed among these distances:
19 18 0.16
21 79 0.69
23 18 0.16
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (21 bp):
CGTTGCGATTTATTCCAAATT
Found at i:3285228 original size:42 final size:42
Alignment explanation
Indices: 3285029--3285241 Score: 304
Period size: 42 Copynumber: 5.1 Consensus size: 42
3285019 TCCAAGTTCG
3285029 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
* *
3285071 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
*
3285113 CGTTGCGATAGTCGAAGTTCGCGTTGTGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
* * * *
3285155 CGTTGCGATTTATTCCAAATT--CATTGCGATTTATTCCAAATT
1 CGTTGCGA--TAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
* * *
3285197 CGTTGCGATAGTCGAAGTTTGCGTTGCGATTTTTTTCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
3285239 CGT
1 CGT
3285242 GGTCGGGTCG
Statistics
Matches: 151, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
40 8 0.05
42 135 0.89
44 8 0.05
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (42 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
Found at i:3285435 original size:20 final size:20
Alignment explanation
Indices: 3285394--3285454 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 20
3285384 AACTTCGACT
**
3285394 ATCGCAATGCGAATA-TATAA
1 ATCGCAATGCG-ATAGTCGAA
3285414 ATCGCAATGCGATAGTCGAA
1 ATCGCAATGCGATAGTCGAA
**
3285434 ATTCGCGTTGCGATAGTCGAA
1 A-TCGCAATGCGATAGTCGAA
3285455 TTTAGAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
19 3 0.09
20 15 0.43
21 17 0.49
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATAGTCGAA
Found at i:3285549 original size:49 final size:49
Alignment explanation
Indices: 3285477--3285575 Score: 171
Period size: 49 Copynumber: 2.0 Consensus size: 49
3285467 CAACGCGAAC
3285477 TTCGACTATCGCATCACGATTTACATATTCGCATTGCGATAGTCCAAGT
1 TTCGACTATCGCATCACGATTTACATATTCGCATTGCGATAGTCCAAGT
* **
3285526 TTCGACTATCGTATTGCGATTTACATATTCGCATTGCGATAGTCCAAGT
1 TTCGACTATCGCATCACGATTTACATATTCGCATTGCGATAGTCCAAGT
3285575 T
1 T
3285576 CGCATTGCGA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.35
Consensus pattern (49 bp):
TTCGACTATCGCATCACGATTTACATATTCGCATTGCGATAGTCCAAGT
Found at i:3285579 original size:21 final size:21
Alignment explanation
Indices: 3285553--3285606 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
3285543 GATTTACATA
3285553 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
3285574 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
3285595 TTCGCGTTGCGA
1 TTCGCATTGCGA
3285607 ATCTGGAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.20, C:0.22, G:0.28, T:0.30
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:3290499 original size:2 final size:2
Alignment explanation
Indices: 3290494--3290525 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3290484 TAGAGCATAC
3290494 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
3290526 TTTGGGGGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3292144 original size:24 final size:24
Alignment explanation
Indices: 3292117--3292185 Score: 75
Period size: 24 Copynumber: 2.9 Consensus size: 24
3292107 ACGAAGATAT
*
3292117 CAGAAATCAAAACAGAATTTAGAA
1 CAGAAATCAAAACAGAATTCAGAA
* * ** * *
3292141 CAGATATCAGAACAGAACCCATAT
1 CAGAAATCAAAACAGAATTCAGAA
3292165 CAGAAATCAAAACAGAATTCA
1 CAGAAATCAAAACAGAATTCA
3292186 AGTCGGAAAT
Statistics
Matches: 34, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.54, C:0.19, G:0.12, T:0.16
Consensus pattern (24 bp):
CAGAAATCAAAACAGAATTCAGAA
Found at i:3292180 original size:12 final size:12
Alignment explanation
Indices: 3292117--3292186 Score: 50
Period size: 12 Copynumber: 5.8 Consensus size: 12
3292107 ACGAAGATAT
3292117 CAGAAATCAAAA
1 CAGAAATCAAAA
* * *
3292129 CAGAATTTAGAA
1 CAGAAATCAAAA
* *
3292141 CAGATATCAGAA
1 CAGAAATCAAAA
** * *
3292153 CAGAACCCATAT
1 CAGAAATCAAAA
3292165 CAGAAATCAAAA
1 CAGAAATCAAAA
*
3292177 CAGAATTCAA
1 CAGAAATCAA
3292187 GTCGGAAATC
Statistics
Matches: 42, Mismatches: 16, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
12 42 1.00
ACGTcount: A:0.54, C:0.19, G:0.11, T:0.16
Consensus pattern (12 bp):
CAGAAATCAAAA
Found at i:3293979 original size:36 final size:36
Alignment explanation
Indices: 3293932--3294004 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
3293922 GATAAATTAT
*
3293932 AATCTATATATCCATGGCTGATTCTTTTATCACTTA
1 AATCTACATATCCATGGCTGATTCTTTTATCACTTA
3293968 AATCTACATATCCATGGCTGATTCTTTTATCACTTA
1 AATCTACATATCCATGGCTGATTCTTTTATCACTTA
3294004 A
1 A
3294005 TTCCAGAACT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.29, C:0.21, G:0.08, T:0.42
Consensus pattern (36 bp):
AATCTACATATCCATGGCTGATTCTTTTATCACTTA
Found at i:3304090 original size:13 final size:13
Alignment explanation
Indices: 3304072--3304099 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3304062 AAAAACTGAA
3304072 AAACTAGCAAAGC
1 AAACTAGCAAAGC
3304085 AAACTAGCAAAGC
1 AAACTAGCAAAGC
3304098 AA
1 AA
3304100 GAGCAGATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.57, C:0.21, G:0.14, T:0.07
Consensus pattern (13 bp):
AAACTAGCAAAGC
Found at i:3305018 original size:27 final size:27
Alignment explanation
Indices: 3304966--3305021 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
3304956 CCGCCATCAC
* *
3304966 CACTTTGAACTTGAAACTATATAACAT
1 CACTTTGAACTTGAAACTACACAACAT
* *
3304993 CACTTTGAACTTGAAAGTCCACAACAT
1 CACTTTGAACTTGAAACTACACAACAT
3305020 CA
1 CA
3305022 AGATCTTCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.39, C:0.23, G:0.09, T:0.29
Consensus pattern (27 bp):
CACTTTGAACTTGAAACTACACAACAT
Found at i:3306213 original size:20 final size:20
Alignment explanation
Indices: 3306170--3306214 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
3306160 ATAAAAACAA
3306170 AAATTAAAAAAAAAATATTT
1 AAATTAAAAAAAAAATATTT
* *
3306190 -AATTAAAAAATAAATGTTT
1 AAATTAAAAAAAAAATATTT
3306209 AAATTA
1 AAATTA
3306215 TATTTCTTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (20 bp):
AAATTAAAAAAAAAATATTT
Found at i:3307931 original size:15 final size:15
Alignment explanation
Indices: 3307908--3307937 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3307898 TAATTTTAAG
3307908 TTTTAAAAAAATAAA
1 TTTTAAAAAAATAAA
*
3307923 TTTTTAAAAAATAAA
1 TTTTAAAAAAATAAA
3307938 AAATATGTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TTTTAAAAAAATAAA
Found at i:3308183 original size:17 final size:18
Alignment explanation
Indices: 3308146--3308190 Score: 74
Period size: 17 Copynumber: 2.6 Consensus size: 18
3308136 TTTCTGAGGA
3308146 AATTGGAATCTGTGAAGG
1 AATTGGAATCTGTGAAGG
*
3308164 AATTGGAATCTGT-CAGG
1 AATTGGAATCTGTGAAGG
3308181 AATTGGAATC
1 AATTGGAATC
3308191 CAATTACATA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 13 0.50
18 13 0.50
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (18 bp):
AATTGGAATCTGTGAAGG
Found at i:3308609 original size:65 final size:63
Alignment explanation
Indices: 3308492--3308699 Score: 197
Period size: 65 Copynumber: 3.2 Consensus size: 63
3308482 TTTCAGAATG
* * ** *
3308492 ATGCACCGATGCACAAATCCATGCATCGATGCAC-CATGGAATAAATTG-AACATCGAATACATT
1 ATGCATCGATGCAC-AA-CCATGCATCGATGCACTCA--GACTATTTTGAAACATCGAATGCATT
3308555 TC
62 TC
* * * *
3308557 ATGCACCGATGCACATACTATGCATCGATGCACTTAGAGT-TTTATGAAAACATCGAATGCATTT
1 ATGCATCGATGCACA-ACCATGCATCGATGCACTCAGACTATTT-TG-AAACATCGAATGCATTT
*
3308621 G
63 C
* * *
3308622 ATGCATCGATGCACCAGCCATGCATCGATGCACTCATACTATTTTGAAACATCGAATGCATTTT
1 ATGCATCGATGCA-CAACCATGCATCGATGCACTCAGACTATTTTGAAACATCGAATGCATTTC
*
3308686 ATGTATCGATGCAC
1 ATGCATCGATGCAC
3308700 TCTTAGTGCA
Statistics
Matches: 121, Mismatches: 15, Indels: 16
0.80 0.10 0.11
Matches are distributed among these distances:
62 1 0.01
63 6 0.05
64 45 0.37
65 64 0.53
66 5 0.04
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (63 bp):
ATGCATCGATGCACAACCATGCATCGATGCACTCAGACTATTTTGAAACATCGAATGCATTTC
Found at i:3314561 original size:22 final size:21
Alignment explanation
Indices: 3314475--3314610 Score: 93
Period size: 22 Copynumber: 6.4 Consensus size: 21
3314465 TTGTGCTTAA
*
3314475 TGCATCGATACACC-T-AAGAG
1 TGCATCGATACACCTTGAA-TG
*
3314495 TGCATCGATGCATCCTTGAATG
1 TGCATCGATACA-CCTTGAATG
* * *
3314517 TGTATCGACACA-C-T-AAGAG
1 TGCATCGATACACCTTGAA-TG
3314536 TGCATCGATACATCCTTGAATG
1 TGCATCGATACA-CCTTGAATG
* *
3314558 TGCATCGATACACCATGAAGG
1 TGCATCGATACACCTTGAATG
* * *
3314579 TGCACCGATGCACGCCTTGAATA
1 TGCATCGAT--ACACCTTGAATG
3314602 TGCATCGAT
1 TGCATCGAT
3314611 GCACAAGGCC
Statistics
Matches: 89, Mismatches: 17, Indels: 17
0.72 0.14 0.14
Matches are distributed among these distances:
18 2 0.02
19 12 0.13
20 12 0.13
21 18 0.20
22 25 0.28
23 20 0.22
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.25
Consensus pattern (21 bp):
TGCATCGATACACCTTGAATG
Found at i:3314600 original size:44 final size:42
Alignment explanation
Indices: 3314475--3314610 Score: 177
Period size: 41 Copynumber: 3.2 Consensus size: 42
3314465 TTGTGCTTAA
3314475 TGCATCGATACACCTAAGAGTGCATCGATGCATCCTTGAATG
1 TGCATCGATACACCTAAGAGTGCATCGATGCATCCTTGAATG
* * *
3314517 TGTATCGACACA-CTAAGAGTGCATCGATACATCCTTGAATG
1 TGCATCGATACACCTAAGAGTGCATCGATGCATCCTTGAATG
* * *
3314558 TGCATCGATACACCATGAAG-GTGCACCGATGCACGCCTTGAATA
1 TGCATCGATACACC-T-AAGAGTGCATCGATGCA-TCCTTGAATG
3314602 TGCATCGAT
1 TGCATCGAT
3314611 GCACAAGGCC
Statistics
Matches: 81, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
41 38 0.47
42 11 0.14
43 12 0.15
44 20 0.25
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.25
Consensus pattern (42 bp):
TGCATCGATACACCTAAGAGTGCATCGATGCATCCTTGAATG
Found at i:3317286 original size:29 final size:30
Alignment explanation
Indices: 3317240--3317320 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 30
3317230 CCGAAGGACC
3317240 TATCCAGAGGTCACAAAG-ACCCCGGCAAT
1 TATCCAGAGGTCACAAAGAACCCCGGCAAT
* * * *
3317269 TATCTAGAGGTCATAAAGAACCTCGGCAAC
1 TATCCAGAGGTCACAAAGAACCCCGGCAAT
* * * *
3317299 TGTCCATAGGTCCCGAAGAACC
1 TATCCAGAGGTCACAAAGAACC
3317321 TAGGTAAACT
Statistics
Matches: 41, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
29 16 0.39
30 25 0.61
ACGTcount: A:0.33, C:0.28, G:0.21, T:0.17
Consensus pattern (30 bp):
TATCCAGAGGTCACAAAGAACCCCGGCAAT
Found at i:3317310 original size:30 final size:31
Alignment explanation
Indices: 3317276--3317400 Score: 85
Period size: 31 Copynumber: 4.0 Consensus size: 31
3317266 AATTATCTAG
* * *
3317276 AGGTCATAAAGAACCTCGG-CAACTGTCCAT
1 AGGTCACAAAGAACCTAGGTAAACTGTCCAT
* *
3317306 AGGTCCCGAAGAACCTAGGTAAACTGTCCAT
1 AGGTCACAAAGAACCTAGGTAAACTGTCCAT
* ** * *
3317337 ATGTTC-CTTAGAACATAGGTATACTGTCCAT
1 A-GGTCACAAAGAACCTAGGTAAACTGTCCAT
* * *
3317368 ATGTCTCGAAAG-ACATAGGTAAAACTGTCCAT
1 AGGTCAC-AAAGAACCTAGGT-AAACTGTCCAT
3317400 A
1 A
3317401 TGTTCCGTAG
Statistics
Matches: 75, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
30 17 0.23
31 42 0.56
32 16 0.21
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (31 bp):
AGGTCACAAAGAACCTAGGTAAACTGTCCAT
Found at i:3317406 original size:63 final size:62
Alignment explanation
Indices: 3317297--3317420 Score: 187
Period size: 63 Copynumber: 2.0 Consensus size: 62
3317287 AACCTCGGCA
* *
3317297 ACTGTCCATAGGTCCCGAAGAACCTAGGTAAACTGTCCATATGTTCCTTAGAACATAGGTAT
1 ACTGTCCATAGGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATAGGTAT
* *
3317359 ACTGTCCATATGTCTCGAA-AGACATAGGTAAAACTGTCCATATGTTCCGTAGAACATAGGTA
1 ACTGTCCATAGGTCCCGAAGA-ACATAGGT-AAACTGTCCATATGTTCCGTAGAACATAGGTA
3317421 AACCCTCGAC
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
61 1 0.02
62 24 0.43
63 31 0.55
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.27
Consensus pattern (62 bp):
ACTGTCCATAGGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATAGGTAT
Found at i:3317416 original size:32 final size:31
Alignment explanation
Indices: 3317296--3317423 Score: 152
Period size: 31 Copynumber: 4.1 Consensus size: 31
3317286 GAACCTCGGC
* * * *
3317296 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
*
3317327 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
* *
3317358 TACTGTCCATATG-TCTCG-AAAGACATAGGTAA
1 AACTGTCCATATGTTC-CGTAGA-ACATAGGT-A
3317390 AACTGTCCATATGTTCCGTAGAACATAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
3317421 AAC
1 AAC
3317424 CCTCGACTCT
Statistics
Matches: 82, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
30 4 0.05
31 51 0.62
32 23 0.28
33 4 0.05
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGTAGAACATAGGTA
Found at i:3318285 original size:64 final size:63
Alignment explanation
Indices: 3318175--3318312 Score: 145
Period size: 64 Copynumber: 2.2 Consensus size: 63
3318165 TTAACATGTG
* * *
3318175 CATCGATGCACTACCCATGCATCGATACACAAATTACCTTCGATGTTTTCAT-TTTAAAGTGATA
1 CATCGATGCACTACCCATGCATCGATACACAAATTACATTCAATG-TTTCATCTTTAAAGAG-TA
* * * * * * *
3318239 CATCGATGCACT-CCTTATGCATCGATGCACCATTTGCATTCAATGTTTCTTCTTTAAAGAGTG
1 CATCGATGCACTACC-CATGCATCGATACACAAATTACATTCAATGTTTCATCTTTAAAGAGTA
3318302 CATCGATGCAC
1 CATCGATGCAC
3318313 ATTCAATGTG
Statistics
Matches: 62, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
63 19 0.31
64 43 0.69
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (63 bp):
CATCGATGCACTACCCATGCATCGATACACAAATTACATTCAATGTTTCATCTTTAAAGAGTA
Found at i:3320121 original size:64 final size:65
Alignment explanation
Indices: 3320002--3320122 Score: 167
Period size: 64 Copynumber: 1.9 Consensus size: 65
3319992 TGCACATACT
3320002 ATGCATCAATGCACTCAGAGTTTTATGAAAACATAGAATGCATTTGATGCATCGATGTACCAGCC
1 ATGCATCAATGCACTCAGAGTTTTATGAAAACATAGAATGCATTTGATGCATCGATGTACCAGCC
* * * *
3320067 ATGCATCGATGCACTCAG-GCTATTT-TG-AAACATCGAATGCATTTTATGTATCGATG
1 ATGCATCAATGCACTCAGAG-T-TTTATGAAAACATAGAATGCATTTGATGCATCGATG
3320123 CACTCTTAGT
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
64 27 0.54
65 20 0.40
66 3 0.06
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (65 bp):
ATGCATCAATGCACTCAGAGTTTTATGAAAACATAGAATGCATTTGATGCATCGATGTACCAGCC
Found at i:3323547 original size:25 final size:25
Alignment explanation
Indices: 3323519--3323569 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
3323509 AATATTTTAT
3323519 ATATAAT-TAATATAAAAAATATAAA
1 ATATAATAT-ATATAAAAAATATAAA
* **
3323544 ATATTATATATATAATTAATATAAA
1 ATATAATATATATAAAAAATATAAA
3323569 A
1 A
3323570 AATATAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 21 0.95
26 1 0.05
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (25 bp):
ATATAATATATATAAAAAATATAAA
Found at i:3323554 original size:34 final size:34
Alignment explanation
Indices: 3323507--3323591 Score: 161
Period size: 34 Copynumber: 2.5 Consensus size: 34
3323497 CCCGACCCCG
*
3323507 AAAATATTTTATATATAATTAATATAAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
3323541 AAAATATTATATATATAATTAATATAAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
3323575 AAAATATTATATATATA
1 AAAATATTATATATATA
3323592 TATATATATA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 50 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (34 bp):
AAAATATTATATATATAATTAATATAAAAAATAT
Found at i:3333561 original size:2 final size:2
Alignment explanation
Indices: 3333554--3333590 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3333544 GGAAATATGA
3333554 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3333591 AAAAAACAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3341371 original size:27 final size:27
Alignment explanation
Indices: 3341333--3341395 Score: 126
Period size: 27 Copynumber: 2.3 Consensus size: 27
3341323 AGCTTGGAGC
3341333 AGGCAATCCAAGGGTGCGCATTTATAA
1 AGGCAATCCAAGGGTGCGCATTTATAA
3341360 AGGCAATCCAAGGGTGCGCATTTATAA
1 AGGCAATCCAAGGGTGCGCATTTATAA
3341387 AGGCAATCC
1 AGGCAATCC
3341396 TTTAATTGGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.21
Consensus pattern (27 bp):
AGGCAATCCAAGGGTGCGCATTTATAA
Found at i:3346368 original size:16 final size:16
Alignment explanation
Indices: 3346349--3346379 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3346339 AATTTAAATT
3346349 TTATTTAATTAATTAA
1 TTATTTAATTAATTAA
*
3346365 TTATTTTATTAATTA
1 TTATTTAATTAATTA
3346380 TATTTATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTATTTAATTAATTAA
Found at i:3346400 original size:17 final size:18
Alignment explanation
Indices: 3346348--3346405 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 18
3346338 AAATTTAAAT
* *
3346348 TTTATTTAATTAATTA-A
1 TTTATTTTATAAATTATA
*
3346365 -TTATTTTATTAATTATA
1 TTTATTTTATAAATTATA
*
3346382 TTTATTTTA-AAATTTTA
1 TTTATTTTATAAATTATA
3346399 TTT-TTTT
1 TTTATTTT
3346406 CATTTGAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
16 18 0.50
17 10 0.28
18 8 0.22
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTATTTTATAAATTATA
Found at i:3349403 original size:16 final size:17
Alignment explanation
Indices: 3349372--3349417 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 17
3349362 CTTTAAGTAA
3349372 AAATTATTAAAATAAAT
1 AAATTATTAAAATAAAT
*
3349389 AAATT-TTAAATTAAA-
1 AAATTATTAAAATAAAT
3349404 AAACTTACTTAAAA
1 AAA-TTA-TTAAAA
3349418 GTTATCAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
15 3 0.12
16 11 0.46
17 5 0.21
18 5 0.21
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (17 bp):
AAATTATTAAAATAAAT
Found at i:3349810 original size:2 final size:2
Alignment explanation
Indices: 3349803--3349827 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3349793 ATAATAAAAT
3349803 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 T
3349828 CATGGATAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3354024 original size:18 final size:18
Alignment explanation
Indices: 3354001--3354060 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 18
3353991 CAAAATAATT
3354001 TTAAAACTTAATTTAAAA
1 TTAAAACTTAATTTAAAA
** *
3354019 TTAAAAAATAATTT-AGA
1 TTAAAACTTAATTTAAAA
3354036 TTAAAAACTTCAATGTTAAAA
1 TT-AAAACTT-AAT-TTAAAA
3354057 TTAA
1 TTAA
3354061 TATGAAATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
17 4 0.12
18 17 0.53
19 3 0.09
20 4 0.12
21 4 0.12
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (18 bp):
TTAAAACTTAATTTAAAA
Found at i:3354350 original size:60 final size:59
Alignment explanation
Indices: 3354226--3354351 Score: 146
Period size: 60 Copynumber: 2.1 Consensus size: 59
3354216 ATTGTATCAT
* * * * * *
3354226 ACATCTTCAAATTATGATTCTCATTCTAAATTGATCTTTAAACTTTTGAAAATATTAATT
1 ACATCCTCAAATTATGATTCACATTCTAAACTGATCCTCAAACTTTTG-AAATATTAATA
* *
3354286 ACATCCTCAAATTATGATTCACATTCTAAACTGGTCCTCAAACTTTTG-AGTATTCCAATA
1 ACATCCTCAAATTATGATTCACATTCTAAACTGATCCTCAAACTTTTGAAATATT--AATA
3354346 ACATCC
1 ACATCC
3354352 CATAAATCAT
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
58 5 0.09
60 51 0.91
ACGTcount: A:0.35, C:0.20, G:0.06, T:0.39
Consensus pattern (59 bp):
ACATCCTCAAATTATGATTCACATTCTAAACTGATCCTCAAACTTTTGAAATATTAATA
Found at i:3355309 original size:21 final size:21
Alignment explanation
Indices: 3355267--3355310 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3355257 CGTATGCAGA
* *
3355267 TTTTATGATATGATGTATAAT
1 TTTTATGATATAATGTAAAAT
3355288 TTTTAT-ATATAATGTTAAAAT
1 TTTTATGATATAATG-TAAAAT
3355309 TT
1 TT
3355311 ATTTTGTCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (21 bp):
TTTTATGATATAATGTAAAAT
Found at i:3370449 original size:21 final size:21
Alignment explanation
Indices: 3370423--3370469 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
3370413 TTCTTCTTCC
3370423 TCTTCCTCTTGC-T-CTGCATCT
1 TCTTCC-CTTGCATCCT-CATCT
3370444 TCTTCCCTTGCATCCTCATCT
1 TCTTCCCTTGCATCCTCATCT
3370465 TCTTC
1 TCTTC
3370470 TCCACCCCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.21
21 17 0.71
22 2 0.08
ACGTcount: A:0.06, C:0.40, G:0.06, T:0.47
Consensus pattern (21 bp):
TCTTCCCTTGCATCCTCATCT
Found at i:3373685 original size:104 final size:104
Alignment explanation
Indices: 3373551--3373759 Score: 355
Period size: 104 Copynumber: 2.0 Consensus size: 104
3373541 ATAATGAATC
*
3373551 AGAAGAATGATATCCTACCGCTGCTCCCTTTCCTTTGAAGGTGGTTTGATTCTATGCGGAGGACC
1 AGAAGAATGAGATCCTACCGCTGCTCCCTTTCCTTTGAAGGTGGTTTGATTCTATGCGGAGGACC
* *
3373616 CTCGCGGATCTTACCATCAGATCTCCCCGTGATTCAGCT
66 CTCACAGATCTTACCATCAGATCTCCCCGTGATTCAGCT
* *
3373655 AGAAGAATGAGATCCTACTGCTGCTCCCTTTCCTTTGAAGGTGGTTTGATTCTATGCGGAGGACG
1 AGAAGAATGAGATCCTACCGCTGCTCCCTTTCCTTTGAAGGTGGTTTGATTCTATGCGGAGGACC
* *
3373720 CTCACAGATCTTACCATGAGATCTCCCCGTGATTCGGCT
66 CTCACAGATCTTACCATCAGATCTCCCCGTGATTCAGCT
3373759 A
1 A
3373760 TGATTGTTTT
Statistics
Matches: 98, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
104 98 1.00
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.30
Consensus pattern (104 bp):
AGAAGAATGAGATCCTACCGCTGCTCCCTTTCCTTTGAAGGTGGTTTGATTCTATGCGGAGGACC
CTCACAGATCTTACCATCAGATCTCCCCGTGATTCAGCT
Found at i:3373831 original size:31 final size:31
Alignment explanation
Indices: 3373796--3373867 Score: 144
Period size: 31 Copynumber: 2.3 Consensus size: 31
3373786 TTTAGATACC
3373796 ATTAAATTTTATCCTTTTATACATTTATATT
1 ATTAAATTTTATCCTTTTATACATTTATATT
3373827 ATTAAATTTTATCCTTTTATACATTTATATT
1 ATTAAATTTTATCCTTTTATACATTTATATT
3373858 ATTAAATTTT
1 ATTAAATTTT
3373868 TAGTTTTATC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.58
Consensus pattern (31 bp):
ATTAAATTTTATCCTTTTATACATTTATATT
Found at i:3376548 original size:41 final size:41
Alignment explanation
Indices: 3376502--3376580 Score: 131
Period size: 41 Copynumber: 1.9 Consensus size: 41
3376492 TATGGGAGTA
* * *
3376502 GTTAGTTTTATCGAAATAATACAGAATAAATATAATAAGTG
1 GTTAGTTTTATCAAAAGAATAAAGAATAAATATAATAAGTG
3376543 GTTAGTTTTATCAAAAGAATAAAGAATAAATATAATAA
1 GTTAGTTTTATCAAAAGAATAAAGAATAAATATAATAA
3376581 AATCATGGGC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.51, C:0.04, G:0.13, T:0.33
Consensus pattern (41 bp):
GTTAGTTTTATCAAAAGAATAAAGAATAAATATAATAAGTG
Found at i:3384514 original size:22 final size:22
Alignment explanation
Indices: 3384468--3384569 Score: 74
Period size: 22 Copynumber: 4.8 Consensus size: 22
3384458 ATCTTTTTTT
* *
3384468 ATATATTAT-TAAAATAA-AAA
1 ATATATTATATAATATAATTAA
3384488 TATATATTATATAATATAATTAA
1 -ATATATTATATAATATAATTAA
3384511 ATATATTAT-T-ATA-ACATTAA
1 ATATATTATATAATATA-ATTAA
* * *
3384531 AAATATTATATTATATTATTAA
1 ATATATTATATAATATAATTAA
3384553 A-ACTATTA-ATAAATATA
1 ATA-TATTATAT-AATATA
3384570 TTTTTAATAA
Statistics
Matches: 67, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
19 1 0.01
20 16 0.24
21 14 0.21
22 34 0.51
23 2 0.03
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
ATATATTATATAATATAATTAA
Found at i:3384578 original size:15 final size:16
Alignment explanation
Indices: 3384558--3384596 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
3384548 ATTAAAACTA
3384558 TTAATAAAT-ATATTT
1 TTAATAAATAATATTT
*
3384573 TTAATAATTAATATTT
1 TTAATAAATAATATTT
*
3384589 TTATTAAA
1 TTAATAAA
3384597 ATAGTATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTAATAAATAATATTT
Found at i:3384650 original size:61 final size:64
Alignment explanation
Indices: 3384530--3384650 Score: 153
Period size: 62 Copynumber: 1.9 Consensus size: 64
3384520 TATAACATTA
* * *
3384530 AAAATATTATATTATATTATTAAAACTATTAATAAATATATTTTTAATAATTAATATTTTTATT
1 AAAATAGTATATTATATTATTAAAACTATAAATAAATATATTTTAAATAATTAATATTTTTATT
*
3384594 AAAATAGTATATTA-A-TATTAAATAC-ATAAAT-AATATTATTTTAAAT-ATTTATATTTT
1 AAAATAGTATATTATATTATTAAA-ACTATAAATAAATA-TATTTTAAATAATTAATATTTT
3384651 GAAGTAAAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
61 14 0.27
62 21 0.41
63 3 0.06
64 13 0.25
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.50
Consensus pattern (64 bp):
AAAATAGTATATTATATTATTAAAACTATAAATAAATATATTTTAAATAATTAATATTTTTATT
Found at i:3389527 original size:22 final size:24
Alignment explanation
Indices: 3389485--3389528 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
3389475 TAAAATTTTA
*
3389485 TTTATATTTATCTGATATAAAAAG
1 TTTATATTTATCTAATATAAAAAG
3389509 TTTATA-TTAT-TAATATAAAA
1 TTTATATTTATCTAATATAAAA
3389529 TAATTATTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (24 bp):
TTTATATTTATCTAATATAAAAAG
Found at i:3403440 original size:2 final size:2
Alignment explanation
Indices: 3403433--3403466 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3403423 AAAACCTGTC
3403433 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
3403467 GATGACATCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3405227 original size:2 final size:2
Alignment explanation
Indices: 3405222--3405246 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3405212 TGTGTGTGTG
3405222 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 T
3405247 GATTATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3406755 original size:40 final size:40
Alignment explanation
Indices: 3406711--3406786 Score: 98
Period size: 40 Copynumber: 1.9 Consensus size: 40
3406701 ATTATCATTC
* * * *
3406711 TTGTATTTAGGTGTGTATCTCGTACAATACATCACCTTAT
1 TTGTAGTTAGATGTATATCCCGTACAATACATCACCTTAT
**
3406751 TTGTAGTTAGATGTATATCCCGTGTAATACATCACC
1 TTGTAGTTAGATGTATATCCCGTACAATACATCACC
3406787 ACTTTCGTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 30 1.00
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.39
Consensus pattern (40 bp):
TTGTAGTTAGATGTATATCCCGTACAATACATCACCTTAT
Found at i:3406898 original size:39 final size:39
Alignment explanation
Indices: 3406853--3406927 Score: 105
Period size: 39 Copynumber: 1.9 Consensus size: 39
3406843 TAATACCACT
* * *
3406853 ATTCTGGTACCTATACTCTGAAATGGTACCAATACTGAA
1 ATTCTGGTACCTATAATATGAAATAGTACCAATACTGAA
* *
3406892 ATTCTGGTATCTATAATATGAAATAGTTCCAATACT
1 ATTCTGGTACCTATAATATGAAATAGTACCAATACT
3406928 AGCATCTTGG
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:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (39 bp):
ATTCTGGTACCTATAATATGAAATAGTACCAATACTGAA
Found at i:3409078 original size:26 final size:26
Alignment explanation
Indices: 3409049--3409127 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 26
3409039 AATGATGATC
3409049 AATACGTGATTAATCAGTTGATAACA
1 AATACGTGATTAATCAGTTGATAACA
** *
3409075 AATAC-TCCTCTAA--AG--GATGATC-
1 AATACGTGAT-TAATCAGTTGAT-AACA
3409097 AATACGTGATTAATCAGTTGATAACA
1 AATACGTGATTAATCAGTTGATAACA
3409123 AATAC
1 AATAC
3409128 TCCTCTAAAG
Statistics
Matches: 39, Mismatches: 6, Indels: 16
0.64 0.10 0.26
Matches are distributed among these distances:
22 11 0.28
23 4 0.10
24 4 0.10
25 4 0.10
26 16 0.41
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (26 bp):
AATACGTGATTAATCAGTTGATAACA
Found at i:3409113 original size:48 final size:48
Alignment explanation
Indices: 3409042--3409139 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
3409032 GAGCAAGAAT
3409042 GATGATCAATACGTGATTAATCAGTTGATAACAAATACTCCTCTAAAG
1 GATGATCAATACGTGATTAATCAGTTGATAACAAATACTCCTCTAAAG
3409090 GATGATCAATACGTGATTAATCAGTTGATAACAAATACTCCTCTAAAG
1 GATGATCAATACGTGATTAATCAGTTGATAACAAATACTCCTCTAAAG
3409138 GA
1 GA
3409140 CATTGAGGTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (48 bp):
GATGATCAATACGTGATTAATCAGTTGATAACAAATACTCCTCTAAAG
Found at i:3413843 original size:24 final size:27
Alignment explanation
Indices: 3413814--3413863 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
3413804 ATAATATATA
3413814 TAAATA-TTATTA-TTA-TTAAATTAG
1 TAAATATTTATTATTTAGTTAAATTAG
*
3413838 TAAATATTTTTTATTTAGTTAAATTA
1 TAAATATTTATTATTTAGTTAAATTA
3413864 AATTATTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 6 0.27
25 5 0.23
26 3 0.14
27 8 0.36
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (27 bp):
TAAATATTTATTATTTAGTTAAATTAG
Found at i:3415404 original size:4 final size:4
Alignment explanation
Indices: 3415395--3415422 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
3415385 TTAAATATTC
3415395 TCTT TCTT TCTT TCTT TCTT TCTT TCTT
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT
3415423 CGAATGGCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TCTT
Found at i:3416780 original size:6 final size:6
Alignment explanation
Indices: 3416769--3416800 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
3416759 ATAAGAAAAA
*
3416769 TGGATT TGGATT TGGATA TGGATT TGGATT TG
1 TGGATT TGGATT TGGATT TGGATT TGGATT TG
3416801 AACTAATCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.19, C:0.00, G:0.34, T:0.47
Consensus pattern (6 bp):
TGGATT
Found at i:3421054 original size:16 final size:16
Alignment explanation
Indices: 3421019--3421054 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3421009 ATAAAATTAG
**
3421019 ATTTATTATTTTAATT
1 ATTTATTATTTTAAAA
3421035 ATTTATTATTTTAAAA
1 ATTTATTATTTTAAAA
3421051 ATTT
1 ATTT
3421055 GACTGAACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATTTATTATTTTAAAA
Found at i:3421665 original size:28 final size:25
Alignment explanation
Indices: 3421634--3421692 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 25
3421624 AAAATTTGTA
3421634 AAATTACAATAATAGTCTAAACTTTTAT
1 AAATTACAATAA-AG-CT-AACTTTTAT
* *
3421662 AAATTACAATTAAGCTAATTTTTAT
1 AAATTACAATAAAGCTAACTTTTAT
3421687 AAATTA
1 AAATTA
3421693 AGAAAAAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 14 0.48
26 2 0.07
27 2 0.07
28 11 0.38
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.41
Consensus pattern (25 bp):
AAATTACAATAAAGCTAACTTTTAT
Found at i:3421745 original size:28 final size:27
Alignment explanation
Indices: 3421624--3421786 Score: 100
Period size: 28 Copynumber: 6.0 Consensus size: 27
3421614 TAAATTTGTT
* * *
3421624 AAAATTTGTA-AAATTACAATAATAGTC
1 AAAATTTTTATAAATTACAA-AAAAGGC
* * **
3421651 TAAACTTTTATAAATTACAATTAA-GC
1 AAAATTTTTATAAATTACAAAAAAGGC
* * *
3421677 -TAATTTTTATAAATTAAGAAAAAAGAC
1 AAAATTTTTATAAATT-ACAAAAAAGGC
* * *
3421704 AGAATTTTTCTAAATTACAAAAAAGGG
1 AAAATTTTTATAAATTACAAAAAAGGC
* *
3421731 AAAATTATTTATAAATTATAATAAAGGAC
1 AAAATT-TTTATAAATTACAAAAAAGG-C
*
3421760 AAAACATTTTATAAATTA-AAATAAAGG
1 AAAA-TTTTTATAAATTACAAA-AAAGG
3421787 ACACAACTTC
Statistics
Matches: 103, Mismatches: 25, Indels: 14
0.73 0.18 0.10
Matches are distributed among these distances:
25 13 0.13
26 6 0.06
27 22 0.21
28 41 0.40
29 20 0.19
30 1 0.01
ACGTcount: A:0.53, C:0.06, G:0.08, T:0.33
Consensus pattern (27 bp):
AAAATTTTTATAAATTACAAAAAAGGC
Found at i:3421811 original size:29 final size:29
Alignment explanation
Indices: 3421743--3421812 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
3421733 AATTATTTAT
* *
3421743 AAATTATAATAAAGGACAAAACATTTTAT
1 AAATTATAATAAAGGACAAAACATTTCAC
* *
3421772 AAATTAAAATAAAGGACACAAC-TTCTCAC
1 AAATTATAATAAAGGACAAAACATT-TCAC
*
3421801 AAATTGTAATAA
1 AAATTATAATAA
3421813 CAACATATAC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 2 0.06
29 32 0.94
ACGTcount: A:0.54, C:0.11, G:0.07, T:0.27
Consensus pattern (29 bp):
AAATTATAATAAAGGACAAAACATTTCAC
Found at i:3425052 original size:2 final size:2
Alignment explanation
Indices: 3425045--3425454 Score: 303
Period size: 2 Copynumber: 213.0 Consensus size: 2
3425035 GTTGTTACTA
* * *
3425045 CT CT CT CT CT CT CT CT CT CT CT CT CC CT CT CC CT CC CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
* * *
3425087 CT CT CT CT CT C- CT CT CC CT CT CT CT CT CC CT CT CT CT CC CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
* *
3425128 CT C- CT C- CT CT CT CT C- CT CC CT C- CT CT CT CT CT CT CC CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
* *
3425166 CT CT C- CT CT CT CT CT CT CT C- CT CT CC CT CT CT CT CT CT CC
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
* * *
3425206 CT C- CT C- CC CT CT C- CT CT CT CT CT CT CC CT CC CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
* * * * *
3425245 CT CT CT AT CT CC CT CT CC CT CC CT CT CT CT CC CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
* * * * * * * * * * * * * *
3425287 C- CC CC CC CT CC CT CC CT CC CC CC CC CT CC CC CC CT CC CT CC
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
* * * * * * * * * *
3425328 CC CT CC CC CC CC CT C- CT CC CT CC CT C- CT CC CT CC CT CC CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
* * *
3425368 C- CC CT CC CT CC CT C- CT C- CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3425407 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3425449 CT CT CT
1 CT CT CT
3425455 GTATAAGAAA
Statistics
Matches: 327, Mismatches: 65, Indels: 32
0.77 0.15 0.08
Matches are distributed among these distances:
1 16 0.05
2 311 0.95
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.37
Consensus pattern (2 bp):
CT
Found at i:3426191 original size:23 final size:23
Alignment explanation
Indices: 3426165--3426228 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
3426155 CTAAGATTCA
*
3426165 TGAACATATTAGTTTAATATTGG
1 TGAACATATTGGTTTAATATTGG
3426188 TGAACATATTGGTTTAATATTGG
1 TGAACATATTGGTTTAATATTGG
**
3426211 TGAATGTATTGGTTTAAT
1 TGAACATATTGGTTTAAT
3426229 GTTTCAAAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.31, C:0.03, G:0.20, T:0.45
Consensus pattern (23 bp):
TGAACATATTGGTTTAATATTGG
Found at i:3431279 original size:2 final size:2
Alignment explanation
Indices: 3431272--3431305 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3431262 TATATGATGA
3431272 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3431306 CATGTATGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3438300 original size:21 final size:21
Alignment explanation
Indices: 3438276--3438315 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3438266 TTTATTTTAT
3438276 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
3438297 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
3438316 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:3438363 original size:33 final size:33
Alignment explanation
Indices: 3438310--3438408 Score: 155
Period size: 33 Copynumber: 3.0 Consensus size: 33
3438300 TTTGTTTCAA
3438310 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
*
3438342 TTATCGAACTTGGAAGTTTTTAAGTTTTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
3438375 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
3438408 T
1 T
3438409 ATGTTGAGTT
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
32 11 0.18
33 50 0.82
ACGTcount: A:0.31, C:0.07, G:0.15, T:0.46
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:3438670 original size:21 final size:21
Alignment explanation
Indices: 3438644--3438700 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
3438634 TGGAGCGTGG
*
3438644 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
*
3438665 GGGAATCGGTTTCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
3438686 GGGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
3438701 AAGTGTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:3438919 original size:15 final size:15
Alignment explanation
Indices: 3438867--3438922 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
3438857 ATCTGGAATA
*
3438867 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
3438882 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
* *
3438897 TAAAAAAACTGGTTTTT
1 T--TAAAACCGGTTTTT
3438914 TTAAAACCG
1 TTAAAACCG
3438923 AAACCGGTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
15 20 0.62
17 12 0.38
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.45
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:3449354 original size:6 final size:6
Alignment explanation
Indices: 3449345--3449376 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
3449335 GTATAGGGAC
*
3449345 TAAAAT TAAAAT TAAAAT TAGAAT TAAAAT TA
1 TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TA
3449377 GATTCCTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (6 bp):
TAAAAT
Found at i:3460818 original size:34 final size:34
Alignment explanation
Indices: 3460780--3460849 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
3460770 TAAGAAAGAA
3460780 AACCTCTCAGTTTAGTTTGAATACTTCTTGGTTC
1 AACCTCTCAGTTTAGTTTGAATACTTCTTGGTTC
3460814 AACCTCTCAGTTTAGTTTGAATACTTCTTGGTTC
1 AACCTCTCAGTTTAGTTTGAATACTTCTTGGTTC
3460848 AA
1 AA
3460850 AGTTATAAGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.23, C:0.20, G:0.14, T:0.43
Consensus pattern (34 bp):
AACCTCTCAGTTTAGTTTGAATACTTCTTGGTTC
Done.