Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008242.1 Hibiscus syriacus cultivar Beakdansim tig00110890_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: 16962412
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 73
Found at i:1950345 original size:43 final size:43
Alignment explanation
Indices: 1950291--1950624 Score: 499
Period size: 43 Copynumber: 7.7 Consensus size: 43
1950281 TAAAAAAGGC
* *
1950291 AAGGTCTTACCCTTGCACATAACAAAAGAACCTGGGGAAACTGT
1 AAGG-CTTACCCTTGCACACAACAAAGGAACCTGGGGAAACTGT
1950335 AAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACTGT
1 AAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACTGT
* * *
1950378 AAGGCTTACCCTTGCACATAGA-AAATGAACCTGGGGAAACTCT
1 AAGGCTTACCCTTGCACACA-ACAAAGGAACCTGGGGAAACTGT
*
1950421 AAGGCTTACCCTTGCACACAACAAAAGAACCTGGGGAAACTGT
1 AAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACTGT
*
1950464 AAGGCTTACCCTTGCACACAACAAAGGAACCTAGGGAAACTGT
1 AAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACTGT
**
1950507 AAGGCTTACCCTTGCACACAGTAAAGGAACCTGGGGAAACTGT
1 AAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACTGT
* * * **
1950550 AAGGCTTACCCCTACACATAGTAAAGGAACCTGGGGAAACTGT
1 AAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACTGT
* *
1950593 AAAGCTTACCCTTGCACACAGCAAAGGAACCT
1 AAGGCTTACCCTTGCACACAACAAAGGAACCT
1950625 TTATACAAAA
Statistics
Matches: 267, Mismatches: 21, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
42 1 0.00
43 261 0.98
44 5 0.02
ACGTcount: A:0.36, C:0.25, G:0.22, T:0.18
Consensus pattern (43 bp):
AAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACTGT
Found at i:1955154 original size:43 final size:43
Alignment explanation
Indices: 1955087--1955255 Score: 169
Period size: 43 Copynumber: 3.9 Consensus size: 43
1955077 AAGCATGTAA
* * * *
1955087 AAACGGTAAGGTCTTACCCTTGCACATAGCAAAAAAACCTAGGG
1 AAACTGTAAGG-CTTACCCTTGCACACAACAAAAAAACCTGGGG
* * * * ** *
1955131 AAATTGTCAGGCCTACCTTTGCACACAACAAAGGAACATGGGG
1 AAACTGTAAGGCTTACCCTTGCACACAACAAAAAAACCTGGGG
* * **
1955174 AAACCGTAAGGCTTACCCTTGCACATAGA-AAAGGAACCTGGGG
1 AAACTGTAAGGCTTACCCTTGCACACA-ACAAAAAAACCTGGGG
*
1955217 AAACTGTAAGGCTTACCCTTGCACACAACAAAGAAACCT
1 AAACTGTAAGGCTTACCCTTGCACACAACAAAAAAACCT
1955256 TTATACAAAA
Statistics
Matches: 102, Mismatches: 21, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
42 1 0.01
43 92 0.90
44 9 0.09
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.18
Consensus pattern (43 bp):
AAACTGTAAGGCTTACCCTTGCACACAACAAAAAAACCTGGGG
Found at i:1955201 original size:86 final size:87
Alignment explanation
Indices: 1955087--1955249 Score: 240
Period size: 86 Copynumber: 1.9 Consensus size: 87
1955077 AAGCATGTAA
* * * *
1955087 AAACGGTAAGGTCTTACCCTTGCACATAGCAAAA-AAACCTAGGGAAATTGTCAGGCCTACCTTT
1 AAACCGTAAGGTCTTACCCTTGCACATAG-AAAAGAAACCTAGGGAAACTGTAAGGCCTACCCTT
1955151 GCACACAACAAAGGAACATGGGG
65 GCACACAACAAAGGAACATGGGG
* * *
1955174 AAACCGTAAGG-CTTACCCTTGCACATAGAAAAGGAACCTGGGGAAACTGTAAGGCTTACCCTTG
1 AAACCGTAAGGTCTTACCCTTGCACATAGAAAAGAAACCTAGGGAAACTGTAAGGCCTACCCTTG
1955238 CACACAACAAAG
66 CACACAACAAAG
1955250 AAACCTTTAT
Statistics
Matches: 68, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
85 4 0.06
86 54 0.79
87 10 0.15
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.18
Consensus pattern (87 bp):
AAACCGTAAGGTCTTACCCTTGCACATAGAAAAGAAACCTAGGGAAACTGTAAGGCCTACCCTTG
CACACAACAAAGGAACATGGGG
Found at i:1958540 original size:28 final size:28
Alignment explanation
Indices: 1958500--1958556 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
1958490 TCATACAACT
1958500 CATATATGTCCCGAAAGACCACGTAGAA
1 CATATATGTCCCGAAAGACCACGTAGAA
*
1958528 CATATATGTCCCGAAGGACCACGTAGAA
1 CATATATGTCCCGAAAGACCACGTAGAA
1958556 C
1 C
1958557 CCTCGACTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.18
Consensus pattern (28 bp):
CATATATGTCCCGAAAGACCACGTAGAA
Found at i:1960255 original size:2 final size:2
Alignment explanation
Indices: 1960248--1960272 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1960238 ATTTATTCTG
1960248 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 A
1960273 AAGTGGTGGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1962789 original size:18 final size:18
Alignment explanation
Indices: 1962763--1962802 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1962753 GTTTATAATT
1962763 ATCAGATGATTTTCAGTG
1 ATCAGATGATTTTCAGTG
* *
1962781 ATCATATGATTTTCAGTT
1 ATCAGATGATTTTCAGTG
1962799 ATCA
1 ATCA
1962803 AATAATTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.42
Consensus pattern (18 bp):
ATCAGATGATTTTCAGTG
Found at i:1973809 original size:40 final size:41
Alignment explanation
Indices: 1973698--1974029 Score: 492
Period size: 40 Copynumber: 8.1 Consensus size: 41
1973688 CACCAGTCGT
*
1973698 AACGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGC
1 AACGAATTTGG-ATAAATCGCAACGCGAACTTCGACTATCGC
*
1973740 AACGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGC
1 AACGAATTTGG-ATAAATCGCAACGCGAACTTCGACTATCGC
* * *
1973782 AATGAATTTGGA-AAATCGCAACACGAACTTCTACTATCGC
1 AACGAATTTGGATAAATCGCAACGCGAACTTCGACTATCGC
1973822 AACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGC
1 AACGAATTTGG-ATAAATCGCAACGCGAACTTCGACTATCGC
* * **
1973864 AACGAATTTAGA-AAATCGCAACGCGAACTTTGACTAAAGC
1 AACGAATTTGGATAAATCGCAACGCGAACTTCGACTATCGC
*
1973904 AACGAATTTGGA-AAATCACAACGCGAACTTCGACTATCGC
1 AACGAATTTGGATAAATCGCAACGCGAACTTCGACTATCGC
*
1973944 AACGAATTTTGAATAAATCGCAACGCGAACTTCGACTATCGC
1 AACGAA-TTTGGATAAATCGCAACGCGAACTTCGACTATCGC
*
1973986 AACGAATTT-GAAAAATCGCAACGCGAACTTCGACTATCGC
1 AACGAATTTGGATAAATCGCAACGCGAACTTCGACTATCGC
1974026 AACG
1 AACG
1974030 CGAACTTGGA
Statistics
Matches: 266, Mismatches: 20, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
40 134 0.50
41 11 0.04
42 121 0.45
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (41 bp):
AACGAATTTGGATAAATCGCAACGCGAACTTCGACTATCGC
Found at i:1974028 original size:122 final size:122
Alignment explanation
Indices: 1973698--1974029 Score: 540
Period size: 122 Copynumber: 2.7 Consensus size: 122
1973688 CACCAGTCGT
*
1973698 AACGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAAATCGCAA
1 AACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTT-GAA-AAATCGCAA
* * * *
1973763 CGCGAACTTGGACTATCGCAATGAATTTGGAAAATCGCAACACGAACTTCTACTATCGC
64 CGCGAACTTCGACTATCGCAACGAATTTGGAAAATCACAACACGAACTTCGACTATCGC
1973822 AACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTT-AGAAAATCGCAAC
1 AACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGA-AAAATCGCAAC
* ** *
1973886 GCGAACTTTGACTAAAGCAACGAATTTGGAAAATCACAACGCGAACTTCGACTATCGC
65 GCGAACTTCGACTATCGCAACGAATTTGGAAAATCACAACACGAACTTCGACTATCGC
*
1973944 AACGAATTTTGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGAAAAATCGCAACG
1 AACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGAAAAATCGCAACG
1974009 CGAACTTCGACTATCGCAACG
66 CGAACTTCGACTATCGCAACG
1974030 CGAACTTGGA
Statistics
Matches: 194, Mismatches: 12, Indels: 6
0.92 0.06 0.03
Matches are distributed among these distances:
122 142 0.73
123 2 0.01
124 50 0.26
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (122 bp):
AACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGAAAAATCGCAACG
CGAACTTCGACTATCGCAACGAATTTGGAAAATCACAACACGAACTTCGACTATCGC
Found at i:1974054 original size:82 final size:82
Alignment explanation
Indices: 1973698--1974029 Score: 501
Period size: 82 Copynumber: 4.0 Consensus size: 82
1973688 CACCAGTCGT
*
1973698 AACGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAAATCGCAA
1 AACGAATTTGG-A-AAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAATCGCAA
*
1973763 CGCGAACTTGGACTATCGC
64 CGCGAACTTCGACTATCGC
* * *
1973782 AATGAATTTGGAAAATCGCAACACGAACTTCTACTATCGCAACGAATTTGGAATAAATCGCAACG
1 AACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAATCGCAACG
1973847 CGAACTTCGACTATCGC
66 CGAACTTCGACTATCGC
* * ** *
1973864 AACGAATTTAGAAAATCGCAACGCGAACTTTGACTAAAGCAACGAATTTGG-A-AAATCACAACG
1 AACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAATCGCAACG
1973927 CGAACTTCGACTATCGC
66 CGAACTTCGACTATCGC
*
1973944 AACGAATTTTGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTT-GAA-AAATCGCAA
1 AACGAA-TTTGGA-AAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAATCGCAA
1974007 CGCGAACTTCGACTATCGC
64 CGCGAACTTCGACTATCGC
1974026 AACG
1 AACG
1974030 CGAACTTGGA
Statistics
Matches: 226, Mismatches: 19, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
80 33 0.15
81 6 0.03
82 176 0.78
83 1 0.00
84 10 0.04
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (82 bp):
AACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAATCGCAACG
CGAACTTCGACTATCGC
Found at i:1974096 original size:21 final size:21
Alignment explanation
Indices: 1974063--1974115 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
1974053 AATATGTAAA
* *
1974063 TCGCATTGTGATAGTCCAAGT
1 TCGCGTTGCGATAGTCCAAGT
*
1974084 TCGCGTTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCCAAGT
1974105 TCGCGTTGCGA
1 TCGCGTTGCGA
1974116 ATCTGTAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.19, C:0.21, G:0.30, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCCAAGT
Found at i:1976143 original size:21 final size:22
Alignment explanation
Indices: 1976119--1976161 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1976109 GTAAAGAAAG
*
1976119 AAATC-AAATAAACAACCAAAT
1 AAATCAAAATAAACAACAAAAT
*
1976140 AAATCAAAATCAACAACAAAAT
1 AAATCAAAATAAACAACAAAAT
1976162 CATATTATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.67, C:0.19, G:0.00, T:0.14
Consensus pattern (22 bp):
AAATCAAAATAAACAACAAAAT
Found at i:1976776 original size:17 final size:18
Alignment explanation
Indices: 1976749--1976782 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1976739 ATATCAAAAC
*
1976749 ATCATTAAACATGATCAT
1 ATCATTAAACATCATCAT
1976767 ATCA-TAAACATCATCA
1 ATCATTAAACATCATCA
1976783 AAATGAACCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.47, C:0.21, G:0.03, T:0.29
Consensus pattern (18 bp):
ATCATTAAACATCATCAT
Found at i:1976788 original size:26 final size:26
Alignment explanation
Indices: 1976739--1976788 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
1976729 TGCATTTTAA
*
1976739 ATATCAAAACATCATTAAACATGATC
1 ATATCAAAACATCATCAAACATGATC
1976765 ATATCATAAACATCATCAAA-ATGA
1 ATATCA-AAACATCATCAAACATGA
1976789 ACCTATTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 10 0.45
27 12 0.55
ACGTcount: A:0.52, C:0.18, G:0.04, T:0.26
Consensus pattern (26 bp):
ATATCAAAACATCATCAAACATGATC
Found at i:1977331 original size:38 final size:37
Alignment explanation
Indices: 1977287--1977489 Score: 145
Period size: 37 Copynumber: 5.5 Consensus size: 37
1977277 GAAAGCATAT
1977287 AATATATATATATATATTTTAAAAAATCAATTTTTGAA
1 AATATATATATATATATTTTAAAAAA-CAATTTTTGAA
* * *
1977325 AATATATATA-ATATGGTTTT-GAAAACACCTTTTTGAA
1 AATATATATATATAT-ATTTTAAAAAACA-ATTTTTGAA
* *
1977362 AACGTGTATA-ATATATAGTTTTAAAAAA-ATGGTTTTTGAA
1 AA--TATATATATATATA-TTTTAAAAAACA--ATTTTTGAA
* * *
1977402 AATGTATATA-ATATAGTTTAGAAAAC-ATTTTTGAA
1 AATATATATATATATATTTTAAAAAACAATTTTTGAA
* *
1977437 AA-ATATATATATAGT-TTTT-TAAAACGATTTTTGAA
1 AATATATATATATA-TATTTTAAAAAACAATTTTTGAA
* *
1977472 AACATGTATAATATATAT
1 AATATATAT-ATATATAT
1977490 AATTTTTGAT
Statistics
Matches: 134, Mismatches: 15, Indels: 33
0.74 0.08 0.18
Matches are distributed among these distances:
34 11 0.08
35 27 0.20
36 9 0.07
37 32 0.24
38 26 0.19
39 15 0.11
40 14 0.10
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.42
Consensus pattern (37 bp):
AATATATATATATATATTTTAAAAAACAATTTTTGAA
Found at i:1977403 original size:77 final size:75
Alignment explanation
Indices: 1977291--1977486 Score: 201
Period size: 77 Copynumber: 2.7 Consensus size: 75
1977281 GCATATAATA
* *
1977291 TATATATATATATTTTAAAAAATCAATTTTTGAAAATATATATAATATGGTTTTGAAAACACCTT
1 TATATATATATATTTTAAAAAATCAATTTTTGAAAATATATATAATATAGTTTAGAAAACA--TT
1977356 TTTGAAAACGTG
64 TTTGAAAACGTG
** *
1977368 TATA-ATATATAGTTTTAAAAAAAT-GGTTTTTGAAAATGTATATAATATAGTTTAGAAAACATT
1 TATATATATATA-TTTT-AAAAAATCAATTTTTGAAAATATATATAATATAGTTTAGAAAACATT
1977431 TTTGAAAA----
64 TTTGAAAACGTG
** * * *
1977439 -ATATATATATAGTTTTTTAAAA-CGATTTTTGAAAACATGTATAATATA
1 TATATATATATA-TTTTAAAAAATCAATTTTTGAAAATATATATAATATA
1977487 TATAATTTTT
Statistics
Matches: 104, Mismatches: 11, Indels: 15
0.80 0.08 0.12
Matches are distributed among these distances:
70 28 0.27
71 12 0.12
75 10 0.10
76 7 0.07
77 40 0.38
78 7 0.07
ACGTcount: A:0.44, C:0.04, G:0.10, T:0.42
Consensus pattern (75 bp):
TATATATATATATTTTAAAAAATCAATTTTTGAAAATATATATAATATAGTTTAGAAAACATTTT
TGAAAACGTG
Found at i:1977527 original size:21 final size:21
Alignment explanation
Indices: 1977481--1977533 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
1977471 AAACATGTAT
1977481 AATA-TATATAATTTTTGATA
1 AATATTATATAATTTTTGATA
1977501 ACATATTATATAATTTTTTGA-A
1 A-ATATTATATAA-TTTTTGATA
*
1977523 AATATAATATA
1 AATATTATATA
1977534 TGTTATATAC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 1 0.03
21 12 0.41
22 9 0.31
23 7 0.24
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (21 bp):
AATATTATATAATTTTTGATA
Found at i:1977533 original size:23 final size:24
Alignment explanation
Indices: 1977478--1977534 Score: 73
Period size: 23 Copynumber: 2.4 Consensus size: 24
1977468 TGAAAACATG
*
1977478 TATAATATATATAATTTTTGATAA
1 TATAATATATATAATTTTTGAAAA
*
1977502 CAT-AT-TATATAATTTTTTGAAAA
1 TATAATATATATAA-TTTTTGAAAA
1977525 TATAATATAT
1 TATAATATAT
1977535 GTTATATACT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
22 7 0.26
23 13 0.48
24 4 0.15
25 3 0.11
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.49
Consensus pattern (24 bp):
TATAATATATATAATTTTTGAAAA
Found at i:1977570 original size:5 final size:5
Alignment explanation
Indices: 1977553--1977619 Score: 54
Period size: 5 Copynumber: 14.2 Consensus size: 5
1977543 CTTTTTATTA
* **
1977553 TATAT TATTT TATAT TAT-T TATAT TATTAT TAGGT TATAT TAT-T TAT-T
1 TATAT TATAT TATAT TATAT TATAT TA-TAT TATAT TATAT TATAT TATAT
*
1977601 TAT-T TAT-T TATTT TATAT T
1 TATAT TATAT TATAT TATAT T
1977620 TTAACAAGTC
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
4 20 0.38
5 27 0.52
6 5 0.10
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (5 bp):
TATAT
Found at i:1977570 original size:17 final size:17
Alignment explanation
Indices: 1977544--1977619 Score: 54
Period size: 17 Copynumber: 4.5 Consensus size: 17
1977534 TGTTATATAC
1977544 TTTT-TATTATATATTA
1 TTTTATATTATATATTA
*
1977560 TTTTATATTATTTA-TA
1 TTTTATATTATATATTA
*
1977576 TTAT-TATTAGGTTATATTA
1 TTTTATATTA---TATATTA
*
1977595 -TTTAT-TTATTTATTTA
1 TTTTATATTATATA-TTA
1977611 TTTTATATT
1 TTTTATATT
1977620 TTAACAAGTC
Statistics
Matches: 46, Mismatches: 5, Indels: 16
0.69 0.07 0.24
Matches are distributed among these distances:
15 8 0.17
16 12 0.26
17 13 0.28
18 10 0.22
19 3 0.07
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (17 bp):
TTTTATATTATATATTA
Found at i:1977590 original size:25 final size:25
Alignment explanation
Indices: 1977535--1977604 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 25
1977525 TATAATATAT
* *
1977535 GTTATA-TACTTTTTATTATATATTAT
1 GTTATATTA-TTTATATTAT-TATTAG
*
1977561 TTTATATTATTTATATTATTATTAG
1 GTTATATTATTTATATTATTATTAG
1977586 GTTATATTATTTAT-TTATT
1 GTTATATTATTTATATTATT
1977605 TATTTATTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
24 5 0.13
25 18 0.46
26 14 0.36
27 2 0.05
ACGTcount: A:0.30, C:0.01, G:0.04, T:0.64
Consensus pattern (25 bp):
GTTATATTATTTATATTATTATTAG
Found at i:1977601 original size:4 final size:4
Alignment explanation
Indices: 1977546--1977613 Score: 50
Period size: 4 Copynumber: 15.8 Consensus size: 4
1977536 TTATATACTT
*
1977546 TTTA TTATA TATTA TTTTA TATTA TTTA TATTA -TTA -TTA GGTTA TATTA
1 TTTA TT-TA T-TTA -TTTA T-TTA TTTA T-TTA TTTA TTTA -TTTA T-TTA
1977595 TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTT
1977614 TATATTTTAA
Statistics
Matches: 55, Mismatches: 1, Indels: 16
0.76 0.01 0.22
Matches are distributed among these distances:
3 6 0.11
4 25 0.45
5 22 0.40
6 2 0.04
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (4 bp):
TTTA
Found at i:1977603 original size:8 final size:9
Alignment explanation
Indices: 1977547--1977619 Score: 66
Period size: 9 Copynumber: 8.2 Consensus size: 9
1977537 TATATACTTT
1977547 TTATTATATA
1 TTATT-TATA
1977557 TTATTTTATA
1 TTA-TTTATA
1977567 TTATTTATA
1 TTATTTATA
1977576 TTA--T-TA
1 TTATTTATA
*
1977582 TTAGGTTATA
1 TTA-TTTATA
1977592 TTATTTAT-
1 TTATTTATA
1977600 TTATTTAT-
1 TTATTTATA
1977608 TTATTTTATA
1 TTA-TTTATA
1977618 TT
1 TT
1977620 TTAACAAGTC
Statistics
Matches: 55, Mismatches: 1, Indels: 14
0.79 0.01 0.20
Matches are distributed among these distances:
6 5 0.09
7 1 0.02
8 11 0.20
9 19 0.35
10 17 0.31
11 2 0.04
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (9 bp):
TTATTTATA
Found at i:1979794 original size:23 final size:23
Alignment explanation
Indices: 1979768--1979811 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1979758 ACTAACTTGT
* * *
1979768 TTCTTTTCATTTTCTTCATTTTA
1 TTCTTATCATTTGCATCATTTTA
1979791 TTCTTATCATTTGCATCATTT
1 TTCTTATCATTTGCATCATTT
1979812 AAAGAGGTGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.16, C:0.18, G:0.02, T:0.64
Consensus pattern (23 bp):
TTCTTATCATTTGCATCATTTTA
Found at i:1989656 original size:21 final size:20
Alignment explanation
Indices: 1989628--1989690 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 20
1989618 CATTTTGGTG
1989628 CAGAGGGAATCGATCCCCCC
1 CAGAGGGAATCGATCCCCCC
*
1989648 CATGAGGGAACCGATTCCCCCC
1 CA-GAGGGAATCGA-TCCCCCC
1989670 ACAG-GGGAATCGATACCCCCC
1 -CAGAGGGAATCGAT-CCCCCC
1989691 TGGGGTTCTG
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
20 3 0.08
21 24 0.65
22 8 0.22
23 2 0.05
ACGTcount: A:0.25, C:0.40, G:0.24, T:0.11
Consensus pattern (20 bp):
CAGAGGGAATCGATCCCCCC
Found at i:1994531 original size:22 final size:22
Alignment explanation
Indices: 1994471--1994555 Score: 82
Period size: 22 Copynumber: 3.9 Consensus size: 22
1994461 GATTTTCTCC
* *
1994471 TATCAATGCTGAGACACTTTAG
1 TATCAGTGCTAAGACACTTTAG
* * *
1994493 TATAAGTGCAAATACACTTCT-G
1 TATCAGTGCTAAGACACTT-TAG
* *
1994515 TATCACTGCTGAGACACTTTAG
1 TATCAGTGCTAAGACACTTTAG
*
1994537 TATCAGTGCTAAGGCACTT
1 TATCAGTGCTAAGACACTT
1994556 CAATTATTCG
Statistics
Matches: 48, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
21 1 0.02
22 46 0.96
23 1 0.02
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.32
Consensus pattern (22 bp):
TATCAGTGCTAAGACACTTTAG
Found at i:1994555 original size:44 final size:44
Alignment explanation
Indices: 1994471--1994556 Score: 127
Period size: 44 Copynumber: 2.0 Consensus size: 44
1994461 GATTTTCTCC
*
1994471 TATCAATGCTGAGACACTTTAGTATAAGTGCAAATACACTTCTG
1 TATCAATGCTGAGACACTTTAGTATAAGTGCAAAGACACTTCTG
* * * *
1994515 TATCACTGCTGAGACACTTTAGTATCAGTGCTAAGGCACTTC
1 TATCAATGCTGAGACACTTTAGTATAAGTGCAAAGACACTTC
1994557 AATTATTCGA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.31
Consensus pattern (44 bp):
TATCAATGCTGAGACACTTTAGTATAAGTGCAAAGACACTTCTG
Found at i:1995250 original size:2 final size:2
Alignment explanation
Indices: 1995243--1995268 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1995233 CAACTTTTTA
1995243 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
1995269 TAGTTGGGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2000555 original size:19 final size:21
Alignment explanation
Indices: 2000511--2000556 Score: 53
Period size: 19 Copynumber: 2.3 Consensus size: 21
2000501 TACAACGCCC
2000511 AAAATTGGTACTTTTTAATTA
1 AAAATTGGTACTTTTTAATTA
*
2000532 TAAATT-GT-CTTTATTAA-TA
1 AAAATTGGTACTTT-TTAATTA
2000551 AAAATT
1 AAAATT
2000557 TAAAAATTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 11 0.50
20 6 0.27
21 5 0.23
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.48
Consensus pattern (21 bp):
AAAATTGGTACTTTTTAATTA
Found at i:2002275 original size:10 final size:10
Alignment explanation
Indices: 2002252--2002283 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
2002242 AATTATTTTT
2002252 TAATAATA-A
1 TAATAATATA
2002261 TAATAATATA
1 TAATAATATA
2002271 TAATAATATA
1 TAATAATATA
2002281 TAA
1 TAA
2002284 ATAAATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
TAATAATATA
Found at i:2002275 original size:16 final size:16
Alignment explanation
Indices: 2002254--2002291 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
2002244 TTATTTTTTA
2002254 ATAATAATA-ATAATAT
1 ATAATAATATATAA-AT
2002270 ATAATAATATATAAAT
1 ATAATAATATATAAAT
2002286 A-AATAA
1 ATAATAA
2002292 AATGGGTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.24
16 12 0.57
17 4 0.19
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
ATAATAATATATAAAT
Found at i:2002673 original size:124 final size:123
Alignment explanation
Indices: 2002487--2003336 Score: 752
Period size: 124 Copynumber: 6.9 Consensus size: 123
2002477 GGGATGATAA
* * * ** * * *
2002487 TATCTCCTTCTGTGAT-GTAAT-TTGGAAAAGGGTTGAACAAGTTCTTCTTATTATAAAATTCTT
1 TATCTCCTTCTGTGATAG-AGTCATGCAAAA-GGTTGAACAAACTCTTCTCATTATGAACTTCTT
* *
2002550 CTTCCTTCTTCAAATGAGTTCTTCTTATTATGAACTTTACCTGGAAAAGTTGATGTTGA-C
64 CTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-CCTGGAAAAGTTGATGTTGATC
* * *
2002610 ATATTTCCTTCTGTGATAGAGTCATTCAAAAGGTTGAATAAACTCTTCTCATTATGAACTTCTTC
1 -TATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTC
* * * *
2002675 TTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGTTGATGCTAATC
65 TTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTC-CTGGAAAAGTTGATGTTGATC
* * * * *
2002735 TATCTCCTTCTGTGATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTGTAAAC-T-TT-T
1 TATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCT
* *
2002797 T-CTTCTTCAGATGAGTTCTTCTCATGATGAACTTTCTCTGG-AAA----A-GCTGATC
66 TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTC-CTGGAAAAGTTGATGTTGATC
* *** ** * * *
2002849 CATCAAATGATG-GAT---TTGA-GCAAAAGGTTGAACAAATTCTTCTCATTATGAA--T-TTCT
1 TATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCT
2002906 T-CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCCCTGGAAAAGTTGATGTTTGAAAGAGGT
66 TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-CCTGGAAAAGTTGATG-TT----GA---
2002970 GTC
122 -TC
* * * * * * *
2002973 ATTGATTTAACTTCATATGTGATAAATTAAGGC--AAGGTTGAACAAATTCTTCTCATTATGAA-
1 --T-ATCT-CCTTC---TGTGATAGAGTCATGCAAAAGGTTGAACAAACTCTTCTCATTATGAAC
* * * * *
2003035 TTTTTTTCTCCTTTTTCAGATGAGTTCTTCTCATTATGAACACTT-CTGGAAATGTTGATGTTGA
59 TTCTTCT-TCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTTCCTGGAAAAGTTGATGTTGA
2003099 TC
122 TC
** * *
2003101 TATCTCCTTCTGTGATAGAGTCAAAC-AAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCT
1 TATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCT
* * *
2003165 TCC-TCTTCATATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTGATC
66 TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTC-CTGGAAAAGTTGATGTTGATC
* *
2003223 TATCTCCTTCTATGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCT
1 TATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCT
* *
2003288 TCC-TCTTCAGATAAGTTCTTCTCATTATGAACTTT-CTGGAAATGTTGAT
66 TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCCTGGAAAAGTTGAT
2003337 CCATCGATCA
Statistics
Matches: 606, Mismatches: 77, Indels: 89
0.78 0.10 0.12
Matches are distributed among these distances:
108 3 0.00
109 68 0.11
110 6 0.01
113 3 0.00
114 13 0.02
115 2 0.00
116 1 0.00
119 2 0.00
120 43 0.07
121 52 0.09
122 75 0.12
123 76 0.13
124 151 0.25
125 10 0.02
126 1 0.00
127 2 0.00
128 4 0.01
131 2 0.00
132 5 0.01
134 29 0.05
135 4 0.01
136 7 0.01
137 15 0.02
138 30 0.05
139 2 0.00
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.40
Consensus pattern (123 bp):
TATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCT
TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCCTGGAAAAGTTGATGTTGATC
Found at i:2002881 original size:109 final size:109
Alignment explanation
Indices: 2002759--2002956 Score: 317
Period size: 109 Copynumber: 1.8 Consensus size: 109
2002749 ATAGAATTAT
* *
2002759 GCAAAAGGTTGAACAAGCTCTTCTCATTGTAAACTTT-TTCTTCTTCAGATGAGTTCTTCTCATG
1 GCAAAAGGTTGAACAAACTCTTCTCATTATAAA-TTTCTTCTTCTTCAGATGAGTTCTTCTCATG
*
2002823 ATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
65 ATGAACTTTCCCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
* * *
2002868 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTCAGATGAGTTCTTCTCATTA
1 GCAAAAGGTTGAACAAACTCTTCTCATTATAAATTTCTTCTTCTTCAGATGAGTTCTTCTCATGA
*
2002933 TGAACTTTCCCTGGAAAAGTTGAT
66 TGAACTTTCCCTGGAAAAGCTGAT
2002957 GTTTGAAAGA
Statistics
Matches: 81, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
108 3 0.04
109 78 0.96
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.37
Consensus pattern (109 bp):
GCAAAAGGTTGAACAAACTCTTCTCATTATAAATTTCTTCTTCTTCAGATGAGTTCTTCTCATGA
TGAACTTTCCCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
Found at i:2003205 original size:122 final size:121
Alignment explanation
Indices: 2003006--2003336 Score: 477
Period size: 122 Copynumber: 2.7 Consensus size: 121
2002996 AAATTAAGGC
* * * *
2003006 AAGGTTGAACAAATTCTTCTCATTATGAA-TTTTTTTCTCCTTTTTCAGATGAGTTCTTCTCATT
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCT-TCC-TCTTCAGATAAGTTCTTCTCATT
* * *
2003070 ATGAACACTTCTGGAAATGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCAAAC-A
64 ATGAAC-TTTCTGGAAATGTTGATGCTGATCTATCTCCTTCTATGATAGAGTCAAACAA
* *
2003128 AAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTCTTCATATAAGTTCTTCTCATTAT
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
* **
2003193 GAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTATGATAGAGTCATGCAA
66 GAAC-TT-TCTGGAAATGTTGATGCTGATCTATCTCCTTCTATGATAGAGTCAAACAA
**
2003251 AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
2003316 GAACTTTCTGGAAATGTTGAT
66 GAACTTTCTGGAAATGTTGAT
2003337 CCATCGATCA
Statistics
Matches: 188, Mismatches: 18, Indels: 7
0.88 0.08 0.03
Matches are distributed among these distances:
121 41 0.22
122 76 0.40
123 71 0.38
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (121 bp):
AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
GAACTTTCTGGAAATGTTGATGCTGATCTATCTCCTTCTATGATAGAGTCAAACAA
Found at i:2003682 original size:76 final size:76
Alignment explanation
Indices: 2003551--2003733 Score: 294
Period size: 76 Copynumber: 2.4 Consensus size: 76
2003541 GTTTTAAGAA
* * * * * *
2003551 AAAACATTCTGCACTGTAGGGCTTATAGTTGACCTGAAGGTTTTGAAAACATCAAAAAGCTCCTG
1 AAAACATCCTGCACTGTAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCG
2003616 AAGGCTTTTTG
66 AAGGCTTTTTG
**
2003627 AAAACATCCTGCACTGTAGGGCTTACAGATGACCCGAAGGCTTTGAAAATGTCAAAAAGCTCCCG
1 AAAACATCCTGCACTGTAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCG
2003692 AAGGCTTTTTG
66 AAGGCTTTTTG
2003703 AAAACATCCTGCACTGTAGGGCTTACAGATG
1 AAAACATCCTGCACTGTAGGGCTTACAGATG
2003734 TGGGAAATAG
Statistics
Matches: 99, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
76 99 1.00
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (76 bp):
AAAACATCCTGCACTGTAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCG
AAGGCTTTTTG
Found at i:2004873 original size:54 final size:54
Alignment explanation
Indices: 2004782--2004937 Score: 249
Period size: 54 Copynumber: 2.9 Consensus size: 54
2004772 ATAATCACTG
* * * * *
2004782 GTTCGTAAAACATTTGACAACACATTCTTCATCTCCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGCTCAGAC
*
2004836 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGTTCAGAC
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGCTCAGAC
*
2004890 GTTCGTAAAACATTTGACAACACATTCATCCTTTCTTGTGGTTTCTGC
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGC
2004938 CAAGATTTCT
Statistics
Matches: 94, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 94 1.00
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGCTCAGAC
Found at i:2009363 original size:9 final size:9
Alignment explanation
Indices: 2009345--2009403 Score: 66
Period size: 9 Copynumber: 6.2 Consensus size: 9
2009335 GATTCAATTG
2009345 TTTTCTTTTT
1 TTTTC-TTTT
2009355 TTTTCTTTT
1 TTTTCTTTT
2009364 TTTTCTATTT
1 TTTTCT-TTT
*
2009374 CTTTCCCTTTT
1 -TTT-TCTTTT
2009385 TTTTC-TTT
1 TTTTCTTTT
2009393 TTTTCTTTT
1 TTTTCTTTT
2009402 TT
1 TT
2009404 CCTTTCTTTG
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
8 8 0.19
9 16 0.37
10 11 0.26
11 6 0.14
12 2 0.05
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTTCTTTT
Found at i:2009385 original size:21 final size:19
Alignment explanation
Indices: 2009345--2009397 Score: 70
Period size: 21 Copynumber: 2.7 Consensus size: 19
2009335 GATTCAATTG
**
2009345 TTTTCTTTTTTTTTCTTTT
1 TTTTCTTTTTTTCCCTTTT
2009364 TTTTCTATTTCTTTCCCTTTT
1 TTTTCT-TTT-TTTCCCTTTT
2009385 TTTTCTTTTTTTC
1 TTTTCTTTTTTTC
2009398 TTTTTTCCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 10 0.33
20 6 0.20
21 14 0.47
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTTCTTTTTTTCCCTTTT
Found at i:2009403 original size:10 final size:10
Alignment explanation
Indices: 2009345--2009396 Score: 61
Period size: 10 Copynumber: 5.2 Consensus size: 10
2009335 GATTCAATTG
2009345 TTTTCTTTTT
1 TTTTCTTTTT
2009355 TTTTC-TTTT
1 TTTTCTTTTT
*
2009364 TTTTCTATTTC
1 TTTTCT-TTTT
* *
2009375 TTTCCCTTTT
1 TTTTCTTTTT
2009385 TTTTCTTTTT
1 TTTTCTTTTT
2009395 TT
1 TT
2009397 CTTTTTTCCT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
9 9 0.26
10 18 0.53
11 7 0.21
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:2009430 original size:27 final size:26
Alignment explanation
Indices: 2009392--2009445 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
2009382 TTTTTTTCTT
*
2009392 TTTTTCTTTTTTCCTTTCTTTGCTGGA
1 TTTTTCTCTTTT-CTTTCTTTGCTGGA
*
2009419 TTTTTCTCTTTTCTTTCTTTGTTGGA
1 TTTTTCTCTTTTCTTTCTTTGCTGGA
2009445 T
1 T
2009446 GAGTATAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 14 0.56
27 11 0.44
ACGTcount: A:0.04, C:0.17, G:0.11, T:0.69
Consensus pattern (26 bp):
TTTTTCTCTTTTCTTTCTTTGCTGGA
Found at i:2009739 original size:2 final size:2
Alignment explanation
Indices: 2009732--2009761 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2009722 ACAACAAAGG
2009732 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
2009762 TAAAGGATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2018014 original size:26 final size:26
Alignment explanation
Indices: 2017978--2018038 Score: 106
Period size: 26 Copynumber: 2.3 Consensus size: 26
2017968 TCCCCCTTTT
2017978 CATCATCACTG-TATGATTTCGTTCGA
1 CATCATCACTGCTA-GATTTCGTTCGA
2018004 CATCATCACTGCTAGATTTCGTTCGA
1 CATCATCACTGCTAGATTTCGTTCGA
2018030 CATCATCAC
1 CATCATCAC
2018039 CTACAACTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
26 32 0.94
27 2 0.06
ACGTcount: A:0.25, C:0.28, G:0.13, T:0.34
Consensus pattern (26 bp):
CATCATCACTGCTAGATTTCGTTCGA
Found at i:2024176 original size:13 final size:13
Alignment explanation
Indices: 2024158--2024182 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2024148 TACAATCAAG
2024158 GATGAGAAATTTA
1 GATGAGAAATTTA
2024171 GATGAGAAATTT
1 GATGAGAAATTT
2024183 TCAGTCTCGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.24, T:0.32
Consensus pattern (13 bp):
GATGAGAAATTTA
Found at i:2025522 original size:37 final size:37
Alignment explanation
Indices: 2025433--2025536 Score: 127
Period size: 37 Copynumber: 2.8 Consensus size: 37
2025423 CTTTTCGTCA
* * *
2025433 TACTAGGATTCAAACTCCTAAAAATAGGATATAATTT
1 TACTAGGATTCAAACTCCTAAAAATATGATAGAATTC
* *
2025470 TGCTAGGATTCAAACTCCTAAAAATATGATAGAGTTC
1 TACTAGGATTCAAACTCCTAAAAATATGATAGAATTC
** * *
2025507 TACTATTATTTAAACTCCTAAAGATATGAT
1 TACTAGGATTCAAACTCCTAAAAATATGAT
2025537 CCACAAGTAC
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (37 bp):
TACTAGGATTCAAACTCCTAAAAATATGATAGAATTC
Found at i:2025711 original size:12 final size:12
Alignment explanation
Indices: 2025694--2025725 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
2025684 TTTGTTTCTC
2025694 TTTTTTTATATA
1 TTTTTTTATATA
*
2025706 TTTTTTTATTTA
1 TTTTTTTATATA
2025718 TTTTTTTA
1 TTTTTTTA
2025726 CTTACTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTTTTTATATA
Found at i:2030093 original size:13 final size:12
Alignment explanation
Indices: 2030077--2030120 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 12
2030067 AAGGGCAAAA
2030077 AAAAAAAAGAAGC
1 AAAAAAAAGAA-C
*
2030090 AAAAAAGAAGAAA
1 AAAAAA-AAGAAC
2030103 AAAAATAAAGAAC
1 AAAAA-AAAGAAC
2030116 AAAAA
1 AAAAA
2030121 TCAAAAAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 21 0.78
14 6 0.22
ACGTcount: A:0.82, C:0.05, G:0.11, T:0.02
Consensus pattern (12 bp):
AAAAAAAAGAAC
Found at i:2030132 original size:27 final size:27
Alignment explanation
Indices: 2030073--2030133 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 27
2030063 CAAAAAGGGC
* *
2030073 AAAAAAAAAAAAGAAGCAAAAAAGAAG
1 AAAAAAAAAAAAGAAGCAAAAAACAAA
* *
2030100 AAAAAAAATAAAGAA-CAAAAATCAAA
1 AAAAAAAAAAAAGAAGCAAAAAACAAA
*
2030126 AAGAAAAA
1 AAAAAAAA
2030134 GGGACAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 15 0.52
27 14 0.48
ACGTcount: A:0.82, C:0.05, G:0.10, T:0.03
Consensus pattern (27 bp):
AAAAAAAAAAAAGAAGCAAAAAACAAA
Found at i:2030765 original size:22 final size:22
Alignment explanation
Indices: 2030737--2030791 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
2030727 GCTACCCCAT
2030737 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
*
2030759 CAAACCTTTGAGCATCAAATGT
1 CAAACCTTTGAGCATCAAATGC
*
2030781 AAAACCTTTGA
1 CAAACCTTTGA
2030792 CCAAACACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.25
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:2031809 original size:106 final size:106
Alignment explanation
Indices: 2031534--2032830 Score: 1892
Period size: 106 Copynumber: 12.3 Consensus size: 106
2031524 TCGAGAGTAG
*
2031534 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * * *
2031599 ATCGCTGGTTGTCAACAAAC-ACTTCTCGATTTTAGAGCCA
66 ACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCA
* *
2031639 ATTTCAACTTCAAAATGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
2031704 ACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCA
66 ACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCA
* * * * *
2031745 ATTTTAACTTCACAGCGTAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCATGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
2031810 ACCGCTGGTTGTCAATAAACAATTTCTCAATTTCAGAGCCA
66 ACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCA
* *
2031851 ATTTCAACTTCACAACGTAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * *
2031916 ACCACTGGTTATCAATAAACAGCTTCCCAATTTCAAAGCCA
66 ACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCA
* *
2031957 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCATGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * *
2032022 ACCGTTGGTTGTCAACAAACAACTTCTCAATTTCAGAGTCA
66 ACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCA
*
2032063 ATTTCAACTTCACAACAAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
2032128 ACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
66 ACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCA
*
2032169 ATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
2032234 ACCACTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCA
66 ACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCA
* *
2032275 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
** * *
2032340 ACCGCTGGTTGTCAACGAACAACTTCTCAATTTTAGAGCCA
66 ACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCA
2032381 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
2032446 ACCGCTGGTTGTCAATAAACAATTTCTCAATTTCAGAGCCA
66 ACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCA
* * *
2032487 ATTTCAACTTCACAGCGTAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
2032552 ATCGCTAGTTGTCAATAAACAACTTCCCAATTTCAGAGCCA
66 ACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCA
* * * * * * *
2032593 ATTTCAACTTCTCAGCGAAGGATCTTGGAC-CCAAAACAACACAAGCTCAACTTCACGAGGAAGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCC-AGACAACGCAAGTTCAACTTCACGACGAAGG
* * * * * *
2032657 GGCGGCTGATTGTCAA-CAA-AA-TT-TC-A-TTCAGAGTCA
65 GACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCA
* * * *
2032693 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * *
2032758 A-CGACTGGTTGTCAACAAACAATTTCCCAGTTCCAGAGCCA
66 ACCG-CTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCA
* *
2032799 ATTTCAACTGCACAACGGAGGATATTGGACTC
1 ATTTCAACTTCACAACGAAGGATATTGGACTC
2032831 GGAACAATGC
Statistics
Matches: 1077, Mismatches: 105, Indels: 19
0.90 0.09 0.02
Matches are distributed among these distances:
99 1 0.00
100 75 0.07
101 4 0.00
102 3 0.00
103 4 0.00
104 3 0.00
105 83 0.08
106 904 0.84
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (106 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCA
Found at i:2033616 original size:37 final size:37
Alignment explanation
Indices: 2033564--2033743 Score: 209
Period size: 37 Copynumber: 4.8 Consensus size: 37
2033554 CTTTTCAACA
2033564 TACTAGGATTCAAACTCCTAAAAATAGGATATAATTT
1 TACTAGGATTCAAACTCCTAAAAATAGGATATAATTT
* * * **
2033601 TGCTAGGATTCAAACTCCTAAAAATAGGCCTTTTCAA-CA
1 TACTAGGATTCAAACTCCTAAAAATAGG--ATAT-AATTT
2033640 TACTAGGATTCAAACTCCTAAAAATAGGATATAATTT
1 TACTAGGATTCAAACTCCTAAAAATAGGATATAATTT
* * * *
2033677 TGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTTC
1 TACTAGGATTCAAACTCCTAAAAATAGGATATAATTT
** * *
2033714 TACTATTATTTAAACTCCTAAAGATAGGAT
1 TACTAGGATTCAAACTCCTAAAAATAGGAT
2033744 CCACAAGCAC
Statistics
Matches: 120, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
36 2 0.02
37 87 0.73
39 29 0.24
40 2 0.02
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.31
Consensus pattern (37 bp):
TACTAGGATTCAAACTCCTAAAAATAGGATATAATTT
Found at i:2033679 original size:76 final size:76
Alignment explanation
Indices: 2033553--2033704 Score: 304
Period size: 76 Copynumber: 2.0 Consensus size: 76
2033543 TGTCAACACA
2033553 CCTTTTCAACATACTAGGATTCAAACTCCTAAAAATAGGATATAATTTTGCTAGGATTCAAACTC
1 CCTTTTCAACATACTAGGATTCAAACTCCTAAAAATAGGATATAATTTTGCTAGGATTCAAACTC
2033618 CTAAAAATAGG
66 CTAAAAATAGG
2033629 CCTTTTCAACATACTAGGATTCAAACTCCTAAAAATAGGATATAATTTTGCTAGGATTCAAACTC
1 CCTTTTCAACATACTAGGATTCAAACTCCTAAAAATAGGATATAATTTTGCTAGGATTCAAACTC
2033694 CTAAAAATAGG
66 CTAAAAATAGG
2033705 ATAGAGTTCT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.30
Consensus pattern (76 bp):
CCTTTTCAACATACTAGGATTCAAACTCCTAAAAATAGGATATAATTTTGCTAGGATTCAAACTC
CTAAAAATAGG
Found at i:2034350 original size:23 final size:22
Alignment explanation
Indices: 2034298--2034341 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
2034288 TTCTTTGCAT
2034298 TTTTATTATT-CTATTATATTTA
1 TTTTATT-TTACTATTATATTTA
2034320 TTATTATTTTACTATTATATTT
1 TT-TTATTTTACTATTATATTT
2034342 TCCTTTATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTTATTTTACTATTATATTTA
Found at i:2034451 original size:12 final size:11
Alignment explanation
Indices: 2034429--2034469 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
2034419 TCTTTCTTTT
2034429 TATTATTCTTG
1 TATTATTCTTG
2034440 TATTATTACTTG
1 TATTATT-CTTG
* *
2034452 TATTATTTTTA
1 TATTATTCTTG
2034463 TATTATT
1 TATTATT
2034470 TATTTTGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (11 bp):
TATTATTCTTG
Found at i:2034634 original size:32 final size:31
Alignment explanation
Indices: 2034593--2034656 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 31
2034583 TATATTTTTC
2034593 TATTAATTTTCTATATTTTTTATT-ATCATTA
1 TATTAATTTTCTATATTTTTTATTGAT-ATTA
* * *
2034624 TATTATATTTTTTTTCTTTTTTATTGATATTA
1 TATTA-ATTTTCTATATTTTTTATTGATATTA
2034656 T
1 T
2034657 TGTTGTTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 5 0.18
32 21 0.75
33 2 0.07
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.69
Consensus pattern (31 bp):
TATTAATTTTCTATATTTTTTATTGATATTA
Found at i:2034698 original size:2 final size:2
Alignment explanation
Indices: 2034691--2034721 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2034681 CTAGTATTAT
2034691 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2034722 TCTACACAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2035107 original size:27 final size:24
Alignment explanation
Indices: 2035057--2035107 Score: 57
Period size: 27 Copynumber: 2.0 Consensus size: 24
2035047 TTCTTTTTCT
*
2035057 TTTTTTTTATATATTTTTTATTTG
1 TTTTTTTTATATATTTTATATTTG
*
2035081 TTTTTTTTACTTACTATTTTATCTTTG
1 TTTTTTTTA--TA-TATTTTATATTTG
2035108 CTTTCTTCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 9 0.41
26 2 0.09
27 11 0.50
ACGTcount: A:0.16, C:0.06, G:0.04, T:0.75
Consensus pattern (24 bp):
TTTTTTTTATATATTTTATATTTG
Found at i:2038709 original size:40 final size:39
Alignment explanation
Indices: 2038654--2038921 Score: 260
Period size: 40 Copynumber: 6.8 Consensus size: 39
2038644 AGCCACTATC
* * *
2038654 GAAACCTAAAATTTTAGGCTT-CAACTTGATTTATCTTATA
1 GAAACCT-AATTTTTAGG-TTGCAACCTGATTTATCATATA
* *
2038694 GAAACCTGAATTTTTAGGTTGAAACCTAATTTATCATATA
1 GAAACCT-AATTTTTAGGTTGCAACCTGATTTATCATATA
*
2038734 GAAACATGAATTTTTAGGTTGCAACCTGATTTATCATATA
1 GAAACCT-AATTTTTAGGTTGCAACCTGATTTATCATATA
* *
2038774 AAAACCTAGATTTTTAGGTTGCAACCTGATTTATCTTATA
1 GAAACCTA-ATTTTTAGGTTGCAACCTGATTTATCATATA
* * * * * *
2038814 GAAATCTAGATTTTTAGGTTACAATCTAATTGATCACATCA
1 GAAACCTA-ATTTTTAGGTTGCAACCTGATTTATCATAT-A
* * *
2038855 -AAACTTGATTTTTA-GTTGCAACCTGATTTTTGCATATA
1 GAAACCTAATTTTTAGGTTGCAACCTGATTTAT-CATATA
2038893 G-AACC-AGA-TTTTAGGTTGCAACCTGATTT
1 GAAACCTA-ATTTTTAGGTTGCAACCTGATTT
2038922 TTTTTATGGA
Statistics
Matches: 190, Mismatches: 31, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
37 5 0.03
38 32 0.17
39 14 0.07
40 138 0.73
41 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (39 bp):
GAAACCTAATTTTTAGGTTGCAACCTGATTTATCATATA
Found at i:2038719 original size:20 final size:20
Alignment explanation
Indices: 2038694--2038762 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
2038684 TTATCTTATA
2038694 GAAACCTGAATTTTTAGGTT
1 GAAACCTGAATTTTTAGGTT
* ** *
2038714 GAAACCT-AATTTATCATATA
1 GAAACCTGAATTT-TTAGGTT
*
2038734 GAAACATGAATTTTTAGGTT
1 GAAACCTGAATTTTTAGGTT
*
2038754 GCAACCTGA
1 GAAACCTGA
2038763 TTTATCATAT
Statistics
Matches: 36, Mismatches: 11, Indels: 4
0.71 0.22 0.08
Matches are distributed among these distances:
19 5 0.14
20 26 0.72
21 5 0.14
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (20 bp):
GAAACCTGAATTTTTAGGTT
Found at i:2038746 original size:21 final size:21
Alignment explanation
Indices: 2038682--2038780 Score: 62
Period size: 20 Copynumber: 4.9 Consensus size: 21
2038672 CTTCAACTTG
*
2038682 ATTTATCTTATAGAAACCTGA
1 ATTTATCATATAGAAACCTGA
* ** *
2038703 ATTT-TTAGGTTGAAACCT-A
1 ATTTATCATATAGAAACCTGA
*
2038722 ATTTATCATATAGAAACATGA
1 ATTTATCATATAGAAACCTGA
* ** * *
2038743 ATTT-TTAGGTTGCAACCTG-
1 ATTTATCATATAGAAACCTGA
*
2038762 ATTTATCATATAAAAACCT
1 ATTTATCATATAGAAACCT
2038781 AGATTTTTAG
Statistics
Matches: 53, Mismatches: 22, Indels: 7
0.65 0.27 0.09
Matches are distributed among these distances:
19 9 0.17
20 35 0.66
21 9 0.17
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.38
Consensus pattern (21 bp):
ATTTATCATATAGAAACCTGA
Found at i:2038787 original size:80 final size:80
Alignment explanation
Indices: 2038665--2038960 Score: 263
Period size: 80 Copynumber: 3.8 Consensus size: 80
2038655 AAACCTAAAA
* * * *
2038665 TTTTAGGCTT-CAACTTGATTTATCTTATAGAAACCT-GAATTTTTAGGTTGAAACCTAATTTAT
1 TTTTAGG-TTGCAACCTGATTTATCATATAAAAACCTAG-ATTTTTAGGTTGAAACCTGATTTAT
2038728 CATATAGAAACATGAAT
64 CATATAGAAACATGAAT
* *
2038745 TTTTAGGTTGCAACCTGATTTATCATATAAAAACCTAGATTTTTAGGTTGCAACCTGATTTATCT
1 TTTTAGGTTGCAACCTGATTTATCATATAAAAACCTAGATTTTTAGGTTGAAACCTGATTTATCA
2038810 TATAGAAATC-T-AGAT
66 TATAGAAA-CATGA-AT
* * * * * * * * *
2038825 TTTTAGGTTACAATCTAATTGATCACATCAAAA-CTTGATTTTTA-GTTGCAACCTGATTTTTGC
1 TTTTAGGTTGCAACCTGATTTATCATATAAAAACCTAGATTTTTAGGTTGAAACCTGATTTAT-C
*
2038888 ATATAGAACCA-G-A-
65 ATATAGAAACATGAAT
* ** ** *
2038901 TTTTAGGTTGCAACCTGATTTTTTTTATGGAAACC-AGA-TTTTAGGTTGGAAACCTTATTT
1 TTTTAGGTTGCAACCTGATTTATCATATAAAAACCTAGATTTTTAGGTT-GAAACCTGATTT
2038961 TTCTATAAAA
Statistics
Matches: 177, Mismatches: 29, Indels: 23
0.77 0.13 0.10
Matches are distributed among these distances:
75 5 0.03
76 28 0.16
77 12 0.07
78 17 0.10
79 21 0.12
80 92 0.52
81 2 0.01
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.41
Consensus pattern (80 bp):
TTTTAGGTTGCAACCTGATTTATCATATAAAAACCTAGATTTTTAGGTTGAAACCTGATTTATCA
TATAGAAACATGAAT
Found at i:2038883 original size:18 final size:18
Alignment explanation
Indices: 2038860--2038923 Score: 53
Period size: 18 Copynumber: 3.4 Consensus size: 18
2038850 CATCAAAACT
2038860 TGATTTTTAGTTGCAACC
1 TGATTTTTAGTTGCAACC
2038878 TGATTTTT-GCATATAG-AACC
1 TGATTTTTAG--T-T-GCAACC
*
2038898 AGA-TTTTAGGTTGCAACC
1 TGATTTTTA-GTTGCAACC
2038916 TGATTTTT
1 TGATTTTT
2038924 TTTATGGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 15
0.68 0.04 0.28
Matches are distributed among these distances:
17 2 0.06
18 15 0.42
19 10 0.28
20 7 0.19
21 2 0.06
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.44
Consensus pattern (18 bp):
TGATTTTTAGTTGCAACC
Found at i:2038950 original size:19 final size:19
Alignment explanation
Indices: 2038894--2038954 Score: 61
Period size: 20 Copynumber: 3.2 Consensus size: 19
2038884 TTGCATATAG
*
2038894 AACCAGATTTTAGGTT-GC
1 AACCAGATTTTAGGTTGGA
* ***
2038912 AACCTGATTTTTTTTATGGA
1 AACCAGATTTTAGGT-TGGA
2038932 AACCAGATTTTAGGTTGGA
1 AACCAGATTTTAGGTTGGA
2038951 AACC
1 AACC
2038955 TTATTTTTCT
Statistics
Matches: 32, Mismatches: 9, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
18 11 0.34
19 9 0.28
20 12 0.38
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.36
Consensus pattern (19 bp):
AACCAGATTTTAGGTTGGA
Found at i:2038976 original size:38 final size:36
Alignment explanation
Indices: 2038705--2038976 Score: 136
Period size: 40 Copynumber: 7.0 Consensus size: 36
2038695 AAACCTGAAT
* *
2038705 TTTTAGGTTGAAACCTAATTTATCATATAGAAA-CATGAA
1 TTTTAGGTTGAAACCTGATTTTTC-TATA-AAACCA-G-A
* *
2038744 TTTTTAGGTTGCAACCTGATTTATCATATAAAAACCTAGA
1 -TTTTAGGTTGAAACCTGATTTTTC-TAT-AAAACC-AGA
* * *
2038784 TTTTTAGGTTGCAACCTGATTTATCTTATAGAAATCTAGA
1 -TTTTAGGTTGAAACCTGATTTTTC-TATA-AAA-CCAGA
* * ** * **
2038824 TTTTTAGGTT-ACAATCTAATTGATCACATCAAAACTTGA
1 -TTTTAGGTTGA-AACCTGATTTTTC-TAT-AAAACCAGA
* *
2038863 TTTTTA-GTTGCAACCTGATTTTTGCATATAGAACCAGA
1 -TTTTAGGTTGAAACCTGATTTTT-C-TATAAAACCAGA
* * *
2038901 TTTTAGGTTGCAACCTGATTTTTTTTATGGAAACCAGA
1 TTTTAGGTTGAAACCTGA-TTTTTCTAT-AAAACCAGA
*
2038939 TTTTAGGTTGGAAACCTTATTTTTCTATAAAATCCAGA
1 TTTTAGGTT-GAAACCTGATTTTTCTATAAAA-CCAGA
2038977 GTTCCAGTTG
Statistics
Matches: 191, Mismatches: 27, Indels: 30
0.77 0.11 0.12
Matches are distributed among these distances:
37 11 0.06
38 58 0.30
39 27 0.14
40 89 0.47
41 5 0.03
42 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.40
Consensus pattern (36 bp):
TTTTAGGTTGAAACCTGATTTTTCTATAAAACCAGA
Found at i:2041748 original size:2 final size:2
Alignment explanation
Indices: 2041741--2041806 Score: 107
Period size: 2 Copynumber: 33.5 Consensus size: 2
2041731 ATTACACTCG
* *
2041741 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA TA TA GA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2041783 TA TA TA TA TA T- TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2041807 TATTTACACA
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
1 1 0.02
2 58 0.98
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2043474 original size:21 final size:22
Alignment explanation
Indices: 2043436--2043476 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2043426 ACAACTTTTT
*
2043436 TTTTTCTTTTTTTCTTCGAACA
1 TTTTTCTTTCTTTCTTCGAACA
2043458 TTTTTCTTTCTTT-TTCGAA
1 TTTTTCTTTCTTTCTTCGAA
2043477 TTTTTTTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.12, C:0.17, G:0.05, T:0.66
Consensus pattern (22 bp):
TTTTTCTTTCTTTCTTCGAACA
Found at i:2043482 original size:21 final size:22
Alignment explanation
Indices: 2043434--2043484 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
2043424 AAACAACTTT
*
2043434 TTTTTTTCTTTTTTTCTTCGAA
1 TTTTTTTCTTTCTTTCTTCGAA
**
2043456 CATTTTTCTTTCTTT-TTCGAA
1 TTTTTTTCTTTCTTTCTTCGAA
2043477 TTTTTTTC
1 TTTTTTTC
2043485 ATGGACCATG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.10, C:0.16, G:0.04, T:0.71
Consensus pattern (22 bp):
TTTTTTTCTTTCTTTCTTCGAA
Found at i:2044118 original size:20 final size:20
Alignment explanation
Indices: 2044090--2044140 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
2044080 TACACTGCAT
2044090 GAACCGATTCCTTATGATGG
1 GAACCGATTCCTTATGATGG
*
2044110 GAACTGATTCCTTATGATGG
1 GAACCGATTCCTTATGATGG
* *
2044130 GTATCGATTCC
1 GAACCGATTCC
2044141 CCCACACTCC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (20 bp):
GAACCGATTCCTTATGATGG
Found at i:2046392 original size:26 final size:26
Alignment explanation
Indices: 2046362--2046414 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
2046352 CTACACAAAT
2046362 GGATACCTAAGGGGACTAGGATTTTG
1 GGATACCTAAGGGGACTAGGATTTTG
2046388 GGATACCTAAGGGGACTAGGATTTTG
1 GGATACCTAAGGGGACTAGGATTTTG
2046414 G
1 G
2046415 AAACTAATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.26, C:0.11, G:0.36, T:0.26
Consensus pattern (26 bp):
GGATACCTAAGGGGACTAGGATTTTG
Found at i:2049879 original size:22 final size:22
Alignment explanation
Indices: 2049849--2049908 Score: 75
Period size: 23 Copynumber: 2.7 Consensus size: 22
2049839 TAGTGCAGGA
* *
2049849 GGAATCGATACCCCCTTGAAGG
1 GGAACCGATTCCCCCTTGAAGG
*
2049871 GGAACCGATTCCCCTTTTGAAGG
1 GGAACCGATTCCCC-CTTGAAGG
*
2049894 GGAACCTATTCCCCC
1 GGAACCGATTCCCCC
2049909 CGGGGGAATC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 12 0.38
23 20 0.62
ACGTcount: A:0.23, C:0.32, G:0.23, T:0.22
Consensus pattern (22 bp):
GGAACCGATTCCCCCTTGAAGG
Found at i:2049894 original size:23 final size:23
Alignment explanation
Indices: 2049864--2049907 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
2049854 CGATACCCCC
2049864 TTGAAGGGGAACCGATTCCCCTT
1 TTGAAGGGGAACCGATTCCCCTT
*
2049887 TTGAAGGGGAACCTATTCCCC
1 TTGAAGGGGAACCGATTCCCC
2049908 CCGGGGGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.23, C:0.27, G:0.25, T:0.25
Consensus pattern (23 bp):
TTGAAGGGGAACCGATTCCCCTT
Found at i:2050671 original size:21 final size:21
Alignment explanation
Indices: 2050647--2050693 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
2050637 AACAAATTCT
*
2050647 TAATCCCAATCCCGATGATCC
1 TAATACCAATCCCGATGATCC
2050668 TAATACCAATCCCGATGATCC
1 TAATACCAATCCCGATGATCC
2050689 TAATA
1 TAATA
2050694 TGACCATTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.34, C:0.32, G:0.09, T:0.26
Consensus pattern (21 bp):
TAATACCAATCCCGATGATCC
Found at i:2052111 original size:20 final size:21
Alignment explanation
Indices: 2052065--2052111 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
2052055 GGGAGGGGAG
*
2052065 TAATTTCAAAACTTAAGTTTT
1 TAATTTCAAAACATAAGTTTT
*
2052086 TTATTTCAAAA-ATAA-TTTT
1 TAATTTCAAAACATAAGTTTT
2052105 TCAATTT
1 T-AATTT
2052112 AGAAAATCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 5 0.23
20 7 0.32
21 10 0.45
ACGTcount: A:0.38, C:0.09, G:0.02, T:0.51
Consensus pattern (21 bp):
TAATTTCAAAACATAAGTTTT
Found at i:2054022 original size:102 final size:102
Alignment explanation
Indices: 2053901--2054104 Score: 408
Period size: 102 Copynumber: 2.0 Consensus size: 102
2053891 TACTGAGGAC
2053901 TCCTACTATCGGGAATAAAATTGCAAGGGTCTGCCGATGGCGAATGAACATCGGGACCGGTGGAG
1 TCCTACTATCGGGAATAAAATTGCAAGGGTCTGCCGATGGCGAATGAACATCGGGACCGGTGGAG
2053966 GGAGCGAAGAACGAGATCAATTATCTATGCTAGTCTA
66 GGAGCGAAGAACGAGATCAATTATCTATGCTAGTCTA
2054003 TCCTACTATCGGGAATAAAATTGCAAGGGTCTGCCGATGGCGAATGAACATCGGGACCGGTGGAG
1 TCCTACTATCGGGAATAAAATTGCAAGGGTCTGCCGATGGCGAATGAACATCGGGACCGGTGGAG
2054068 GGAGCGAAGAACGAGATCAATTATCTATGCTAGTCTA
66 GGAGCGAAGAACGAGATCAATTATCTATGCTAGTCTA
2054105 GACTAAAAAT
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
102 102 1.00
ACGTcount: A:0.30, C:0.19, G:0.29, T:0.22
Consensus pattern (102 bp):
TCCTACTATCGGGAATAAAATTGCAAGGGTCTGCCGATGGCGAATGAACATCGGGACCGGTGGAG
GGAGCGAAGAACGAGATCAATTATCTATGCTAGTCTA
Found at i:2055720 original size:16 final size:16
Alignment explanation
Indices: 2055677--2055724 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
2055667 GACAAAAGAA
*
2055677 AACCA-AACCGAAAGT
1 AACCAGAACCGAAAGC
* *
2055692 AACCATAATCGAAAGC
1 AACCAGAACCGAAAGC
*
2055708 AACTAGAACCGAAAGC
1 AACCAGAACCGAAAGC
2055724 A
1 A
2055725 GTCTGAATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
15 5 0.19
16 22 0.81
ACGTcount: A:0.52, C:0.25, G:0.15, T:0.08
Consensus pattern (16 bp):
AACCAGAACCGAAAGC
Found at i:2056436 original size:31 final size:32
Alignment explanation
Indices: 2056390--2056450 Score: 97
Period size: 31 Copynumber: 1.9 Consensus size: 32
2056380 ACTAAACCTG
*
2056390 AACCAAATCTAATCTGACCTGAACTGAATCTA
1 AACCAAATCTAATCTGACCTGAAATGAATCTA
*
2056422 AACCAAA-GTAATCTGACCTGAAATGAATC
1 AACCAAATCTAATCTGACCTGAAATGAATC
2056451 GAACTGAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 20 0.74
32 7 0.26
ACGTcount: A:0.43, C:0.23, G:0.11, T:0.23
Consensus pattern (32 bp):
AACCAAATCTAATCTGACCTGAAATGAATCTA
Found at i:2059866 original size:56 final size:56
Alignment explanation
Indices: 2059802--2059930 Score: 222
Period size: 56 Copynumber: 2.3 Consensus size: 56
2059792 CTATATCCAA
* *
2059802 TTTTGGGCACCTATAGCAAAACAAGCAATTTCTTAATTTTTGTCGACTAGAGCCAG
1 TTTTGGGCACCTCTAGCAAAACAAGCAATTTCTTAATTTTTGTCGAATAGAGCCAG
*
2059858 TTTTGGGCACCTCTAGCAAAGCAAGCAATTTCTTAATTTTTGTCGAATAGAGCCAG
1 TTTTGGGCACCTCTAGCAAAACAAGCAATTTCTTAATTTTTGTCGAATAGAGCCAG
*
2059914 TTTCGGGCACCTCTAGC
1 TTTTGGGCACCTCTAGC
2059931 GATTCTTGAA
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 69 1.00
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (56 bp):
TTTTGGGCACCTCTAGCAAAACAAGCAATTTCTTAATTTTTGTCGAATAGAGCCAG
Found at i:2060019 original size:47 final size:47
Alignment explanation
Indices: 2059905--2060022 Score: 112
Period size: 47 Copynumber: 2.5 Consensus size: 47
2059895 TTTTGTCGAA
* * * * * *
2059905 TAGAGCCAGTTTCGGGCACCTCTAGCGATTCTTGAATGAGTAGCAAC
1 TAGAGCAAGTTTCGAGCACCTCTAACAATTCATGAATGAGTAACAAC
** * * * *
2059952 TAGAGCTTG-TTCCAGACACCTCTAATAATTCATGAATGTGTAATAAC
1 TAGAGCAAGTTTCGAG-CACCTCTAACAATTCATGAATGAGTAACAAC
2059999 TAGAGCAAGTTTCGAGCACCTCTA
1 TAGAGCAAGTTTCGAGCACCTCTA
2060023 GCATGCAATT
Statistics
Matches: 55, Mismatches: 14, Indels: 4
0.75 0.19 0.05
Matches are distributed among these distances:
46 4 0.07
47 46 0.84
48 5 0.09
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (47 bp):
TAGAGCAAGTTTCGAGCACCTCTAACAATTCATGAATGAGTAACAAC
Found at i:2061596 original size:22 final size:22
Alignment explanation
Indices: 2061557--2061618 Score: 56
Period size: 22 Copynumber: 2.8 Consensus size: 22
2061547 AATTGAACTT
*
2061557 CAAAAAT-AAAATCCAAAGAAAA
1 CAAAAATAAAAAT-AAAAGAAAA
*
2061579 CAAAAATAAAAATAAAAGGAAA
1 CAAAAATAAAAATAAAAGAAAA
* *
2061601 -AAAATTCAACAATAAAAG
1 CAAAAAT-AAAAATAAAAG
2061619 TACTGAATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
21 5 0.15
22 24 0.71
23 5 0.15
ACGTcount: A:0.73, C:0.10, G:0.06, T:0.11
Consensus pattern (22 bp):
CAAAAATAAAAATAAAAGAAAA
Found at i:2071595 original size:20 final size:22
Alignment explanation
Indices: 2071547--2071596 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
2071537 ATAGAATTAC
* *
2071547 TGACATGACATTTTTTTCAATGA
1 TGACATGACATTATCTT-AATGA
2071570 TGACATGACATTATCTT-ATG-
1 TGACATGACATTATCTTAATGA
2071590 TGACATG
1 TGACATG
2071597 TAATCATCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 7 0.28
21 3 0.12
23 15 0.60
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (22 bp):
TGACATGACATTATCTTAATGA
Found at i:2074352 original size:17 final size:18
Alignment explanation
Indices: 2074332--2074365 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2074322 TTATTAATTC
*
2074332 AACTAGTTCAT-TATTTA
1 AACTAGCTCATGTATTTA
2074349 AACTAGCTCATGTATTT
1 AACTAGCTCATGTATTT
2074366 TTTCATGACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.32, C:0.15, G:0.09, T:0.44
Consensus pattern (18 bp):
AACTAGCTCATGTATTTA
Found at i:2074853 original size:244 final size:245
Alignment explanation
Indices: 2074424--2074915 Score: 977
Period size: 244 Copynumber: 2.0 Consensus size: 245
2074414 TTTTTGTGTC
2074424 TGGTGCATAAGGGAAGTTGAATGGTCTCGATAGATGTAAGAATTTCAGCCAGTTTGTTTTCAATT
1 TGGTGCATAAGGGAAGTTGAATGGTCTCGATAGATGTAAGAATTTCAGCCAGTTTGTTTTCAATT
2074489 TATGGATACGATACATATGTTTTTGGGTCCTGAAATCAACTAGATATTATTCCTCCATCTCTTAG
66 TATGGATACGATACATATGTTTTTGGGTCCTGAAATCAACTAGATATTATTCCTCCATCTCTTAG
2074554 CTTTCAAACGCTTTTGAATCACCTCAATACGATATTGGGAGCTTGGATATAAATGATTTACCGAA
131 CTTTCAAACGCTTTTGAATCACCTCAATACGATATTGGGAGCTTGGATATAAATGATTTACCGAA
2074619 GACAGTGCACGCTAAAATTTTCATTACGGAAA-TTTAAGCATGGATGATT
196 GACAGTGCACGCTAAAATTTTCATTACGGAAATTTTAAGCATGGATGATT
2074668 TGGTGCATAAGGGAAGTTGAATGGTCTCGATAGATGTAAGAATTTCAGCCAGTTTGTTTTCAATT
1 TGGTGCATAAGGGAAGTTGAATGGTCTCGATAGATGTAAGAATTTCAGCCAGTTTGTTTTCAATT
2074733 TATGGATACGATACATATGTTTTTGGGTCCTGAAATCAACTAGATATTATTCCTCCATCTCTTAG
66 TATGGATACGATACATATGTTTTTGGGTCCTGAAATCAACTAGATATTATTCCTCCATCTCTTAG
2074798 CTTTCAAACGCTTTTGAATCACCTCAATACGATATTGGGAGCTTGGATATAAATGATTTACCGAA
131 CTTTCAAACGCTTTTGAATCACCTCAATACGATATTGGGAGCTTGGATATAAATGATTTACCGAA
2074863 GACAGTGCACGCTAAAATTTTCATTACGGAAATTTTAAGCATGGATGATT
196 GACAGTGCACGCTAAAATTTTCATTACGGAAATTTTAAGCATGGATGATT
2074913 TGG
1 TGG
2074916 ATTAAATTTG
Statistics
Matches: 247, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
244 227 0.92
245 20 0.08
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (245 bp):
TGGTGCATAAGGGAAGTTGAATGGTCTCGATAGATGTAAGAATTTCAGCCAGTTTGTTTTCAATT
TATGGATACGATACATATGTTTTTGGGTCCTGAAATCAACTAGATATTATTCCTCCATCTCTTAG
CTTTCAAACGCTTTTGAATCACCTCAATACGATATTGGGAGCTTGGATATAAATGATTTACCGAA
GACAGTGCACGCTAAAATTTTCATTACGGAAATTTTAAGCATGGATGATT
Found at i:2076616 original size:5 final size:5
Alignment explanation
Indices: 2076606--2076635 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
2076596 AAACTTTAGT
2076606 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
2076636 GTACTCCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:2076759 original size:31 final size:31
Alignment explanation
Indices: 2076685--2076744 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
2076675 ATAAAACTCT
***
2076685 TTAGGTACTAAAACAAACTAAAATTGGTAGA
1 TTAGGTACTAAAACAAACTAAAATAAATAGA
*
2076716 TTAGGTATTAAAACAAACTAAAATAAATA
1 TTAGGTACTAAAACAAACTAAAATAAATA
2076745 TTTTGAGTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.53, C:0.08, G:0.12, T:0.27
Consensus pattern (31 bp):
TTAGGTACTAAAACAAACTAAAATAAATAGA
Found at i:2077754 original size:13 final size:13
Alignment explanation
Indices: 2077736--2077762 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2077726 CTTGAACTAA
2077736 CCCGTTGGTAGTG
1 CCCGTTGGTAGTG
2077749 CCCGTTGGTAGTG
1 CCCGTTGGTAGTG
2077762 C
1 C
2077763 TTTGATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.26, G:0.37, T:0.30
Consensus pattern (13 bp):
CCCGTTGGTAGTG
Found at i:2077786 original size:2 final size:2
Alignment explanation
Indices: 2077781--2077824 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
2077771 ATTTTAACAT
2077781 TA TA TA TA TA TA TA TA TA TA TA -A TA -A 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
2077821 TA TA
1 TA TA
2077825 AACTAACTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2082228 original size:17 final size:18
Alignment explanation
Indices: 2082206--2082243 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
2082196 CCCAAACATG
*
2082206 CCTCTCC-TAATTTCCCT
1 CCTCTCCATAATTACCCT
*
2082223 CCTCTCCATCATTACCCT
1 CCTCTCCATAATTACCCT
2082241 CCT
1 CCT
2082244 GGTCATAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.13, C:0.50, G:0.00, T:0.37
Consensus pattern (18 bp):
CCTCTCCATAATTACCCT
Found at i:2091628 original size:18 final size:19
Alignment explanation
Indices: 2091605--2091641 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2091595 AAAACTAGGC
2091605 AACA-TTCATAGGATATTA
1 AACATTTCATAGGATATTA
*
2091623 AACATTTCATATGATATTA
1 AACATTTCATAGGATATTA
2091642 TTAAATAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.43, C:0.11, G:0.08, T:0.38
Consensus pattern (19 bp):
AACATTTCATAGGATATTA
Found at i:2092464 original size:17 final size:17
Alignment explanation
Indices: 2092424--2092466 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
2092414 TTTAAGCATA
* *
2092424 TAGTTCATTTAGTTATG
1 TAGTTCATTTAATTAAG
* *
2092441 CACTTCATTTAATTAAG
1 TAGTTCATTTAATTAAG
2092458 TAGTTCATT
1 TAGTTCATT
2092467 GTGCATATGA
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.49
Consensus pattern (17 bp):
TAGTTCATTTAATTAAG
Found at i:2092520 original size:17 final size:17
Alignment explanation
Indices: 2092498--2092533 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
2092488 AAGTTGGTTT
2092498 ATTAATTAAACTAGTTC
1 ATTAATTAAACTAGTTC
2092515 ATTAATTAAACTAGTTC
1 ATTAATTAAACTAGTTC
2092532 AT
1 AT
2092534 GTATTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.11, G:0.06, T:0.42
Consensus pattern (17 bp):
ATTAATTAAACTAGTTC
Found at i:2094338 original size:24 final size:24
Alignment explanation
Indices: 2094285--2094331 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
2094275 AATATGTTAT
2094285 ACTTGAAGTTCCAAAAGATGTGTC
1 ACTTGAAGTTCCAAAAGATGTGTC
* **
2094309 AGTTGAAGTTCCAAGTGATGTGT
1 ACTTGAAGTTCCAAAAGATGTGT
2094332 TCCTTGATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.30, C:0.13, G:0.26, T:0.32
Consensus pattern (24 bp):
ACTTGAAGTTCCAAAAGATGTGTC
Found at i:2095451 original size:17 final size:17
Alignment explanation
Indices: 2095429--2095478 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
2095419 ATAAAGTTGG
2095429 TTTATTAATTAAACTAA
1 TTTATTAATTAAACTAA
* *
2095446 TTTATTCATTAAACTAG
1 TTTATTAATTAAACTAA
* *
2095463 TTCAATAATTAAACTA
1 TTTATTAATTAAACTA
2095479 TCTCATTTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (17 bp):
TTTATTAATTAAACTAA
Found at i:2096603 original size:22 final size:21
Alignment explanation
Indices: 2096560--2096604 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
2096550 TCAGGTTAGT
*
2096560 GAAAAAAGGAAAAAATTAAAA
1 GAAAAAAAGAAAAAATTAAAA
* *
2096581 GAAAAAAAGAGAAAAGTTTAAA
1 GAAAAAAAGA-AAAAATTAAAA
2096603 GA
1 GA
2096605 GGGAGGGGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.71, C:0.00, G:0.18, T:0.11
Consensus pattern (21 bp):
GAAAAAAAGAAAAAATTAAAA
Found at i:2107884 original size:22 final size:22
Alignment explanation
Indices: 2107856--2107899 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2107846 AGATAACATT
2107856 GGAGCTCCATTGTAAACTTTCA
1 GGAGCTCCATTGTAAACTTTCA
*
2107878 GGAGCTCCATTTTAAACTTTCA
1 GGAGCTCCATTGTAAACTTTCA
2107900 TATACTGACC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (22 bp):
GGAGCTCCATTGTAAACTTTCA
Found at i:2119266 original size:24 final size:24
Alignment explanation
Indices: 2119239--2119323 Score: 111
Period size: 24 Copynumber: 3.5 Consensus size: 24
2119229 TTTGAAATTT
2119239 TTTTTCTCTTTTTCTCTTTTTCTC
1 TTTTTCTCTTTTTCTCTTTTTCTC
2119263 TTTTTCTCTTTTTCTCTTTTTCTC
1 TTTTTCTCTTTTTCTCTTTTTCTC
* * *
2119287 TTTTTGC-CTTTTTCTTTTTCTTTTT
1 TTTTT-CTCTTTTTCTCTTT-TTCTC
2119312 TTTTTCT-TTTTT
1 TTTTTCTCTTTTT
2119324 ATTTTGTTTT
Statistics
Matches: 55, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
24 46 0.84
25 9 0.16
ACGTcount: A:0.00, C:0.20, G:0.01, T:0.79
Consensus pattern (24 bp):
TTTTTCTCTTTTTCTCTTTTTCTC
Found at i:2119323 original size:8 final size:8
Alignment explanation
Indices: 2119239--2119305 Score: 111
Period size: 8 Copynumber: 8.5 Consensus size: 8
2119229 TTTGAAATTT
2119239 TTTTTCTC
1 TTTTTCTC
2119247 TTTTTCTC
1 TTTTTCTC
2119255 TTTTTCTC
1 TTTTTCTC
2119263 TTTTTCTC
1 TTTTTCTC
2119271 TTTTTCTC
1 TTTTTCTC
2119279 TTTTTCTC
1 TTTTTCTC
2119287 TTTTTGC-C
1 TTTTT-CTC
2119295 TTTTTCT-
1 TTTTTCTC
2119302 TTTT
1 TTTT
2119306 CTTTTTTTTT
Statistics
Matches: 57, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
7 5 0.09
8 51 0.89
9 1 0.02
ACGTcount: A:0.00, C:0.22, G:0.01, T:0.76
Consensus pattern (8 bp):
TTTTTCTC
Found at i:2119328 original size:6 final size:6
Alignment explanation
Indices: 2119248--2119322 Score: 52
Period size: 6 Copynumber: 12.8 Consensus size: 6
2119238 TTTTTTCTCT
* * * *
2119248 TTTTCTC TTTTTC -TCTT- TTTCTC TTTTTC -TCTT- TTTCTC TTTTTGCC
1 TTTT-TC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT--C
2119295 TTTTTC TTTTTC TTTTT- TTTTTC TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
2119323 TATTTTGTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 15
0.70 0.11 0.20
Matches are distributed among these distances:
5 15 0.28
6 28 0.53
7 4 0.08
8 6 0.11
ACGTcount: A:0.00, C:0.20, G:0.01, T:0.79
Consensus pattern (6 bp):
TTTTTC
Found at i:2119328 original size:17 final size:18
Alignment explanation
Indices: 2119280--2119333 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 18
2119270 CTTTTTCTCT
2119280 TTTTCTCTTTTTGCCTTTTTC
1 TTTT-TCTTTTTG--TTTTTC
2119301 TTTTTCTTTTT-TTTTTC
1 TTTTTCTTTTTGTTTTTC
2119318 TTTTT-TATTTTGTTTT
1 TTTTTCT-TTTTGTTTT
2119334 AGATGAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
16 1 0.03
17 15 0.48
18 4 0.13
20 7 0.23
21 4 0.13
ACGTcount: A:0.02, C:0.13, G:0.04, T:0.81
Consensus pattern (18 bp):
TTTTTCTTTTTGTTTTTC
Found at i:2141060 original size:9 final size:9
Alignment explanation
Indices: 2141033--2141075 Score: 54
Period size: 9 Copynumber: 5.0 Consensus size: 9
2141023 GTCTTGTAAT
2141033 TATAATA-A
1 TATAATATA
2141041 TATAATA-A
1 TATAATATA
*
2141049 TATTATATA
1 TATAATATA
*
2141058 TATAATAAA
1 TATAATATA
2141067 TATAATATA
1 TATAATATA
2141076 AACATCACTC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
8 14 0.47
9 16 0.53
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
TATAATATA
Found at i:2141462 original size:35 final size:35
Alignment explanation
Indices: 2141393--2141464 Score: 85
Period size: 35 Copynumber: 2.1 Consensus size: 35
2141383 AAGAATCTGT
* * *
2141393 TTCACTACTCTTCTGTGAAGATCATATTTGATTAC
1 TTCACTACTCTTCCGTGAAGAGCATAATTGATTAC
2141428 TTCACTACTCTTCCGTGAAG-GC-TGAATTGAATTAC
1 TTCACTACTCTTCCGTGAAGAGCAT-AATTG-ATTAC
2141463 TT
1 TT
2141465 GAGAAGAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
33 1 0.03
34 5 0.16
35 26 0.81
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (35 bp):
TTCACTACTCTTCCGTGAAGAGCATAATTGATTAC
Found at i:2141617 original size:20 final size:20
Alignment explanation
Indices: 2141592--2141673 Score: 137
Period size: 20 Copynumber: 4.1 Consensus size: 20
2141582 ATACGGACAG
*
2141592 ATGACCCGAAGGATTTACAA
1 ATGACCCGAAGGTTTTACAA
*
2141612 ATGACCCAAAGGTTTTACAA
1 ATGACCCGAAGGTTTTACAA
*
2141632 ATGACCTGAAGGTTTTACAA
1 ATGACCCGAAGGTTTTACAA
2141652 ATGACCCGAAGGTTTTACAA
1 ATGACCCGAAGGTTTTACAA
2141672 AT
1 AT
2141674 TCGTGGGAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 57 1.00
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (20 bp):
ATGACCCGAAGGTTTTACAA
Found at i:2169677 original size:22 final size:22
Alignment explanation
Indices: 2169626--2169684 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
2169616 ACGTGATTCT
2169626 GACTATCGCATTGCGATTTTCC
1 GACTATCGCATTGCGATTTTCC
* * * *
2169648 AAAT-TCGCGTTGCGATTTTTC
1 GACTATCGCATTGCGATTTTCC
*
2169669 GACTATCGCAATGCGA
1 GACTATCGCATTGCGA
2169685 ATATGTAAAT
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
21 17 0.61
22 11 0.39
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (22 bp):
GACTATCGCATTGCGATTTTCC
Found at i:2169716 original size:20 final size:20
Alignment explanation
Indices: 2169669--2169806 Score: 143
Period size: 20 Copynumber: 6.9 Consensus size: 20
2169659 GCGATTTTTC
* *
2169669 GACTATCGCAATGCGAATAT
1 GACTATCGCAACGCGATTAT
* * *
2169689 GTA-AATCGCAATGCGAGTAT
1 G-ACTATCGCAACGCGATTAT
2169709 GACTATCGCAACGCGATTAT
1 GACTATCGCAACGCGATTAT
* *
2169729 GACTATCGCAACGAGATTCT
1 GACTATCGCAACGCGATTAT
* *
2169749 AACTATCGCAACGCGATTCT
1 GACTATCGCAACGCGATTAT
* **
2169769 GACTGTCGCAACGCGATGCT
1 GACTATCGCAACGCGATTAT
*
2169789 GACTATCGCAATGCGATT
1 GACTATCGCAACGCGATT
2169807 TTCAAAGCGC
Statistics
Matches: 101, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
19 1 0.01
20 99 0.98
21 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.25
Consensus pattern (20 bp):
GACTATCGCAACGCGATTAT
Found at i:2170006 original size:22 final size:22
Alignment explanation
Indices: 2169981--2170023 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2169971 GGTGACATCC
2169981 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
2170003 GTCCCCATCTCCGGCGAAATC
1 GTCCCCATCTCCGACGAAATC
2170024 CGTCTATCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.42, G:0.16, T:0.19
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:2170433 original size:19 final size:19
Alignment explanation
Indices: 2170411--2170452 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
2170401 AATCGCAATG
2170411 CGATTCT-AGTTTCGCGTTA
1 CGATTCTCA-TTTCGCGTTA
* *
2170430 CGATTTTCATTTCGCGTTG
1 CGATTCTCATTTCGCGTTA
2170449 CGAT
1 CGAT
2170453 AGTCAAATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 19 0.95
20 1 0.05
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.43
Consensus pattern (19 bp):
CGATTCTCATTTCGCGTTA
Found at i:2170529 original size:40 final size:39
Alignment explanation
Indices: 2170420--2170532 Score: 136
Period size: 40 Copynumber: 2.8 Consensus size: 39
2170410 GCGATTCTAG
*
2170420 TTTCGCGTTACGATTTTCATTTCGCGTTGCGATAGTCAA
1 TTTCGCGTTGCGATTTTCATTTCGCGTTGCGATAGTCAA
* ** * *
2170459 ATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATTTTC-ATTTCGCGTTGCGATAGTCAA
* *
2170499 TTTCGTGTTGCGATTTTCATTTTCGTGTTGCGAT
1 TTTCGCGTTGCGATTTTCA-TTTCGCGTTGCGAT
2170533 TTTAAGTTTC
Statistics
Matches: 60, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
39 15 0.25
40 45 0.75
ACGTcount: A:0.17, C:0.19, G:0.23, T:0.42
Consensus pattern (39 bp):
TTTCGCGTTGCGATTTTCATTTCGCGTTGCGATAGTCAA
Found at i:2170535 original size:20 final size:20
Alignment explanation
Indices: 2170420--2170532 Score: 120
Period size: 20 Copynumber: 5.7 Consensus size: 20
2170410 GCGATTCTAG
* **
2170420 TTTCGCGTTACGATTTTC-A
1 TTTCGCGTTGCGATAGTCAA
2170439 TTTCGCGTTGCGATAGTCAA
1 TTTCGCGTTGCGATAGTCAA
*
2170459 ATTCGCGTTGCGATAGTCAA
1 TTTCGCGTTGCGATAGTCAA
* *
2170479 ATTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAA
* ** *
2170499 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATAGTCAA
*
2170519 TTTCGTGTTGCGAT
1 TTTCGCGTTGCGAT
2170533 TTTAAGTTTC
Statistics
Matches: 84, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
19 15 0.18
20 69 0.82
ACGTcount: A:0.17, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAA
Found at i:2170542 original size:20 final size:20
Alignment explanation
Indices: 2170499--2170542 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
2170489 CGATAGTCAT
* *
2170499 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
2170519 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
2170539 TTTC
1 TTTC
2170543 ATAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:2172275 original size:18 final size:17
Alignment explanation
Indices: 2172252--2172301 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 17
2172242 TTTACTCGTA
2172252 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATT-ACC
2172270 ATTTCACTTAGATGTACC
1 ATTTCACTTAGAT-TACC
2172288 ATTTCACTTAGATT
1 ATTTCACTTAGATT
2172302 GCTTAGTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
17 1 0.03
18 29 0.94
19 1 0.03
ACGTcount: A:0.30, C:0.20, G:0.08, T:0.42
Consensus pattern (17 bp):
ATTTCACTTAGATTACC
Found at i:2172573 original size:20 final size:20
Alignment explanation
Indices: 2172519--2172574 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
2172509 GCGATTCTCT
**
2172519 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
*
2172539 CGCTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
2172559 CGTTGCGATAGTCATT
1 CGTTGCGATAGTCATT
2172575 CGTGTTGCGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.20, C:0.21, G:0.25, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:2172581 original size:18 final size:18
Alignment explanation
Indices: 2172519--2172585 Score: 80
Period size: 20 Copynumber: 3.5 Consensus size: 18
2172509 GCGATTCTCT
2172519 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTC--ATTCG
*
2172539 CGCTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCA--TTCG
2172559 CGTTGCGATAGTCATTCG
1 CGTTGCGATAGTCATTCG
*
2172577 TGTTGCGAT
1 CGTTGCGAT
2172586 TTTAAGTTTC
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
18 13 0.31
20 29 0.69
ACGTcount: A:0.18, C:0.21, G:0.27, T:0.34
Consensus pattern (18 bp):
CGTTGCGATAGTCATTCG
Found at i:2174802 original size:20 final size:20
Alignment explanation
Indices: 2174749--2174802 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
2174739 AGGTACACTT
* **
2174749 TCGCAACGCTAAACTCAAAA
1 TCGCAACGCGAAAGACAAAA
*
2174769 TCGCAATGCGAAAGACAAAA
1 TCGCAACGCGAAAGACAAAA
*
2174789 TTGCAACGCGAAAG
1 TCGCAACGCGAAAG
2174803 TCAATTCGCG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.44, C:0.24, G:0.19, T:0.13
Consensus pattern (20 bp):
TCGCAACGCGAAAGACAAAA
Found at i:2174871 original size:20 final size:20
Alignment explanation
Indices: 2174846--2175089 Score: 208
Period size: 20 Copynumber: 12.8 Consensus size: 20
2174836 CGATTTTCTG
* *
2174846 GTTGCGATAGTCAAATACCC
1 GTTGCGATAGTCAAATTCGC
*
2174866 GTTGCGATAATCAAATTCGC
1 GTTGCGATAGTCAAATTCGC
*
2174886 GTTGCGATACTCAAATTCGC
1 GTTGCGATAGTCAAATTCGC
* *
2174906 ATTGCGATAGTCAAA-TAGCC
1 GTTGCGATAGTCAAATTCG-C
*
2174926 ATTGCGATAGTCAAATTCGC
1 GTTGCGATAGTCAAATTCGC
**
2174946 GTTGCGATAAACAAATTCGC
1 GTTGCGATAGTCAAATTCGC
*
2174966 GTTGCGAT--T----TTTGC
1 GTTGCGATAGTCAAATTCGC
* *
2174980 GTTGCGATAGTCATATTCGT
1 GTTGCGATAGTCAAATTCGC
*
2175000 ATTGCGATAGTCAAATTCGC
1 GTTGCGATAGTCAAATTCGC
* *
2175020 GTTGCGAT--T----TTTGA
1 GTTGCGATAGTCAAATTCGC
* *
2175034 GTTGCGATAATCAAATTCTC
1 GTTGCGATAGTCAAATTCGC
* *
2175054 TTTGCGATAGTCAAATTCAC
1 GTTGCGATAGTCAAATTCGC
*
2175074 GTTGCGATATTCAAAT
1 GTTGCGATAGTCAAAT
2175090 GAATGTGTAA
Statistics
Matches: 181, Mismatches: 29, Indels: 28
0.76 0.12 0.12
Matches are distributed among these distances:
14 23 0.13
16 2 0.01
18 1 0.01
19 2 0.01
20 151 0.83
21 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.33
Consensus pattern (20 bp):
GTTGCGATAGTCAAATTCGC
Found at i:2175005 original size:54 final size:54
Alignment explanation
Indices: 2174927--2175081 Score: 213
Period size: 54 Copynumber: 2.9 Consensus size: 54
2174917 CAAATAGCCA
** ** *
2174927 TTGCGATAGTCAAATTCGCGTTGCGATAAACAAATTCGCGTTGCGATTTTTGCG
1 TTGCGATAGTCAAATTCGTATTGCGATAGTCAAATTCGCGTTGCGATTTTTGAG
*
2174981 TTGCGATAGTCATATTCGTATTGCGATAGTCAAATTCGCGTTGCGATTTTTGAG
1 TTGCGATAGTCAAATTCGTATTGCGATAGTCAAATTCGCGTTGCGATTTTTGAG
* * *
2175035 TTGCGATAATCAAATTC-TCTTTGCGATAGTCAAATTCACGTTGCGAT
1 TTGCGATAGTCAAATTCGT-ATTGCGATAGTCAAATTCGCGTTGCGAT
2175082 ATTCAAATGA
Statistics
Matches: 90, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
53 1 0.01
54 89 0.99
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (54 bp):
TTGCGATAGTCAAATTCGTATTGCGATAGTCAAATTCGCGTTGCGATTTTTGAG
Found at i:2175312 original size:140 final size:140
Alignment explanation
Indices: 2175060--2175329 Score: 504
Period size: 140 Copynumber: 1.9 Consensus size: 140
2175050 TCTCTTTGCG
2175060 ATAGTCAAATTCACGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCACGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
* * *
2175125 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAACAGTTTACACATAA
66 TAACAATGTTAAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
2175190 AATACACATA
131 AATACACATA
*
2175200 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCACGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
2175265 TAACAATGTTAAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAACAATGTTAAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
2175330 TACAACGTTT
Statistics
Matches: 126, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 126 1.00
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.29
Consensus pattern (140 bp):
ATAGTCAAATTCACGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
TAACAATGTTAAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:2175412 original size:18 final size:18
Alignment explanation
Indices: 2175389--2175423 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2175379 AAGTCGGTTG
*
2175389 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
2175407 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
2175424 GCCTTTTTCT
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):
TGATTGCGATTTTGATTT
Found at i:2177692 original size:24 final size:24
Alignment explanation
Indices: 2177665--2177718 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2177655 TTGAAACATC
*
2177665 ATCAAAATCTGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
2177689 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
2177713 ATCAAA
1 ATCAAA
2177719 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:2178597 original size:19 final size:20
Alignment explanation
Indices: 2178540--2178601 Score: 90
Period size: 20 Copynumber: 3.1 Consensus size: 20
2178530 AAATTCAGTG
* *
2178540 TTGCGACAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCA
2178560 TTGCGATAGTCAGAATCGCA
1 TTGCGATAGTCAGAATCGCA
*
2178580 TTGCGATAGT-ATAATCGCA
1 TTGCGATAGTCAGAATCGCA
2178599 TTG
1 TTG
2178602 TGATTTACAT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 11 0.28
20 28 0.72
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.27
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCA
Found at i:2178652 original size:21 final size:21
Alignment explanation
Indices: 2178628--2178667 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2178618 ATTGCGATAA
2178628 TTGGAAAATAGCAACGCGAAT
1 TTGGAAAATAGCAACGCGAAT
* *
2178649 TTGGAAAATCGCAATGCGA
1 TTGGAAAATAGCAACGCGA
2178668 TAGTCAGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.15, G:0.25, T:0.20
Consensus pattern (21 bp):
TTGGAAAATAGCAACGCGAAT
Found at i:2180250 original size:6 final size:6
Alignment explanation
Indices: 2180239--2180265 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2180229 GTCCGTCTCG
2180239 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
2180266 AATACGTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:2180393 original size:22 final size:22
Alignment explanation
Indices: 2180366--2180439 Score: 130
Period size: 22 Copynumber: 3.4 Consensus size: 22
2180356 AATTTGGAAA
*
2180366 ATCGCAACGACAACTGTAGACT
1 ATCGCAACAACAACTGTAGACT
*
2180388 ATCGCAACAATAACTGTAGACT
1 ATCGCAACAACAACTGTAGACT
2180410 ATCGCAACAACAACTGTAGACT
1 ATCGCAACAACAACTGTAGACT
2180432 ATCGCAAC
1 ATCGCAAC
2180440 GCGAAATGGA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.39, C:0.27, G:0.15, T:0.19
Consensus pattern (22 bp):
ATCGCAACAACAACTGTAGACT
Found at i:2180457 original size:20 final size:20
Alignment explanation
Indices: 2180432--2180487 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
2180422 ACTGTAGACT
*
2180432 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGAAAA
*
2180452 ATCGCAACACGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
2180472 ATCGCAACGCGAAATG
1 ATCGCAACGCGAAATG
2180488 CAACGCGAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.11
Consensus pattern (20 bp):
ATCGCAACGCGAAATGAAAA
Done.