Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009344.1 Hibiscus syriacus cultivar Beakdansim tig00113124_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: 4287485
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 24
Found at i:1021946 original size:40 final size:41
Alignment explanation
Indices: 1021891--1021972 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
1021881 AATAGAATGT
*
1021891 CCAGGGGGTACAGATT-CCCCCCAGGGGGTACCGATTCCCC
1 CCAGGGGGAACAGATTCCCCCCCAGGGGGTACCGATTCCCC
*
1021931 CCAGGGGGAACAGATTCCCCCCCAGGGGGTATCGATTCCCC
1 CCAGGGGGAACAGATTCCCCCCCAGGGGGTACCGATTCCCC
1021972 C
1 C
1021973 TGTCTAACGG
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
40 15 0.38
41 24 0.62
ACGTcount: A:0.18, C:0.38, G:0.29, T:0.15
Consensus pattern (41 bp):
CCAGGGGGAACAGATTCCCCCCCAGGGGGTACCGATTCCCC
Found at i:1024748 original size:20 final size:20
Alignment explanation
Indices: 1024723--1024782 Score: 95
Period size: 20 Copynumber: 3.0 Consensus size: 20
1024713 AACAGAATGT
1024723 CCAGGGGGTACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
*
1024743 CCAGGGGATACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
*
1024763 CCA-GGGGTACCGATTCCCC
1 CCAGGGGGTACAGATTCCCC
1024782 C
1 C
1024783 TCTGTGTAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
19 15 0.41
20 22 0.59
ACGTcount: A:0.20, C:0.38, G:0.27, T:0.15
Consensus pattern (20 bp):
CCAGGGGGTACAGATTCCCC
Found at i:1025169 original size:34 final size:32
Alignment explanation
Indices: 1025130--1025199 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
1025120 TTTTGTAAAG
* *
1025130 GGGAAATGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
1025164 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
1025196 GGGA
1 GGGA
1025200 GTTTGTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:1027150 original size:39 final size:39
Alignment explanation
Indices: 1027107--1027247 Score: 174
Period size: 39 Copynumber: 3.6 Consensus size: 39
1027097 GGGCTTACCC
*
1027107 TGTGCACAAAGCATAGGAGCCTGCGGTAAGGTCTTATCA
1 TGTGCACAAAGCAGAGGAGCCTGCGGTAAGGTCTTATCA
* * * * * *
1027146 TGTGCACAAAGTAGAGGAGCCTACAGTAAGGACTTACCC
1 TGTGCACAAAGCAGAGGAGCCTGCGGTAAGGTCTTATCA
* * *
1027185 TGAGCACAAAGCCGAGGAGCCTGCGGTAAGGTCTTATCT
1 TGTGCACAAAGCAGAGGAGCCTGCGGTAAGGTCTTATCA
* *
1027224 TGTGCACAAAGTAGATGAGCCTGC
1 TGTGCACAAAGCAGAGGAGCCTGC
1027248 ACAAAACGGT
Statistics
Matches: 83, Mismatches: 19, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
39 83 1.00
ACGTcount: A:0.29, C:0.22, G:0.28, T:0.21
Consensus pattern (39 bp):
TGTGCACAAAGCAGAGGAGCCTGCGGTAAGGTCTTATCA
Found at i:1027228 original size:78 final size:78
Alignment explanation
Indices: 1027094--1027245 Score: 250
Period size: 78 Copynumber: 1.9 Consensus size: 78
1027084 GTACACCCAA
* * *
1027094 TAAGGGCTTACCCTGTGCACAAAGCATAGGAGCCTGCGGTAAGGTCTTATCATGTGCACAAAGTA
1 TAAGGACTTACCCTGAGCACAAAGCAGAGGAGCCTGCGGTAAGGTCTTATCATGTGCACAAAGTA
1027159 GAGGAGCCTACAG
66 GAGGAGCCTACAG
* *
1027172 TAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTGCGGTAAGGTCTTATCTTGTGCACAAAGTA
1 TAAGGACTTACCCTGAGCACAAAGCAGAGGAGCCTGCGGTAAGGTCTTATCATGTGCACAAAGTA
*
1027237 GATGAGCCT
66 GAGGAGCCT
1027246 GCACAAAACG
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
78 68 1.00
ACGTcount: A:0.29, C:0.22, G:0.28, T:0.21
Consensus pattern (78 bp):
TAAGGACTTACCCTGAGCACAAAGCAGAGGAGCCTGCGGTAAGGTCTTATCATGTGCACAAAGTA
GAGGAGCCTACAG
Found at i:1027876 original size:21 final size:22
Alignment explanation
Indices: 1027852--1027893 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1027842 TTCCATGATC
*
1027852 AAATCCTAAAAA-ATTAAGCAA
1 AAATCCTAAAAACACTAAGCAA
*
1027873 AAATGCTAAAAACACTAAGCA
1 AAATCCTAAAAACACTAAGCA
1027894 TTTTCGGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.60, C:0.17, G:0.07, T:0.17
Consensus pattern (22 bp):
AAATCCTAAAAACACTAAGCAA
Found at i:1028534 original size:11 final size:11
Alignment explanation
Indices: 1028507--1028545 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
1028497 TTTCTTTTTG
*
1028507 AATTTAGATCCA
1 AATTTA-ATCAA
1028519 AATTTAATCAA
1 AATTTAATCAA
1028530 AATTTAATCAA
1 AATTTAATCAA
1028541 AATTT
1 AATTT
1028546 CACTTTGATC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
11 20 0.77
12 6 0.23
ACGTcount: A:0.49, C:0.10, G:0.03, T:0.38
Consensus pattern (11 bp):
AATTTAATCAA
Found at i:1031637 original size:29 final size:29
Alignment explanation
Indices: 1031602--1031685 Score: 150
Period size: 29 Copynumber: 2.9 Consensus size: 29
1031592 CGTAAGTTCC
**
1031602 AAAAATAATGGTTTGATCACTGAAGTTTT
1 AAAAATAATAATTTGATCACTGAAGTTTT
1031631 AAAAATAATAATTTGATCACTGAAGTTTT
1 AAAAATAATAATTTGATCACTGAAGTTTT
1031660 AAAAATAATAATTTGATCACTGAAGT
1 AAAAATAATAATTTGATCACTGAAGT
1031686 CATTGTTTTA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.36
Consensus pattern (29 bp):
AAAAATAATAATTTGATCACTGAAGTTTT
Found at i:1032930 original size:18 final size:17
Alignment explanation
Indices: 1032907--1032940 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1032897 ATAATAAAAA
1032907 TAAATAAAAATAAATATT
1 TAAATAAAAA-AAATATT
*
1032925 TAAATACAAAAAATAT
1 TAAATAAAAAAAATAT
1032941 ATAATTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
TAAATAAAAAAAATATT
Found at i:1046878 original size:16 final size:16
Alignment explanation
Indices: 1046857--1046895 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1046847 ATTGATTTTT
1046857 GGGTCGGGTCAATATC
1 GGGTCGGGTCAATATC
* *
1046873 GGGTCGAGTTAATATC
1 GGGTCGGGTCAATATC
*
1046889 GGATCGG
1 GGGTCGG
1046896 TTGATTATCG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.21, C:0.15, G:0.38, T:0.26
Consensus pattern (16 bp):
GGGTCGGGTCAATATC
Found at i:1047374 original size:21 final size:22
Alignment explanation
Indices: 1047348--1047388 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1047338 AAAGTCAAAG
*
1047348 GGGGGCACC-AGTTTGCTTGGT
1 GGGGGCACCGACTTTGCTTGGT
1047369 GGGGGCACCGACTTTGCTTG
1 GGGGGCACCGACTTTGCTTG
1047389 ATATTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.10, C:0.22, G:0.41, T:0.27
Consensus pattern (22 bp):
GGGGGCACCGACTTTGCTTGGT
Found at i:1051964 original size:21 final size:22
Alignment explanation
Indices: 1051930--1051970 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1051920 AAAAGTCAAA
1051930 GGGGGCACCAGC-TTGCTTGGT
1 GGGGGCACCAGCTTTGCTTGGT
**
1051951 GGGGGCACTGGCTTTGCTTG
1 GGGGGCACCAGCTTTGCTTG
1051971 ATATTTTTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.07, C:0.22, G:0.44, T:0.27
Consensus pattern (22 bp):
GGGGGCACCAGCTTTGCTTGGT
Found at i:1052632 original size:19 final size:20
Alignment explanation
Indices: 1052610--1052672 Score: 74
Period size: 22 Copynumber: 3.0 Consensus size: 20
1052600 TTTCATTAGT
*
1052610 TTGCTTTT-GGTGTTGTATA
1 TTGCTTTTAGGAGTTGTATA
1052629 TTGCTTTATTAGGAGTTGTATA
1 TTGC-TT-TTAGGAGTTGTATA
1052651 TTGCTTTATTAGGAGTTGTATA
1 TTGC-TT-TTAGGAGTTGTATA
1052673 GATTTTTTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
19 4 0.10
20 2 0.05
21 2 0.05
22 32 0.80
ACGTcount: A:0.19, C:0.05, G:0.24, T:0.52
Consensus pattern (20 bp):
TTGCTTTTAGGAGTTGTATA
Found at i:1052649 original size:22 final size:22
Alignment explanation
Indices: 1052621--1052672 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
1052611 TGCTTTTGGT
1052621 GTTGTATATTGCTTTATTAGGA
1 GTTGTATATTGCTTTATTAGGA
1052643 GTTGTATATTGCTTTATTAGGA
1 GTTGTATATTGCTTTATTAGGA
1052665 GTTGTATA
1 GTTGTATA
1052673 GATTTTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.23, C:0.04, G:0.23, T:0.50
Consensus pattern (22 bp):
GTTGTATATTGCTTTATTAGGA
Found at i:1057869 original size:44 final size:44
Alignment explanation
Indices: 1057806--1057894 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
1057796 TAATCTTATA
1057806 AATACCCTAAAGTCTAGTGACTAAAGTTAGTAATTATCCCTTCC
1 AATACCCTAAAGTCTAGTGACTAAAGTTAGTAATTATCCCTTCC
1057850 AATACCCTAAAGTCTAGTGACTAAAGTTAGTAATTATCCCTTCC
1 AATACCCTAAAGTCTAGTGACTAAAGTTAGTAATTATCCCTTCC
1057894 A
1 A
1057895 TTTTCAACAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.31
Consensus pattern (44 bp):
AATACCCTAAAGTCTAGTGACTAAAGTTAGTAATTATCCCTTCC
Found at i:1070511 original size:29 final size:30
Alignment explanation
Indices: 1070478--1070540 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
1070468 ATTAAATTTT
*
1070478 AAAACTACGATC-CTGATAACAAATATTGA
1 AAAACTACGATCTCTAATAACAAATATTGA
** *
1070507 AAAACTTGGATCTCTAATAATAAATATTGA
1 AAAACTACGATCTCTAATAACAAATATTGA
1070537 AAAA
1 AAAA
1070541 ATTGAGTCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 10 0.34
30 19 0.66
ACGTcount: A:0.51, C:0.13, G:0.10, T:0.27
Consensus pattern (30 bp):
AAAACTACGATCTCTAATAACAAATATTGA
Found at i:1070615 original size:30 final size:31
Alignment explanation
Indices: 1070571--1070712 Score: 105
Period size: 30 Copynumber: 4.4 Consensus size: 31
1070561 TGTTAGAAAA
1070571 AAATATTA-ACAAAAAATTAAACACTTAT-AT
1 AAATATTAGA-AAAAAATTAAACACTTATAAT
* *
1070601 AAATATTAGAAAAAAGTTATAAAAGTAAACCCTAATAAT
1 AAATATTAGAAAAAA---AT-----TAAACACTTATAAT
*
1070640 AAATATTAG-AAAAAATTAAACACATAGTAAT
1 AAATATTAGAAAAAAATTAAACACTTA-TAAT
* **
1070671 AAATATTAGAGAAAAATT-AACTTTTATAAT
1 AAATATTAGAAAAAAATTAAACACTTATAAT
1070701 AAATATTA-AAAA
1 AAATATTAGAAAA
1070713 TAAGTGAACC
Statistics
Matches: 90, Mismatches: 10, Indels: 25
0.72 0.08 0.20
Matches are distributed among these distances:
29 3 0.03
30 32 0.36
31 19 0.21
32 7 0.08
33 2 0.02
35 2 0.02
38 14 0.16
39 11 0.12
ACGTcount: A:0.60, C:0.06, G:0.05, T:0.29
Consensus pattern (31 bp):
AAATATTAGAAAAAAATTAAACACTTATAAT
Found at i:1071088 original size:20 final size:20
Alignment explanation
Indices: 1071065--1071131 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
1071055 AACTCTAATT
1071065 TCGCAACACAGATTCCAAAA
1 TCGCAACACAGATTCCAAAA
* ***
1071085 TCGCAACGC-GAATTTGTAAA
1 TCGCAACACAG-ATTCCAAAA
*
1071105 TCGCAACACAGTTTCCAAAA
1 TCGCAACACAGATTCCAAAA
1071125 TCGCAAC
1 TCGCAAC
1071132 GCGAATATGT
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
19 1 0.03
20 34 0.94
21 1 0.03
ACGTcount: A:0.39, C:0.28, G:0.13, T:0.19
Consensus pattern (20 bp):
TCGCAACACAGATTCCAAAA
Found at i:1071109 original size:40 final size:40
Alignment explanation
Indices: 1071065--1071168 Score: 181
Period size: 40 Copynumber: 2.6 Consensus size: 40
1071055 AACTCTAATT
* *
1071065 TCGCAACACAGATTCCAAAATCGCAACGCGAATTTGTAAA
1 TCGCAACACAGTTTCCAAAATCGCAACGCGAATATGTAAA
1071105 TCGCAACACAGTTTCCAAAATCGCAACGCGAATATGTAAA
1 TCGCAACACAGTTTCCAAAATCGCAACGCGAATATGTAAA
*
1071145 TCGCAGCACAGTTTCCAAAATCGC
1 TCGCAACACAGTTTCCAAAATCGC
1071169 GTTGCGATAG
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 61 1.00
ACGTcount: A:0.38, C:0.27, G:0.15, T:0.20
Consensus pattern (40 bp):
TCGCAACACAGTTTCCAAAATCGCAACGCGAATATGTAAA
Found at i:1071145 original size:20 final size:20
Alignment explanation
Indices: 1071082--1071149 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
1071072 ACAGATTCCA
1071082 AAATCGCAACGCGAATTTGT
1 AAATCGCAACGCGAATTTGT
* * **
1071102 AAATCGCAACAC-AGTTTCCA
1 AAATCGCAACGCGAATTT-GT
*
1071122 AAATCGCAACGCGAATATGT
1 AAATCGCAACGCGAATTTGT
1071142 AAATCGCA
1 AAATCGCA
1071150 GCACAGTTTC
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
19 4 0.11
20 30 0.81
21 3 0.08
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.21
Consensus pattern (20 bp):
AAATCGCAACGCGAATTTGT
Found at i:1071229 original size:20 final size:20
Alignment explanation
Indices: 1071204--1071249 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
1071194 TTGATAATTA
1071204 GCGTTGCGAATTTGAAAATC
1 GCGTTGCGAATTTGAAAATC
*
1071224 GCGTTGCGAATTTGGAAATC
1 GCGTTGCGAATTTGAAAATC
*
1071244 GTGTTG
1 GCGTTG
1071250 TGATAACACT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.24, C:0.13, G:0.30, T:0.33
Consensus pattern (20 bp):
GCGTTGCGAATTTGAAAATC
Found at i:1071243 original size:77 final size:77
Alignment explanation
Indices: 1071162--1071309 Score: 215
Period size: 77 Copynumber: 1.9 Consensus size: 77
1071152 ACAGTTTCCA
** * *
1071162 AAATCGCGTTGCGATAGTACTGTTTACCTATATTGATAATTAGCGTTGCGAATTTGAAAATCGCG
1 AAATCGCGTTGCGATAACACTGTTTACCTACATCGATAATTAGCGTTGCGAATTTGAAAATCGCG
1071227 TTGCGAATTTGG
66 TTGCGAATTTGG
* * * * *
1071239 AAATCGTGTTGTGATAACACTGTTTCCCTACATCGGTAATTAGCGTTGCGAATTTGAAAATCTCG
1 AAATCGCGTTGCGATAACACTGTTTACCTACATCGATAATTAGCGTTGCGAATTTGAAAATCGCG
1071304 TTGCGA
66 TTGCGA
1071310 TCCTACATCG
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
77 62 1.00
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.34
Consensus pattern (77 bp):
AAATCGCGTTGCGATAACACTGTTTACCTACATCGATAATTAGCGTTGCGAATTTGAAAATCGCG
TTGCGAATTTGG
Found at i:1071445 original size:77 final size:77
Alignment explanation
Indices: 1071364--1071555 Score: 312
Period size: 77 Copynumber: 2.5 Consensus size: 77
1071354 GATAACACTA
*
1071364 TTTACGTATGTCGGTAATTAGCGTTGCGAATTTTAAAATCTCATTGCGAATTTGTAAACCGTGTT
1 TTTACCTATGTCGGTAATTAGCGTTGCGAATTTTAAAATCTCATTGCGAATTTGTAAACCGTGTT
1071429 GCGATAGTAATG
66 GCGATAGTAATG
* * *
1071441 TTTACCTATGTCGGTAATTAGCGTTGCGAATTTGAAAATCTCGTTGCGAATTTGTAAATCGTGTT
1 TTTACCTATGTCGGTAATTAGCGTTGCGAATTTTAAAATCTCATTGCGAATTTGTAAACCGTGTT
*
1071506 GCGATAGTACTG
66 GCGATAGTAATG
* *
1071518 TTTACCTATATTGGTAATTAGCGTTGCGAATTTGTAAA
1 TTTACCTATGTCGGTAATTAGCGTTGCGAATTT-TAAA
1071556 TCGCGTTGCA
Statistics
Matches: 106, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
77 103 0.97
78 3 0.03
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.39
Consensus pattern (77 bp):
TTTACCTATGTCGGTAATTAGCGTTGCGAATTTTAAAATCTCATTGCGAATTTGTAAACCGTGTT
GCGATAGTAATG
Found at i:1071487 original size:20 final size:21
Alignment explanation
Indices: 1071462--1071509 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
1071452 CGGTAATTAG
1071462 CGTTGCGAATTTGAAAATC-T
1 CGTTGCGAATTTGAAAATCGT
*
1071482 CGTTGCGAATTTGTAAATCGT
1 CGTTGCGAATTTGAAAATCGT
1071503 -GTTGCGA
1 CGTTGCGA
1071510 TAGTACTGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 25 0.96
21 1 0.04
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (21 bp):
CGTTGCGAATTTGAAAATCGT
Found at i:1071570 original size:57 final size:57
Alignment explanation
Indices: 1071482--1071621 Score: 208
Period size: 57 Copynumber: 2.5 Consensus size: 57
1071472 TTGAAAATCT
* * * *
1071482 CGTTGCGAATTTGTAAATCGTGTTGCGATAGTACTGTTTACCTATATTGGTAATTAG
1 CGTTGCGAATTTGTAAATCGCGTTGCAATAGTACTATTTACCTATATCGGTAATTAG
*
1071539 CGTTGCGAATTTGTAAATCGCGTTGCAATAGTACTATTTACCTATGTCGGTAATTAG
1 CGTTGCGAATTTGTAAATCGCGTTGCAATAGTACTATTTACCTATATCGGTAATTAG
* * *
1071596 CATTGCGAATTTGAAAATCTCGTTGC
1 CGTTGCGAATTTGTAAATCGCGTTGC
1071622 GAATTTGTAA
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 75 1.00
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (57 bp):
CGTTGCGAATTTGTAAATCGCGTTGCAATAGTACTATTTACCTATATCGGTAATTAG
Found at i:1071579 original size:134 final size:134
Alignment explanation
Indices: 1071407--1071834 Score: 622
Period size: 134 Copynumber: 3.2 Consensus size: 134
1071397 TAAAATCTCA
* * * * *
1071407 TTGCGAATTTGTAAACCGTGTTGCGATAGTAATGTTTACCTATGTCGGTAATTAGCGTTGCGAAT
1 TTGCGAATTTATAAATCGCGTTGCAATAGTACTGTTTACCTATGTCGGTAATTAGCGTTGCGAAT
* * *
1071472 TTGAAAATCTCGTTGCGAATTTGTAAATCGTGTTGCGATAGTACTGTTTACCTATATTGGTAATT
66 TTGAAAATCTCGTTGCGAATTTGTAAATCGCGTTGCGATAGTACTGTTTACCTATATCGATAATT
1071537 AGCG
131 AGCG
* * *
1071541 TTGCGAATTTGTAAATCGCGTTGCAATAGTACTATTTACCTATGTCGGTAATTAGCATTGCGAAT
1 TTGCGAATTTATAAATCGCGTTGCAATAGTACTGTTTACCTATGTCGGTAATTAGCGTTGCGAAT
*
1071606 TTGAAAATCTCGTTGCGAATTTGTAAATCGCGTTGCGATAGTACTATTTACCTATATCGATAATT
66 TTGAAAATCTCGTTGCGAATTTGTAAATCGCGTTGCGATAGTACTGTTTACCTATATCGATAATT
1071671 AGCG
131 AGCG
* * *
1071675 TTGCGAATTTATAAATCGCGTAGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAAT
1 TTGCGAATTTATAAATCGCGTTGCAATAGTACTGTTTACCTATGTCGGTAATTAGCGTTGCGAAT
* * * * * * * * *
1071740 TTGAAAATCGCATTGCAAATTTGAAAATCGCATTGCGATGGTACTGTTTATCTATGTCGCTAATT
66 TTGAAAATCTCGTTGCGAATTTGTAAATCGCGTTGCGATAGTACTGTTTACCTATATCGATAATT
1071805 AGCG
131 AGCG
* *
1071809 TTGCGAATTTAAAAATCTCGTTGCAA
1 TTGCGAATTTATAAATCGCGTTGCAA
1071835 ATTTGTAAAT
Statistics
Matches: 264, Mismatches: 30, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
134 264 1.00
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (134 bp):
TTGCGAATTTATAAATCGCGTTGCAATAGTACTGTTTACCTATGTCGGTAATTAGCGTTGCGAAT
TTGAAAATCTCGTTGCGAATTTGTAAATCGCGTTGCGATAGTACTGTTTACCTATATCGATAATT
AGCG
Found at i:1071593 original size:211 final size:211
Alignment explanation
Indices: 1071319--1071968 Score: 674
Period size: 211 Copynumber: 3.1 Consensus size: 211
1071309 ATCCTACATC
* ** *
1071319 GGTAATTAGCGTTGCG-ATTT-ACATATTCGCATTGCGATAACACTATTTACGTATGTCGGTAAT
1 GGTAATTAGCGTTGCGAATTTGA-A-AATCGCATTGCGATAGTACTATTTACCTATGTCGGTAAT
* * * * *
1071382 TAGCGTTGCGAATTTTAAAATCTCATTGCGAATTTGTAAACCGTGTTGCGATAGTAATGTTTACC
64 TAGCGTTGCGAATTTAAAAATCTCGTTGCGAATTTGTAAATCGCGTTGCGATAGTACTGTTTACC
*
1071447 TATGTCGGTAATTAGCGTTGCGAATTTGAAAATCTCGTTGCGAATTTGTAAATCGTGTTGCGATA
129 TATATCGGTAATTAGCGTTGCGAATTTGAAAATCTCGTTGCGAATTTGTAAATCGTGTTGCGATA
1071512 GTACTGTTTACCTATATT
194 GTACTGTTTACCTATATT
* * *
1071530 GGTAATTAGCGTTGCGAATTTGTAAATCGCGTTGCAATAGTACTATTTACCTATGTCGGTAATTA
1 GGTAATTAGCGTTGCGAATTTGAAAATCGCATTGCGATAGTACTATTTACCTATGTCGGTAATTA
* * *
1071595 GCATTGCGAATTTGAAAATCTCGTTGCGAATTTGTAAATCGCGTTGCGATAGTACTATTTACCTA
66 GCGTTGCGAATTTAAAAATCTCGTTGCGAATTTGTAAATCGCGTTGCGATAGTACTGTTTACCTA
* * * * * * *
1071660 TATCGATAATTAGCGTTGCGAATTT-ATAAATCGCGTAGCG-A-TAGT-ACT-GT-TTAC-CTA-
131 TATCGGTAATTAGCGTTGCGAATTTGA-AAATCTCGTTGCGAATTTGTAAATCGTGTTGCGATAG
* *
1071717 TATCGGTAATTAGCGT-TGCGAATT
195 TA-CTGT--TTA-CCTAT----ATT
* * * * * * * * * *
1071741 TGAAAATCGCATTGCAAATTTGAAAATCGCATTGCGATGGTACTGTTTATCTATGTCGCTAATTA
1 GGTAATTAGCGTTGCGAATTTGAAAATCGCATTGCGATAGTACTATTTACCTATGTCGGTAATTA
* * *
1071806 GCGTTGCGAATTTAAAAATCTCGTTGCAAATTTGTAAATCGCGTTGCGATAGTACTGTTTACTTT
66 GCGTTGCGAATTTAAAAATCTCGTTGCGAATTTGTAAATCGCGTTGCGATAGTACTGTTTACCTA
** * ** * *
1071871 TATAAGTAATTAGCGTTGCGAATTTGAAAATCTTGTTGCGAATTTAAAAATCGCGTTGAGATAGT
131 TATCGGTAATTAGCGTTGCGAATTTGAAAATCTCGTTGCGAATTTGTAAATCGTGTTGCGATAGT
** * *
1071936 TTTGTTTACCTACATC
196 ACTGTTTACCTATATT
*
1071952 GGTAATAAGCGTTGCGA
1 GGTAATTAGCGTTGCGA
1071969 TTTACATATT
Statistics
Matches: 349, Mismatches: 70, Indels: 40
0.76 0.15 0.09
Matches are distributed among these distances:
204 2 0.01
205 5 0.01
206 3 0.01
207 6 0.02
208 4 0.01
209 3 0.01
210 2 0.01
211 301 0.86
212 7 0.02
213 1 0.00
214 4 0.01
215 4 0.01
216 2 0.01
217 4 0.01
218 1 0.00
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.37
Consensus pattern (211 bp):
GGTAATTAGCGTTGCGAATTTGAAAATCGCATTGCGATAGTACTATTTACCTATGTCGGTAATTA
GCGTTGCGAATTTAAAAATCTCGTTGCGAATTTGTAAATCGCGTTGCGATAGTACTGTTTACCTA
TATCGGTAATTAGCGTTGCGAATTTGAAAATCTCGTTGCGAATTTGTAAATCGTGTTGCGATAGT
ACTGTTTACCTATATT
Found at i:1071623 original size:20 final size:20
Alignment explanation
Indices: 1071598--1071643 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
1071588 GTAATTAGCA
*
1071598 TTGCGAATTTGAAAATCTCG
1 TTGCGAATTTGAAAATCGCG
*
1071618 TTGCGAATTTGTAAATCGCG
1 TTGCGAATTTGAAAATCGCG
1071638 TTGCGA
1 TTGCGA
1071644 TAGTACTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (20 bp):
TTGCGAATTTGAAAATCGCG
Found at i:1071691 original size:77 final size:77
Alignment explanation
Indices: 1071538--1071700 Score: 256
Period size: 77 Copynumber: 2.1 Consensus size: 77
1071528 TTGGTAATTA
* *
1071538 GCGTTGCGAATTTGTAAATCGCGTTGCAATAGTACTATTTACCTATGTCGGTAATTAGCATTGCG
1 GCGTTGCGAATTTGTAAATCGCGTTGCAATAGTACTATTTACCTATATCGATAATTAGCATTGCG
1071603 AATTTGAAAATC
66 AATTTGAAAATC
* * *
1071615 TCGTTGCGAATTTGTAAATCGCGTTGCGATAGTACTATTTACCTATATCGATAATTAGCGTTGCG
1 GCGTTGCGAATTTGTAAATCGCGTTGCAATAGTACTATTTACCTATATCGATAATTAGCATTGCG
1071680 AATTT-ATAAATC
66 AATTTGA-AAATC
*
1071692 GCGTAGCGA
1 GCGTTGCGA
1071701 TAGTACTGTT
Statistics
Matches: 78, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
76 1 0.01
77 77 0.99
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (77 bp):
GCGTTGCGAATTTGTAAATCGCGTTGCAATAGTACTATTTACCTATATCGATAATTAGCATTGCG
AATTTGAAAATC
Found at i:1071704 original size:57 final size:57
Alignment explanation
Indices: 1071616--1071750 Score: 218
Period size: 57 Copynumber: 2.4 Consensus size: 57
1071606 TTGAAAATCT
* *
1071616 CGTTGCGAATTTGTAAATCGCGTTGCGATAGTACTATTTACCTATATCGATAATTAG
1 CGTTGCGAATTTATAAATCGCGTAGCGATAGTACTATTTACCTATATCGATAATTAG
* *
1071673 CGTTGCGAATTTATAAATCGCGTAGCGATAGTACTGTTTACCTATATCGGTAATTAG
1 CGTTGCGAATTTATAAATCGCGTAGCGATAGTACTATTTACCTATATCGATAATTAG
1071730 CGTTGCGAATTTGA-AAATCGC
1 CGTTGCGAATTT-ATAAATCGC
1071751 ATTGCAAATT
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
57 72 0.99
58 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (57 bp):
CGTTGCGAATTTATAAATCGCGTAGCGATAGTACTATTTACCTATATCGATAATTAG
Found at i:1071760 original size:20 final size:20
Alignment explanation
Indices: 1071732--1071775 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
1071722 GTAATTAGCG
*
1071732 TTGCGAATTTGAAAATCGCA
1 TTGCAAATTTGAAAATCGCA
1071752 TTGCAAATTTGAAAATCGCA
1 TTGCAAATTTGAAAATCGCA
1071772 TTGC
1 TTGC
1071776 GATGGTACTG
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:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (20 bp):
TTGCAAATTTGAAAATCGCA
Found at i:1071832 original size:20 final size:20
Alignment explanation
Indices: 1071806--1071854 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
1071796 TCGCTAATTA
1071806 GCGTTGCGAATTTAAAAATC
1 GCGTTGCGAATTTAAAAATC
* * **
1071826 TCGTTGCAAATTTGTAAATC
1 GCGTTGCGAATTTAAAAATC
1071846 GCGTTGCGA
1 GCGTTGCGA
1071855 TAGTACTGTT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (20 bp):
GCGTTGCGAATTTAAAAATC
Found at i:1071910 original size:20 final size:20
Alignment explanation
Indices: 1071885--1071922 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1071875 AGTAATTAGC
*
1071885 GTTGCGAATTTGAAAATCTT
1 GTTGCGAATTTAAAAATCTT
1071905 GTTGCGAATTTAAAAATC
1 GTTGCGAATTTAAAAATC
1071923 GCGTTGAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37
Consensus pattern (20 bp):
GTTGCGAATTTAAAAATCTT
Found at i:1071928 original size:20 final size:20
Alignment explanation
Indices: 1071883--1071928 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1071873 TAAGTAATTA
*
1071883 GCGTTGCGAATTTGAAAATC
1 GCGTTGCGAATTTAAAAATC
**
1071903 TTGTTGCGAATTTAAAAATC
1 GCGTTGCGAATTTAAAAATC
1071923 GCGTTG
1 GCGTTG
1071929 AGATAGTTTT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.28, C:0.13, G:0.24, T:0.35
Consensus pattern (20 bp):
GCGTTGCGAATTTAAAAATC
Found at i:1071986 original size:77 final size:78
Alignment explanation
Indices: 1071672--1072007 Score: 371
Period size: 77 Copynumber: 4.3 Consensus size: 78
1071662 TCGATAATTA
*
1071672 GCGTTGCGAATTT-ATAAATCGCGTAGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGC
1 GCGTTGCGAATTTGA-AAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGC
1071736 GAATTTGAAAATC-
65 GAATTTGAAAATCT
* * * * * * *
1071749 GCATTGCAAATTTGAAAATCGCATTGCGATGGTACTGTTTATCTATGTCGCTAATTAGCGTTGCG
1 GCGTTGCGAATTTGAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCG
*
1071814 AATTTAAAAATCT
66 AATTTGAAAATCT
* * * * **
1071827 -CGTTGCAAATTTGTAAATCGCGTTGCGATAGTACTGTTTACTTTTATAAGTAATTAGCGTTGCG
1 GCGTTGCGAATTTGAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCG
1071891 AATTTGAAAATCT
66 AATTTGAAAATCT
* * * ** * *
1071904 -TGTTGCGAATTTAAAAATCGCGTTGAGATAGTTTTGTTTACCTACATCGGTAATAAGCGTTGCG
1 GCGTTGCGAATTTGAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCG
*
1071968 -ATTT-ACATAT-T
66 AATTTGA-AAATCT
*
1071979 GGCGTTGCGAATTTGGAAAATGGCGTTGC
1 -GCGTTGCGAATTT-GAAAATCGCGTTGC
1072008 AATTTTGGAA
Statistics
Matches: 214, Mismatches: 39, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
75 2 0.01
76 7 0.03
77 193 0.90
78 12 0.06
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (78 bp):
GCGTTGCGAATTTGAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCG
AATTTGAAAATCT
Found at i:1072002 original size:21 final size:21
Alignment explanation
Indices: 1071978--1072033 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
1071968 ATTTACATAT
1071978 TGGCGTTGCGAA-TTTGGAAAA
1 TGGCGTTGC-AATTTTGGAAAA
1071999 TGGCGTTGCAATTTTGGAAAA
1 TGGCGTTGCAATTTTGGAAAA
*
1072020 CT-GCATTGCAATTT
1 -TGGCGTTGCAATTT
1072034 ACATATTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 2 0.06
21 29 0.91
22 1 0.03
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.34
Consensus pattern (21 bp):
TGGCGTTGCAATTTTGGAAAA
Found at i:1072053 original size:20 final size:20
Alignment explanation
Indices: 1072025--1072073 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
1072015 GAAAACTGCA
* *
1072025 TTGCAATTTACATATTATTG
1 TTGCGATTTACATATTAGTG
*
1072045 TTGCGATTTACATATTCGTG
1 TTGCGATTTACATATTAGTG
1072065 TTGCGATTT
1 TTGCGATTT
1072074 TGGAACATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.22, C:0.12, G:0.16, T:0.49
Consensus pattern (20 bp):
TTGCGATTTACATATTAGTG
Found at i:1074330 original size:3 final size:3
Alignment explanation
Indices: 1074322--1074356 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1074312 TCTTGCACCT
1074322 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1074357 TCTCTTTCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1078140 original size:16 final size:17
Alignment explanation
Indices: 1078119--1078150 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1078109 TGATCGTAAG
1078119 TTTTTTTTCT-TTTTCT
1 TTTTTTTTCTATTTTCT
1078135 TTTTTTTTCTATTTTC
1 TTTTTTTTCTATTTTC
1078151 ATGTTTGTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.84
Consensus pattern (17 bp):
TTTTTTTTCTATTTTCT
Found at i:1080370 original size:19 final size:19
Alignment explanation
Indices: 1080346--1080401 Score: 103
Period size: 19 Copynumber: 2.9 Consensus size: 19
1080336 ATGACCAACA
1080346 AAATCGCAATGCGATCTCT
1 AAATCGCAATGCGATCTCT
1080365 AAATCGCAATGCGATCTCT
1 AAATCGCAATGCGATCTCT
*
1080384 AAATCGCAACGCGATCTC
1 AAATCGCAATGCGATCTC
1080402 CAGTATCGCA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.23
Consensus pattern (19 bp):
AAATCGCAATGCGATCTCT
Found at i:1080704 original size:17 final size:17
Alignment explanation
Indices: 1080682--1080719 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1080672 TGACATTCGT
*
1080682 TCCTATATCTAACGACA
1 TCCTATATCCAACGACA
*
1080699 TCCTATATCCATCGACA
1 TCCTATATCCAACGACA
1080716 TCCT
1 TCCT
1080720 TCCCCATCCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.29, C:0.34, G:0.05, T:0.32
Consensus pattern (17 bp):
TCCTATATCCAACGACA
Found at i:1081426 original size:24 final size:24
Alignment explanation
Indices: 1081367--1081426 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
1081357 TAGTCAGTAT
* *
1081367 TCGAAATTTGAACTTGGTCAATAC
1 TCGAATTTTGATCTTGGTCAATAC
* *
1081391 CCGGATTTTGATCTTGGTCAATAC
1 TCGAATTTTGATCTTGGTCAATAC
1081415 TCGAATTTTGAT
1 TCGAATTTTGAT
1081427 GATATTTCAG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (24 bp):
TCGAATTTTGATCTTGGTCAATAC
Found at i:1081893 original size:5 final size:5
Alignment explanation
Indices: 1081883--1081908 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1081873 TGACTTAGAA
1081883 ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG A
1081909 AATAATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:1084117 original size:18 final size:18
Alignment explanation
Indices: 1084094--1084128 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1084084 AGTAAAAGAC
1084094 AATCAAAATCGCAATCAA
1 AATCAAAATCGCAATCAA
*
1084112 AATCAAAATCTCAATCA
1 AATCAAAATCGCAATCA
1084129 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:1084324 original size:20 final size:20
Alignment explanation
Indices: 1084299--1084515 Score: 335
Period size: 20 Copynumber: 10.8 Consensus size: 20
1084289 TTACACATTC
*
1084299 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
1084319 ATTTGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
*
1084339 ATTTGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
* *
1084359 ATTTGATTATCGCAACGGGA
1 ATTTGACTATCGCAACGCGA
*
1084379 ATTTGACTATCGCAATGCGA
1 ATTTGACTATCGCAACGCGA
*
1084399 ATTTGACTATCACAACGCGA
1 ATTTGACTATCGCAACGCGA
1084419 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
1084439 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
1084459 ATTTGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
* * *
1084479 ATTTGATTATCGTAACGGGA
1 ATTTGACTATCGCAACGCGA
1084499 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
1084516 AGAAAACCGT
Statistics
Matches: 181, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 181 1.00
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:1084584 original size:20 final size:20
Alignment explanation
Indices: 1084555--1084618 Score: 92
Period size: 20 Copynumber: 3.2 Consensus size: 20
1084545 GCAACGCGAA
*
1084555 TTGACTTTCGCGTTGCGATT
1 TTGACTTTCGCATTGCGATT
* *
1084575 TTGGCTTTCGCATTGTGATT
1 TTGACTTTCGCATTGCGATT
*
1084595 TTAACTTTCGCATTGCGATT
1 TTGACTTTCGCATTGCGATT
1084615 TTGA
1 TTGA
1084619 GTTTAGCGTT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.14, C:0.17, G:0.22, T:0.47
Consensus pattern (20 bp):
TTGACTTTCGCATTGCGATT
Found at i:1084771 original size:14 final size:14
Alignment explanation
Indices: 1084752--1084788 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
1084742 CATCAATTAA
1084752 ACAAATCAACTTTT
1 ACAAATCAACTTTT
1084766 ACAAATCAACTTTT
1 ACAAATCAACTTTT
1084780 ACAAATCAA
1 ACAAATCAA
1084789 TTAAACAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1086286 original size:42 final size:42
Alignment explanation
Indices: 1086181--1086286 Score: 104
Period size: 42 Copynumber: 2.5 Consensus size: 42
1086171 TTGAATGGTG
* * * * *
1086181 GGAGAGACCTCTTCAACGATAATAGGGGCCTCTTGAACGGCG
1 GGAGAGGCCTCTTGAACGATGATAGGGGCCTCTTGAACGACA
* * ** *
1086223 GGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGATA
1 GGAGAGGCCTCTTGAACGATGATAGGGGCCTCTTGAACGACA
* *
1086265 TGAGAGGCCTCTTGAATGATGA
1 GGAGAGGCCTCTTGAACGATGA
1086287 CAGGTGAGTC
Statistics
Matches: 49, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.25, C:0.18, G:0.35, T:0.22
Consensus pattern (42 bp):
GGAGAGGCCTCTTGAACGATGATAGGGGCCTCTTGAACGACA
Found at i:1086642 original size:33 final size:34
Alignment explanation
Indices: 1086587--1086662 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 34
1086577 AGCAATGACT
* *
1086587 ATCGCAACGGGATAATCACAATGC-GAAATAAAA
1 ATCGCAACGGGAAAATCACAATGCAAAAATAAAA
* ** *
1086620 ATCGCAACGTGAAAATTGCAATGCAAAAATGAAA
1 ATCGCAACGGGAAAATCACAATGCAAAAATAAAA
1086654 ATCGCAACG
1 ATCGCAACG
1086663 CGAATTTAGT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
33 20 0.56
34 16 0.44
ACGTcount: A:0.47, C:0.18, G:0.18, T:0.16
Consensus pattern (34 bp):
ATCGCAACGGGAAAATCACAATGCAAAAATAAAA
Found at i:1086771 original size:20 final size:20
Alignment explanation
Indices: 1086742--1086810 Score: 95
Period size: 20 Copynumber: 3.5 Consensus size: 20
1086732 GCGATTATCC
* *
1086742 CGTTGTGATAGTCAAATTCG
1 CGTTGCGATAGTCAATTTCG
1086762 CGTTGCGATAGTC-ATTTCTG
1 CGTTGCGATAGTCAATTTC-G
*
1086782 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAATTTCG
1086802 CGTTGCGAT
1 CGTTGCGAT
1086811 TTTAAGTTTC
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
19 4 0.09
20 36 0.82
21 4 0.09
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTTCG
Found at i:1088743 original size:21 final size:21
Alignment explanation
Indices: 1088703--1088798 Score: 92
Period size: 21 Copynumber: 4.8 Consensus size: 21
1088693 TTTGAAACTT
1088703 AAAATCGCAACACG-AAAATG
1 AAAATCGCAACACGAAAAATG
1088723 AAAATCGCAACACGAAAAATG
1 AAAATCGCAACACGAAAAATG
** * **
1088744 ACTATCGCAACGCG-AATTTG
1 AAAATCGCAACACGAAAAATG
1088764 AAAA--GCAACACGAAAAATG
1 AAAATCGCAACACGAAAAATG
** *
1088783 ACTATCGCAACGCGAA
1 AAAATCGCAACACGAA
1088799 TTTGACTATC
Statistics
Matches: 59, Mismatches: 13, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
18 7 0.12
19 6 0.10
20 20 0.34
21 26 0.44
ACGTcount: A:0.49, C:0.22, G:0.17, T:0.12
Consensus pattern (21 bp):
AAAATCGCAACACGAAAAATG
Found at i:1088781 original size:39 final size:40
Alignment explanation
Indices: 1088706--1088803 Score: 153
Period size: 39 Copynumber: 2.5 Consensus size: 40
1088696 GAAACTTAAA
* **
1088706 ATCGCAACACGAAAATGAAAATCGCAACACGAAAAATGACT
1 ATCGCAACGCGAATTTGAAAA-CGCAACACGAAAAATGACT
1088747 ATCGCAACGCGAATTTGAAAA-GCAACACGAAAAATGACT
1 ATCGCAACGCGAATTTGAAAACGCAACACGAAAAATGACT
1088786 ATCGCAACGCGAATTTGA
1 ATCGCAACGCGAATTTGA
1088804 CTATCGCAAC
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
39 36 0.67
41 18 0.33
ACGTcount: A:0.46, C:0.21, G:0.17, T:0.15
Consensus pattern (40 bp):
ATCGCAACGCGAATTTGAAAACGCAACACGAAAAATGACT
Found at i:1088806 original size:20 final size:20
Alignment explanation
Indices: 1088742--1088814 Score: 78
Period size: 20 Copynumber: 3.7 Consensus size: 20
1088732 ACACGAAAAA
1088742 TGACTATCGCAACGCGAATT
1 TGACTATCGCAACGCGAATT
** * **
1088762 TGA--AAAGCAACACGAAAAA
1 TGACTATCGCAACGCG-AATT
1088781 TGACTATCGCAACGCGAATT
1 TGACTATCGCAACGCGAATT
1088801 TGACTATCGCAACG
1 TGACTATCGCAACG
1088815 AGATAATCGC
Statistics
Matches: 40, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
18 8 0.20
19 5 0.12
20 19 0.47
21 8 0.20
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.19
Consensus pattern (20 bp):
TGACTATCGCAACGCGAATT
Found at i:1088843 original size:19 final size:19
Alignment explanation
Indices: 1088819--1088862 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
1088809 GCAACGAGAT
*
1088819 AATCGCAACGTGAAA-TGAA
1 AATCGCAACGCGAAACT-AA
1088838 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
1088857 AATCGC
1 AATCGC
1088863 GTTGCGATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 22 0.96
20 1 0.04
ACGTcount: A:0.45, C:0.23, G:0.18, T:0.14
Consensus pattern (19 bp):
AATCGCAACGCGAAACTAA
Found at i:1088900 original size:19 final size:19
Alignment explanation
Indices: 1088876--1088923 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
1088866 GCGATTTTGT
1088876 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
1088895 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
1088914 CGTTGCGATT
1 CGTTGCGATT
1088924 CTCGTTTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.10, C:0.21, G:0.23, T:0.46
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:1089297 original size:22 final size:22
Alignment explanation
Indices: 1089270--1089327 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
1089260 GATGGAGATA
1089270 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
1089292 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
1089314 GACGGATGTCGCCG
1 GACGGATTTCGCCG
1089328 TAGAGAGTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.17, C:0.19, G:0.45, T:0.19
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:1089512 original size:20 final size:20
Alignment explanation
Indices: 1089487--1089558 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
1089477 ATTTTGTATT
*
1089487 ATCGCGTTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCAAA
* *
1089507 ATCGCGTTGCGAT-TTACATA
1 ATCGCGTTGCGATAGT-CAAA
* *
1089527 TTCGCATTGCGATAGTCAAA
1 ATCGCGTTGCGATAGTCAAA
1089547 ATCGCGTTGCGA
1 ATCGCGTTGCGA
1089559 ATCTGGAAAC
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
19 1 0.02
20 40 0.95
21 1 0.02
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAAA
Found at i:1090249 original size:33 final size:33
Alignment explanation
Indices: 1090183--1090278 Score: 97
Period size: 33 Copynumber: 2.9 Consensus size: 33
1090173 TCTCATCTGC
* **
1090183 CTTCTGCA-AGGTTTCTGCTGCATGTTTATCCGT
1 CTTCTGCACA-GTTTCTGCTGCAGGTTTCGCCGT
*
1090216 CTTCTGCACAGTTTCTGCTACAGGTTTCGCCGT
1 CTTCTGCACAGTTTCTGCTGCAGGTTTCGCCGT
* * *
1090249 CTT-TTCAACAGTTCCTGGTGCAGGTTTCGC
1 CTTCTGC-ACAGTTTCTGCTGCAGGTTTCGC
1090279 ATTTTCTTCA
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
32 2 0.04
33 50 0.94
34 1 0.02
ACGTcount: A:0.12, C:0.27, G:0.22, T:0.39
Consensus pattern (33 bp):
CTTCTGCACAGTTTCTGCTGCAGGTTTCGCCGT
Found at i:1091521 original size:17 final size:17
Alignment explanation
Indices: 1091499--1091531 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1091489 TTACCGGATT
1091499 AAAAACCAGTTTTTTTA
1 AAAAACCAGTTTTTTTA
*
1091516 AAAAACCGGTTTTTTT
1 AAAAACCAGTTTTTTT
1091532 CAAACAGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.42
Consensus pattern (17 bp):
AAAAACCAGTTTTTTTA
Found at i:1098140 original size:57 final size:57
Alignment explanation
Indices: 1098052--1098167 Score: 232
Period size: 57 Copynumber: 2.0 Consensus size: 57
1098042 GATAATTTGG
1098052 GACCCAACAAACAGATGGCAAATGGAATACAATCGTTTGAGAATCACGAAAGGCGCT
1 GACCCAACAAACAGATGGCAAATGGAATACAATCGTTTGAGAATCACGAAAGGCGCT
1098109 GACCCAACAAACAGATGGCAAATGGAATACAATCGTTTGAGAATCACGAAAGGCGCT
1 GACCCAACAAACAGATGGCAAATGGAATACAATCGTTTGAGAATCACGAAAGGCGCT
1098166 GA
1 GA
1098168 GGAACGAGGA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 59 1.00
ACGTcount: A:0.41, C:0.21, G:0.23, T:0.16
Consensus pattern (57 bp):
GACCCAACAAACAGATGGCAAATGGAATACAATCGTTTGAGAATCACGAAAGGCGCT
Found at i:1103592 original size:23 final size:23
Alignment explanation
Indices: 1103547--1103643 Score: 140
Period size: 23 Copynumber: 4.2 Consensus size: 23
1103537 CACCGAAGTG
* *
1103547 CCACGTAGAATTTGTCCCGAAGGA
1 CCACGTAGAA-ATGTCCCAAAGGA
* *
1103571 TCGCGTAGAAATGTCCCAAAGGA
1 CCACGTAGAAATGTCCCAAAGGA
1103594 CCACGTAGAAATGTCCCAAAGGA
1 CCACGTAGAAATGTCCCAAAGGA
*
1103617 CCACGTAGAAATGTCCCGAAGGA
1 CCACGTAGAAATGTCCCAAAGGA
1103640 CCAC
1 CCAC
1103644 ATCGATTTTT
Statistics
Matches: 66, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
23 58 0.88
24 8 0.12
ACGTcount: A:0.34, C:0.27, G:0.24, T:0.15
Consensus pattern (23 bp):
CCACGTAGAAATGTCCCAAAGGA
Found at i:1103662 original size:46 final size:46
Alignment explanation
Indices: 1103547--1103672 Score: 153
Period size: 46 Copynumber: 2.7 Consensus size: 46
1103537 CACCGAAGTG
* *
1103547 CCACGTAGAATTTGTCCCGAAGGATCGCGTAGAAATGTCCCAAAGGA
1 CCACATAG-ATTTGTCCCGAAGGACCGCGTAGAAATGTCCCAAAGGA
* ** * * *
1103594 CCACGTAGAAATGTCCCAAAGGACCACGTAGAAATGTCCCGAAGGA
1 CCACATAGATTTGTCCCGAAGGACCGCGTAGAAATGTCCCAAAGGA
* *
1103640 CCACATCGATTTTTCCCGAAGGACCGCGTAGAA
1 CCACATAGATTTGTCCCGAAGGACCGCGTAGAA
1103673 CTCTCGACTC
Statistics
Matches: 66, Mismatches: 13, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
46 58 0.88
47 8 0.12
ACGTcount: A:0.33, C:0.26, G:0.24, T:0.17
Consensus pattern (46 bp):
CCACATAGATTTGTCCCGAAGGACCGCGTAGAAATGTCCCAAAGGA
Found at i:1104402 original size:21 final size:19
Alignment explanation
Indices: 1104373--1104420 Score: 53
Period size: 21 Copynumber: 2.5 Consensus size: 19
1104363 TCCCCCTCAA
*
1104373 TATTTATATTGCTTCAATCAG
1 TATTCATATTG-TTC-ATCAG
*
1104394 TATTGATATTGTTCATCAG
1 TATTCATATTGTTCATCAG
1104413 -ATTCATAT
1 TATTCATAT
1104421 ATTTTCCTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 7 0.28
19 5 0.20
20 3 0.12
21 10 0.40
ACGTcount: A:0.29, C:0.12, G:0.10, T:0.48
Consensus pattern (19 bp):
TATTCATATTGTTCATCAG
Found at i:1108177 original size:19 final size:19
Alignment explanation
Indices: 1108136--1108182 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
1108126 ATGGTTATCG
* *
1108136 AAGCAACAATCCGAGTTGG
1 AAGCAACAATCCGAGTCGA
1108155 AAGCAACAATCCGAGTCGA
1 AAGCAACAATCCGAGTCGA
*
1108174 AAGCCACAA
1 AAGCAACAA
1108183 ACTTAAACGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.43, C:0.26, G:0.21, T:0.11
Consensus pattern (19 bp):
AAGCAACAATCCGAGTCGA
Found at i:1112842 original size:200 final size:203
Alignment explanation
Indices: 1112499--1112901 Score: 776
Period size: 200 Copynumber: 2.0 Consensus size: 203
1112489 TCATTGTTTA
1112499 AGTTAGGATATTCTTGATAATGAATAGCATTAATTGTGATAAGTTGATGTTTTTGTGATATTCCA
1 AGTTAGGATATTCTTGATAATGAATAGCATTAATTGTGATAAGTTGATGTTTTTGTGATATTCCA
1112564 TGACTTTGTTGGTTGTAATGTGATTAGCTCAATGAATGAAAACAATTTGGTGATATTTGAGCCTT
66 TGACTTTGTTGGTTGTAATGTGATTAGCTCAATGAATGAAAACAATTTGGTGATATTTGAGCCTT
1112629 TACGAGCATATCA-TTTTCGCTCTCATTTTGTTGGATTGAGTGTGTCAAA-TTGGCATTGGT-CT
131 TACGAGCATATCATTTTTCGCTCTCATTTTGTTGGATTGAGTGTGTCAAATTTGGCATTGGTACT
1112691 CTAGAACC
196 CTAGAACC
1112699 AGTTAGGATATTCTTGATAATGAATAGCATTAATTGTGATAAGTTGATGTTTTTGTGATATTCCA
1 AGTTAGGATATTCTTGATAATGAATAGCATTAATTGTGATAAGTTGATGTTTTTGTGATATTCCA
1112764 TGACTTTGTTGGTTGTAATGTGATTAGCTCAATGAATGAAAACAATTTGGTGATATTTGAGCCTT
66 TGACTTTGTTGGTTGTAATGTGATTAGCTCAATGAATGAAAACAATTTGGTGATATTTGAGCCTT
*
1112829 TACGAGCATATCATTTTTCGCTCTCATTTTGTTGGATTGAGTGTGTCAAATTTGGCATTGGTATT
131 TACGAGCATATCATTTTTCGCTCTCATTTTGTTGGATTGAGTGTGTCAAATTTGGCATTGGTACT
1112894 CTAGAACC
196 CTAGAACC
1112902 TGCATGTTAA
Statistics
Matches: 199, Mismatches: 1, Indels: 3
0.98 0.00 0.01
Matches are distributed among these distances:
200 143 0.72
201 36 0.18
202 11 0.06
203 9 0.05
ACGTcount: A:0.27, C:0.11, G:0.21, T:0.41
Consensus pattern (203 bp):
AGTTAGGATATTCTTGATAATGAATAGCATTAATTGTGATAAGTTGATGTTTTTGTGATATTCCA
TGACTTTGTTGGTTGTAATGTGATTAGCTCAATGAATGAAAACAATTTGGTGATATTTGAGCCTT
TACGAGCATATCATTTTTCGCTCTCATTTTGTTGGATTGAGTGTGTCAAATTTGGCATTGGTACT
CTAGAACC
Found at i:1116233 original size:31 final size:31
Alignment explanation
Indices: 1116211--1116319 Score: 191
Period size: 31 Copynumber: 3.5 Consensus size: 31
1116201 ATAGATCTCA
* *
1116211 AAGAACCTAGGTAAACAGTCCATATATCCCG
1 AAGAACATAGGTAAACAGTCCATATGTCCCG
1116242 AAGAACATAGGTAAACAGTCCATATGTCCCG
1 AAGAACATAGGTAAACAGTCCATATGTCCCG
*
1116273 AAGAACATAGGTAAACAGTTCATATGTCCCG
1 AAGAACATAGGTAAACAGTCCATATGTCCCG
1116304 AAGAACATAGGTAAAC
1 AAGAACATAGGTAAAC
1116320 CCTCGACCCT
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 75 1.00
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.19
Consensus pattern (31 bp):
AAGAACATAGGTAAACAGTCCATATGTCCCG
Found at i:1120415 original size:20 final size:21
Alignment explanation
Indices: 1120381--1120419 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
1120371 TACATAATGC
1120381 ATACTTATACATATCATTAAT
1 ATACTTATACATATCATTAAT
1120402 ATACTTAT-CATATCATTA
1 ATACTTATACATATCATTA
1120420 TTACTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (21 bp):
ATACTTATACATATCATTAAT
Found at i:1120720 original size:31 final size:31
Alignment explanation
Indices: 1120682--1120805 Score: 205
Period size: 31 Copynumber: 4.0 Consensus size: 31
1120672 CCAAAGGACG
*
1120682 AGTCCATA-GATCCCGAAGAACCTAGGTAAAC
1 AGTCCATATG-TCCCGAAGAACATAGGTAAAC
1120713 AGTCCATATGTCCCGAAGAACATAGGTAAAC
1 AGTCCATATGTCCCGAAGAACATAGGTAAAC
*
1120744 AATCCATATGTCCCGAAGAACATAGGTAAAC
1 AGTCCATATGTCCCGAAGAACATAGGTAAAC
*
1120775 AGTTCATATGTCCCGAAGAACATAGGTAAAC
1 AGTCCATATGTCCCGAAGAACATAGGTAAAC
1120806 CCTCGACCCT
Statistics
Matches: 88, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 87 0.99
32 1 0.01
ACGTcount: A:0.40, C:0.23, G:0.19, T:0.19
Consensus pattern (31 bp):
AGTCCATATGTCCCGAAGAACATAGGTAAAC
Found at i:1121537 original size:19 final size:19
Alignment explanation
Indices: 1121513--1121560 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
1121503 TATTACTGGG
*
1121513 ATGCATCGATTCACTACTT
1 ATGCATCGATGCACTACTT
*
1121532 ATGCATCGATGCACTTCTT
1 ATGCATCGATGCACTACTT
*
1121551 GTGCATCGAT
1 ATGCATCGAT
1121561 ACACCTTCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (19 bp):
ATGCATCGATGCACTACTT
Found at i:1127933 original size:35 final size:35
Alignment explanation
Indices: 1127888--1127957 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
1127878 ACCAAAGGAT
1127888 CACAACAATTAATTTTCTAAGTTTAAAGGCTTGTA
1 CACAACAATTAATTTTCTAAGTTTAAAGGCTTGTA
1127923 CACAACAATTAATTTTCTAAGTTTAAAGGCTTGTA
1 CACAACAATTAATTTTCTAAGTTTAAAGGCTTGTA
1127958 ATTGGATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.37
Consensus pattern (35 bp):
CACAACAATTAATTTTCTAAGTTTAAAGGCTTGTA
Found at i:1133631 original size:20 final size:20
Alignment explanation
Indices: 1133606--1133653 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
1133596 CAGTCTGTTG
*
1133606 CTTCAGGTACTTGACCGATT
1 CTTCAGATACTTGACCGATT
1133626 CTTCAGATACTTGACCGATT
1 CTTCAGATACTTGACCGATT
1133646 CTTCAGAT
1 CTTCAGAT
1133654 GTTGAGCATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (20 bp):
CTTCAGATACTTGACCGATT
Found at i:1139701 original size:2 final size:2
Alignment explanation
Indices: 1139662--1139688 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1139652 GATGTGTAAG
1139662 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 A
1139689 CAAAAGTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1148396 original size:29 final size:29
Alignment explanation
Indices: 1148353--1148417 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
1148343 TAAAAGAACC
*
1148353 ATCATCAAGGCTCTTAACATAGACACAATA
1 ATCAT-AAGGCTCTTAACATAGACACAACA
1148383 ATCATAAGGCTCTTAACATAGACACAACA
1 ATCATAAGGCTCTTAACATAGACACAACA
1148412 ATCATA
1 ATCATA
1148418 CTCACATCGC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 29 0.85
30 5 0.15
ACGTcount: A:0.45, C:0.23, G:0.09, T:0.23
Consensus pattern (29 bp):
ATCATAAGGCTCTTAACATAGACACAACA
Found at i:1149665 original size:30 final size:28
Alignment explanation
Indices: 1149610--1149665 Score: 78
Period size: 27 Copynumber: 1.9 Consensus size: 28
1149600 AATCACTTCA
1149610 AATACTATTATTTTATATATTTAATATT
1 AATACTATTATTTTATATATTTAATATT
1149638 AATA-TATTATTTTAGTATCATTTTAATA
1 AATACTATTATTTTA-TAT-A-TTTAATA
1149666 CAAATATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 10 0.40
28 7 0.28
29 1 0.04
30 7 0.28
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (28 bp):
AATACTATTATTTTATATATTTAATATT
Found at i:1149672 original size:30 final size:27
Alignment explanation
Indices: 1149608--1149672 Score: 76
Period size: 30 Copynumber: 2.3 Consensus size: 27
1149598 ATAATCACTT
1149608 CAAATACTATTATTTTATATATTTAATA
1 CAAATA-TATTATTTTATATATTTAATA
**
1149636 TTAATATATTATTTTAGTATCATTTTAATA
1 CAAATATATTATTTTA-TAT-A-TTTAATA
1149666 CAAATAT
1 CAAATAT
1149673 TAATTATTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
27 10 0.33
28 7 0.23
29 1 0.03
30 12 0.40
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.51
Consensus pattern (27 bp):
CAAATATATTATTTTATATATTTAATA
Found at i:1149705 original size:18 final size:17
Alignment explanation
Indices: 1149669--1149713 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
1149659 TTTAATACAA
1149669 ATATTAATTATTAAATT
1 ATATTAATTATTAAATT
* *
1149686 ATATTTATTGTTAGAATT
1 ATATTAATTATTA-AATT
1149704 ATATT-ATTAT
1 ATATTAATTAT
1149714 AATATATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 15 0.62
18 9 0.38
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (17 bp):
ATATTAATTATTAAATT
Found at i:1149855 original size:21 final size:21
Alignment explanation
Indices: 1149830--1149894 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
1149820 AATATACTTC
1149830 TTAAAATATAATATTATTATT
1 TTAAAATATAATATTATTATT
1149851 TTAAAATAATAAT-TT-TTAATAT
1 TTAAAAT-ATAATATTATT-AT-T
1149873 TT--AA-ATAATATTATTATT
1 TTAAAATATAATATTATTATT
1149891 TTAA
1 TTAA
1149895 TAAGTAATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 15
0.71 0.00 0.29
Matches are distributed among these distances:
18 8 0.22
19 4 0.11
20 6 0.16
21 11 0.30
22 8 0.22
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTAAAATATAATATTATTATT
Found at i:1149888 original size:40 final size:38
Alignment explanation
Indices: 1149837--1149975 Score: 131
Period size: 40 Copynumber: 3.5 Consensus size: 38
1149827 TTCTTAAAAT
** *
1149837 ATAATATTATTATTTTAAAATAA-TAATTTTTAATATTTAA
1 ATAATATTATTATTTT--AATAAGTAATTAAT-ATAATTAA
1149877 ATAATATTATTATTTTAATAAGTAATTAATATAATTAA
1 ATAATATTATTATTTTAATAAGTAATTAATATAATTAA
* * *
1149915 ATAATATATTATCTTATTTTAATAAATAATTAGTATAATT-T
1 AT-A-ATATTA--TTATTTTAATAAGTAATTAATATAATTAA
1149956 ATAATCATT-TTATTTTAATA
1 ATAAT-ATTATTATTTTAATA
1149976 GAATAGAATA
Statistics
Matches: 87, Mismatches: 6, Indels: 15
0.81 0.06 0.14
Matches are distributed among these distances:
37 11 0.13
38 14 0.16
39 9 0.10
40 26 0.30
41 2 0.02
42 25 0.29
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (38 bp):
ATAATATTATTATTTTAATAAGTAATTAATATAATTAA
Found at i:1149902 original size:21 final size:20
Alignment explanation
Indices: 1149837--1149944 Score: 73
Period size: 21 Copynumber: 5.2 Consensus size: 20
1149827 TTCTTAAAAT
1149837 ATAATATTATTATTTTAA-A
1 ATAATATTATTATTTTAATA
*
1149856 ATAATAATTTTTAATATTT-A-A
1 ATAAT-ATTATT-AT-TTTAATA
1149877 ATAATATTATTATTTTAATA
1 ATAATATTATTATTTTAATA
* * *
1149897 AGTAAT-TAATATAATTAAATA
1 A-TAATATTAT-TATTTTAATA
1149918 AT-ATATTATCTTATTTTAATAA
1 ATAATATTA--TTATTTTAAT-A
1149940 ATAAT
1 ATAAT
1149945 TAGTATAATT
Statistics
Matches: 69, Mismatches: 8, Indels: 20
0.71 0.08 0.21
Matches are distributed among these distances:
18 3 0.04
19 10 0.14
20 18 0.26
21 29 0.42
22 7 0.10
23 2 0.03
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (20 bp):
ATAATATTATTATTTTAATA
Found at i:1149906 original size:25 final size:25
Alignment explanation
Indices: 1149864--1149913 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1149854 AAATAATAAT
** *
1149864 TTTTAATATTTAAATAATATTATTA
1 TTTTAATAAGTAAATAATATAATTA
*
1149889 TTTTAATAAGTAATTAATATAATTA
1 TTTTAATAAGTAAATAATATAATTA
1149914 AATAATATAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TTTTAATAAGTAAATAATATAATTA
Found at i:1149956 original size:21 final size:20
Alignment explanation
Indices: 1149890--1149956 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 20
1149880 ATATTATTAT
*
1149890 TTTAATAAGTAATTAATATAA
1 TTTAATAAATAATT-ATATAA
* * *
1149911 TTAAAT-AATATATTATCTTAT
1 TTTAATAAATA-ATTAT-ATAA
1149932 TTTAATAAATAATTAGTATAA
1 TTTAATAAATAATTA-TATAA
1149953 TTTA
1 TTTA
1149957 TAATCATTTT
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
20 5 0.14
21 25 0.71
22 5 0.14
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (20 bp):
TTTAATAAATAATTATATAA
Found at i:1150014 original size:32 final size:34
Alignment explanation
Indices: 1149948--1150019 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 34
1149938 AAATAATTAG
*
1149948 TATAATTTATAATCATTTTATTTTAATAGAATAGA
1 TATAATCT-TAATCATTTTATTTTAATAGAATAGA
1149983 -ATAATCTTAAT-ATTTTA-TTTAATA-ATTATAGA
1 TATAATCTTAATCATTTTATTTTAATAGA--ATAGA
1150015 TATAA
1 TATAA
1150020 CATTTTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
30 1 0.03
31 7 0.21
32 11 0.33
33 8 0.24
34 6 0.18
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.49
Consensus pattern (34 bp):
TATAATCTTAATCATTTTATTTTAATAGAATAGA
Found at i:1151117 original size:41 final size:39
Alignment explanation
Indices: 1151043--1151119 Score: 109
Period size: 41 Copynumber: 1.9 Consensus size: 39
1151033 GCTATTGACT
* * *
1151043 TTATATTTATATTTTAAAAATTAAACTATAATTATATAA
1 TTATATTTATATTATAAAAATTAAAATACAATTATATAA
1151082 TTATAATTTATATTATAAATAATTAAAATACAATTATA
1 TTAT-ATTTATATTATAAA-AATTAAAATACAATTATA
1151120 CTCTATCCAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 4 0.12
40 13 0.39
41 16 0.48
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.47
Consensus pattern (39 bp):
TTATATTTATATTATAAAAATTAAAATACAATTATATAA
Found at i:1152470 original size:20 final size:20
Alignment explanation
Indices: 1152445--1152493 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
1152435 CGATTTCGAA
* *
1152445 TTCGCAACACGAACTCTACT
1 TTCGCAACACGAACTCCAAT
1152465 TTCGCAACACGAACTCCAAT
1 TTCGCAACACGAACTCCAAT
1152485 TTCGCAACA
1 TTCGCAACA
1152494 TAGTTTCCGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.35, G:0.10, T:0.22
Consensus pattern (20 bp):
TTCGCAACACGAACTCCAAT
Found at i:1152525 original size:20 final size:20
Alignment explanation
Indices: 1152502--1152582 Score: 65
Period size: 20 Copynumber: 4.0 Consensus size: 20
1152492 CATAGTTTCC
*
1152502 GAATTCGCAACTCGAATTTG
1 GAATTCGCAACACGAATTTG
* *
1152522 GAATTCGCAACACAGAA-GTC
1 GAATTCGCAACAC-GAATTTG
* **
1152542 GAATTCACAACTTGAATTTG
1 GAATTCGCAACACGAATTTG
*
1152562 ACAATTTCGCAACACGAATTT
1 -GAA-TTCGCAACACGAATTT
1152583 CTTTTTTGCA
Statistics
Matches: 45, Mismatches: 12, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
19 3 0.07
20 24 0.53
21 5 0.11
22 13 0.29
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27
Consensus pattern (20 bp):
GAATTCGCAACACGAATTTG
Found at i:1152641 original size:40 final size:40
Alignment explanation
Indices: 1152567--1152662 Score: 108
Period size: 40 Copynumber: 2.4 Consensus size: 40
1152557 ATTTGACAAT
* * * *
1152567 TTCGCAACACGAATTTCTTTTTTGCAAATCGATTTT-TAAA
1 TTCGCAACACGAGTTTCGTTTTCGCAAATAGATTTTCT-AA
1152607 TTCGCAACACGAGTTTCGTTTTCGCAACA-AGATTTTCTAA
1 TTCGCAACACGAGTTTCGTTTTCGCAA-ATAGATTTTCTAA
1152647 TTCGCAA-AGCGAGTTT
1 TTCGCAACA-CGAGTTT
1152663 TAATTTCTTA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
39 1 0.02
40 46 0.94
41 2 0.04
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.38
Consensus pattern (40 bp):
TTCGCAACACGAGTTTCGTTTTCGCAAATAGATTTTCTAA
Found at i:1152650 original size:20 final size:21
Alignment explanation
Indices: 1152605--1152653 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
1152595 TCGATTTTTA
*
1152605 AATTCGCAACACGAGTTTCGT
1 AATTCGCAACAAGAGTTTCGT
* *
1152626 -TTTCGCAACAAGATTTTC-T
1 AATTCGCAACAAGAGTTTCGT
1152645 AATTCGCAA
1 AATTCGCAA
1152654 AGCGAGTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 1 0.04
20 22 0.96
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (21 bp):
AATTCGCAACAAGAGTTTCGT
Found at i:1152701 original size:60 final size:60
Alignment explanation
Indices: 1152566--1152733 Score: 174
Period size: 60 Copynumber: 2.8 Consensus size: 60
1152556 AATTTGACAA
* * * * * *
1152566 TTTCGCAACACGAATTTCTTTTTTGCAAATCGATTTTTAAATTCGCAACACGAGTTTCGT
1 TTTCGCAACACGATTTTCTATTTCGCAAAGCGAGTTTTAAATTCGCAACACGAATTTCGT
* * * ** *
1152626 TTTCGCAACAAGATTTTCTAATTCGCAAAGCGAGTTTTAATTTCTTAACATGAATTTCGT
1 TTTCGCAACACGATTTTCTATTTCGCAAAGCGAGTTTTAAATTCGCAACACGAATTTCGT
* * * * * *
1152686 TTTCGCAACTCGATTTTATATTTCGCAACGCGAATTTAAAATTAGCAA
1 TTTCGCAACACGATTTTCTATTTCGCAAAGCGAGTTTTAAATTCGCAA
1152734 ATCAATTTAT
Statistics
Matches: 85, Mismatches: 23, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
60 85 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (60 bp):
TTTCGCAACACGATTTTCTATTTCGCAAAGCGAGTTTTAAATTCGCAACACGAATTTCGT
Found at i:1152723 original size:20 final size:20
Alignment explanation
Indices: 1152686--1152723 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1152676 TGAATTTCGT
* *
1152686 TTTCGCAACTCGATTTTATA
1 TTTCGCAACGCGAATTTATA
1152706 TTTCGCAACGCGAATTTA
1 TTTCGCAACGCGAATTTA
1152724 AAATTAGCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.39
Consensus pattern (20 bp):
TTTCGCAACGCGAATTTATA
Found at i:1153270 original size:20 final size:20
Alignment explanation
Indices: 1153245--1153340 Score: 80
Period size: 20 Copynumber: 5.1 Consensus size: 20
1153235 AAAATGAAAA
1153245 TCGAGTTGCGAATTTCATTT
1 TCGAGTTGCGAATTTCATTT
*
1153265 TCGAGTTACG------ATTT
1 TCGAGTTGCGAATTTCATTT
* * *
1153279 TCGTGTTGCGAATTTAAGTT
1 TCGAGTTGCGAATTTCATTT
*
1153299 TCGAATTGCGAA-TTCGATTT
1 TCGAGTTGCGAATTTC-ATTT
*
1153319 TCGAGTTGCGAATTTGATTT
1 TCGAGTTGCGAATTTCATTT
1153339 TC
1 TC
1153341 TTGAAAATTT
Statistics
Matches: 58, Mismatches: 10, Indels: 16
0.69 0.12 0.19
Matches are distributed among these distances:
14 12 0.21
19 2 0.03
20 42 0.72
21 2 0.03
ACGTcount: A:0.21, C:0.14, G:0.22, T:0.44
Consensus pattern (20 bp):
TCGAGTTGCGAATTTCATTT
Found at i:1154773 original size:42 final size:42
Alignment explanation
Indices: 1154714--1154921 Score: 296
Period size: 42 Copynumber: 5.0 Consensus size: 42
1154704 CCCCAATTTT
* * *
1154714 TCATCAAGTTGATTCTCCACTTCGATACCGAGATCCATCACC
1 TCATCGAGTCGATTCTCCACTTCGACACCGAGATCCATCACC
1154756 TCATCGAGTCGATTCTCCACTTCGACACCGAGATCCATCACC
1 TCATCGAGTCGATTCTCCACTTCGACACCGAGATCCATCACC
*
1154798 TCATCGAGTCGATTCTCCACTTCGACACTGAGATCCATCACC
1 TCATCGAGTCGATTCTCCACTTCGACACCGAGATCCATCACC
* * *
1154840 TCATCGAGCCGATTCTACACCTCGACACCGAGATCCATCACC
1 TCATCGAGTCGATTCTCCACTTCGACACCGAGATCCATCACC
* * * *
1154882 TC-T--AGCCGACTCTACACCTCGACACCGAGATCCATCACC
1 TCATCGAGTCGATTCTCCACTTCGACACCGAGATCCATCACC
1154921 T
1 T
1154922 ATTCCATCAC
Statistics
Matches: 157, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
39 36 0.23
41 1 0.01
42 120 0.76
ACGTcount: A:0.25, C:0.38, G:0.13, T:0.24
Consensus pattern (42 bp):
TCATCGAGTCGATTCTCCACTTCGACACCGAGATCCATCACC
Found at i:1155059 original size:21 final size:21
Alignment explanation
Indices: 1155035--1155211 Score: 135
Period size: 21 Copynumber: 8.4 Consensus size: 21
1155025 AGTTAACTGA
* *
1155035 TTTACGTGATGAGGTCGGTGT
1 TTTACGTGATGAGGTAGGTGC
* * *
1155056 TTTACATGATGAGGTCGTTGC
1 TTTACGTGATGAGGTAGGTGC
* **
1155077 TTTACATGATGA-CAATGGTGC
1 TTTACGTGATGAGGTA-GGTGC
* *
1155098 TTTACGTGATGTGGTAGGTGA
1 TTTACGTGATGAGGTAGGTGC
* * *
1155119 TTTACGTGGTGAGGTAGATGT
1 TTTACGTGATGAGGTAGGTGC
**
1155140 TTTACGTGATGA-CAATGGTGC
1 TTTACGTGATGAGGTA-GGTGC
* *
1155161 TTTACGTTG-TGAGGTAGTTGT
1 TTTACG-TGATGAGGTAGGTGC
*
1155182 TTTACGTGATGAGGTGGGTGC
1 TTTACGTGATGAGGTAGGTGC
*
1155203 TCTACGTGA
1 TTTACGTGA
1155212 GATTGTTTCA
Statistics
Matches: 121, Mismatches: 29, Indels: 12
0.75 0.18 0.07
Matches are distributed among these distances:
20 3 0.02
21 114 0.94
22 4 0.03
ACGTcount: A:0.19, C:0.10, G:0.33, T:0.37
Consensus pattern (21 bp):
TTTACGTGATGAGGTAGGTGC
Found at i:1155209 original size:63 final size:63
Alignment explanation
Indices: 1155035--1155211 Score: 221
Period size: 63 Copynumber: 2.8 Consensus size: 63
1155025 AGTTAACTGA
* * * * *
1155035 TTTACGTGATGAGGTCGGTGTTTTACATGATGAGGTCGTTGCTTTACATGATGACAATGGTGC
1 TTTACGTGATGAGGTAGGTGTTTTACGTGATGAGGTAGATGCTTTACGTGATGACAATGGTGC
* * * *
1155098 TTTACGTGATGTGGTAGGTGATTTACGTGGTGAGGTAGATGTTTTACGTGATGACAATGGTGC
1 TTTACGTGATGAGGTAGGTGTTTTACGTGATGAGGTAGATGCTTTACGTGATGACAATGGTGC
* * * *
1155161 TTTACGTTG-TGAGGTAGTTGTTTTACGTGATGAGGTGGGTGCTCTACGTGA
1 TTTACG-TGATGAGGTAGGTGTTTTACGTGATGAGGTAGATGCTTTACGTGA
1155212 GATTGTTTCA
Statistics
Matches: 96, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
63 94 0.98
64 2 0.02
ACGTcount: A:0.19, C:0.10, G:0.33, T:0.37
Consensus pattern (63 bp):
TTTACGTGATGAGGTAGGTGTTTTACGTGATGAGGTAGATGCTTTACGTGATGACAATGGTGC
Found at i:1155627 original size:21 final size:21
Alignment explanation
Indices: 1155534--1155645 Score: 68
Period size: 21 Copynumber: 5.3 Consensus size: 21
1155524 AAAGAAGCCT
* * *
1155534 GATCCACTTACCATTGTTCAG
1 GATCCACCTCCCATCGTTCAG
* * * *
1155555 GATTCACCTCCCATTGTTTAT
1 GATCCACCTCCCATCGTTCAG
* * *
1155576 GATTCACCTCTCATCATTCCAAAG
1 GATCCACCTCCCATCGTT-C--AG
1155600 G--CC-CCTCCCATCGTTCAG
1 GATCCACCTCCCATCGTTCAG
**
1155618 GATCCACCTCGTATCGTTCAG
1 GATCCACCTCCCATCGTTCAG
1155639 GATCCAC
1 GATCCAC
1155646 ATTCCATTAT
Statistics
Matches: 70, Mismatches: 15, Indels: 12
0.72 0.15 0.12
Matches are distributed among these distances:
18 3 0.04
20 3 0.04
21 61 0.87
22 1 0.01
24 2 0.03
ACGTcount: A:0.21, C:0.35, G:0.13, T:0.30
Consensus pattern (21 bp):
GATCCACCTCCCATCGTTCAG
Found at i:1157611 original size:20 final size:20
Alignment explanation
Indices: 1157586--1157689 Score: 109
Period size: 20 Copynumber: 5.2 Consensus size: 20
1157576 CTATCTTTAA
1157586 GAAAATCAAATTCGCAACTC
1 GAAAATCAAATTCGCAACTC
* * *
1157606 GGAAATCGAATTCACAACTC
1 GAAAATCAAATTCGCAACTC
* * *
1157626 GATATTAAAATTCGCAACTC
1 GAAAATCAAATTCGCAACTC
* * *
1157646 AAAAATCGAATTCGAAACTC
1 GAAAATCAAATTCGCAACTC
* *
1157666 GAAAATGAAATTCGCAATTC
1 GAAAATCAAATTCGCAACTC
1157686 GAAA
1 GAAA
1157690 TTGAGTTGCG
Statistics
Matches: 64, Mismatches: 20, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 64 1.00
ACGTcount: A:0.45, C:0.20, G:0.12, T:0.22
Consensus pattern (20 bp):
GAAAATCAAATTCGCAACTC
Found at i:1157652 original size:40 final size:40
Alignment explanation
Indices: 1157586--1157682 Score: 124
Period size: 40 Copynumber: 2.4 Consensus size: 40
1157576 CTATCTTTAA
* **
1157586 GAAAATCAAATTCGCAACTCGGAAATCGAATTC-ACAACTC
1 GAAAATAAAATTCGCAACTCAAAAATCGAATTCGA-AACTC
* *
1157626 GATATTAAAATTCGCAACTCAAAAATCGAATTCGAAACTC
1 GAAAATAAAATTCGCAACTCAAAAATCGAATTCGAAACTC
*
1157666 GAAAATGAAATTCGCAA
1 GAAAATAAAATTCGCAA
1157683 TTCGAAATTG
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
40 47 0.98
41 1 0.02
ACGTcount: A:0.45, C:0.21, G:0.12, T:0.22
Consensus pattern (40 bp):
GAAAATAAAATTCGCAACTCAAAAATCGAATTCGAAACTC
Found at i:1157717 original size:20 final size:20
Alignment explanation
Indices: 1157692--1157841 Score: 137
Period size: 20 Copynumber: 7.7 Consensus size: 20
1157682 ATTCGAAATT
*
1157692 GAGTTGCGAATTTCATTTTC
1 GAGTTGCGAATTTGATTTTC
*
1157712 GAGTTGAGAATTTGATTTTC
1 GAGTTGCGAATTTGATTTTC
* *
1157732 GAGTTGCGAATTTGAATATC
1 GAGTTGCGAATTTGATTTTC
*
1157752 GAGTTGCGAA--T--TTTGC
1 GAGTTGCGAATTTGATTTTC
* *
1157768 GAATTGCGAATTAGATTTTC
1 GAGTTGCGAATTTGATTTTC
* * *
1157788 GAGTTGCGAATTTTAATATC
1 GAGTTGCGAATTTGATTTTC
* * * *
1157808 TAGTTACGATTTTCAATTTTC
1 GAGTTGCGAATTT-GATTTTC
1157829 GAGTTGCGAATTT
1 GAGTTGCGAATTT
1157842 TCACTATGCA
Statistics
Matches: 100, Mismatches: 25, Indels: 9
0.75 0.19 0.07
Matches are distributed among these distances:
16 11 0.11
18 1 0.01
20 74 0.74
21 14 0.14
ACGTcount: A:0.25, C:0.11, G:0.22, T:0.42
Consensus pattern (20 bp):
GAGTTGCGAATTTGATTTTC
Found at i:1157790 original size:36 final size:35
Alignment explanation
Indices: 1157726--1157801 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 35
1157716 TGAGAATTTG
* *
1157726 ATTTTCGAGTTGCGAATTTGAATATCGAGTTGCGA
1 ATTTTCGAATTGCGAATTAGAATATCGAGTTGCGA
* *
1157761 ATTTTGCGAATTGCGAATTAGATTTTCGAGTTGCGA
1 ATTTT-CGAATTGCGAATTAGAATATCGAGTTGCGA
1157797 ATTTT
1 ATTTT
1157802 AATATCTAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
35 5 0.14
36 31 0.86
ACGTcount: A:0.25, C:0.11, G:0.24, T:0.41
Consensus pattern (35 bp):
ATTTTCGAATTGCGAATTAGAATATCGAGTTGCGA
Found at i:1157843 original size:56 final size:56
Alignment explanation
Indices: 1157706--1157820 Score: 162
Period size: 56 Copynumber: 2.1 Consensus size: 56
1157696 TGCGAATTTC
* * * *
1157706 ATTTT-CGAGTTGAGAATTTGATTTTCGAGTTGCGAATTTGAATATCGAGTTGCGA
1 ATTTTGCGAATTGCGAATTAGATTTTCGAGTTGCGAATTTGAATATCGAGTTACGA
* *
1157761 ATTTTGCGAATTGCGAATTAGATTTTCGAGTTGCGAATTTTAATATCTAGTTACG-
1 ATTTTGCGAATTGCGAATTAGATTTTCGAGTTGCGAATTTGAATATCGAGTTACGA
1157816 ATTTT
1 ATTTT
1157821 CAATTTTCGA
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
55 10 0.19
56 43 0.81
ACGTcount: A:0.26, C:0.10, G:0.22, T:0.43
Consensus pattern (56 bp):
ATTTTGCGAATTGCGAATTAGATTTTCGAGTTGCGAATTTGAATATCGAGTTACGA
Found at i:1158395 original size:18 final size:18
Alignment explanation
Indices: 1158374--1158408 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1158364 AGGTGATTGG
*
1158374 GATTGGGATTTTGATTTT
1 GATTGCGATTTTGATTTT
1158392 GATTGCGATTTTGATTT
1 GATTGCGATTTTGATTT
1158409 CCCTTTATTT
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:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
GATTGCGATTTTGATTTT
Found at i:1160564 original size:24 final size:24
Alignment explanation
Indices: 1160513--1160565 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
1160503 AAAATCCAAG
**
1160513 TATTGACCAAGATCAAAGTTCGGG
1 TATTGACCAAGATCAAAGTTCGAA
* *
1160537 TATTGACCAAGATCAAATTTTGAA
1 TATTGACCAAGATCAAAGTTCGAA
1160561 TATTG
1 TATTG
1160566 TCTAGTACTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (24 bp):
TATTGACCAAGATCAAAGTTCGAA
Found at i:1161505 original size:20 final size:20
Alignment explanation
Indices: 1161480--1161517 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1161470 CCAAAACATT
*
1161480 TGTGTTGTAAAATTAAAAGA
1 TGTGTTGCAAAATTAAAAGA
*
1161500 TGTGTTGCGAAATTAAAA
1 TGTGTTGCAAAATTAAAA
1161518 TTCGCGTTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.03, G:0.21, T:0.34
Consensus pattern (20 bp):
TGTGTTGCAAAATTAAAAGA
Found at i:1161526 original size:20 final size:20
Alignment explanation
Indices: 1161503--1161672 Score: 76
Period size: 20 Copynumber: 8.4 Consensus size: 20
1161493 TAAAAGATGT
*
1161503 GTTGCGAAATTAAAATTCGC
1 GTTGCGAAATTAAAATTCGA
* *
1161523 GTTGCG-AATACAAAAATCGA
1 GTTGCGAAAT-TAAAATTCGA
* ***
1161543 GTTACGAAAACGAAATTC-A
1 GTTGCGAAATTAAAATTCGA
* * * *
1161562 TGTTGTGAAATTGAAACTCGC
1 -GTTGCGAAATTAAAATTCGA
** * **
1161583 GTTATG-AATTAGAAAATCTT
1 GTTGCGAAATTA-AAATTCGA
* *
1161603 GTTGCGAATTTAAAAATCGA
1 GTTGCGAAATTAAAATTCGA
** *
1161623 GTTGCGAAAAGAAAATTCGT
1 GTTGCGAAATTAAAATTCGA
*
1161643 GTTGCGAAATTGTCAAATTCGA
1 GTTGCGAAA-T-TAAAATTCGA
1161665 GTTGCGAA
1 GTTGCGAA
1161673 TTCGACTTTT
Statistics
Matches: 110, Mismatches: 32, Indels: 14
0.71 0.21 0.09
Matches are distributed among these distances:
19 8 0.07
20 81 0.74
21 6 0.05
22 15 0.14
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (20 bp):
GTTGCGAAATTAAAATTCGA
Found at i:1161648 original size:40 final size:40
Alignment explanation
Indices: 1161503--1161672 Score: 128
Period size: 40 Copynumber: 4.2 Consensus size: 40
1161493 TAAAAGATGT
** * **
1161503 GTTGCGAAATTAAAATTCGCGTTGCGAATACAAAAATCGA
1 GTTGCGAAAAGAAAATTCGTGTTGCGAATTTAAAAATCGA
* * * * * * *
1161543 GTTACGAAAACG-AAATTCATGTTGTGAAATTGAAACTCGC
1 GTTGCGAAAA-GAAAATTCGTGTTGCGAATTTAAAAATCGA
** * *
1161583 GTTATGAATTAGAAAA-TCTTGTTGCGAATTTAAAAATCGA
1 GTTGCGAA-AAGAAAATTCGTGTTGCGAATTTAAAAATCGA
* *
1161623 GTTGCGAAAAGAAAATTCGTGTTGCGAAATTGTCAAATTCGA
1 GTTGCGAAAAGAAAATTCGTGTTGCG-AATT-TAAAAATCGA
1161665 GTTGCGAA
1 GTTGCGAA
1161673 TTCGACTTTT
Statistics
Matches: 98, Mismatches: 26, Indels: 10
0.73 0.19 0.07
Matches are distributed among these distances:
39 6 0.06
40 68 0.69
41 8 0.08
42 16 0.16
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (40 bp):
GTTGCGAAAAGAAAATTCGTGTTGCGAATTTAAAAATCGA
Found at i:1161694 original size:20 final size:19
Alignment explanation
Indices: 1161665--1161758 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 19
1161655 TCAAATTCGA
*
1161665 GTTGCGAATTCGACTTTTGT
1 GTTGCAAATTCGA-TTTTGT
*
1161685 GTTGCAAATTCCAAATTTTGT
1 GTTGCAAATT-C-GATTTTGT
***
1161706 GTTGCAAATTCGGAAACTGT
1 GTTGCAAATTC-GATTTTGT
* *
1161726 GCTGCGAAATTGGATTTTGT
1 GTTGC-AAATTCGATTTTGT
1161746 GTTGCAAATTCGA
1 GTTGCAAATTCGA
1161759 AATTGAGTTG
Statistics
Matches: 57, Mismatches: 14, Indels: 7
0.73 0.18 0.09
Matches are distributed among these distances:
19 7 0.12
20 27 0.47
21 22 0.39
22 1 0.02
ACGTcount: A:0.24, C:0.14, G:0.23, T:0.38
Consensus pattern (19 bp):
GTTGCAAATTCGATTTTGT
Found at i:1165332 original size:15 final size:14
Alignment explanation
Indices: 1165312--1165363 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 14
1165302 ATAACCAGTT
1165312 AAATTATAAATAAA
1 AAATTATAAATAAA
* *
1165326 AATATTATTTACTAAA
1 AA-ATTA-TAAATAAA
*
1165342 CAATTATAAATAAAA
1 AAATTATAAAT-AAA
1165357 AAATTAT
1 AAATTAT
1165364 TTATTAAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
14 5 0.17
15 17 0.59
16 7 0.24
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATTATAAATAAA
Found at i:1165349 original size:30 final size:30
Alignment explanation
Indices: 1165313--1165371 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
1165303 TAACCAGTTA
*
1165313 AATTATAAATAAAAATATTATTTACTAAAC
1 AATTATAAATAAAAAAATTATTTACTAAAC
*
1165343 AATTATAAATAAAAAAATTATTTATTAAA
1 AATTATAAATAAAAAAATTATTTACTAAA
1165372 AAATAAATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.37
Consensus pattern (30 bp):
AATTATAAATAAAAAAATTATTTACTAAAC
Found at i:1165372 original size:15 final size:15
Alignment explanation
Indices: 1165322--1165375 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
1165312 AAATTATAAA
*
1165322 TAAAAATATTATTTAC
1 TAAAAA-ATTATTTAT
* **
1165338 TAAACAATTATAAAT
1 TAAAAAATTATTTAT
*
1165353 AAAAAAATTATTTAT
1 TAAAAAATTATTTAT
1165368 TAAAAAAT
1 TAAAAAAT
1165376 AAATCTATTT
Statistics
Matches: 29, Mismatches: 9, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
15 24 0.83
16 5 0.17
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAAAAATTATTTAT
Found at i:1166577 original size:27 final size:27
Alignment explanation
Indices: 1166518--1166588 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 27
1166508 AAATATTTAT
* *
1166518 ATTTAAAAAAAACAAATAAACCCTTAA
1 ATTTAAAAAAATCAATTAAACCCTTAA
* * *
1166545 ACTTTAAAAAAATCAATTCAGCCCTTGA
1 A-TTTAAAAAAATCAATTAAACCCTTAA
1166573 ATTT-AAAAAATCAATT
1 ATTTAAAAAAATCAATT
1166589 TAACTCATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
26 12 0.32
27 4 0.11
28 22 0.58
ACGTcount: A:0.54, C:0.15, G:0.03, T:0.28
Consensus pattern (27 bp):
ATTTAAAAAAATCAATTAAACCCTTAA
Found at i:1169440 original size:26 final size:26
Alignment explanation
Indices: 1169411--1169469 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
1169401 ATATATTATT
1169411 TAAATAAATAATCTT-TTAAAAAAAGA
1 TAAATAAATAATCTTATTAAAAAAA-A
* * *
1169437 TAAATTAATAATTTTATTATAAAAAA
1 TAAATAAATAATCTTATTAAAAAAAA
1169463 T-AATAAA
1 TAAATAAA
1169470 AGAGTTTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
25 5 0.18
26 15 0.54
27 8 0.29
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (26 bp):
TAAATAAATAATCTTATTAAAAAAAA
Found at i:1170856 original size:23 final size:23
Alignment explanation
Indices: 1170830--1170901 Score: 92
Period size: 23 Copynumber: 3.1 Consensus size: 23
1170820 AACGAAGTTT
*
1170830 CACATAGAAATGTCTCGAA-GAAC
1 CACATAGAAATGTCCCGAATG-AC
* *
1170853 CACATAGTATTGTCCCGAATGAC
1 CACATAGAAATGTCCCGAATGAC
*
1170876 CGCATAGAAATGTCCCGAATGAC
1 CACATAGAAATGTCCCGAATGAC
1170899 CAC
1 CAC
1170902 GTATAATTGT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
23 40 0.98
24 1 0.02
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.19
Consensus pattern (23 bp):
CACATAGAAATGTCCCGAATGAC
Found at i:1170901 original size:46 final size:46
Alignment explanation
Indices: 1170832--1170930 Score: 121
Period size: 46 Copynumber: 2.2 Consensus size: 46
1170822 CGAAGTTTCA
* * *
1170832 CATAGAAATGTCTCGAAGAACCACATAGT-ATTGTCCCGAATGACCG
1 CATAGAAATGTCCCGAAGAACCACATA-TAATTGTCCCAAAGGACCG
*
1170878 CATAGAAATGTCCCGAATG-ACCACGTATAATTGTCCCAAAGGACCG
1 CATAGAAATGTCCCGAA-GAACCACATATAATTGTCCCAAAGGACCG
*
1170924 CGTAGAA
1 CATAGAA
1170931 CCCTCGACTC
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
45 1 0.02
46 44 0.96
47 1 0.02
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.20
Consensus pattern (46 bp):
CATAGAAATGTCCCGAAGAACCACATATAATTGTCCCAAAGGACCG
Found at i:1170912 original size:23 final size:23
Alignment explanation
Indices: 1170830--1170914 Score: 91
Period size: 23 Copynumber: 3.7 Consensus size: 23
1170820 AACGAAGTTT
* *
1170830 CACATAGAAATGTCTCGAA-GAAC
1 CACATAGAATTGTCCCGAATG-AC
*
1170853 CACATAGTATTGTCCCGAATGAC
1 CACATAGAATTGTCCCGAATGAC
* *
1170876 CGCATAGAAATGTCCCGAATGAC
1 CACATAGAATTGTCCCGAATGAC
* *
1170899 CACGTATAATTGTCCC
1 CACATAGAATTGTCCC
1170915 AAAGGACCGC
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
23 50 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (23 bp):
CACATAGAATTGTCCCGAATGAC
Found at i:1171118 original size:14 final size:14
Alignment explanation
Indices: 1171099--1171207 Score: 60
Period size: 14 Copynumber: 7.4 Consensus size: 14
1171089 ACATAATTCA
1171099 ATATCACATAGCTT
1 ATATCACATAGCTT
1171113 ATATCACAT-G-TT
1 ATATCACATAGCTT
* *
1171125 CACATAATCACATAGATC
1 ---AT-ATCACATAGCTT
**
1171143 ATATCACATATTTT
1 ATATCACATAGCTT
** *
1171157 ATATCACATTTTCAT
1 ATATCACA-TAGCTT
* *
1171172 ATGTTCACATAGTTT
1 AT-ATCACATAGCTT
1171187 AGTATCACATAGCTT
1 A-TATCACATAGCTT
1171202 ATATCA
1 ATATCA
1171208 TTTTTCTCAC
Statistics
Matches: 72, Mismatches: 14, Indels: 18
0.69 0.13 0.17
Matches are distributed among these distances:
12 2 0.03
13 1 0.01
14 31 0.43
15 23 0.32
16 13 0.18
17 1 0.01
18 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.06, T:0.39
Consensus pattern (14 bp):
ATATCACATAGCTT
Found at i:1171121 original size:45 final size:45
Alignment explanation
Indices: 1171057--1171250 Score: 203
Period size: 45 Copynumber: 4.3 Consensus size: 45
1171047 CTGTCAGTTG
* * *
1171057 TCACATGGCTTATTTCACATTTTCAGATATTCACATA-ATTCAATA
1 TCACATAGCTTATATCACATTTTCACATATTCACATAGA-TCAATA
* *
1171102 TCACATAGCTTATATCACATGTTCACATAATCACATAGATC-ATA
1 TCACATAGCTTATATCACATTTTCACATATTCACATAGATCAATA
** * * * * *
1171146 TCACATATTTTATATCACATTTTCATATGTTCACATAGTTTAGTA
1 TCACATAGCTTATATCACATTTTCACATATTCACATAGATCAATA
** *
1171191 TCACATAGCTTATATCATTTTTCTCACATATTCACATAGATCACGTA
1 TCACATAGCTTATATCACATTT-TCACATATTCACATAGATCA-ATA
*
1171238 ACACATAGCTTAT
1 TCACATAGCTTAT
1171251 GTATAACAAT
Statistics
Matches: 122, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
44 36 0.30
45 54 0.44
46 17 0.14
47 15 0.12
ACGTcount: A:0.34, C:0.21, G:0.07, T:0.39
Consensus pattern (45 bp):
TCACATAGCTTATATCACATTTTCACATATTCACATAGATCAATA
Found at i:1171164 original size:89 final size:90
Alignment explanation
Indices: 1171066--1171233 Score: 239
Period size: 89 Copynumber: 1.9 Consensus size: 90
1171056 GTCACATGGC
*
1171066 TTATTTCACATTTTCAGATATTCACATAATTCAATATCACATAGCTTATATCACATGT-TCACAT
1 TTATATCACATTTTCAGATATTCACATAATTCAATATCACATAGCTTATATCACATGTCTCACAT
1171130 AATCACATAGATCATATCACATATT
66 AATCACATAGATCATATCACATATT
* * * * * ** *
1171155 TTATATCACATTTTCATATGTTCACATAGTTTAGTATCACATAGCTTATATCATTTTTCTCACAT
1 TTATATCACATTTTCAGATATTCACATAATTCAATATCACATAGCTTATATCACATGTCTCACAT
*
1171220 ATTCACATAGATCA
66 AATCACATAGATCA
1171234 CGTAACACAT
Statistics
Matches: 68, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
89 49 0.72
90 19 0.28
ACGTcount: A:0.35, C:0.20, G:0.05, T:0.40
Consensus pattern (90 bp):
TTATATCACATTTTCAGATATTCACATAATTCAATATCACATAGCTTATATCACATGTCTCACAT
AATCACATAGATCATATCACATATT
Found at i:1173042 original size:23 final size:23
Alignment explanation
Indices: 1173016--1173065 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
1173006 TACAACACTC
1173016 AATAAAATTATTCAATATAGGGA
1 AATAAAATTATTCAATATAGGGA
*
1173039 AATAAAATTATTCAATATAGGTA
1 AATAAAATTATTCAATATAGGGA
1173062 AATA
1 AATA
1173066 CTTATTATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.54, C:0.04, G:0.10, T:0.32
Consensus pattern (23 bp):
AATAAAATTATTCAATATAGGGA
Found at i:1175357 original size:33 final size:34
Alignment explanation
Indices: 1175320--1175428 Score: 100
Period size: 35 Copynumber: 3.2 Consensus size: 34
1175310 GGTAAGAAAT
* * *
1175320 TTATTTTTATGTTAGTAT-TTT-TTTAAATAGTTA
1 TTATTTTTATATTAATATATTTATGTAAATA-TTA
1175353 TTATTTTTATATTAATATATTTATGTAAATATTA
1 TTATTTTTATATTAATATATTTATGTAAATATTA
* *
1175387 TT-TTTTT-TATTAAAATAATATTTATATAATTATTA
1 TTATTTTTATATT--AAT-ATATTTATGTAAATATTA
1175422 TTTATTT
1 -TTATTT
1175429 AGAATTATTT
Statistics
Matches: 64, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
32 4 0.06
33 21 0.33
34 11 0.17
35 23 0.36
36 2 0.03
37 3 0.05
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (34 bp):
TTATTTTTATATTAATATATTTATGTAAATATTA
Found at i:1175382 original size:35 final size:32
Alignment explanation
Indices: 1175320--1175399 Score: 92
Period size: 33 Copynumber: 2.5 Consensus size: 32
1175310 GGTAAGAAAT
* * *
1175320 TTATTTTTATGTTAGTATTTTTTTAAATAGTTA
1 TTATTTTTATATTAATATTTTTGTAAATA-TTA
1175353 TTATTTTTATATTAATATATTTATGTAAATATTA
1 TTATTTTTATATTAATAT-TTT-TGTAAATATTA
1175387 TT-TTTTT-TATTAA
1 TTATTTTTATATTAA
1175400 AATAATATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
32 6 0.14
33 21 0.50
34 8 0.19
35 7 0.17
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (32 bp):
TTATTTTTATATTAATATTTTTGTAAATATTA
Found at i:1175590 original size:17 final size:17
Alignment explanation
Indices: 1175568--1175621 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
1175558 AATGTTAATA
1175568 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
1175585 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
1175602 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
1175619 TTT
1 TTT
1175622 TTATAATGTT
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
Done.