Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A12
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: 102106374
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3186644 characters in sequence are not A, C, G, or T
File 6 of 311
Found at i:1597115 original size:16 final size:16
Alignment explanation
Indices: 1597094--1597128 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1597084 GCACTTTGAC
1597094 TAAAATTAATAGGCTG
1 TAAAATTAATAGGCTG
*
1597110 TAAAATTAATAGGTTG
1 TAAAATTAATAGGCTG
1597126 TAA
1 TAA
1597129 GACTTGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.46, C:0.03, G:0.17, T:0.34
Consensus pattern (16 bp):
TAAAATTAATAGGCTG
Found at i:1603870 original size:17 final size:17
Alignment explanation
Indices: 1603845--1603879 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1603835 TTAGTTCGAG
* *
1603845 ATATCAAAATTTTAAAA
1 ATATAAAAATTATAAAA
1603862 ATATAAAAATTATAAAA
1 ATATAAAAATTATAAAA
1603879 A
1 A
1603880 AATGACTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (17 bp):
ATATAAAAATTATAAAA
Found at i:1608123 original size:7 final size:7
Alignment explanation
Indices: 1608111--1608135 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1608101 TTGCGTTTCA
1608111 TTTTTAT
1 TTTTTAT
1608118 TTTTTAT
1 TTTTTAT
1608125 TTTTTAT
1 TTTTTAT
1608132 TTTT
1 TTTT
1608136 CATTCTTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTAT
Found at i:1608144 original size:14 final size:13
Alignment explanation
Indices: 1608106--1608144 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
1608096 TGGATTTGCG
1608106 TTTCATTTTTATT
1 TTTCATTTTTATT
*
1608119 TTTTATTTTTTATT
1 TTTCA-TTTTTATT
1608133 TTTCATTCTTTA
1 TTTCATT-TTTA
1608145 CTTCTCTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 6 0.27
14 16 0.73
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTCATTTTTATT
Found at i:1612693 original size:35 final size:35
Alignment explanation
Indices: 1612647--1612716 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
1612637 ACAATCGTTT
1612647 TTATTACAAAACGATTGTTGAAGGGAGAATAAAGA
1 TTATTACAAAACGATTGTTGAAGGGAGAATAAAGA
1612682 TTATTACAAAACGATTGTTGAAGGGAGAATAAAGA
1 TTATTACAAAACGATTGTTGAAGGGAGAATAAAGA
1612717 GAGAAGAAAG
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:0.46, C:0.06, G:0.23, T:0.26
Consensus pattern (35 bp):
TTATTACAAAACGATTGTTGAAGGGAGAATAAAGA
Found at i:1618765 original size:216 final size:216
Alignment explanation
Indices: 1618391--1619042 Score: 1214
Period size: 216 Copynumber: 3.0 Consensus size: 216
1618381 ACCAATAGAT
*
1618391 TAGAGACATCAGTTTAGGTTTCAAACATTTGATCTAAGCCATTTCATAAAATTATTTAAATTTAA
1 TAGAGACATCAGTTTAGGTTTCAGACATTTGATCTAAGCCATTTCATAAAATTATTTAAATTTAA
*
1618456 AGCTAATTTAGATTGGAAGGATAATAAAATGAATTATGCTCAACTTATACATCTATAACTAAATG
66 ACCTAATTTAGATTGGAAGGATAATAAAATGAATTATGCTCAACTTATACATCTATAACTAAATG
**
1618521 GCACAAAGTTAAAATATTAAGTCTTTTGGAAAACAGATGATAAATTAATTGTTTTATGACATGTT
131 GCACAAAGTTAAAATATTAAGTCTTTTGGAAAACAGATGATAAATTAATTGTTTTATGACATGGA
1618586 AAACAGATGACTCCTCTAAAC
196 AAACAGATGACTCCTCTAAAC
1618607 TAGAGACATCAGTTTAGGTTTCAGACATTTGATCTAAGCCATTTCATAAAATTATTTAAATTTAA
1 TAGAGACATCAGTTTAGGTTTCAGACATTTGATCTAAGCCATTTCATAAAATTATTTAAATTTAA
* *
1618672 ATCTAATTTAGATTGGAAGGATAATAAAATGAATTATGCTCAACTTATACATCTATAACTAGATG
66 ACCTAATTTAGATTGGAAGGATAATAAAATGAATTATGCTCAACTTATACATCTATAACTAAATG
* *
1618737 GCACAAAGTTAAAATATTAAGTCTTTTGGAAAACAGATGATAAACTAATTGTTTTATGATATGGA
131 GCACAAAGTTAAAATATTAAGTCTTTTGGAAAACAGATGATAAATTAATTGTTTTATGACATGGA
1618802 AAACAGATGACTCCTCTAAAC
196 AAACAGATGACTCCTCTAAAC
1618823 TAGAGACATCAGTTTAGGTTTCAGACATTTGATCTAAGCCATTTCATAAAATTATTTAAATTTAA
1 TAGAGACATCAGTTTAGGTTTCAGACATTTGATCTAAGCCATTTCATAAAATTATTTAAATTTAA
1618888 ACCTAATTTAGATTGGAAGGATAATAAAATGAATTATGCTCAACTTATACATCTATAACTAAATG
66 ACCTAATTTAGATTGGAAGGATAATAAAATGAATTATGCTCAACTTATACATCTATAACTAAATG
* *
1618953 GCACAAAGTTAAAATATCAAGTCTTTTGGAGAACAGATGATAAATTAATTGTTTTATGACATGGA
131 GCACAAAGTTAAAATATTAAGTCTTTTGGAAAACAGATGATAAATTAATTGTTTTATGACATGGA
1619018 AAACAGATGACTCCTCTAAAC
196 AAACAGATGACTCCTCTAAAC
1619039 TAGA
1 TAGA
1619043 TTAGGTTCAA
Statistics
Matches: 423, Mismatches: 13, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
216 423 1.00
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.34
Consensus pattern (216 bp):
TAGAGACATCAGTTTAGGTTTCAGACATTTGATCTAAGCCATTTCATAAAATTATTTAAATTTAA
ACCTAATTTAGATTGGAAGGATAATAAAATGAATTATGCTCAACTTATACATCTATAACTAAATG
GCACAAAGTTAAAATATTAAGTCTTTTGGAAAACAGATGATAAATTAATTGTTTTATGACATGGA
AAACAGATGACTCCTCTAAAC
Found at i:1620577 original size:166 final size:166
Alignment explanation
Indices: 1620388--1620723 Score: 645
Period size: 166 Copynumber: 2.0 Consensus size: 166
1620378 GAGCTTGAAT
1620388 TAACAATGTTTCATAAATCCAACTACCCTGACTACAAATCCACTCACAATGAAAGGATATCATAA
1 TAACAATGTTTCATAAATCCAACTACCCTGACTACAAATCCACTCACAATGAAAGGATATCATAA
1620453 TCAAAGAAAAATCATAACATGTGAGTTTGTGAGCATCTTGATTACCAAGCAGCAATGAAAAGTCA
66 TCAAAGAAAAATCATAACATGTGAGTTTGTGAGCATCTTGATTACCAAGCAGCAATGAAAAGTCA
1620518 TGTTCAGATAGATGAGTAAAGCTTTAGAATGATAAC
131 TGTTCAGATAGATGAGTAAAGCTTTAGAATGATAAC
1620554 TAACAATGTTTCATAAATCCAACTACCCTGACTACAAATCCACTCACAATGAAAGGATATCATAA
1 TAACAATGTTTCATAAATCCAACTACCCTGACTACAAATCCACTCACAATGAAAGGATATCATAA
* *
1620619 TCAAAGTAAAATCATAACATGTGAGTTTGTGAGCATCTTGATTACCAAGCAGCAATGAAGAGTCA
66 TCAAAGAAAAATCATAACATGTGAGTTTGTGAGCATCTTGATTACCAAGCAGCAATGAAAAGTCA
*
1620684 TGTTCAGATAGATGAGTAAAGCTTTGGAATGATAAC
131 TGTTCAGATAGATGAGTAAAGCTTTAGAATGATAAC
1620720 TAAC
1 TAAC
1620724 TCTTACACCC
Statistics
Matches: 167, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
166 167 1.00
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.26
Consensus pattern (166 bp):
TAACAATGTTTCATAAATCCAACTACCCTGACTACAAATCCACTCACAATGAAAGGATATCATAA
TCAAAGAAAAATCATAACATGTGAGTTTGTGAGCATCTTGATTACCAAGCAGCAATGAAAAGTCA
TGTTCAGATAGATGAGTAAAGCTTTAGAATGATAAC
Found at i:1620948 original size:205 final size:205
Alignment explanation
Indices: 1620554--1620955 Score: 599
Period size: 205 Copynumber: 2.0 Consensus size: 205
1620544 GAATGATAAC
* *
1620554 TAACAATGTTTCATAAATCCAACTACCCTGACTACAAATCCACTCACAATGAAAGGATATCATAA
1 TAACAATGTTTCATAAATCCAACTACCCTGACTACAAATCCACCCACAATGAAAAGATATCATAA
* * * * *
1620619 TCAAAGTAAAATCATAACATGTGAGTTTGTGAGCATCTTGATTACCAAGCAGCAATGAAGAGTCA
66 TCAAAGTAAAATCATAACATGCGAGTTTGGGAGAATCTTGAGTACCAAGCAGCAATGAAAAGTCA
** * * * *
1620684 TGTTCAGATAGATGAGTAAAGCTTTGGAATGATAACTAACTCTTACACCCAGACCTCGAACTAAG
131 CATTCAGATAGAAGAGTAAAGCTTTAGAATGATAACCAACTCTGACACCCAGACCTCGAACTAAG
1620749 AAACTTGAAT
196 AAACTTGAAT
1620759 TAACAATGTTTCATAAATCCAACTACCCTGACTACAAATCCACCCACAATGAAAAGATATCATAA
1 TAACAATGTTTCATAAATCCAACTACCCTGACTACAAATCCACCCACAATGAAAAGATATCATAA
* *
1620824 TCGAAGTAAAATCATAACATGCGAGTTTGGGAGAATCTTG-GTAGCCAAGCAGCTATGAAAAGTC
66 TCAAAGTAAAATCATAACATGCGAGTTTGGGAGAATCTTGAGTA-CCAAGCAGCAATGAAAAGTC
* * *** *
1620888 ACATTCAGATAGAAGAGTAATGCTTTAGAATGGTAACCAACTCTGACACTTGGGCCTCGAACTAA
130 ACATTCAGATAGAAGAGTAAAGCTTTAGAATGATAACCAACTCTGACACCCAGACCTCGAACTAA
1620953 GAA
195 GAA
1620956 GAAACTTATT
Statistics
Matches: 175, Mismatches: 21, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
204 2 0.01
205 173 0.99
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (205 bp):
TAACAATGTTTCATAAATCCAACTACCCTGACTACAAATCCACCCACAATGAAAAGATATCATAA
TCAAAGTAAAATCATAACATGCGAGTTTGGGAGAATCTTGAGTACCAAGCAGCAATGAAAAGTCA
CATTCAGATAGAAGAGTAAAGCTTTAGAATGATAACCAACTCTGACACCCAGACCTCGAACTAAG
AAACTTGAAT
Found at i:1627464 original size:11 final size:11
Alignment explanation
Indices: 1627448--1627472 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1627438 ATATGATATT
1627448 TTATTATTTTA
1 TTATTATTTTA
1627459 TTATTATTTTA
1 TTATTATTTTA
1627470 TTA
1 TTA
1627473 GTATATATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:1627712 original size:38 final size:38
Alignment explanation
Indices: 1627670--1627744 Score: 150
Period size: 38 Copynumber: 2.0 Consensus size: 38
1627660 CTATGGGGAG
1627670 TTAGAATATCAAATTGGATTCAAGGAATAGAAGCTGGT
1 TTAGAATATCAAATTGGATTCAAGGAATAGAAGCTGGT
1627708 TTAGAATATCAAATTGGATTCAAGGAATAGAAGCTGG
1 TTAGAATATCAAATTGGATTCAAGGAATAGAAGCTGG
1627745 AGGAGAGAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.40, C:0.08, G:0.24, T:0.28
Consensus pattern (38 bp):
TTAGAATATCAAATTGGATTCAAGGAATAGAAGCTGGT
Found at i:1628400 original size:18 final size:19
Alignment explanation
Indices: 1628367--1628402 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1628357 GTCAGACAAC
*
1628367 AGAATAGAAGTGAATTTAA
1 AGAATAGAACTGAATTTAA
1628386 AGAATA-AACTGAATTTA
1 AGAATAGAACTGAATTTA
1628403 TTGGCTAAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.53, C:0.03, G:0.17, T:0.28
Consensus pattern (19 bp):
AGAATAGAACTGAATTTAA
Found at i:1631153 original size:16 final size:17
Alignment explanation
Indices: 1631132--1631163 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1631122 CATTGGGTTG
1631132 AGAAAATT-ATTTAATT
1 AGAAAATTAATTTAATT
1631148 AGAAAATTAATTTAAT
1 AGAAAATTAATTTAAT
1631164 AAATAATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (17 bp):
AGAAAATTAATTTAATT
Found at i:1634706 original size:20 final size:19
Alignment explanation
Indices: 1634663--1634706 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
1634653 ATGGTTATAT
*
1634663 TTTTAATATTTAAAATATA
1 TTTTAATATTTAAAATAAA
* *
1634682 GTTTATATATTTAAATTAAA
1 TTTTA-ATATTTAAAATAAA
1634702 TTTTA
1 TTTTA
1634707 CAAACAATTA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (19 bp):
TTTTAATATTTAAAATAAA
Found at i:1640812 original size:33 final size:33
Alignment explanation
Indices: 1640770--1640835 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
1640760 AAAGGAGAAA
1640770 GACGCATATCACATGCATAGTATAAGCTTTGGT
1 GACGCATATCACATGCATAGTATAAGCTTTGGT
1640803 GACGCATATCACATGCATAGTATAAGCTTTGGT
1 GACGCATATCACATGCATAGTATAAGCTTTGGT
1640836 CCTTAAGAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.30
Consensus pattern (33 bp):
GACGCATATCACATGCATAGTATAAGCTTTGGT
Found at i:1648387 original size:20 final size:21
Alignment explanation
Indices: 1648362--1648405 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
1648352 TATAAATATT
**
1648362 AATATTTATTAAATTATTA-A
1 AATATTTAAAAAATTATTATA
1648382 AATATTTAAAAAATTATTATA
1 AATATTTAAAAAATTATTATA
1648403 AAT
1 AAT
1648406 TGAAGTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AATATTTAAAAAATTATTATA
Found at i:1650735 original size:39 final size:39
Alignment explanation
Indices: 1650691--1650933 Score: 324
Period size: 39 Copynumber: 6.0 Consensus size: 39
1650681 ATTATATTAT
* * *
1650691 CAGCACAAAGCCTGCGGGACTTTAACCCGGATAAATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
* *
1650730 CAGCACGAAGCCTGCAGGACTTTGGCCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
*
1650769 CAGCACGAAGCCTGCGGGACTTTGGCCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
*
1650808 CAGCACGAAGCCTGCGGGACTTTAGTCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
*
1650847 CATATATTTCCTGCACGAAGCCTGTGGGACTTTAGCCCGGATACATTTC
1 C----A------GCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
1650896 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
1650934 TCAGTGTCTT
Statistics
Matches: 183, Mismatches: 11, Indels: 20
0.86 0.05 0.09
Matches are distributed among these distances:
39 145 0.79
43 1 0.01
45 1 0.01
49 36 0.20
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.23
Consensus pattern (39 bp):
CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
Found at i:1650913 original size:88 final size:88
Alignment explanation
Indices: 1650764--1650933 Score: 304
Period size: 88 Copynumber: 1.9 Consensus size: 88
1650754 GCCCGGATAC
*
1650764 ATTTCCAGCACGAAGCCTGCGGGACTTTGGCCCGGATACATTTCCAGCACGAAGCCTGCGGGACT
1 ATTTCCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTCCAGCACGAAGCCTGCGGGACT
*
1650829 TTAGTCCGGATACATTTCCATAT
66 TTAGCCCGGATACATTTCCATAT
* *
1650852 ATTTCCTGCACGAAGCCTGTGGGACTTTAGCCCGGATACATTTCCAGCACGAAGCCTGCGGGACT
1 ATTTCCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTCCAGCACGAAGCCTGCGGGACT
1650917 TTAGCCCGGATACATTT
66 TTAGCCCGGATACATTT
1650934 TCAGTGTCTT
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
88 78 1.00
ACGTcount: A:0.22, C:0.28, G:0.24, T:0.25
Consensus pattern (88 bp):
ATTTCCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTCCAGCACGAAGCCTGCGGGACT
TTAGCCCGGATACATTTCCATAT
Found at i:1657507 original size:40 final size:40
Alignment explanation
Indices: 1657463--1657539 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
1657453 ACCAACACAA
* *
1657463 TTCCTACGGGTCTTTAAGCCTGGATATAATTCCAGCATAT
1 TTCCTACGGGTCTTTAAGCCCGGATACAATTCCAGCATAT
*
1657503 TTCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCA
1 TTCCTACGGGTCTTTAAGCCCGGATACAATTCCAGCA
1657540 CGAAGCTTGC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.31
Consensus pattern (40 bp):
TTCCTACGGGTCTTTAAGCCCGGATACAATTCCAGCATAT
Found at i:1657551 original size:40 final size:40
Alignment explanation
Indices: 1657469--1657723 Score: 193
Period size: 39 Copynumber: 6.5 Consensus size: 40
1657459 ACAATTCCTA
* * * * **
1657469 CGGGTCTTTAAGCCTGGATATAATTCCAGCA-TATTTCCTG
1 CGGGACTTTAAGCCCGGATACAATTCCAGCACGA-AGCCTG
* *
1657509 CGGGTCTTTAAGCCCGGATACAATTCCAGCACGAAGCTTG
1 CGGGACTTTAAGCCCGGATACAATTCCAGCACGAAGCCTG
* *
1657549 C-GGACCTTAAGTCCGGATACAATTCCAGCACGAAGCCTG
1 CGGGACTTTAAGCCCGGATACAATTCCAGCACGAAGCCTG
* * * * *
1657588 C-GGACCTTAAGTCAGGATACAATTCTAGCACAAAGCCTG
1 CGGGACTTTAAGCCCGGATACAATTCCAGCACGAAGCCTG
* ** *
1657627 CGGGACTTT-AGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTTAAGCCCGGATACAATTCCAGCACGAA-GCCTG
* * * ** *
1657667 CGGGGC-TTAA-CTCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTTAAGCCCGGATACAATTCCAGCACGAA-GCCTG
*
1657706 TGGGAC-TTAA-CCCGGATA
1 CGGGACTTTAAGCCCGGATA
1657724 TAACACCATT
Statistics
Matches: 184, Mismatches: 27, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
39 134 0.73
40 49 0.27
41 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (40 bp):
CGGGACTTTAAGCCCGGATACAATTCCAGCACGAAGCCTG
Found at i:1657837 original size:28 final size:28
Alignment explanation
Indices: 1657804--1657876 Score: 110
Period size: 28 Copynumber: 2.6 Consensus size: 28
1657794 ATTTAATCAT
*
1657804 TCAATATTTTGCACACTAAGTGTCATTC
1 TCAATATTTCGCACACTAAGTGTCATTC
* *
1657832 TCAATATCTCGCACATTAAGTGTCATTC
1 TCAATATTTCGCACACTAAGTGTCATTC
*
1657860 TCAATATTTCGTACACT
1 TCAATATTTCGCACACT
1657877 GAGTACCATA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.38
Consensus pattern (28 bp):
TCAATATTTCGCACACTAAGTGTCATTC
Found at i:1660909 original size:11 final size:11
Alignment explanation
Indices: 1660895--1660947 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
1660885 ATTATCATTT
1660895 TATTATTAAAA
1 TATTATTAAAA
*
1660906 TATTATAAAAA
1 TATTATTAAAA
* *
1660917 TATATAATTTAAT
1 TAT-T-ATTAAAA
*
1660930 TATTATTAATA
1 TATTATTAAAA
1660941 TATTATT
1 TATTATT
1660948 TAATTAAATA
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
11 24 0.73
12 2 0.06
13 7 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
TATTATTAAAA
Found at i:1660962 original size:22 final size:21
Alignment explanation
Indices: 1660913--1660963 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
1660903 AAATATTATA
*
1660913 AAAATATATAATTTAATTATT
1 AAAATATATAATTTAATTAAT
* *
1660934 ATTAATATATTATTTAATTAAAT
1 A-AAATATATAATTTAATT-AAT
1660957 AAAATAT
1 AAAATAT
1660964 TCAAAATATC
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
21 1 0.04
22 20 0.83
23 3 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
AAAATATATAATTTAATTAAT
Found at i:1663471 original size:24 final size:24
Alignment explanation
Indices: 1663439--1663486 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1663429 GGCCTTGCAG
1663439 CCCAAATATCAATACCTACAAATC
1 CCCAAATATCAATACCTACAAATC
1663463 CCCAAATATCAATACCTACAAATC
1 CCCAAATATCAATACCTACAAATC
1663487 AAGTACCGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.33, G:0.00, T:0.21
Consensus pattern (24 bp):
CCCAAATATCAATACCTACAAATC
Found at i:1664069 original size:24 final size:23
Alignment explanation
Indices: 1664029--1664083 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
1664019 ATTTTTAGAT
* *
1664029 TTTAATCATGAAAATA-TATATAA
1 TTTAATTATAAAAATATTAT-TAA
1664052 TTTAATTATAAAATATATTATTAA
1 TTTAATTATAAAA-ATATTATTAA
*
1664076 ATTAATTA
1 TTTAATTA
1664084 ATTATAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 11 0.41
24 13 0.48
25 3 0.11
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
TTTAATTATAAAAATATTATTAA
Found at i:1664087 original size:28 final size:26
Alignment explanation
Indices: 1664053--1664110 Score: 82
Period size: 25 Copynumber: 2.2 Consensus size: 26
1664043 TATATATAAT
1664053 TTAATTATAAAATATATTATTAAATT-AA
1 TTAATTAT-AAATATA--ATTAAATTAAA
1664081 TTAATTATAAATATAATTAAATTAAA
1 TTAATTATAAATATAATTAAATTAAA
1664107 TTAA
1 TTAA
1664111 AGTCAAATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
25 8 0.28
26 6 0.21
27 7 0.24
28 8 0.28
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
TTAATTATAAATATAATTAAATTAAA
Found at i:1664097 original size:16 final size:16
Alignment explanation
Indices: 1664046--1664100 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
1664036 ATGAAAATAT
1664046 ATATAATTTAATTATAA
1 ATATAA-TTAATTATAA
1664063 A-AT-A-T-ATTATTAA
1 ATATAATTAATTA-TAA
1664076 AT-TAATTAATTATAA
1 ATATAATTAATTATAA
1664091 ATATAATTAA
1 ATATAATTAA
1664101 ATTAAATTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 13
0.71 0.00 0.29
Matches are distributed among these distances:
12 4 0.12
13 6 0.19
14 1 0.03
15 7 0.22
16 13 0.41
17 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATATAATTAATTATAA
Found at i:1664226 original size:16 final size:16
Alignment explanation
Indices: 1664207--1664256 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
1664197 AAATAGATAT
1664207 TTATTATTTATCATTA
1 TTATTATTTATCATTA
*
1664223 TTATTATTCTATCA-AA
1 TTATTATT-TATCATTA
*
1664239 TTATAATTTAT-ATTA
1 TTATTATTTATCATTA
1664254 TTA
1 TTA
1664257 AATTATGATT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
14 1 0.03
15 7 0.24
16 16 0.55
17 5 0.17
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (16 bp):
TTATTATTTATCATTA
Found at i:1664270 original size:19 final size:20
Alignment explanation
Indices: 1664236--1664277 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
1664226 TTATTCTATC
1664236 AAATTATAATTTATATTATT
1 AAATTATAATTTATATTATT
*
1664256 AAATTATGA-TTATATTATT
1 AAATTATAATTTATATTATT
1664275 AAA
1 AAA
1664278 AAAATTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
AAATTATAATTTATATTATT
Found at i:1667086 original size:13 final size:13
Alignment explanation
Indices: 1667068--1667092 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1667058 TATAAAAATA
1667068 TATTTTTATATTT
1 TATTTTTATATTT
1667081 TATTTTTATATT
1 TATTTTTATATT
1667093 AAGTCATATT
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TATTTTTATATTT
Found at i:1668760 original size:8 final size:8
Alignment explanation
Indices: 1668746--1668776 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
1668736 TTTAAAGATT
1668746 ATATAAAA
1 ATATAAAA
*
1668754 TTATAAAA
1 ATATAAAA
1668762 ATATAAAA
1 ATATAAAA
1668770 ATATAAA
1 ATATAAA
1668777 GAAAATGCGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (8 bp):
ATATAAAA
Found at i:1675928 original size:23 final size:25
Alignment explanation
Indices: 1675902--1675948 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
1675892 TATCATTCAT
*
1675902 TTCATTATAT-CA-ATATTTTATGC
1 TTCATCATATCCATATATTTTATGC
*
1675925 TTCATCATTTCCATATATTTTATG
1 TTCATCATATCCATATATTTTATG
1675949 TATATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 2 0.10
25 10 0.50
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.53
Consensus pattern (25 bp):
TTCATCATATCCATATATTTTATGC
Found at i:1676269 original size:46 final size:46
Alignment explanation
Indices: 1676209--1676474 Score: 325
Period size: 46 Copynumber: 6.0 Consensus size: 46
1676199 TTTGACGTGA
* * * * * *
1676209 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
** * * *
1676255 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
* * *
1676301 TTCTATGGTATCTTTCAACCATGGTCTTACACATCTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1676347 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1676393 TGCCATGGTATCTTTCAACCATGGTCTT--ACA---C--A-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
1676431 TGCCATGGTATCTTTCAACCATAGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1676475 AGAGCACACT
Statistics
Matches: 193, Mismatches: 18, Indels: 18
0.84 0.08 0.08
Matches are distributed among these distances:
38 32 0.17
39 1 0.01
40 3 0.02
41 1 0.01
43 1 0.01
44 3 0.02
45 5 0.03
46 147 0.76
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:1676439 original size:38 final size:38
Alignment explanation
Indices: 1676388--1676463 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
1676378 CATTTCATAT
*
1676388 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATAGTCTTACACA
1676426 CAGGTTGCCATGGTATCTTTCAACCATAGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATAGTCTTACACA
1676464 TTTCATATCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (38 bp):
CAGGTTGCCATGGTATCTTTCAACCATAGTCTTACACA
Found at i:1680188 original size:46 final size:44
Alignment explanation
Indices: 1680085--1680192 Score: 137
Period size: 44 Copynumber: 2.4 Consensus size: 44
1680075 TGTCTTTGAC
** * *
1680085 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAATGCCATATATAAT
*
1680129 ATGGACTTACATGGCTCAATCCTGTCTCCAAAT-CCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCC-AATGCCATA--TATAAT
1680175 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
1680193 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
44 30 0.54
45 3 0.05
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAATGCCATATATAAT
Found at i:1685987 original size:41 final size:40
Alignment explanation
Indices: 1685925--1686189 Score: 372
Period size: 41 Copynumber: 6.6 Consensus size: 40
1685915 TATTCGGATG
* *
1685925 ATATTCGGGCTAAGACCCGAAGGCACTTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCA-TTTGTGCTAGTGACT
* *
1685966 ATATCCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACG
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
*
1686006 ATATCCGGGCTAAGACCCGAAGGCATTTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCA-TTTGTGCTAGTGACT
* *
1686047 ATATCCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACG
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
*
1686087 ATATCCGGGCTAAGACCCGAAGGCATTTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCA-TTTGTGCTAGTGACT
* *
1686128 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGATTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTA-GTGACT
* *
1686168 ATATCC-GGTTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
1686190 TACTTGGGTT
Statistics
Matches: 203, Mismatches: 18, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
39 14 0.07
40 90 0.44
41 99 0.49
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:1686175 original size:81 final size:81
Alignment explanation
Indices: 1685924--1686156 Score: 448
Period size: 81 Copynumber: 2.9 Consensus size: 81
1685914 TTATTCGGAT
* *
1685924 GATATTCGGGCTAAGACCCGAAGGCACTTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGG
1 GATATCCGGGCTAAGACCCGAAGGCATTTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGG
1685989 CATTTGCGCTAGTGAC
66 CATTTGCGCTAGTGAC
1686005 GATATCCGGGCTAAGACCCGAAGGCATTTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGG
1 GATATCCGGGCTAAGACCCGAAGGCATTTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGG
1686070 CATTTGCGCTAGTGAC
66 CATTTGCGCTAGTGAC
1686086 GATATCCGGGCTAAGACCCGAAGGCATTTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGG
1 GATATCCGGGCTAAGACCCGAAGGCATTTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGG
1686151 CATTTG
66 CATTTG
1686157 TGCGATTTGC
Statistics
Matches: 150, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 150 1.00
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
GATATCCGGGCTAAGACCCGAAGGCATTTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGG
CATTTGCGCTAGTGAC
Found at i:1694095 original size:40 final size:40
Alignment explanation
Indices: 1694009--1694313 Score: 407
Period size: 40 Copynumber: 7.6 Consensus size: 40
1693999 TATTCGGATG
*
1694009 ATATCCGGGCTAAGACCCGAAGGCACTTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCA-TTTGTGCTAGTGACT
* *
1694050 ATATCCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACG
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
1694090 ATATCCGGGCTAAGACCCGAAGGCATTTTGTGTTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCA-TTTGTGCTAGTGACT
* *
1694131 ATATCCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACG
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
*
1694171 ATATCCGGGCTAAGACCCGAAGGCATTTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCA-TTTGTGCTAGTGACT
* * *
1694212 ATATCCGGGCTAAGTTCCGAAGGCATTTGTGCGAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
** * *
1694252 ATATCCGGGCTAAGTCCTAAAGGCATTTGTGCGATTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTA-GTGACT
* *
1694292 ATATCC-GGTTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
1694314 TACTTGGGTT
Statistics
Matches: 234, Mismatches: 27, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
39 12 0.05
40 125 0.53
41 97 0.41
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:1694143 original size:81 final size:81
Alignment explanation
Indices: 1694008--1694313 Score: 456
Period size: 81 Copynumber: 3.8 Consensus size: 81
1693998 TTATTCGGAT
*
1694008 GATATCCGGGCTAAGACCCGAAGGCACTTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGG
1 GATATCCGGGCTAAGACCCGAAGGCATTTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGG
1694073 CATTTGCGCTAGTGAC
66 CATTTGCGCTAGTGAC
*
1694089 GATATCCGGGCTAAGACCCGAAGGCATTTTGTGTTAGTGACTATATCCGGGCTAAGTCCCGAAGG
1 GATATCCGGGCTAAGACCCGAAGGCATTTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGG
1694154 CATTTGCGCTAGTGAC
66 CATTTGCGCTAGTGAC
*
1694170 GATATCCGGGCTAAGACCCGAAGGCATTTTGTGCTAGTGACTATATCCGGGCTAAGTTCCGAAGG
1 GATATCCGGGCTAAGACCCGAAGGCATTTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGG
* * *
1694235 CATTTGTGCGAGTTAC
66 CATTTGCGCTAGTGAC
* * ** * * * *
1694251 TATATCCGGGCTAAGTCCTAAAGGCA-TTTGTGCGATTTG-CTATATCC-GGTTAAATCCCGAAG
1 GATATCCGGGCTAAGACCCGAAGGCATTTTGTGCTA-GTGACTATATCCGGGCTAAGTCCCGAAG
1694313 G
65 G
1694314 TACTTGGGTT
Statistics
Matches: 208, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
79 13 0.06
80 16 0.08
81 179 0.86
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.26
Consensus pattern (81 bp):
GATATCCGGGCTAAGACCCGAAGGCATTTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGG
CATTTGCGCTAGTGAC
Found at i:1696441 original size:58 final size:58
Alignment explanation
Indices: 1696356--1696511 Score: 185
Period size: 58 Copynumber: 2.7 Consensus size: 58
1696346 ATATATTATG
**
1696356 ATTTTTATT-AATTCATATTTTAATAATAATTATATTAAGAATGTTATTAAA-TTATACATT
1 ATTTTTATTAAATT-ATA-TTTAATAATAATTATATTAA-AA-AATATTAAATTTATACATT
* **
1696416 A-TTTTATTAAATTATATTTAATAATAATTATGTTAAAAAATATTAAATTTATTTATT
1 ATTTTTATTAAATTATATTTAATAATAATTATATTAAAAAATATTAAATTTATACATT
*
1696473 ATTTTTATTAAATTATATTCAATAATAATCT-TATTAAAA
1 ATTTTTATTAAATTATATTTAATAATAAT-TATATTAAAA
1696512 TTTAATAATA
Statistics
Matches: 85, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
56 7 0.08
57 10 0.12
58 52 0.61
59 11 0.13
60 5 0.06
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (58 bp):
ATTTTTATTAAATTATATTTAATAATAATTATATTAAAAAATATTAAATTTATACATT
Found at i:1696674 original size:16 final size:16
Alignment explanation
Indices: 1696655--1696698 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
1696645 TTGATTATAA
*
1696655 CTCTATTCCATTACAT
1 CTCTATTCCATTACAG
* *
1696671 CTCTTTTCTATTACAG
1 CTCTATTCCATTACAG
1696687 CTCTATTCCATT
1 CTCTATTCCATT
1696699 CCATTGTACC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.20, C:0.30, G:0.02, T:0.48
Consensus pattern (16 bp):
CTCTATTCCATTACAG
Found at i:1696730 original size:78 final size:78
Alignment explanation
Indices: 1696601--1696854 Score: 499
Period size: 78 Copynumber: 3.3 Consensus size: 78
1696591 AAAAGAATAT
1696601 TATTACAGCTCTATTCCATTCCATTGTACCAAACAATTGAATTATTGATTATAACTCTATTCCAT
1 TATTACAGCTCTATTCCATTCCATTGTACCAAACAATTGAATTATTGATTATAACTCTATTCCAT
1696666 TACATCTCTTTTC
66 TACATCTCTTTTC
1696679 TATTACAGCTCTATTCCATTCCATTGTACCAAACAATTGAATTATTGATTATAACTCTATTCCAT
1 TATTACAGCTCTATTCCATTCCATTGTACCAAACAATTGAATTATTGATTATAACTCTATTCCAT
1696744 TACATCTCTTTTC
66 TACATCTCTTTTC
1696757 TATTACAGCTCTATTCCATTCCATTGTACCAAACAATTGAATTATTGATTATAACTCTATTCCAT
1 TATTACAGCTCTATTCCATTCCATTGTACCAAACAATTGAATTATTGATTATAACTCTATTCCAT
*
1696822 TGCATCTCTTTTC
66 TACATCTCTTTTC
1696835 TATTACAGCTCTATTCCATT
1 TATTACAGCTCTATTCCATT
1696855 TACCACAATC
Statistics
Matches: 175, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 175 1.00
ACGTcount: A:0.29, C:0.23, G:0.06, T:0.43
Consensus pattern (78 bp):
TATTACAGCTCTATTCCATTCCATTGTACCAAACAATTGAATTATTGATTATAACTCTATTCCAT
TACATCTCTTTTC
Found at i:1696752 original size:16 final size:16
Alignment explanation
Indices: 1696733--1696776 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
1696723 TTGATTATAA
*
1696733 CTCTATTCCATTACAT
1 CTCTATTCCATTACAG
* *
1696749 CTCTTTTCTATTACAG
1 CTCTATTCCATTACAG
1696765 CTCTATTCCATT
1 CTCTATTCCATT
1696777 CCATTGTACC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.20, C:0.30, G:0.02, T:0.48
Consensus pattern (16 bp):
CTCTATTCCATTACAG
Found at i:1705591 original size:27 final size:25
Alignment explanation
Indices: 1705529--1705597 Score: 75
Period size: 25 Copynumber: 2.7 Consensus size: 25
1705519 GAGATAGAGT
* *
1705529 TGCTCACACGAGCTGTGAATATAAG
1 TGCTCACATGAGCTGTGAAAATAAG
* **
1705554 TGCTTACATGAGCTGTGAAAATTGG
1 TGCTCACATGAGCTGTGAAAATAAG
1705579 CCTGCTCACATGAGCTGTG
1 --TGCTCACATGAGCTGTG
1705598 GGTCACGATG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
25 20 0.56
27 16 0.44
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (25 bp):
TGCTCACATGAGCTGTGAAAATAAG
Found at i:1707839 original size:197 final size:197
Alignment explanation
Indices: 1707500--1707895 Score: 677
Period size: 197 Copynumber: 2.0 Consensus size: 197
1707490 CAAACATAAC
*
1707500 ATAAACACTTATGTCACACCCAAAAATGTTAAAAGAGAAGTACAACAGTAATTTTGGGTATCTAA
1 ATAAACACTTATGTCACACCCAAAAATGTTAAAAGAGAAGTACAACAGTAATTCTGGGTATCTAA
1707565 TTATAAAACTTCCTATTTATAAGGGTATTAGTGTAATTACGTGAATCTTGCTAACTGATTTGGTA
66 TTATAAAACTTCCTATTTATAAGGGTATTAGTGTAATTACGTGAATCTTGCTAACTGATTTGGTA
* * *
1707630 ATTGGCCAGATTTCAACTATTAGTTTCGTTACATTAGAACT-AGGTATTTGCTTTAGTGGGAAAT
131 ATTGGCCAGATTTCAACTATTAGTTTCGTTAAATTAGAACTGA-GCATTTACTTTAGTGGGAAAT
1707694 ATT
195 ATT
* *
1707697 ATAAACACTTATGTCACACCCAAAAATGTTAAAGGATAAGTACAACAGTAATTCTGGGTATCTAA
1 ATAAACACTTATGTCACACCCAAAAATGTTAAAAGAGAAGTACAACAGTAATTCTGGGTATCTAA
* * * *
1707762 TTATAAAACTTTCTGTTTATAAGGGTCTTAGTGTAATTATGTGAATCTTGCTAACTGATTTGGTA
66 TTATAAAACTTCCTATTTATAAGGGTATTAGTGTAATTACGTGAATCTTGCTAACTGATTTGGTA
*
1707827 ATTGGTCAGATTTCAACTATTAGTTTCGTTAAATTAGAACTGAGCATTTACTTTAGTGGGAAATA
131 ATTGGCCAGATTTCAACTATTAGTTTCGTTAAATTAGAACTGAGCATTTACTTTAGTGGGAAATA
1707892 TT
196 TT
1707894 AT
1 AT
1707896 GATAAAGAAC
Statistics
Matches: 187, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
197 186 0.99
198 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (197 bp):
ATAAACACTTATGTCACACCCAAAAATGTTAAAAGAGAAGTACAACAGTAATTCTGGGTATCTAA
TTATAAAACTTCCTATTTATAAGGGTATTAGTGTAATTACGTGAATCTTGCTAACTGATTTGGTA
ATTGGCCAGATTTCAACTATTAGTTTCGTTAAATTAGAACTGAGCATTTACTTTAGTGGGAAATA
TT
Found at i:1708795 original size:32 final size:32
Alignment explanation
Indices: 1708759--1708826 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
1708749 GTGTGGAGGT
* *
1708759 ATGTAATGGTGGATGGAAGTTGAAGAAATGTC
1 ATGTAATAGCGGATGGAAGTTGAAGAAATGTC
1708791 ATGTAATAGCGGATGGAAGTTGAAGAAATGTC
1 ATGTAATAGCGGATGGAAGTTGAAGAAATGTC
1708823 ATGT
1 ATGT
1708827 TGTGCACCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.35, C:0.04, G:0.32, T:0.28
Consensus pattern (32 bp):
ATGTAATAGCGGATGGAAGTTGAAGAAATGTC
Found at i:1711147 original size:17 final size:17
Alignment explanation
Indices: 1711119--1711153 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
1711109 TTCACTACAT
1711119 TTTTATTTCACATATTCA
1 TTTTATTTCACA-ATTCA
1711137 TTTTA-TTCACAATTCA
1 TTTTATTTCACAATTCA
1711153 T
1 T
1711154 AAATTACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 6 0.35
18 5 0.29
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTTATTTCACAATTCA
Found at i:1711908 original size:17 final size:17
Alignment explanation
Indices: 1711870--1711913 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
1711860 GAAAATTTTC
**
1711870 TTTCTTT-TTCTCTGTT
1 TTTCTTTCTTCTCTCCT
1711886 TCTTCTTTCTTCTCTCCT
1 T-TTCTTTCTTCTCTCCT
1711904 TTTCTTTCTT
1 TTTCTTTCTT
1711914 TTTTATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 1 0.04
17 15 0.62
18 8 0.33
ACGTcount: A:0.00, C:0.27, G:0.02, T:0.70
Consensus pattern (17 bp):
TTTCTTTCTTCTCTCCT
Found at i:1711912 original size:21 final size:18
Alignment explanation
Indices: 1711865--1711916 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
1711855 TTAGGGAAAA
1711865 TTTTCTTTCTTTTTCTCT
1 TTTTCTTTCTTTTTCTCT
*
1711883 GTTTC-TTCTTTCTTCTCT
1 TTTTCTTTCTTT-TTCTCT
1711901 CCTTTTCTTTCTTTTT
1 --TTTTCTTTCTTTTT
1711917 TATTTTTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
17 6 0.21
18 10 0.36
20 6 0.21
21 6 0.21
ACGTcount: A:0.00, C:0.25, G:0.02, T:0.73
Consensus pattern (18 bp):
TTTTCTTTCTTTTTCTCT
Found at i:1717698 original size:20 final size:20
Alignment explanation
Indices: 1717661--1717696 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 20
1717651 ATATTAATCG
1717661 AAATAAATAATATATTTTAT
1 AAATAAATAATATATTTTAT
1717681 AAAT-AAT-ATATATTTT
1 AAATAAATAATATATTTT
1717697 TTGAACTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.56
19 3 0.19
20 4 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AAATAAATAATATATTTTAT
Found at i:1718736 original size:3 final size:3
Alignment explanation
Indices: 1718728--1718753 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1718718 TCCACCCACA
1718728 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
1718754 ATAAGTGTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1721279 original size:27 final size:27
Alignment explanation
Indices: 1721241--1721296 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
1721231 ATAGTTCCAT
1721241 TTCTCAGAGTTTGATCTTACAGATAGA
1 TTCTCAGAGTTTGATCTTACAGATAGA
1721268 TTCTCAGAGTTTGATCTTACAGATAGA
1 TTCTCAGAGTTTGATCTTACAGATAGA
1721295 TT
1 TT
1721297 TAAATCTTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (27 bp):
TTCTCAGAGTTTGATCTTACAGATAGA
Found at i:1724161 original size:50 final size:46
Alignment explanation
Indices: 1724090--1724211 Score: 136
Period size: 46 Copynumber: 2.6 Consensus size: 46
1724080 TGTCTTCGAC
** * *
1724090 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATATATCTAAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCC----ATATATCTAAT
* * *
1724140 ATGGGCTTACATGGCTCATTCCTATCTCCAAAGCCATATATCTGAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCATATATCTAAT
*
1724186 ATGGACTTACATGGCTCATTTCTGTC
1 ATGGACTTACATGGCTCATTCCTGTC
1724212 CTGTCCTATC
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
46 33 0.53
50 29 0.47
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (46 bp):
ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCATATATCTAAT
Found at i:1728536 original size:46 final size:47
Alignment explanation
Indices: 1728430--1728551 Score: 147
Period size: 46 Copynumber: 2.6 Consensus size: 47
1728420 TGTCTTTGAC
** * *
1728430 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATATATCTAAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCC--A-ATATATCTAAT
* *
1728480 ATGGTCTTACATGGCTCATTCCTGTCTCCAAAGCC-ATATATCTGAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCAATATATCTAAT
*
1728526 ATGGACTTACATGGCTCATTTCTGTC
1 ATGGACTTACATGGCTCATTCCTGTC
1728552 CTATCATGTC
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
46 34 0.53
50 30 0.47
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (47 bp):
ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCAATATATCTAAT
Found at i:1739167 original size:13 final size:13
Alignment explanation
Indices: 1739136--1739161 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1739126 CAATTAAATC
1739136 AAATTTCTTTTTA
1 AAATTTCTTTTTA
1739149 AAATTTCTTTTTA
1 AAATTTCTTTTTA
1739162 TCATTTTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (13 bp):
AAATTTCTTTTTA
Found at i:1748757 original size:18 final size:19
Alignment explanation
Indices: 1748734--1748771 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
1748724 GTCTTTTACC
*
1748734 TTTATTTATTTATT-TTAT
1 TTTATTTATTAATTATTAT
1748752 TTTATTTATTAATTATTAT
1 TTTATTTATTAATTATTAT
1748771 T
1 T
1748772 AAATTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTATTTATTAATTATTAT
Found at i:1748799 original size:22 final size:22
Alignment explanation
Indices: 1748774--1748845 Score: 81
Period size: 22 Copynumber: 3.2 Consensus size: 22
1748764 TTATTATTAA
*
1748774 ATTTAAAAAATTTGAAATATAT
1 ATTTAAAAAATTTTAAATATAT
* *
1748796 ATTTGAAATATTTTATTAATATAT
1 ATTTAAAAAATTTTA--AATATAT
**
1748820 ATTTTTAAAATTTTAAATATAT
1 ATTTAAAAAATTTTAAATATAT
1748842 ATTT
1 ATTT
1748846 TGAAATTATT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
22 23 0.55
24 19 0.45
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (22 bp):
ATTTAAAAAATTTTAAATATAT
Found at i:1748821 original size:24 final size:25
Alignment explanation
Indices: 1748789--1748862 Score: 93
Period size: 24 Copynumber: 3.1 Consensus size: 25
1748779 AAAAATTTGA
1748789 AATATATA-TTTGAAATATTTTATT
1 AATATATATTTTGAAATATTTTATT
*
1748813 AATATATATTTTTAAA-ATTTTA--
1 AATATATATTTTGAAATATTTTATT
*
1748835 AATATATATTTTGAAATTATTTTTTT
1 AATATATATTTTGAAA-TATTTTATT
1748861 AA
1 AA
1748863 ATTTTAAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
22 15 0.36
24 19 0.45
25 6 0.14
26 2 0.05
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (25 bp):
AATATATATTTTGAAATATTTTATT
Found at i:1748866 original size:21 final size:20
Alignment explanation
Indices: 1748842--1748899 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 20
1748832 TTAAATATAT
1748842 ATTTTGAAATTATTTTTTTAA
1 ATTTT-AAATTATTTTTTTAA
1748863 ATTTTAAA-TATTATTTTTTAA
1 ATTTTAAATTA-T-TTTTTTAA
*
1748884 ATATTAAA-TATTTTTT
1 ATTTTAAATTATTTTTT
1748900 AATATTATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
19 7 0.21
20 5 0.15
21 22 0.65
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
ATTTTAAATTATTTTTTTAA
Found at i:1748912 original size:20 final size:19
Alignment explanation
Indices: 1748855--1748914 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
1748845 TTGAAATTAT
*
1748855 TTTTTTAAATTTTAAATATTA
1 TTTTTTAAATTATAAA-A-TA
*
1748876 TTTTTTAAA-TATTAAATA
1 TTTTTTAAATTATAAAATA
1748894 TTTTTTAATATTATAAAATA
1 TTTTTTAA-ATTATAAAATA
1748914 T
1 T
1748915 GTAAATATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 10 0.29
19 2 0.06
20 13 0.38
21 9 0.26
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTTTTAAATTATAAAATA
Found at i:1749137 original size:20 final size:18
Alignment explanation
Indices: 1749105--1749141 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 18
1749095 TAATAAAAAA
1749105 TTAAAAAATATTTATTTG
1 TTAAAAAATATTTATTTG
1749123 TTAAAAAATGAATTTATTT
1 TTAAAAAAT--ATTTATTT
1749142 AAAAATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
20 8 0.47
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (18 bp):
TTAAAAAATATTTATTTG
Found at i:1749158 original size:13 final size:13
Alignment explanation
Indices: 1749140--1749188 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
1749130 ATGAATTTAT
* *
1749140 TTAAAAATATATA
1 TTAAAAATAAAAA
1749153 TTAAAAATTAAAAA
1 TTAAAAA-TAAAAA
* *
1749167 TTGAAATTAAAAA
1 TTAAAAATAAAAA
1749180 TTAAAAATA
1 TTAAAAATA
1749189 TATAATATAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
13 20 0.69
14 9 0.31
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (13 bp):
TTAAAAATAAAAA
Found at i:1749164 original size:7 final size:7
Alignment explanation
Indices: 1749152--1749187 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
1749142 AAAAATATAT
1749152 ATTAAAA
1 ATTAAAA
1749159 ATTAAAA
1 ATTAAAA
*
1749166 ATT-GAA
1 ATTAAAA
1749172 ATTAAAA
1 ATTAAAA
1749179 ATTAAAA
1 ATTAAAA
1749186 AT
1 AT
1749188 ATATAATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 5 0.19
7 21 0.81
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (7 bp):
ATTAAAA
Found at i:1749165 original size:20 final size:20
Alignment explanation
Indices: 1749140--1749192 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
1749130 ATGAATTTAT
1749140 TTAAAAATATATATTAAAAA
1 TTAAAAATATATATTAAAAA
*
1749160 TTAAAAAT-TGAAATTAAAAA
1 TTAAAAATAT-ATATTAAAAA
1749180 TTAAAAATATATA
1 TTAAAAATATATA
1749193 ATATAACTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 1 0.03
20 27 0.93
21 1 0.03
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (20 bp):
TTAAAAATATATATTAAAAA
Found at i:1749237 original size:18 final size:17
Alignment explanation
Indices: 1749210--1749252 Score: 70
Period size: 18 Copynumber: 2.5 Consensus size: 17
1749200 TAGTCACATC
1749210 ATATTTTTTTAACAAAT
1 ATATTTTTTTAACAAAT
1749227 ATATATTTTTTAACAAAT
1 ATAT-TTTTTTAACAAAT
1749245 AT-TTTTTT
1 ATATTTTTT
1749253 ATTAATTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.20
17 5 0.20
18 15 0.60
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (17 bp):
ATATTTTTTTAACAAAT
Found at i:1749257 original size:18 final size:18
Alignment explanation
Indices: 1749213--1749257 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
1749203 TCACATCATA
1749213 TTTTTTTAACAAATATAT
1 TTTTTTTAACAAATATAT
*
1749231 ATTTTTTAACAAATAT-T
1 TTTTTTTAACAAATATAT
1749248 TTTTTATTAA
1 TTTTT-TTAA
1749258 TTCAAATTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 5 0.21
18 19 0.79
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTTTTTAACAAATATAT
Found at i:1749361 original size:24 final size:24
Alignment explanation
Indices: 1749306--1749371 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
1749296 TATCTTTTTC
* *
1749306 TTTAAATTTTTTCTTTTTTTAAGT
1 TTTATATTTTTTCTTATTTTAAGT
1749330 TTTATATTTTTTCTTATTTT-A-T
1 TTTATATTTTTTCTTATTTTAAGT
*
1749352 TTTATTTATTTTTTGTTATT
1 TTTA--TATTTTTTCTTATT
1749372 AATTTTGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
22 5 0.14
23 1 0.03
24 31 0.84
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.76
Consensus pattern (24 bp):
TTTATATTTTTTCTTATTTTAAGT
Found at i:1749415 original size:4 final size:4
Alignment explanation
Indices: 1749406--1749454 Score: 55
Period size: 4 Copynumber: 11.8 Consensus size: 4
1749396 ATTTGAAATG
*
1749406 TTTA TTTA TTTTA TTTA TTT- TTTC TTTA TCTTTA TTTA TTTA TTTA TTT
1 TTTA TTTA -TTTA TTTA TTTA TTTA TTTA --TTTA TTTA TTTA TTTA TTT
1749455 TTATTTTATT
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
3 3 0.08
4 29 0.73
5 4 0.10
6 4 0.10
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:1749457 original size:18 final size:17
Alignment explanation
Indices: 1749410--1749473 Score: 67
Period size: 18 Copynumber: 3.7 Consensus size: 17
1749400 GAAATGTTTA
*
1749410 TTTATTT-TATTTATTT
1 TTTATTTATTTTTATTT
* *
1749426 TTTCTTTATCTTTATTT
1 TTTATTTATTTTTATTT
1749443 ATTTATTTATTTTTATTT
1 -TTTATTTATTTTTATTT
*
1749461 TATTATTAATTTT
1 T-TTATTTATTTT
1749474 AAAAAACTTG
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
16 6 0.15
17 9 0.22
18 25 0.62
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTATTTATTTTTATTT
Found at i:1749467 original size:14 final size:15
Alignment explanation
Indices: 1749410--1749464 Score: 62
Period size: 15 Copynumber: 3.7 Consensus size: 15
1749400 GAAATGTTTA
1749410 TTTATTTTATTTATT
1 TTTATTTTATTTATT
*
1749425 TTT-TCTTTATCTT-TA
1 TTTAT-TTTAT-TTATT
1749440 TTTA-TTTATTTATT
1 TTTATTTTATTTATT
1749454 TTTATTTTATT
1 TTTATTTTATT
1749465 ATTAATTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
13 2 0.06
14 11 0.33
15 18 0.55
16 2 0.06
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTATTTTATTTATT
Found at i:1749564 original size:20 final size:20
Alignment explanation
Indices: 1749539--1749580 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1749529 AAATATATAT
1749539 TTTTAAATTATT-TTTATAAA
1 TTTTAAA-TATTATTTATAAA
*
1749559 TTTTAAATATTATTTTTAAA
1 TTTTAAATATTATTTATAAA
1749579 TT
1 TT
1749581 ATTGTTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTAAATATTATTTATAAA
Found at i:1749566 original size:34 final size:33
Alignment explanation
Indices: 1749514--1749616 Score: 140
Period size: 33 Copynumber: 3.1 Consensus size: 33
1749504 TTATAATATA
*
1749514 TATTTTT-TAAATTCTAAATATATATTTTTAAAT
1 TATTTTTATAAATTTTAAATAT-TATTTTTAAAT
1749547 TATTTTTATAAATTTTAAATATTATTTTTAAAT
1 TATTTTTATAAATTTTAAATATTATTTTTAAAT
*
1749580 TATTGTTTA-AAAATTTAAATATTATTTTCT-AAT
1 TATT-TTTATAAATTTTAAATATTATTTT-TAAAT
1749613 TATT
1 TATT
1749617 AAACATATTT
Statistics
Matches: 65, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
33 47 0.72
34 18 0.28
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.58
Consensus pattern (33 bp):
TATTTTTATAAATTTTAAATATTATTTTTAAAT
Found at i:1749573 original size:22 final size:21
Alignment explanation
Indices: 1749532--1749576 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1749522 AAATTCTAAA
* *
1749532 TATATATTTTTAAATTATTTT
1 TATAAATTTTAAAATTATTTT
1749553 TATAAATTTTAAATATTATTTT
1 TATAAATTTTAAA-ATTATTTT
1749575 TA
1 TA
1749577 AATTATTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TATAAATTTTAAAATTATTTT
Found at i:1749588 original size:12 final size:11
Alignment explanation
Indices: 1749536--1749590 Score: 60
Period size: 12 Copynumber: 4.9 Consensus size: 11
1749526 TCTAAATATA
1749536 TATTTTTAAAT
1 TATTTTTAAAT
1749547 TATTTTTATAA-
1 TATTTTTA-AAT
*
1749558 -ATTTTAAATAT
1 TATTTTTAA-AT
1749569 TATTTTTAAAT
1 TATTTTTAAAT
1749580 TATTGTTTAAA
1 TATT-TTTAAA
1749591 AATTTAAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
9 1 0.03
10 7 0.19
11 14 0.38
12 15 0.41
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (11 bp):
TATTTTTAAAT
Found at i:1749639 original size:20 final size:20
Alignment explanation
Indices: 1749602--1749639 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1749592 ATTTAAATAT
*
1749602 TATTTTCTAATTATTAAACA
1 TATTTTCTAATAATTAAACA
1749622 TATTTT-TAATAATATAAA
1 TATTTTCTAATAAT-TAAA
1749640 ACATTTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (20 bp):
TATTTTCTAATAATTAAACA
Found at i:1749819 original size:21 final size:21
Alignment explanation
Indices: 1749795--1749835 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
1749785 GAAATTTATT
1749795 ATTT-ATTTTATAATATTTTAA
1 ATTTAATTTTA-AATATTTTAA
1749816 ATTTAAATTTTAAATATTTT
1 ATTT-AATTTTAAATATTTT
1749836 TTAAATCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.22
22 8 0.44
23 6 0.33
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
ATTTAATTTTAAATATTTTAA
Found at i:1749858 original size:31 final size:32
Alignment explanation
Indices: 1749798--1749858 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
1749788 ATTTATTATT
* *
1749798 TATTTTATAATATTTTAAATTTAAATTTTAAA
1 TATTTTATAATATCTTAAATATAAATTTTAAA
* *
1749830 TATTTTTTAA-ATCTTAAATATAATTTTTA
1 TATTTTATAATATCTTAAATATAAATTTTA
1749859 TAAATTATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 16 0.64
32 9 0.36
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (32 bp):
TATTTTATAATATCTTAAATATAAATTTTAAA
Found at i:1749866 original size:115 final size:113
Alignment explanation
Indices: 1749651--1749858 Score: 280
Period size: 115 Copynumber: 1.8 Consensus size: 113
1749641 CATTTAAATA
*
1749651 TTTTAAAGATATGACCTTTCAAATTTATTATTAGTTTTATAATATTTAAATGTATATTTTAATTT
1 TTTTAAAGATATGACCTTTCAAATTTATTATTAGTTTTATAATATTTAAATGTAAATTTTAATTT
* * *
1749716 GTTTTATAATTTTTTTAATTATGATTTTTAAATTATTTAAAATATATTAT
66 GTTTTATAA--TTCTTAAATATAATTTTTAAATTATTTAAAATATATTAT
* *
1749766 TTTTAAAGATATGACCTTTGAAATTTATTATTTA-TTTTATAATATTTTAAATTTAAATTTTAAA
1 TTTTAAAGATATGACCTTTCAAATTTATTA-TTAGTTTTATAATA-TTTAAATGTAAATTTT-AA
1749830 TATT-TTTTA-AA-TCTTAAATATAATTTTTA
63 T-TTGTTTTATAATTCTTAAATATAATTTTTA
1749859 TAAATTATAA
Statistics
Matches: 83, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
113 15 0.18
115 39 0.47
116 19 0.23
117 8 0.10
118 2 0.02
ACGTcount: A:0.37, C:0.03, G:0.04, T:0.56
Consensus pattern (113 bp):
TTTTAAAGATATGACCTTTCAAATTTATTATTAGTTTTATAATATTTAAATGTAAATTTTAATTT
GTTTTATAATTCTTAAATATAATTTTTAAATTATTTAAAATATATTAT
Found at i:1750021 original size:7 final size:7
Alignment explanation
Indices: 1750004--1750033 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
1749994 TTTTTTAATA
1750004 TAATAATT
1 TAAT-ATT
1750012 TAATATT
1 TAATATT
1750019 TAATATT
1 TAATATT
1750026 TAATATT
1 TAATATT
1750033 T
1 T
1750034 TATTTTGGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 18 0.82
8 4 0.18
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
TAATATT
Found at i:1753313 original size:30 final size:30
Alignment explanation
Indices: 1753278--1753354 Score: 109
Period size: 30 Copynumber: 2.6 Consensus size: 30
1753268 CGGTGGTTGC
* *
1753278 TCTGGGTGAAATGAACTCGAACTGCCTATG
1 TCTGGGTGATATGAACTCGAACCGCCTATG
*
1753308 TCTGGGTGATATGAACTTGAACCGCCTATG
1 TCTGGGTGATATGAACTCGAACCGCCTATG
**
1753338 TCCAGGTGATATGAACT
1 TCTGGGTGATATGAACT
1753355 ACTCTGGGAC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (30 bp):
TCTGGGTGATATGAACTCGAACCGCCTATG
Found at i:1755631 original size:70 final size:71
Alignment explanation
Indices: 1755551--1755690 Score: 201
Period size: 70 Copynumber: 2.0 Consensus size: 71
1755541 TTAAAACATA
* * * * * * *
1755551 TTTTAAAAATATATTGAATATATTATAATTTTAATATTAGTTATACTTAACA-TTTTTAATATAT
1 TTTTAAAAATACATTAAATATATTAAAATTTTAAAATTAGCTATACATAACATTTTTTAATATAG
1755615 TTAATC
66 TTAATC
*
1755621 TTTTAAAAATACATTAAATATATTAAAATTTTAAAATTCGCTATACATAACATTTTTTAATATAG
1 TTTTAAAAATACATTAAATATATTAAAATTTTAAAATTAGCTATACATAACATTTTTTAATATAG
1755686 TTAAT
66 TTAAT
1755691 ATCTTTAAGT
Statistics
Matches: 61, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
70 45 0.74
71 16 0.26
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.48
Consensus pattern (71 bp):
TTTTAAAAATACATTAAATATATTAAAATTTTAAAATTAGCTATACATAACATTTTTTAATATAG
TTAATC
Found at i:1755793 original size:20 final size:20
Alignment explanation
Indices: 1755770--1755845 Score: 68
Period size: 20 Copynumber: 3.9 Consensus size: 20
1755760 TTAAATACAT
*
1755770 AAATTTATGAATGTATACTA
1 AAATTTATAAATGTATACTA
* *
1755790 AAATTAAAAAAT-TAATA-TA
1 AAATTTATAAATGT-ATACTA
*
1755809 TAAATTTATAAATGTGTACTA
1 -AAATTTATAAATGTATACTA
*
1755830 AAATTTAAAAAT-TATA
1 AAATTTATAAATGTATA
1755846 ATCAACACAT
Statistics
Matches: 44, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
19 6 0.14
20 35 0.80
21 3 0.07
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (20 bp):
AAATTTATAAATGTATACTA
Found at i:1755812 original size:40 final size:40
Alignment explanation
Indices: 1755763--1755843 Score: 126
Period size: 40 Copynumber: 2.0 Consensus size: 40
1755753 AAATATATTA
*
1755763 AATACATAAATTTATGAATGTATACTAAAATTAAAAAATT
1 AATACATAAATTTATAAATGTATACTAAAATTAAAAAATT
* * *
1755803 AATATATAAATTTATAAATGTGTACTAAAATTTAAAAATT
1 AATACATAAATTTATAAATGTATACTAAAATTAAAAAATT
1755843 A
1 A
1755844 TAATCAACAC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.54, C:0.04, G:0.05, T:0.37
Consensus pattern (40 bp):
AATACATAAATTTATAAATGTATACTAAAATTAAAAAATT
Found at i:1756357 original size:19 final size:20
Alignment explanation
Indices: 1756322--1756365 Score: 72
Period size: 19 Copynumber: 2.2 Consensus size: 20
1756312 ATATATTTTT
1756322 AAATAAATTCATTTTTTAAC
1 AAATAAATTCATTTTTTAAC
*
1756342 AAATAAA-TCTTTTTTTAAC
1 AAATAAATTCATTTTTTAAC
1756361 AAATA
1 AAATA
1756366 TTTTTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (20 bp):
AAATAAATTCATTTTTTAAC
Found at i:1756782 original size:21 final size:21
Alignment explanation
Indices: 1756758--1756819 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
1756748 TTTTATATTA
**
1756758 TTAAAAATATATATTTAATGT
1 TTAAAAATATATATTTAAAAT
*
1756779 TTAAAAA-ATAATATTCAAAAT
1 TTAAAAATAT-ATATTTAAAAT
*
1756800 TTTAAAATATA-ATTTAAAAT
1 TTAAAAATATATATTTAAAAT
1756820 AATTTTTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
20 10 0.29
21 22 0.65
22 2 0.06
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (21 bp):
TTAAAAATATATATTTAAAAT
Found at i:1756803 original size:22 final size:20
Alignment explanation
Indices: 1756778--1756819 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
1756768 ATATTTAATG
1756778 TTTAAAAAATAATATTCAAAAT
1 TTTAAAAAATAAT-TT-AAAAT
*
1756800 TTTAAAATATAATTTAAAAT
1 TTTAAAAAATAATTTAAAAT
1756820 AATTTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 2 0.11
22 12 0.63
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
TTTAAAAAATAATTTAAAAT
Found at i:1756818 original size:20 final size:21
Alignment explanation
Indices: 1756761--1756819 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 21
1756751 TATATTATTA
1756761 AAAATATATATTT--AATGTTT
1 AAAATATA-ATTTAAAATGTTT
*
1756781 AAAAAATAATATTCAAAAT-TTT
1 AAAATATAAT-TT-AAAATGTTT
1756803 AAAATATAATTTAAAAT
1 AAAATATAATTTAAAAT
1756820 AATTTTTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
19 2 0.06
20 14 0.42
21 2 0.06
22 12 0.36
23 3 0.09
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (21 bp):
AAAATATAATTTAAAATGTTT
Found at i:1756841 original size:23 final size:23
Alignment explanation
Indices: 1756815--1756887 Score: 65
Period size: 23 Copynumber: 3.1 Consensus size: 23
1756805 AATATAATTT
1756815 AAAATAATTTTTAAAATTTTTAA
1 AAAATAATTTTTAAAATTTTTAA
* ** *
1756838 AAAATATATATTATAAAACATTTCA
1 AAAATA-AT-TTTTAAAATTTTTAA
* * *
1756863 AATATAAATTTTAAATTTTTTAA
1 AAAATAATTTTTAAAATTTTTAA
1756886 AA
1 AA
1756888 TTAATAACAA
Statistics
Matches: 37, Mismatches: 11, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
23 18 0.49
24 3 0.08
25 16 0.43
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (23 bp):
AAAATAATTTTTAAAATTTTTAA
Found at i:1756915 original size:22 final size:21
Alignment explanation
Indices: 1756885--1756926 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1756875 AAATTTTTTA
*
1756885 AAATTAATAACAAAAAATAAAT
1 AAATAAATAA-AAAAAATAAAT
*
1756907 AAATAAATAAACAAAATAAA
1 AAATAAATAAAAAAAATAAA
1756927 ATAAGAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.19
Consensus pattern (21 bp):
AAATAAATAAAAAAAATAAAT
Found at i:1756999 original size:9 final size:9
Alignment explanation
Indices: 1756987--1757012 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1756977 TAAAAATTTT
1756987 AAAAAATTA
1 AAAAAATTA
1756996 AAAAAATTA
1 AAAAAATTA
1757005 AAAAAATT
1 AAAAAATT
1757013 GAAAGATGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (9 bp):
AAAAAATTA
Found at i:1757131 original size:20 final size:20
Alignment explanation
Indices: 1757090--1757132 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
1757080 TTTTATTTTT
* *
1757090 AATTTTAAAATAATATTTAA
1 AATTTAAAAATAATATTCAA
1757110 AATTTAAAAAGTAAT-TTCAA
1 AATTTAAAAA-TAATATTCAA
1757130 AAT
1 AAT
1757133 ATATATTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (20 bp):
AATTTAAAAATAATATTCAA
Found at i:1757132 original size:32 final size:33
Alignment explanation
Indices: 1757089--1757152 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
1757079 TTTTTATTTT
*
1757089 TAATTTTAAAATA-ATATTTAAAATTTAAAAAG
1 TAATTTCAAAATATATATTTAAAATTTAAAAAG
1757121 TAATTTCAAAATATATATTTAAAATTTAAAAA
1 TAATTTCAAAATATATATTTAAAATTTAAAAA
1757153 TATATATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 12 0.40
33 18 0.60
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (33 bp):
TAATTTCAAAATATATATTTAAAATTTAAAAAG
Found at i:1757147 original size:21 final size:22
Alignment explanation
Indices: 1757122--1757164 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
1757112 TTTAAAAAGT
*
1757122 AATTTCAAAATATATAT-TTAA
1 AATTTAAAAATATATATATTAA
1757143 AATTTAAAAATATATATATTAA
1 AATTTAAAAATATATATATTAA
1757165 TAAAATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
AATTTAAAAATATATATATTAA
Found at i:1757226 original size:10 final size:9
Alignment explanation
Indices: 1757204--1757238 Score: 52
Period size: 10 Copynumber: 3.7 Consensus size: 9
1757194 TTTTAAAGTT
1757204 AATAATAATA
1 AATAA-AATA
1757214 AATAAAATAA
1 AATAAAAT-A
1757224 AATAAAATA
1 AATAAAATA
1757233 AATAAA
1 AATAAA
1757239 GGTAAAAGGC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 10 0.42
10 14 0.58
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (9 bp):
AATAAAATA
Found at i:1759624 original size:20 final size:21
Alignment explanation
Indices: 1759601--1759649 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
1759591 GAAAATATAA
*
1759601 TAATATATTTCAT-AAAACAT
1 TAATATATTACATGAAAACAT
*
1759621 TAATATA-CACATGAAAACAT
1 TAATATATTACATGAAAACAT
1759641 TAA-ATATTA
1 TAATATATTA
1759650 ATCATTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.53, C:0.10, G:0.02, T:0.35
Consensus pattern (21 bp):
TAATATATTACATGAAAACAT
Found at i:1769211 original size:5 final size:5
Alignment explanation
Indices: 1769201--1769235 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
1769191 ATGGAATTTG
1769201 AATTA AATTA AATTA AATTA AATTA AATTA AATTA
1 AATTA AATTA AATTA AATTA AATTA AATTA AATTA
1769236 TTTGAGTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AATTA
Found at i:1769880 original size:72 final size:73
Alignment explanation
Indices: 1769757--1769891 Score: 263
Period size: 72 Copynumber: 1.9 Consensus size: 73
1769747 TTTTAGCTTC
1769757 ACAATATTAAATCACTCGATTTTGAGTTAGAGAGTTTAAATTATTACTATTTTAGTGAAGGCTTT
1 ACAATATTAAATCACTCGATTTTGAGTTAGAGAGTTTAAATTATTACTATTTTAGTGAAGGCTTT
1769822 AAATTATT
66 AAATTATT
1769830 ACAAT-TTAAATCACTCGATTTTGAGTTAGAGAGTTTAAATTATTACTATTTTAGTGAAGGCT
1 ACAATATTAAATCACTCGATTTTGAGTTAGAGAGTTTAAATTATTACTATTTTAGTGAAGGCT
1769892 GTGCGAGTAA
Statistics
Matches: 62, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
72 57 0.92
73 5 0.08
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.41
Consensus pattern (73 bp):
ACAATATTAAATCACTCGATTTTGAGTTAGAGAGTTTAAATTATTACTATTTTAGTGAAGGCTTT
AAATTATT
Found at i:1770948 original size:20 final size:20
Alignment explanation
Indices: 1770923--1770960 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1770913 AAAAAATTAA
1770923 AAATCCAAAAATTCAAATTC
1 AAATCCAAAAATTCAAATTC
*
1770943 AAATCCATAAATTCAAAT
1 AAATCCAAAAATTCAAAT
1770961 AATATACACA
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:0.55, C:0.18, G:0.00, T:0.26
Consensus pattern (20 bp):
AAATCCAAAAATTCAAATTC
Found at i:1782691 original size:29 final size:30
Alignment explanation
Indices: 1782640--1782698 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
1782630 GAAAAAAAAT
1782640 AATAAAAATAAAAATATACTCTAAA-ATAA
1 AATAAAAATAAAAATATACTCTAAATATAA
* *
1782669 AATAAAAATAAAACCT-TATTCTAAATATAA
1 AATAAAAATAAAA-ATATACTCTAAATATAA
1782699 GAAGAAAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 21 0.81
30 5 0.19
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.27
Consensus pattern (30 bp):
AATAAAAATAAAAATATACTCTAAATATAA
Found at i:1789787 original size:30 final size:31
Alignment explanation
Indices: 1789753--1789825 Score: 94
Period size: 30 Copynumber: 2.3 Consensus size: 31
1789743 CGGGAGGGCG
*
1789753 AACTGCAGGTATTGGAGCAATA-GGTGGCAC
1 AACTGCAGGTAGTGGAGCAATATGGTGGCAC
* *
1789783 AACTGCTGGTAGTGGAGCAATAGTTGGTGGTAC
1 AACTGCAGGTAGTGGAGCAATA--TGGTGGCAC
1789816 AACTGCAGGT
1 AACTGCAGGT
1789826 GGGACCGCTG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 20 0.56
33 16 0.44
ACGTcount: A:0.27, C:0.15, G:0.34, T:0.23
Consensus pattern (31 bp):
AACTGCAGGTAGTGGAGCAATATGGTGGCAC
Found at i:1791396 original size:14 final size:14
Alignment explanation
Indices: 1791377--1791406 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1791367 TTAGCATAAG
*
1791377 TATTTTAATCGAAA
1 TATTTTAATAGAAA
1791391 TATTTTAATAGAAA
1 TATTTTAATAGAAA
1791405 TA
1 TA
1791407 ATTATATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (14 bp):
TATTTTAATAGAAA
Found at i:1794143 original size:29 final size:29
Alignment explanation
Indices: 1794085--1794145 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
1794075 TTTTGGGGAA
** * *
1794085 TTTCGGGTTTTAGCCAAAGTGTTTTATTC
1 TTTCGGGACTTAGCCAAAGAGCTTTATTC
*
1794114 TTTCGGGACTTAGCCAAAGAGCTTTGTTC
1 TTTCGGGACTTAGCCAAAGAGCTTTATTC
1794143 TTT
1 TTT
1794146 TGGGGTATAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.18, C:0.16, G:0.21, T:0.44
Consensus pattern (29 bp):
TTTCGGGACTTAGCCAAAGAGCTTTATTC
Found at i:1804730 original size:39 final size:39
Alignment explanation
Indices: 1804687--1804762 Score: 125
Period size: 39 Copynumber: 1.9 Consensus size: 39
1804677 GGGGTTTCAA
* * *
1804687 TTTAGCACTTATGTGCTTTAGTTAGCCTTCGGGCTTCCG
1 TTTAGCACTTATGTGCTTCAGCTAGACTTCGGGCTTCCG
1804726 TTTAGCACTTATGTGCTTCAGCTAGACTTCGGGCTTC
1 TTTAGCACTTATGTGCTTCAGCTAGACTTCGGGCTTC
1804763 AGATCACGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.14, C:0.24, G:0.22, T:0.39
Consensus pattern (39 bp):
TTTAGCACTTATGTGCTTCAGCTAGACTTCGGGCTTCCG
Found at i:1806507 original size:19 final size:19
Alignment explanation
Indices: 1806470--1806508 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1806460 TATATCCATA
*
1806470 TTAAATTATAATTATTATT
1 TTAAATTATAACTATTATT
1806489 TTAAATTAATAACTA-TATT
1 TTAAATT-ATAACTATTATT
1806508 T
1 T
1806509 AGTTCTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (19 bp):
TTAAATTATAACTATTATT
Found at i:1812517 original size:31 final size:31
Alignment explanation
Indices: 1812471--1812556 Score: 111
Period size: 31 Copynumber: 2.8 Consensus size: 31
1812461 TCTAAATTCA
*
1812471 TACAATTGAATCAAAATCAAAGTTTTATTTG
1 TACAATTGAATCAAAATCAAAGTTTTACTTG
** * *
1812502 TATGATTGAACCAAAATCAAAATTTTACTTG
1 TACAATTGAATCAAAATCAAAGTTTTACTTG
*
1812533 TACAATTGCATC-AAATCAAAGTTT
1 TACAATTGAATCAAAATCAAAGTTT
1812557 ATGTATCACA
Statistics
Matches: 45, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
30 11 0.24
31 34 0.76
ACGTcount: A:0.42, C:0.13, G:0.09, T:0.36
Consensus pattern (31 bp):
TACAATTGAATCAAAATCAAAGTTTTACTTG
Found at i:1815682 original size:15 final size:15
Alignment explanation
Indices: 1815650--1815683 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1815640 TCCTTTTTCC
**
1815650 TTTTCTTTATTTTGT
1 TTTTCTTTATTTACT
1815665 TTTTCTTTATTTACT
1 TTTTCTTTATTTACT
1815680 TTTT
1 TTTT
1815684 TAAATTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.09, G:0.03, T:0.79
Consensus pattern (15 bp):
TTTTCTTTATTTACT
Found at i:1815830 original size:21 final size:20
Alignment explanation
Indices: 1815763--1815829 Score: 125
Period size: 20 Copynumber: 3.4 Consensus size: 20
1815753 TTTCTAATAT
1815763 TATTTTTAAAAATTTAAACA
1 TATTTTTAAAAATTTAAACA
1815783 TATTTTTAAAAATTTAAACA
1 TATTTTTAAAAATTTAAACA
*
1815803 TATTTTTAAAAATTTAAATA
1 TATTTTTAAAAATTTAAACA
1815823 TATTTTT
1 TATTTTT
1815830 TTAAAATTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (20 bp):
TATTTTTAAAAATTTAAACA
Found at i:1815920 original size:23 final size:23
Alignment explanation
Indices: 1815888--1815941 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 23
1815878 AAATGTATAC
* ** *
1815888 TTTAACATTTTTAAATATTGTTT
1 TTTAAAATTTTTAAATATAATCT
1815911 TTTAAAA-TTTTAAATATAATCT
1 TTTAAAATTTTTAAATATAATCT
1815933 TTTAAAATT
1 TTTAAAATT
1815942 ATTATTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
22 19 0.73
23 7 0.27
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.56
Consensus pattern (23 bp):
TTTAAAATTTTTAAATATAATCT
Found at i:1815959 original size:12 final size:12
Alignment explanation
Indices: 1815942--1816015 Score: 52
Period size: 11 Copynumber: 6.7 Consensus size: 12
1815932 TTTTAAAATT
1815942 ATTATTTTTTAA
1 ATTATTTTTTAA
1815954 ATTA-TTTTTAA
1 ATTATTTTTTAA
*
1815965 A-TA-TATTTAA
1 ATTATTTTTTAA
*
1815975 A-T-TCTTTTAA
1 ATTATTTTTTAA
* *
1815985 ATTATATTTAAA
1 ATTATTTTTTAA
*
1815997 ATT-TTTTTAAA
1 ATTATTTTTTAA
*
1816008 AATATTTT
1 ATTATTTT
1816016 ATTTGGTAGA
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
10 16 0.31
11 18 0.35
12 17 0.33
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (12 bp):
ATTATTTTTTAA
Found at i:1815963 original size:11 final size:11
Alignment explanation
Indices: 1815942--1816007 Score: 66
Period size: 10 Copynumber: 6.1 Consensus size: 11
1815932 TTTTAAAATT
1815942 ATTATTTTTTAA
1 ATTA-TTTTTAA
1815954 ATTATTTTTAA
1 ATTATTTTTAA
*
1815965 A-TATATTTAA
1 ATTATTTTTAA
*
1815975 ATT-CTTTTAA
1 ATTATTTTTAA
*
1815985 ATTATATTTAAA
1 ATTAT-TTTTAA
1815997 ATT-TTTTTAA
1 ATTATTTTTAA
1816007 A
1 A
1816008 AATATTTTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
10 23 0.51
11 10 0.22
12 12 0.27
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (11 bp):
ATTATTTTTAA
Found at i:1815974 original size:21 final size:20
Alignment explanation
Indices: 1815949--1816014 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 20
1815939 ATTATTATTT
1815949 TTTAAATTATTTTTAAATATA
1 TTTAAATT-TTTTTAAATATA
*
1815970 TTTAAATTCTTTTAAATTATA
1 TTTAAATTTTTTTAAA-TATA
*
1815991 TTTAAAATTTTTTTAAAAATA
1 TTT-AAATTTTTTTAAATATA
1816012 TTT
1 TTT
1816015 TATTTGGTAG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
20 7 0.17
21 21 0.52
22 12 0.30
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTAAATTTTTTTAAATATA
Found at i:1816003 original size:104 final size:104
Alignment explanation
Indices: 1815805--1816002 Score: 246
Period size: 104 Copynumber: 1.9 Consensus size: 104
1815795 TTTAAACATA
* *
1815805 TTTTTAAAAATTTAAATATATTTTTTTAAAATTATATGATCTTTTAAATTTATTATTTATTTTAT
1 TTTTTAAAAATTTAAATATAATCTTTTAAAATTATATGATCTTTTAAATTTATTATTTATTTTAT
*
1815870 AATATTTTAAATGTATACTTTAACATTTTTAAATATTGT
66 AATATTTTAAATGTATACTTTAAAATTTTTAAATATTGT
* * *
1815909 TTTTTAAAATTTTAAATATAATCTTTTAAAATTAT-T-ATTTTTTAAA-TTATTTTTAAATATAT
1 TTTTTAAAAATTTAAATATAATCTTTTAAAATTATATGATCTTTTAAATTTATTATT---TAT-T
*
1815971 TTA-AATTCTTTTAAAT-TATA-TTTAAAATTTTT
62 TTATAA-TATTTTAAATGTATACTTTAAAATTTTT
1816003 TTAAAAATAT
Statistics
Matches: 82, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
101 7 0.09
102 9 0.11
103 12 0.15
104 41 0.50
105 13 0.16
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.58
Consensus pattern (104 bp):
TTTTTAAAAATTTAAATATAATCTTTTAAAATTATATGATCTTTTAAATTTATTATTTATTTTAT
AATATTTTAAATGTATACTTTAAAATTTTTAAATATTGT
Found at i:1816155 original size:13 final size:14
Alignment explanation
Indices: 1816129--1816162 Score: 52
Period size: 13 Copynumber: 2.4 Consensus size: 14
1816119 TACAAGTATA
1816129 GTTTTTTTAAAATAT
1 GTTTTTTT-AAATAT
1816144 GTTTTTTT-AATAT
1 GTTTTTTTAAATAT
1816157 GTTTTT
1 GTTTTT
1816163 GGCTCCACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 11 0.58
15 8 0.42
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.68
Consensus pattern (14 bp):
GTTTTTTTAAATAT
Found at i:1816310 original size:10 final size:10
Alignment explanation
Indices: 1816290--1816318 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1816280 ATTTTTTAAT
1816290 TTTAAAA-AA
1 TTTAAAATAA
1816299 TTTAAAATAA
1 TTTAAAATAA
1816309 TTTAAAATAA
1 TTTAAAATAA
1816319 AAATATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 7 0.37
10 12 0.63
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
TTTAAAATAA
Found at i:1826483 original size:93 final size:93
Alignment explanation
Indices: 1826370--1826541 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
1826360 CGCCCATAAG
* *
1826370 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1826435 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
1826463 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1826528 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
1826542 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:1826538 original size:46 final size:46
Alignment explanation
Indices: 1826363--1826538 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
1826353 TGTAACCCGC
* * *
1826363 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
1826409 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
1826459 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
1826502 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
1826539 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:1833745 original size:44 final size:44
Alignment explanation
Indices: 1833600--1833741 Score: 155
Period size: 44 Copynumber: 3.2 Consensus size: 44
1833590 TTTATACAGG
* * *
1833600 TCTTATCTCCCTGAGATTACAGTGGA-CAGACCAAAGAATTCAGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGAAGT-AGA
* ** *
1833644 TCTTATCTCCCTGAGGTTACAGCGGAGCAGATTGAAGCCAG-AGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAG-AAGTAGA
*
1833688 TCTTATCTCCTTGAGATTACAGCGGAGCAGATCAAAGATAGTA-A
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGA-AGTAGA
*
1833732 TCCTATCTCC
1 TCTTATCTCC
1833742 TTGATATACA
Statistics
Matches: 81, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
44 72 0.89
45 8 0.10
46 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.26
Consensus pattern (44 bp):
TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGAAGTAGA
Found at i:1835477 original size:3 final size:3
Alignment explanation
Indices: 1835466--1835545 Score: 67
Period size: 3 Copynumber: 27.0 Consensus size: 3
1835456 ATTATTTTGT
*
1835466 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTTA CTA TTA TTA TCT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA T-TA TTA
* * * * *
1835511 CTA TTA TTG TTA GTA -TA TTA CTA CTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1835546 CTATCATATA
Statistics
Matches: 63, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
2 5 0.08
3 54 0.86
4 4 0.06
ACGTcount: A:0.30, C:0.06, G:0.03, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:1835866 original size:13 final size:12
Alignment explanation
Indices: 1835845--1835878 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
1835835 AATATCACTA
1835845 TTTACTTTTTTAT
1 TTTA-TTTTTTAT
1835858 TTTATTTTTTAT
1 TTTATTTTTTAT
1835870 TATTATTTT
1 T-TTATTTT
1835879 CAAATTTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTATTTTTTAT
Found at i:1851324 original size:44 final size:43
Alignment explanation
Indices: 1851214--1851587 Score: 203
Period size: 44 Copynumber: 8.6 Consensus size: 43
1851204 ATTATACAGG
* *** * *
1851214 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCA---GAGA
* *
1851260 TCTTATCTCCCTGAGGTTACAGCGGAGCAGATTGAAGCCAGAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAG-CAGAGA
* * ** *
1851304 TCTTATCTCCTTGAGATTACAGCGGAGCAGATCAAAG-ATAGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCAGAG--A
* * * * *
1851348 TCCTATCTCCTTGATATTACAATGGAGCGGATT-AA--AG-GA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCAGAGA
* * * * *
1851387 TCTTATCTCTCTGA-AGTTACAGTAGAGAAGA-TCACATCAG-G-
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGA-AGCAGAGA
* * * ** * * *
1851428 TCTTATTTCCCTGAGGTTACAGTGGAGTAGACCGGAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCA---GAGA
*
1851474 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAG-CAGAGA
* * * **
1851518 TCTTATCTCCCTGAGATTACAGCGGAGCAAATCGAAGACA-CTA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAG-CAGAGA
*
1851561 TCCTATCTCCCTGA-AGTTACAGTGGAG
1 TCTTATCTCCCTGAGA-TTACAGTGGAG
1851588 TGGATTAAAA
Statistics
Matches: 257, Mismatches: 54, Indels: 37
0.74 0.16 0.11
Matches are distributed among these distances:
38 2 0.01
39 24 0.09
40 1 0.00
41 28 0.11
42 8 0.03
43 26 0.10
44 102 0.40
45 1 0.00
46 63 0.25
47 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (43 bp):
TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCAGAGA
Found at i:1853130 original size:3 final size:3
Alignment explanation
Indices: 1853119--1853209 Score: 78
Period size: 3 Copynumber: 30.3 Consensus size: 3
1853109 ATTATTTTGT
*
1853119 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTTA CTA TTA TTA TCT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA T-TA TTA
* * * * * * *
1853164 CTA TTA TTG TTA GTA TTA TTA CTA CTA TTA TTA TTA CTA TCA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1853210 ATTTATACCT
Statistics
Matches: 70, Mismatches: 14, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
2 3 0.04
3 63 0.90
4 4 0.06
ACGTcount: A:0.30, C:0.08, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Done.