Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008138.1 Hibiscus syriacus cultivar Beakdansim tig00110694_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: 3838456
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 18
Found at i:1601088 original size:14 final size:15
Alignment explanation
Indices: 1601069--1601097 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1601059 AATATCCTTT
1601069 AAAACAA-TTTAAAA
1 AAAACAATTTTAAAA
1601083 AAAACAATTTTAAAA
1 AAAACAATTTTAAAA
1601098 TATAAAAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAACAATTTTAAAA
Found at i:1604522 original size:30 final size:30
Alignment explanation
Indices: 1604486--1604552 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
1604476 ATCCCACGGC
*
1604486 TGCTGCTC-AGACACTCCTCCATAACCCTGG
1 TGCTGCTCAAG-CACTCCTCAATAACCCTGG
* * *
1604516 TGCTGCTCAAGCACTCTTTAATAATCCTGG
1 TGCTGCTCAAGCACTCCTCAATAACCCTGG
1604546 TGCTGCT
1 TGCTGCT
1604553 TCTCAGGCAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 30 0.94
31 2 0.06
ACGTcount: A:0.19, C:0.33, G:0.18, T:0.30
Consensus pattern (30 bp):
TGCTGCTCAAGCACTCCTCAATAACCCTGG
Found at i:1604655 original size:30 final size:30
Alignment explanation
Indices: 1604612--1604742 Score: 133
Period size: 30 Copynumber: 4.4 Consensus size: 30
1604602 ATAACCCTGG
*
1604612 TGGTG-TGGTCAGCAACTCATGGGCGTTCC
1 TGGTGTTGGTCAGCAACACATGGGCGTTCC
* * **
1604641 TAGTGTTGGCCAGCAACACATGGGCAATCAC
1 TGGTGTTGGTCAGCAACACATGGGCGTTC-C
*
1604672 -GGTGTTGGTCAGCAACACGTGGGC-TATCC
1 TGGTGTTGGTCAGCAACACATGGGCGT-TCC
* *
1604701 TGGTGTTCGTCAGCAACACGTGGGCGTTCC
1 TGGTGTTGGTCAGCAACACATGGGCGTTCC
* *
1604731 TGGAGCTGGTCA
1 TGGTGTTGGTCA
1604743 TGTATCTATC
Statistics
Matches: 84, Mismatches: 13, Indels: 9
0.79 0.12 0.08
Matches are distributed among these distances:
29 5 0.06
30 77 0.92
31 2 0.02
ACGTcount: A:0.18, C:0.24, G:0.33, T:0.24
Consensus pattern (30 bp):
TGGTGTTGGTCAGCAACACATGGGCGTTCC
Found at i:1604695 original size:60 final size:59
Alignment explanation
Indices: 1604613--1604725 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 59
1604603 TAACCCTGGT
* *
1604613 GGTGTGGTCAGCAACTCATGGGCGT-TCCTAGTGTTGGCCAGCAACACATGGGCAATCAC
1 GGTGTGGTCAGCAACACATGGGC-TATCCTAGTGTTCGCCAGCAACACATGGGCAATCAC
* * * *
1604672 GGTGTTGGTCAGCAACACGTGGGCTATCCTGGTGTTCGTCAGCAACACGTGGGC
1 GGTG-TGGTCAGCAACACATGGGCTATCCTAGTGTTCGCCAGCAACACATGGGC
1604726 GTTCCTGGAG
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
59 5 0.11
60 41 0.89
ACGTcount: A:0.19, C:0.25, G:0.33, T:0.23
Consensus pattern (59 bp):
GGTGTGGTCAGCAACACATGGGCTATCCTAGTGTTCGCCAGCAACACATGGGCAATCAC
Found at i:1606847 original size:50 final size:50
Alignment explanation
Indices: 1606772--1606872 Score: 184
Period size: 50 Copynumber: 2.0 Consensus size: 50
1606762 ACCAGAGTTT
1606772 TATTACATAAATGTTTACTTTTGTTACAAGTTCAAGCATCTAATGACAGA
1 TATTACATAAATGTTTACTTTTGTTACAAGTTCAAGCATCTAATGACAGA
* *
1606822 TATTACATAAATGTTTACTTTTGTTACAAGTTCATGCATCTAATGAGAGA
1 TATTACATAAATGTTTACTTTTGTTACAAGTTCAAGCATCTAATGACAGA
1606872 T
1 T
1606873 TTTGAACTTG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (50 bp):
TATTACATAAATGTTTACTTTTGTTACAAGTTCAAGCATCTAATGACAGA
Found at i:1608761 original size:18 final size:18
Alignment explanation
Indices: 1608738--1608774 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1608728 TACGAACAAT
1608738 ATAGGATTTGAGAAGCTC
1 ATAGGATTTGAGAAGCTC
1608756 ATAGGATTTGAGAAGCTC
1 ATAGGATTTGAGAAGCTC
1608774 A
1 A
1608775 CATTGTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.11, G:0.27, T:0.27
Consensus pattern (18 bp):
ATAGGATTTGAGAAGCTC
Found at i:1609564 original size:27 final size:27
Alignment explanation
Indices: 1609533--1609591 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
1609523 TTATTATTTC
* *
1609533 TACCGGTTTTGTTATTATTGGGCGCTT
1 TACCGGTTTTGTTATTATTGGACACTT
*
1609560 TACCGGTTTTGTTATTGTTGGACACTT
1 TACCGGTTTTGTTATTATTGGACACTT
1609587 TACCG
1 TACCG
1609592 AAAATATTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.14, C:0.17, G:0.24, T:0.46
Consensus pattern (27 bp):
TACCGGTTTTGTTATTATTGGACACTT
Found at i:1609626 original size:21 final size:21
Alignment explanation
Indices: 1609601--1609644 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1609591 GAAAATATTA
* *
1609601 AAAAACATTAATGTTTTAGGT
1 AAAAACAATAATATTTTAGGT
*
1609622 AAAAATAATAATATTTTAGGT
1 AAAAACAATAATATTTTAGGT
1609643 AA
1 AA
1609645 TTTTTTTACC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.36
Consensus pattern (21 bp):
AAAAACAATAATATTTTAGGT
Found at i:1611700 original size:59 final size:61
Alignment explanation
Indices: 1611575--1611734 Score: 170
Period size: 59 Copynumber: 2.7 Consensus size: 61
1611565 ACCCTTATTT
* * **
1611575 TAAATTGATCCTTAAACTTTTGAATATTTCATTTTCCATCCCTAAACTATGACTCTCGTTC
1 TAAATTGATCCTTAAACTTTTGAATATTTCAATTTCCATCCCTAAAATATGAAACTCGTTC
* * *
1611636 TAAATT-AGTCCTTAAACTTTT-TATATTTTAATTT-CATCCCTAAAATATGAAACTCTTTC
1 TAAATTGA-TCCTTAAACTTTTGAATATTTCAATTTCCATCCCTAAAATATGAAACTCGTTC
* **
1611695 TAAATTGGT-CTCCAACTTTTGAATA-TTCTAA-TTCCATCCC
1 TAAATTGATCCTTAAACTTTTGAATATTTC-AATTTCCATCCC
1611735 CAAATTCATT
Statistics
Matches: 82, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
58 13 0.16
59 39 0.48
60 11 0.13
61 19 0.23
ACGTcount: A:0.30, C:0.21, G:0.06, T:0.43
Consensus pattern (61 bp):
TAAATTGATCCTTAAACTTTTGAATATTTCAATTTCCATCCCTAAAATATGAAACTCGTTC
Found at i:1611978 original size:60 final size:60
Alignment explanation
Indices: 1611850--1612078 Score: 211
Period size: 59 Copynumber: 3.9 Consensus size: 60
1611840 GAATATACAT
* * * * *
1611850 ATAGTTT-GGGATGAAATTAGA-ATGTTCAAAAAGTTT-GGGACCAATTTAGAATGA-ATTTC
1 ATAGTTTAGGAATGAAATTA-ATATGTTC-AAAAGTTTAGAGACTAATTTAAAATGATA-GTC
* * *
1611909 ATAGGTTAGGGATGAAATTGAA-ATGTTCAAAAGTTTAAAGACTAATTTAAAATGATAGTC
1 ATAGTTTAGGAATGAAATT-AATATGTTCAAAAGTTTAGAGACTAATTTAAAATGATAGTC
* * * * * *
1611969 ATTGTTTAGGAAT-ACATTAATATATTTAAAATTTTAGAGACTAATTTAGAATGATAGTC
1 ATAGTTTAGGAATGAAATTAATATGTTCAAAAGTTTAGAGACTAATTTAAAATGATAGTC
* * * *
1612028 ATAGTTTAAGAATAAAATTAATAT-TTTAAAATTTTAGAGACTAATTTAAAA
1 ATAGTTTAGGAATGAAATTAATATGTTCAAAAGTTTAGAGACTAATTTAAAA
1612079 AGAGTCATAC
Statistics
Matches: 145, Mismatches: 19, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
58 2 0.01
59 88 0.61
60 53 0.37
61 2 0.01
ACGTcount: A:0.43, C:0.05, G:0.16, T:0.36
Consensus pattern (60 bp):
ATAGTTTAGGAATGAAATTAATATGTTCAAAAGTTTAGAGACTAATTTAAAATGATAGTC
Found at i:1612022 original size:59 final size:59
Alignment explanation
Indices: 1611937--1612078 Score: 214
Period size: 59 Copynumber: 2.4 Consensus size: 59
1611927 TGAAATGTTC
* * * * *
1611937 AAAAGTTTAAAGACTAATTTAAAATGATAGTCATTGTTTAGGAAT-ACATTAATATATTT
1 AAAATTTTAGAGACTAATTTAAAATGATAGTCATAGTTTAAGAATAAAATTAATAT-TTT
*
1611996 AAAATTTTAGAGACTAATTTAGAATGATAGTCATAGTTTAAGAATAAAATTAATATTTT
1 AAAATTTTAGAGACTAATTTAAAATGATAGTCATAGTTTAAGAATAAAATTAATATTTT
1612055 AAAATTTTAGAGACTAATTTAAAA
1 AAAATTTTAGAGACTAATTTAAAA
1612079 AGAGTCATAC
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
59 66 0.88
60 9 0.12
ACGTcount: A:0.46, C:0.04, G:0.11, T:0.38
Consensus pattern (59 bp):
AAAATTTTAGAGACTAATTTAAAATGATAGTCATAGTTTAAGAATAAAATTAATATTTT
Found at i:1612267 original size:17 final size:17
Alignment explanation
Indices: 1612245--1612281 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1612235 TATTATCATA
* *
1612245 TAAAGATTAATATAAAT
1 TAAAGATGAATAAAAAT
1612262 TAAAGATGAATAAAAAT
1 TAAAGATGAATAAAAAT
1612279 TAA
1 TAA
1612282 GTATACACGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.30
Consensus pattern (17 bp):
TAAAGATGAATAAAAAT
Found at i:1613689 original size:2 final size:2
Alignment explanation
Indices: 1613684--1613708 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1613674 TAAAAAAAAC
1613684 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
1613709 CCCCCATCCA
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:1613925 original size:24 final size:24
Alignment explanation
Indices: 1613898--1613949 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
1613888 AACGGATATA
*
1613898 TCAAAAATCAAAACATAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
** * *
1613922 TCAAGTATCATATCAGAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
1613946 TCAA
1 TCAA
1613950 GTAACAGATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (24 bp):
TCAAAAATCAAAACAGAAATCAGG
Found at i:1613950 original size:24 final size:24
Alignment explanation
Indices: 1613918--1614035 Score: 150
Period size: 24 Copynumber: 4.9 Consensus size: 24
1613908 AAACATAAAT
*
1613918 CAGGTCAAGTATCATATCAGAAAT-
1 CAGGTCAAGTATCAGATCAG-AATC
*
1613942 CAGGTCAAGTAACAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
* *
1613966 CAAGTCAAGTATCATATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
*
1613990 CATGTC-AGATATCAGATCAGAATC
1 CAGGTCAAG-TATCAGATCAGAATC
*
1614014 CATGTCAAGTATCAGATCAGAA
1 CAGGTCAAGTATCAGATCAGAA
1614036 ATCAAATCAA
Statistics
Matches: 84, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
23 5 0.06
24 77 0.92
25 2 0.02
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (24 bp):
CAGGTCAAGTATCAGATCAGAATC
Found at i:1614052 original size:48 final size:48
Alignment explanation
Indices: 1613921--1614052 Score: 160
Period size: 48 Copynumber: 2.8 Consensus size: 48
1613911 CATAAATCAG
* *
1613921 GTCAAGTATCATATCAGAAATCAGGTCAAGTAA-CAGATCAGAATCCAA
1 GTCAAGTATCATATCAGAAATCAAGTCAA-AAATCAGATCAGAATCCAA
* * * *
1613969 GTCAAGTATCATATCAG-AATCCATGTCAGATATCAGATCAGAATCCAT
1 GTCAAGTATCATATCAGAAAT-CAAGTCAAAAATCAGATCAGAATCCAA
* *
1614017 GTCAAGTATCAGATCAGAAATCAAATCAAAAATCAG
1 GTCAAGTATCATATCAGAAATCAAGTCAAAAATCAG
1614053 GTAAAATATT
Statistics
Matches: 71, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
47 4 0.06
48 64 0.90
49 3 0.04
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.23
Consensus pattern (48 bp):
GTCAAGTATCATATCAGAAATCAAGTCAAAAATCAGATCAGAATCCAA
Found at i:1623620 original size:22 final size:22
Alignment explanation
Indices: 1623595--1623638 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1623585 ATTAACTAAG
1623595 ATTTTAAATAAAAATACATATT
1 ATTTTAAATAAAAATACATATT
* * *
1623617 ATTTTATATAAATATATATATT
1 ATTTTAAATAAAAATACATATT
1623639 TATGGTTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
ATTTTAAATAAAAATACATATT
Found at i:1624952 original size:3 final size:3
Alignment explanation
Indices: 1624944--1624986 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
1624934 AGCATGTTTG
*
1624944 TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA -AA TAA TAA CAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1624987 ATAAATAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 4 0.11
3 33 0.89
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:1625001 original size:9 final size:10
Alignment explanation
Indices: 1624944--1624994 Score: 54
Period size: 9 Copynumber: 5.3 Consensus size: 10
1624934 AGCATGTTTG
1624944 TAATAAT-AA
1 TAATAATAAA
1624953 TAATAAT-AA
1 TAATAATAAA
1624962 TAATAATAAA
1 TAATAATAAA
*
1624972 AAATAAT-AA
1 TAATAATAAA
*
1624981 CAATAAATAAA
1 TAAT-AATAAA
1624992 TAA
1 TAA
1624995 ATAAAATGGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
9 21 0.58
10 11 0.31
11 4 0.11
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (10 bp):
TAATAATAAA
Found at i:1625253 original size:17 final size:17
Alignment explanation
Indices: 1625231--1625288 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
1625221 TTGAACAAGC
1625231 TCTTCTCATTGTGAACT
1 TCTTCTCATTGTGAACT
1625248 TCTTCTTC-TTCAGATG-A-T
1 TCTTC-TCATT--G-TGAACT
1625266 TCTTCTCATTGTGAACT
1 TCTTCTCATTGTGAACT
*
1625283 CCTTCT
1 TCTTCT
1625289 GGAAATGCTG
Statistics
Matches: 33, Mismatches: 1, Indels: 14
0.69 0.02 0.29
Matches are distributed among these distances:
15 2 0.06
16 2 0.06
17 15 0.45
18 10 0.30
19 2 0.06
20 2 0.06
ACGTcount: A:0.16, C:0.26, G:0.10, T:0.48
Consensus pattern (17 bp):
TCTTCTCATTGTGAACT
Found at i:1625369 original size:119 final size:118
Alignment explanation
Indices: 1625216--1625544 Score: 410
Period size: 123 Copynumber: 2.7 Consensus size: 118
1625206 GTAATCTAGC
* *
1625216 AAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTC-TTCTTCAGATGATTCTTCTCATTGTGA
1 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTTCTTCAGATGATTCTTCTCATTATGA
* * * *
1625280 ACTCCTTCTGGAAATGCTGATGATGATATATCTCATTCTGTGATAGAGTCATGCA
66 ACT--TTCTGGAAAAGCTGATGATGATATATCTCATTCTATGATAGAGTCAAGAA
*
1625335 AAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGATTCTTCTCATTA
1 AAAGGTTGAACAAGCTCTTCTCATTATGAA---CTTCTTCTTTCTTCAGATGATTCTTCTCATTA
* * * *
1625400 TGAACTTTCTCTGGAAAAAGTTGATGTTGATCTATCTCCTTCTATGATAGAGTCAAGAA
63 TGAAC-TT-TCTGG-AAAAGCTGATGATGATATATCTCATTCTATGATAGAGTCAAGAA
** *
1625459 AAAGGTTGAACAAAAT-TTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTA
1 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTT--TCTTCAGATGA-TTCTTCTCATTA
*
1625523 TGAACTTTCTGGAAAAGTTGAT
63 TGAACTTTCTGGAAAAGCTGAT
1625545 CCATCGAATG
Statistics
Matches: 185, Mismatches: 15, Indels: 19
0.84 0.07 0.09
Matches are distributed among these distances:
119 28 0.15
120 19 0.10
121 5 0.03
122 20 0.11
123 63 0.34
124 50 0.27
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (118 bp):
AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTTCTTCAGATGATTCTTCTCATTATGA
ACTTTCTGGAAAAGCTGATGATGATATATCTCATTCTATGATAGAGTCAAGAA
Found at i:1625479 original size:123 final size:121
Alignment explanation
Indices: 1625216--1625770 Score: 436
Period size: 113 Copynumber: 4.7 Consensus size: 121
1625206 GTAATCTAGC
* *
1625216 AAAGGTTGAACAAGCTCTTCTCATTGTGAA---CTTCTTCTTCTTCAGATGATTCTTCTCATTGT
1 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGATTCTTCTCATTAT
* * * * * *
1625278 GAACTCCTTCTGGAAATGCTGATGATGATATATCTCATTCTGTGATAGAGTCATGCA
66 GAACTTC-TCTGGAAAAGTTGATGATGATATATCTCATTCTATGATAGAGTCAAGAA
*
1625335 AAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGATTCTTCTCATTA
1 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTC-TTCTTCAGATGATTCTTCTCATTA
* * *
1625400 TGAACTTTCTCTGGAAAAAGTTGATGTTGATCTATCTCCTTCTATGATAGAGTCAAGAA
65 TGAAC-TTCTCTGG-AAAAGTTGATGATGATATATCTCATTCTATGATAGAGTCAAGAA
** * *
1625459 AAAGGTTGAACAAAAT-TTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTA
1 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGA-TTCTTCTCATTA
* *
1625523 TGAACTT-TCTGGAAAA---G-T--TG----ATC-CA-TCGAATGAT-GAATTCAA-ACA
65 TGAACTTCTCTGGAAAAGTTGATGATGATATATCTCATTC-TATGATAG-AGTCAAGA-A
* ** * *
1625568 AAAAGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGACGAGTTCTTCTCATT
1 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGA-TTCTTCTCATT
* * * * * * *
1625633 ATGAA---CTCT---ACA--TGGTAATGCT-GATC-CA-TCAAATGAT-GAATTCAA-ACA
64 ATGAACTTCTCTGGAAAAGTTGATGATGATATATCTCATTC-TATGATAG-AGTCAAGA-A
**
1625681 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGA-TTCTTCTCATT
* *
1625746 ATGAAATTTCTCTGGAAAAGCTGAT
64 ATG-AACTTCTCTGGAAAAGTTGAT
1625771 CCATGAAGTG
Statistics
Matches: 374, Mismatches: 33, Indels: 55
0.81 0.07 0.12
Matches are distributed among these distances:
106 2 0.01
107 1 0.00
108 5 0.01
109 29 0.08
110 26 0.07
111 27 0.07
113 89 0.24
114 4 0.01
116 1 0.00
117 5 0.01
119 28 0.07
120 6 0.02
121 5 0.01
122 22 0.06
123 73 0.20
124 51 0.14
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (121 bp):
AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGATTCTTCTCATTAT
GAACTTCTCTGGAAAAGTTGATGATGATATATCTCATTCTATGATAGAGTCAAGAA
Found at i:1625677 original size:113 final size:112
Alignment explanation
Indices: 1625457--1626117 Score: 813
Period size: 113 Copynumber: 5.9 Consensus size: 112
1625447 TAGAGTCAAG
* *
1625457 AAAAAGGTTGAACAAAAT-TTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCA
1 AAAAA-GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * *
1625520 TTATGAACT-TTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAAC
65 TTATGAACTCTACTGGAAATGCTGATCCATCAAATGATGAATTCAAAC
* *
1625567 AAAAAGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGACGAGTTCTTCTCAT
1 AAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
1625632 TATGAACTCTACATGGTAATGCTGATCCATCAAATGATGAATTCAAAC
66 TATGAACTCTAC-TGGAAATGCTGATCCATCAAATGATGAATTCAAAC
*
1625680 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * * ** *
1625745 TATGAAATTTCT-CTGGAAAAGCTGATCCATGAAGTGATGGATTTGAGC
66 TATG-AA-CTCTACTGGAAATGCTGATCCATCAAATGATGAATTCAAAC
*
1625793 AAAAGGTTGAACAAATTCTTCTCATTATGAA--T-TTCTT-CTTCTTCAGATGACGAGTTCTTCT
1 AAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCT
* * *
1625854 CATTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTTAAAC
63 CATTATGAACTCTA-CTGGAAATGCTGATCCATCAAATGATGAATTCAAAC
* ** *
1625905 AAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTT-TTCTCAT
1 AAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
** * * *
1625969 TATGAACT-TTTTTGAAATGATGATCCATC-GATGATGAATTCAAAC
66 TATGAACTCTACTGGAAATGCTGATCCATCAAATGATGAATTCAAAC
* * *
1626014 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGGGTTCTTCTCGT
1 AAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * **
1626079 TATGAACTCTAACTGGCACTGTTGATCCATTGAATGATG
66 TATGAACTCT-ACTGGAAATGCTGATCCATCAAATGATG
1626118 GATTTAAATC
Statistics
Matches: 479, Mismatches: 53, Indels: 35
0.84 0.09 0.06
Matches are distributed among these distances:
109 89 0.19
110 65 0.14
111 33 0.07
112 104 0.22
113 165 0.34
114 4 0.01
115 8 0.02
116 11 0.02
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (112 bp):
AAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTCTACTGGAAATGCTGATCCATCAAATGATGAATTCAAAC
Found at i:1625912 original size:225 final size:224
Alignment explanation
Indices: 1625458--1626125 Score: 935
Period size: 225 Copynumber: 3.0 Consensus size: 224
1625448 AGAGTCAAGA
1625458 AAAAGGTTGAACAAAAT-TTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCAT
1 AAAAGGTTGAACAAAATCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCAT
* *
1625521 TATG-AACTTTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAACAAAAAGTTGAACAAATTC
66 TATGAAATTTTCTGGAAAAGATGATCCATCGAATGATGAATTCAAACAAAAAGTTGAACAAATTC
** * *
1625585 TTCTCATTATGAATTTCTTCTTCCTTCTTCA-GACGAGTTCTTCTCATTATGAACTCTACATGGT
131 TTCTCATTATGAATTTCTTCTT-CTTC-AGATGACGAGTTCTTCTCATTATGAACTCTACCTGGC
* *
1625649 AATGCTGATCCATCAAATGATGAATTCAAAC
194 AATGTTGATCCATCAAATGATGAATTTAAAC
* *
1625680 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAAATCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCAT
* * ** * *
1625745 TATGAAATTTCTCTGGAAAAGCTGATCCAT-GAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
66 TATGAAATTT-TCTGGAAAAGATGATCCATCGAA-TGATGAATTCAAACAAAAAGTTGAACAAAT
1625809 TCTTCTCATTATGAATTTCTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGC
129 TCTTCTCATTATGAATTTCTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGC
1625874 AATGTTGATCCATCAAATGATGAATTTAAAC
194 AATGTTGATCCATCAAATGATGAATTTAAAC
**
1625905 AAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTT-TTCTCAT
1 AAAAGGTTGAACAAAATCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCAT
* * * *
1625969 TATGAACTTTT-TTGAAATGATGATCCATCG-ATGATGAATTCAAACAAAAAGTTGAACAAGTTC
66 TATGAAATTTTCTGGAAAAGATGATCCATCGAATGATGAATTCAAACAAAAAGTTGAACAAATTC
* *
1626032 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG--G-GTTCTTCTCGTTATGAACTCTAACTG
131 TTCTCATTATGAA--T-TTCTT-CTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTG
* ** *
1626094 GCACTGTTGATCCATTGAATGATGGATTTAAA
192 GCAATGTTGATCCATCAAATGATGAATTTAAA
1626126 TCTTTGCTAA
Statistics
Matches: 401, Mismatches: 34, Indels: 22
0.88 0.07 0.05
Matches are distributed among these distances:
221 39 0.10
222 83 0.21
223 28 0.07
224 47 0.12
225 137 0.34
226 67 0.17
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (224 bp):
AAAAGGTTGAACAAAATCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCAT
TATGAAATTTTCTGGAAAAGATGATCCATCGAATGATGAATTCAAACAAAAAGTTGAACAAATTC
TTCTCATTATGAATTTCTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAA
TGTTGATCCATCAAATGATGAATTTAAAC
Found at i:1627013 original size:114 final size:114
Alignment explanation
Indices: 1626813--1627036 Score: 385
Period size: 114 Copynumber: 2.0 Consensus size: 114
1626803 GATCATACAG
* * * *
1626813 TTCATCTTTCAATTCCAATGATTGGTTCTGGGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAAATCAAAGA
1626878 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
* * *
1626927 TTCATCTTTTAAATCTAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAAATCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAAATCAAAGA
1626992 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAG
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAG
1627037 AACGTGGCAC
Statistics
Matches: 103, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 103 1.00
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.33
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAAATCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
Found at i:1627746 original size:12 final size:13
Alignment explanation
Indices: 1627724--1627792 Score: 56
Period size: 14 Copynumber: 5.4 Consensus size: 13
1627714 TCTTGACCCC
1627724 CTTTTTTTTC-TT
1 CTTTTTTTTCATT
1627736 -TTTTTTCTTC-TT
1 CTTTTTT-TTCATT
**
1627748 CTCTTTTTTTTTTT
1 CT-TTTTTTTCATT
1627762 CTTTTTTTTTCATT
1 C-TTTTTTTTCATT
*
1627776 TTTTTTTTTCATT
1 CTTTTTTTTCATT
1627789 -TTTT
1 CTTTT
1627793 AAGCATAATA
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
11 6 0.12
12 9 0.19
13 15 0.31
14 17 0.35
15 1 0.02
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (13 bp):
CTTTTTTTTCATT
Found at i:1627754 original size:17 final size:17
Alignment explanation
Indices: 1627732--1627764 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1627722 CCCTTTTTTT
1627732 TCTTTTTTTTCTTCTTC
1 TCTTTTTTTTCTTCTTC
*
1627749 TCTTTTTTTTTTTCTT
1 TCTTTTTTTTCTTCTT
1627765 TTTTTTTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (17 bp):
TCTTTTTTTTCTTCTTC
Found at i:1633565 original size:23 final size:23
Alignment explanation
Indices: 1633547--1633606 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
1633537 CTCGTATAAA
1633547 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
1633570 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
*
1633593 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
1633607 ATATAATGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.23, C:0.32, G:0.27, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCCCGTAGAAT
Found at i:1634325 original size:67 final size:66
Alignment explanation
Indices: 1634218--1634367 Score: 246
Period size: 67 Copynumber: 2.3 Consensus size: 66
1634208 TTTTTTTCAT
* * *
1634218 GGGGGAATCGGTTCCCCCCTGGGGTATCGGTTCCCCTCTAGCATTCTGGAATTTCATATCCGTTG
1 GGGGGTATCGGTTCCCCCCTGGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATCCGTTG
1634283 A
66 A
* *
1634284 GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCTAGTATTCTGGAAATTCATATTCGTT
1 GGGGGTATCGGTTCCCCCCT-GGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATCCGTT
1634349 GA
65 GA
1634351 GGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
1634368 TTGAATGGGT
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
66 19 0.24
67 59 0.76
ACGTcount: A:0.15, C:0.26, G:0.29, T:0.31
Consensus pattern (66 bp):
GGGGGTATCGGTTCCCCCCTGGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATCCGTTG
A
Found at i:1634886 original size:22 final size:20
Alignment explanation
Indices: 1634850--1634889 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
1634840 ACGTTGAGAG
1634850 AAGGAAGAGAAGAAGAAAAT
1 AAGGAAGAGAAGAAGAAAAT
1634870 AAGGAAGAAGGAAGAAGAAA
1 AAGGAAG-A-GAAGAAGAAA
1634890 TGGGAGGGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 1 0.06
22 10 0.56
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.03
Consensus pattern (20 bp):
AAGGAAGAGAAGAAGAAAAT
Found at i:1637244 original size:15 final size:15
Alignment explanation
Indices: 1637221--1637252 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1637211 TGCAATGAAT
1637221 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
1637236 AATGCATGTATGCAA
1 AATGAATGTATGCAA
1637251 AA
1 AA
1637253 GGTATTGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:1641207 original size:20 final size:19
Alignment explanation
Indices: 1641168--1641219 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
1641158 TTTCTTTGAT
1641168 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
1641187 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
*
1641207 ATTTATAAAATAA
1 A-TTAAAAAATAA
1641220 GATATTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 7 0.26
20 15 0.56
21 5 0.19
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:1641633 original size:19 final size:20
Alignment explanation
Indices: 1641609--1641659 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
1641599 AATGACCAAT
1641609 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
1641628 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
1641648 AAAATCGCAACG
1 AAAATCGCAACG
1641660 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:1641653 original size:20 final size:20
Alignment explanation
Indices: 1641609--1641863 Score: 138
Period size: 20 Copynumber: 12.6 Consensus size: 20
1641599 AATGACCAAT
* *
1641609 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
1641628 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
1641648 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
1641668 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
1641688 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
1641709 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * * *
1641732 AAAATCGCAATGTGATTGAT
1 AAAATCGCAACGCGATTTAG
* * *
1641752 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * * *
1641772 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * * *
1641792 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * *
1641812 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
*
1641832 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
1641852 AAAATCGCAACG
1 AAAATCGCAACG
1641864 TTGAAAATAA
Statistics
Matches: 192, Mismatches: 35, Indels: 17
0.79 0.14 0.07
Matches are distributed among these distances:
19 17 0.09
20 148 0.77
21 14 0.07
23 13 0.07
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:1641796 original size:40 final size:40
Alignment explanation
Indices: 1641713--1641861 Score: 190
Period size: 40 Copynumber: 3.6 Consensus size: 40
1641703 GCTTCCAAGT
* * *
1641713 TCGCAACGCGATTTAGAAGAAAATCGCAATGTGATTGATAGAA
1 TCGCAATGCGATTTAG-AG--AATCGCAATGCGATTGAGAGAA
* *
1641756 TCGCAATGCGATTTATAGAATCGCAATGCGACTGAGAGAA
1 TCGCAATGCGATTTAGAGAATCGCAATGCGATTGAGAGAA
* *
1641796 TCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAA
1 TCGCAATGCGATTTAGAGAATCGCAATGCGATTGAGAGAA
* *
1641836 TCGCAACGCGATTTAGAAAATCGCAA
1 TCGCAATGCGATTTAGAGAATCGCAA
1641862 CGTTGAAAAT
Statistics
Matches: 93, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
40 77 0.83
42 2 0.02
43 14 0.15
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.21
Consensus pattern (40 bp):
TCGCAATGCGATTTAGAGAATCGCAATGCGATTGAGAGAA
Found at i:1641816 original size:60 final size:60
Alignment explanation
Indices: 1641730--1641861 Score: 183
Period size: 60 Copynumber: 2.2 Consensus size: 60
1641720 GCGATTTAGA
* * * * * *
1641730 AGAAAATCGCAATGTGATTGATAGAATCGCAATGCGATTTATAGAATCGCAATGCGACTG
1 AGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAATCGCAACGCGACTG
* * *
1641790 AGAGAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAATCGCAACGCGATTT
1 AGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAATCGCAACGCGACTG
1641850 AGAAAATCGCAA
1 AGAAAATCGCAA
1641862 CGTTGAAAAT
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.20
Consensus pattern (60 bp):
AGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAATCGCAACGCGACTG
Found at i:1641890 original size:20 final size:20
Alignment explanation
Indices: 1641852--1641890 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1641842 CGCGATTTAG
* *
1641852 AAAATCGCAACGTTGAAAAT
1 AAAATCGCAACGGTCAAAAT
1641872 AAAATCGCAACGGTCAAAA
1 AAAATCGCAACGGTCAAAA
1641891 GAATAGTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.51, C:0.18, G:0.15, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACGGTCAAAAT
Found at i:1641982 original size:6 final size:6
Alignment explanation
Indices: 1641971--1642075 Score: 210
Period size: 6 Copynumber: 17.5 Consensus size: 6
1641961 GACACGTATT
1641971 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1642019 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1642067 ACCACG ACC
1 ACCACG ACC
1642076 CGAGACGAGA
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 99 1.00
ACGTcount: A:0.33, C:0.50, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1642786 original size:6 final size:6
Alignment explanation
Indices: 1642766--1642833 Score: 111
Period size: 6 Copynumber: 11.5 Consensus size: 6
1642756 TCTCGTCTCG
* *
1642766 GGTCG- GGTCGT GGTCGG GGTCGG GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1642813 GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGT
1642834 AATACGTGTC
Statistics
Matches: 60, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
5 5 0.08
6 55 0.92
ACGTcount: A:0.00, C:0.16, G:0.54, T:0.29
Consensus pattern (6 bp):
GGTCGT
Found at i:1642966 original size:20 final size:20
Alignment explanation
Indices: 1642943--1643093 Score: 167
Period size: 20 Copynumber: 7.4 Consensus size: 20
1642933 ATTTTCAACG
* *
1642943 TTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTCAATCGCA
* *
1642963 TTGCGATTCTCTCAGTCGCG
1 TTGCGATTCTCTCAATCGCA
* *
1642983 TTGCGATTTTCTTCTAAATCGCG
1 TTGCGA--TTC-TCTCAATCGCA
* *
1643006 TTGCGACTCTCTCAATCGCG
1 TTGCGATTCTCTCAATCGCA
*
1643026 TTGCGACTCTCTCAATCGCA
1 TTGCGATTCTCTCAATCGCA
* *
1643046 TTGCGATTATATCAATCGCA
1 TTGCGATTCTCTCAATCGCA
*
1643066 TTGCGATTCTATCAATCGCA
1 TTGCGATTCTCTCAATCGCA
1643086 TTGCGATT
1 TTGCGATT
1643094 TTCTTCTAAA
Statistics
Matches: 115, Mismatches: 13, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
20 95 0.83
21 2 0.02
22 3 0.03
23 15 0.13
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.36
Consensus pattern (20 bp):
TTGCGATTCTCTCAATCGCA
Found at i:1642985 original size:40 final size:40
Alignment explanation
Indices: 1642941--1643114 Score: 186
Period size: 40 Copynumber: 4.2 Consensus size: 40
1642931 TTATTTTCAA
*
1642941 CGTTGCGATTCTATAAATCGCATTGCGATTCTCTCAGTCG
1 CGTTGCGATTCTATAAATCGCATTGCGATTCTCTCAATCG
* * *
1642981 CGTTGCGATTTTCTTCTAAATCGCGTTGCGACTCTCTCAATCG
1 CGTTGCGA--TTC-TATAAATCGCATTGCGATTCTCTCAATCG
* * * * *
1643024 CGTTGCGACTCTCTCAATCGCATTGCGATTATATCAATCG
1 CGTTGCGATTCTATAAATCGCATTGCGATTCTCTCAATCG
* * *
1643064 CATTGCGATTCTATCAATCGCATTGCGATTTTCTTCTAAATCG
1 CGTTGCGATTCTATAAATCGCATTGCGA--TTC-TCTCAATCG
1643107 CGTTGCGA
1 CGTTGCGA
1643115 ACTTGGAAGC
Statistics
Matches: 111, Mismatches: 17, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
40 57 0.51
41 2 0.02
42 5 0.05
43 47 0.42
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.36
Consensus pattern (40 bp):
CGTTGCGATTCTATAAATCGCATTGCGATTCTCTCAATCG
Found at i:1643106 original size:83 final size:81
Alignment explanation
Indices: 1642941--1643114 Score: 190
Period size: 83 Copynumber: 2.1 Consensus size: 81
1642931 TTATTTTCAA
* * * * * *
1642941 CGTTGCGATTCTATAAATCGCATTGCGATTCTCTCAGTCGCGTTGCGATTTTCTTCTAAATCGCG
1 CGTTGCGACTCTATAAATCGCATTGCGATTATATCAATCGCATTGCGA-TTTCTTC-AAATCGCA
*
1643006 TTGCGACTCTCTCAATCG
64 TTGCGACTCTCTAAATCG
* *
1643024 CGTTGCGACTCTCTCAATCGCATTGCGATTATATCAATCGCATTGCGA-TTCTATC-AATCGCAT
1 CGTTGCGACTCTATAAATCGCATTGCGATTATATCAATCGCATTGCGATTTCT-TCAAATCGCAT
*
1643087 TGCGATTTTCTTCTAAATCG
65 TGCGA--CTC-TCTAAATCG
1643107 CGTTGCGA
1 CGTTGCGA
1643115 ACTTGGAAGC
Statistics
Matches: 77, Mismatches: 10, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
80 12 0.16
81 4 0.05
82 4 0.05
83 57 0.74
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.36
Consensus pattern (81 bp):
CGTTGCGACTCTATAAATCGCATTGCGATTATATCAATCGCATTGCGATTTCTTCAAATCGCATT
GCGACTCTCTAAATCG
Found at i:1643155 original size:20 final size:20
Alignment explanation
Indices: 1643130--1643181 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
1643120 GAAGCTCGCA
*
1643130 TTGCGATTTTCTTTTGACCG
1 TTGCGATTTTCTTTTGAACG
*
1643150 TTGCGATTTTCTTTTTAACG
1 TTGCGATTTTCTTTTGAACG
1643170 TTGCGATTTTCT
1 TTGCGATTTTCT
1643182 AAATCGCGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.12, C:0.17, G:0.17, T:0.54
Consensus pattern (20 bp):
TTGCGATTTTCTTTTGAACG
Found at i:1643208 original size:19 final size:20
Alignment explanation
Indices: 1643168--1643218 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
1643158 TTCTTTTTAA
*
1643168 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
1643188 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
1643207 CGTTGCGATTTT
1 CGTTGCGATTTT
1643219 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:1644568 original size:3 final size:3
Alignment explanation
Indices: 1644560--1644604 Score: 65
Period size: 3 Copynumber: 15.0 Consensus size: 3
1644550 AGCCTATTTG
*
1644560 TAA TAA TAA TAA TAA TAA TAA TAAA TAA -AA TAA TAA TAA CAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
1644605 ATAAATAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 2 0.05
3 33 0.87
4 3 0.08
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:1644592 original size:24 final size:25
Alignment explanation
Indices: 1644564--1644613 Score: 84
Period size: 24 Copynumber: 2.0 Consensus size: 25
1644554 TATTTGTAAT
*
1644564 AATAATAATAATAAT-AATAAATAA
1 AATAATAATAACAATAAATAAATAA
1644588 AATAATAATAACAATAAATAAATAA
1 AATAATAATAACAATAAATAAATAA
1644613 A
1 A
1644614 TAAAATGGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 14 0.58
25 10 0.42
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (25 bp):
AATAATAATAACAATAAATAAATAA
Found at i:1644616 original size:21 final size:21
Alignment explanation
Indices: 1644561--1644609 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
1644551 GCCTATTTGT
*
1644561 AATAATAATAATAATAATAATA
1 AATAA-AATAATAATAACAATA
1644583 AATAAAATAATAATAACAATA
1 AATAAAATAATAATAACAATA
1644604 AATAAA
1 AATAAA
1644610 TAAATAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 21 0.81
22 5 0.19
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (21 bp):
AATAAAATAATAATAACAATA
Found at i:1645393 original size:29 final size:28
Alignment explanation
Indices: 1645352--1645406 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
1645342 TTTTAAGGGT
*
1645352 AAAGTACACAATGATCCT-TCGACTATTA
1 AAAGTACAAAATGATCCTCT-GACTATTA
1645380 AAAGTTACAAAATGATCCTCTGACTAT
1 AAAG-TACAAAATGATCCTCTGACTAT
1645407 AAGATGTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 4 0.17
29 19 0.79
30 1 0.04
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (28 bp):
AAAGTACAAAATGATCCTCTGACTATTA
Found at i:1654111 original size:18 final size:18
Alignment explanation
Indices: 1654088--1654126 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
1654078 TAAAACTCTC
1654088 TAAATCGTCATTATTATT
1 TAAATCGTCATTATTATT
1654106 TAAATCGTCATTATTATT
1 TAAATCGTCATTATTATT
1654124 TAA
1 TAA
1654127 CCACTTCCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.36, C:0.10, G:0.05, T:0.49
Consensus pattern (18 bp):
TAAATCGTCATTATTATT
Found at i:1657006 original size:13 final size:13
Alignment explanation
Indices: 1656988--1657015 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1656978 ACAAGCTTTT
1656988 TTATTATTATTTA
1 TTATTATTATTTA
1657001 TTATTATTATTTA
1 TTATTATTATTTA
1657014 TT
1 TT
1657016 TGGGGTAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTATTATTATTTA
Found at i:1659283 original size:19 final size:19
Alignment explanation
Indices: 1659259--1659297 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1659249 TCGAATGCAT
1659259 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
1659278 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
1659297 T
1 T
1659298 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:1659396 original size:64 final size:65
Alignment explanation
Indices: 1659245--1659405 Score: 209
Period size: 65 Copynumber: 2.5 Consensus size: 65
1659235 TGAATAATTG
* * *** *
1659245 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
* * **
1659310 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATTCA-TCAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATA-TTTTCA
1659373 A
65 A
1659374 AACATCGAATGCATTTCATGCATCGATGCACA
1 AACATCGAATGCATTTCATGCATCGATGCACA
1659406 CTTGGTGCAC
Statistics
Matches: 84, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
64 37 0.44
65 47 0.56
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:1659425 original size:64 final size:64
Alignment explanation
Indices: 1659197--1659425 Score: 214
Period size: 64 Copynumber: 3.6 Consensus size: 64
1659187 TATTCAAAGG
* * * * *
1659197 CATGCACCGATGCATCAGTACATGCATCGATGCATCGATGAATA-ATT--GAACATCGAATGCAT
1 CATGCATCGATGCA-CACTCCATGCATCGATGCATC-A-GAATATTTTCAAAACATCGAATGCAT
*
1659259 TC
63 TT
* * *
1659261 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTT
1 CATGCATCGATGCACACTCCATGCATCGATGCA-TCAGAATATTTTCAAAACATCGAATGCATTT
* ** * **
1659326 GATGCATCGATGCACAAGCCATGCATCGATTCATCAGGCTATTTTTC-AAACATCGAATGCATTT
1 CATGCATCGATGCACACTCCATGCATCGATGCATCAGAATA-TTTTCAAAACATCGAATGCATTT
*** *
1659390 CATGCATCGATGCACACTTGGTGCACCGATGCATCA
1 CATGCATCGATGCACACTCCATGCATCGATGCATCA
1659426 AGTGTTCCAA
Statistics
Matches: 136, Mismatches: 24, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
62 5 0.04
63 18 0.13
64 66 0.49
65 47 0.35
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (64 bp):
CATGCATCGATGCACACTCCATGCATCGATGCATCAGAATATTTTCAAAACATCGAATGCATTT
Found at i:1665225 original size:20 final size:21
Alignment explanation
Indices: 1665202--1665250 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
1665192 TTCATGCACA
1665202 GATGCAT-TT-AACAATGCATC
1 GATGCATCTTGAA-AATGCATC
*
1665222 GATGCATCCTTGAATATGCATC
1 GATGCAT-CTTGAAAATGCATC
1665244 GATGCAT
1 GATGCAT
1665251 AAGACCATGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 7 0.28
22 16 0.64
23 2 0.08
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (21 bp):
GATGCATCTTGAAAATGCATC
Found at i:1666822 original size:21 final size:21
Alignment explanation
Indices: 1666780--1666823 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1666770 ACCCCGGGAG
*
1666780 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
1666801 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
1666822 CT
1 CT
1666824 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:1667896 original size:19 final size:19
Alignment explanation
Indices: 1667872--1667910 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1667862 TCGAATGCAT
1667872 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
1667891 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
1667910 T
1 T
1667911 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:1668009 original size:64 final size:65
Alignment explanation
Indices: 1667858--1668018 Score: 209
Period size: 65 Copynumber: 2.5 Consensus size: 65
1667848 TGAATAATTG
* * *** *
1667858 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
* * **
1667923 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATTCA-TCAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATA-TTTTCA
1667986 A
65 A
1667987 AACATCGAATGCATTTCATGCATCGATGCACA
1 AACATCGAATGCATTTCATGCATCGATGCACA
1668019 CTTGGTGCAC
Statistics
Matches: 84, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
64 37 0.44
65 47 0.56
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:1668038 original size:64 final size:64
Alignment explanation
Indices: 1667810--1668038 Score: 214
Period size: 64 Copynumber: 3.6 Consensus size: 64
1667800 TATTCAAAGG
* * * * *
1667810 CATGCACCGATGCATCAGTACATGCATCGATGCATCGATGAATA-ATT--GAACATCGAATGCAT
1 CATGCATCGATGCA-CACTCCATGCATCGATGCATC-A-GAATATTTTCAAAACATCGAATGCAT
*
1667872 TC
63 TT
* * *
1667874 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTT
1 CATGCATCGATGCACACTCCATGCATCGATGCA-TCAGAATATTTTCAAAACATCGAATGCATTT
* ** * **
1667939 GATGCATCGATGCACAAGCCATGCATCGATTCATCAGGCTATTTTTC-AAACATCGAATGCATTT
1 CATGCATCGATGCACACTCCATGCATCGATGCATCAGAATA-TTTTCAAAACATCGAATGCATTT
*** *
1668003 CATGCATCGATGCACACTTGGTGCACCGATGCATCA
1 CATGCATCGATGCACACTCCATGCATCGATGCATCA
1668039 AGTGTTCCAA
Statistics
Matches: 136, Mismatches: 24, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
62 5 0.04
63 18 0.13
64 66 0.49
65 47 0.35
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (64 bp):
CATGCATCGATGCACACTCCATGCATCGATGCATCAGAATATTTTCAAAACATCGAATGCATTT
Found at i:1673810 original size:42 final size:42
Alignment explanation
Indices: 1673758--1673916 Score: 241
Period size: 42 Copynumber: 3.8 Consensus size: 42
1673748 GAGCCTAGGA
* *
1673758 AAACTGTAAGGTTTATCCTT-GCACACATCAAAGGGACCTGGG
1 AAACTGTAAGGCTTA-CCTTCGCACACAGCAAAGGGACCTGGG
* *
1673800 AAACTGTAAGGCTTACCCTT-GGACACAGCAAAGGGACCTGGT
1 AAACTGTAAGGCTTA-CCTTCGCACACAGCAAAGGGACCTGGG
*
1673842 AAACTGTAAGGCTTACCTTCGCACACAGCAAAGGGACTTGGG
1 AAACTGTAAGGCTTACCTTCGCACACAGCAAAGGGACCTGGG
1673884 AAACTGTAAGGCTTACCTTCGCACACAGCAAAG
1 AAACTGTAAGGCTTACCTTCGCACACAGCAAAG
1673917 AGACTTGATA
Statistics
Matches: 108, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
41 4 0.04
42 104 0.96
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.20
Consensus pattern (42 bp):
AAACTGTAAGGCTTACCTTCGCACACAGCAAAGGGACCTGGG
Found at i:1684746 original size:29 final size:27
Alignment explanation
Indices: 1684712--1684808 Score: 72
Period size: 29 Copynumber: 3.4 Consensus size: 27
1684702 AAAGGGTCAT
1684712 AGTTTAAGGATGAAATTAGAATGTTCAAA
1 AGTTTAAGGAT-AAATTAGAATG-TCAAA
* *
1684741 AGTTTAATGACT-AATGTAGAATAAGTC-AT
1 AGTTTAAGGA-TAAAT-TAGAAT--GTCAAA
* *
1684770 AGTTTAGGGATAAAATTAGAATAATCAAA
1 AGTTTAAGGAT-AAATTAGAAT-GTCAAA
1684799 AGTTTAAGGA
1 AGTTTAAGGA
1684809 CCATTTAAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
28 7 0.13
29 40 0.74
30 6 0.11
31 1 0.02
ACGTcount: A:0.45, C:0.04, G:0.20, T:0.31
Consensus pattern (27 bp):
AGTTTAAGGATAAATTAGAATGTCAAA
Found at i:1684786 original size:58 final size:58
Alignment explanation
Indices: 1684690--1684805 Score: 162
Period size: 58 Copynumber: 2.0 Consensus size: 58
1684680 AAAATTTGGG
* * **
1684690 GACTAATTTAGAAAAGGGTCATAGTTTAAGGATGAAATTAGAATGTTCAAAAGTTTAAT
1 GACTAATGTAGAAAA-GGTCATAGTTTAAGGATAAAATTAGAATAATCAAAAGTTTAAT
*
1684749 GACTAATGTAGAATAA-GTCATAGTTTAGGGATAAAATTAGAATAATCAAAAGTTTAA
1 GACTAATGTAGAA-AAGGTCATAGTTTAAGGATAAAATTAGAATAATCAAAAGTTTAA
1684806 GGACCATTTA
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
58 37 0.73
59 12 0.24
60 2 0.04
ACGTcount: A:0.45, C:0.05, G:0.19, T:0.31
Consensus pattern (58 bp):
GACTAATGTAGAAAAGGTCATAGTTTAAGGATAAAATTAGAATAATCAAAAGTTTAAT
Found at i:1689825 original size:51 final size:51
Alignment explanation
Indices: 1689745--1689888 Score: 164
Period size: 51 Copynumber: 2.8 Consensus size: 51
1689735 AAATAGTTTC
* ** * * * * *
1689745 CTAAATCAGAAATAAGCAGTGACCCAAATGCGTAAATTGAAAGGACGATAG
1 CTAAATCAGAAATAAACAGTGACTAAAATGCATAAATTAAAAGAACAATGG
* * *
1689796 -TCAAATCAAAAATAAACAGTCACTAAAATGCATAAAATAAAAGAACAATGG
1 CT-AAATCAGAAATAAACAGTGACTAAAATGCATAAATTAAAAGAACAATGG
*
1689847 CTAAATCAGAAATAAACAGTGACTAAGATGCATAAATTAAAA
1 CTAAATCAGAAATAAACAGTGACTAAAATGCATAAATTAAAA
1689889 ATACATAAAA
Statistics
Matches: 76, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
50 1 0.01
51 74 0.97
52 1 0.01
ACGTcount: A:0.53, C:0.14, G:0.15, T:0.19
Consensus pattern (51 bp):
CTAAATCAGAAATAAACAGTGACTAAAATGCATAAATTAAAAGAACAATGG
Found at i:1691944 original size:21 final size:21
Alignment explanation
Indices: 1691896--1691944 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
1691886 TGGCCCGAAT
*
1691896 GACTTATCATCTTGCCTGAAG
1 GACTTATCATCTTGCCTGAAA
1691917 GACTTATCATCTTG-CTCGAAA
1 GACTTATCATCTTGCCT-GAAA
*
1691938 GAGTTAT
1 GACTTAT
1691945 AGATGACCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 2 0.08
21 23 0.92
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (21 bp):
GACTTATCATCTTGCCTGAAA
Found at i:1699272 original size:18 final size:18
Alignment explanation
Indices: 1699251--1699322 Score: 78
Period size: 18 Copynumber: 4.1 Consensus size: 18
1699241 TTTTTAATTT
1699251 TTTTCTTCTTTCTTTTTG
1 TTTTCTTCTTTCTTTTTG
1699269 TTTTCTTCTTTTCTTTTTCG
1 TTTTCTTC-TTTCTTTTT-G
* *
1699289 TTTTTTTCTAT-TTTTT-
1 TTTTCTTCTTTCTTTTTG
*
1699305 TCTT-TTCTTTCTTTTTG
1 TTTTCTTCTTTCTTTTTG
1699322 T
1 T
1699323 AATATATATA
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
15 5 0.11
16 8 0.17
17 1 0.02
18 13 0.28
19 11 0.24
20 8 0.17
ACGTcount: A:0.01, C:0.15, G:0.04, T:0.79
Consensus pattern (18 bp):
TTTTCTTCTTTCTTTTTG
Found at i:1699272 original size:21 final size:21
Alignment explanation
Indices: 1699226--1699297 Score: 69
Period size: 21 Copynumber: 3.4 Consensus size: 21
1699216 CCTATCATTT
**
1699226 TTTTTTCTCTTCTTAT-TTTTAA
1 TTTTTT-TCTTCTT-TCTTTTTG
1699248 TTTTTTTCTTCTTTCTTTTTG
1 TTTTTTTCTTCTTTCTTTTTG
*
1699269 TTTTCTTC-T-TTTCTTTTTCG
1 TTTTTTTCTTCTTTCTTTTT-G
1699289 TTTTTTTCT
1 TTTTTTTCT
1699298 ATTTTTTTCT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
19 9 0.21
20 10 0.23
21 18 0.42
22 6 0.14
ACGTcount: A:0.04, C:0.15, G:0.03, T:0.78
Consensus pattern (21 bp):
TTTTTTTCTTCTTTCTTTTTG
Found at i:1699274 original size:15 final size:15
Alignment explanation
Indices: 1699256--1699314 Score: 63
Period size: 14 Copynumber: 4.0 Consensus size: 15
1699246 AATTTTTTTC
1699256 TTCTTTCTTTT-TGTT
1 TTCTTTCTTTTCT-TT
1699271 TTC-TTCTTTTCTTT
1 TTCTTTCTTTTCTTT
1699285 TTCGTTT-TTTTCTATT
1 TTC-TTTCTTTTCT-TT
1699301 TT-TTTCTTTTCTTT
1 TTCTTTCTTTTCTTT
1699315 CTTTTTGTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
14 17 0.44
15 16 0.41
16 6 0.15
ACGTcount: A:0.02, C:0.15, G:0.03, T:0.80
Consensus pattern (15 bp):
TTCTTTCTTTTCTTT
Found at i:1699281 original size:19 final size:19
Alignment explanation
Indices: 1699251--1699319 Score: 79
Period size: 19 Copynumber: 3.6 Consensus size: 19
1699241 TTTTTAATTT
1699251 TTTTCTTC-TTTCTTTTTG
1 TTTTCTTCTTTTCTTTTTG
1699269 TTTTCTTCTTTTCTTTTTCG
1 TTTTCTTCTTTTCTTTTT-G
* * *
1699289 TTTTTTTCTATT-TTTTTC
1 TTTTCTTCTTTTCTTTTTG
1699307 TTTTCTTTCTTTT
1 TTTTC-TTCTTTT
1699320 TGTAATATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
18 12 0.28
19 20 0.47
20 11 0.26
ACGTcount: A:0.01, C:0.16, G:0.03, T:0.80
Consensus pattern (19 bp):
TTTTCTTCTTTTCTTTTTG
Found at i:1699296 original size:9 final size:8
Alignment explanation
Indices: 1699248--1699320 Score: 53
Period size: 9 Copynumber: 8.6 Consensus size: 8
1699238 TTATTTTTAA
1699248 TTTTTTTC
1 TTTTTTTC
1699256 TTCTTTCTT-
1 TT-TTT-TTC
1699265 TTTGTTTTC
1 TTT-TTTTC
*
1699274 TTCTTTTC
1 TTTTTTTC
1699282 --TTTTTC
1 TTTTTTTC
1699288 GTTTTTTTC
1 -TTTTTTTC
1699297 TATTTTTTTC
1 --TTTTTTTC
1699307 TTTTCTTTC
1 TTTT-TTTC
1699316 TTTTT
1 TTTTT
1699321 GTAATATATA
Statistics
Matches: 53, Mismatches: 3, Indels: 18
0.72 0.04 0.24
Matches are distributed among these distances:
6 5 0.09
8 15 0.28
9 23 0.43
10 10 0.19
ACGTcount: A:0.01, C:0.15, G:0.03, T:0.81
Consensus pattern (8 bp):
TTTTTTTC
Found at i:1699302 original size:10 final size:9
Alignment explanation
Indices: 1699248--1699320 Score: 58
Period size: 10 Copynumber: 7.4 Consensus size: 9
1699238 TTATTTTTAA
1699248 TTTTTTTCT
1 TTTTTTTCT
1699257 TCTTTCTTT-T
1 T-TTT-TTTCT
1699267 TGTTTTCTTCTT
1 T-TTTT-TTC-T
*
1699279 TTCTTTTTCG
1 TT-TTTTTCT
1699289 TTTTTTTCT
1 TTTTTTTCT
1699298 ATTTTTTTCT
1 -TTTTTTTCT
*
1699308 TTTCTTTCT
1 TTTTTTTCT
1699317 TTTT
1 TTTT
1699321 GTAATATATA
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
9 19 0.37
10 21 0.40
11 7 0.13
12 5 0.10
ACGTcount: A:0.01, C:0.15, G:0.03, T:0.81
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:1699319 original size:15 final size:14
Alignment explanation
Indices: 1699224--1699320 Score: 65
Period size: 15 Copynumber: 6.6 Consensus size: 14
1699214 CACCTATCAT
*
1699224 TTTTTTTTCTCTTC
1 TTTTTTTTCTTTTC
**
1699238 TTATTTTTAATTTT-
1 TT-TTTTTTCTTTTC
1699252 TTTCTTCTTTCTTTT-
1 TTT-TT-TTTCTTTTC
*
1699267 TGTTTTCTTCTTTTC
1 T-TTTTTTTCTTTTC
1699282 TTTTTCGTTT-TTTTC
1 TTTTT--TTTCTTTTC
1699297 TATTTTTTTCTTTTC
1 T-TTTTTTTCTTTTC
1699312 TTTCTTTTT
1 TTT-TTTTT
1699321 GTAATATATA
Statistics
Matches: 66, Mismatches: 7, Indels: 19
0.72 0.08 0.21
Matches are distributed among these distances:
13 1 0.02
14 22 0.33
15 35 0.53
16 8 0.12
ACGTcount: A:0.04, C:0.14, G:0.02, T:0.79
Consensus pattern (14 bp):
TTTTTTTTCTTTTC
Found at i:1699320 original size:25 final size:25
Alignment explanation
Indices: 1699223--1699314 Score: 73
Period size: 26 Copynumber: 3.6 Consensus size: 25
1699213 GCACCTATCA
* *
1699223 TTTTTT-TTTCTCTTCTTATTTTTAAT
1 TTTTTTCTTTTTCTTTTTA-TTTT-AT
* *
1699249 TTTTTTCTTCTTTCTTTTTGTTTTCT
1 TTTTTTCTT-TTTCTTTTTATTTTAT
* *
1699275 TCTTTTCTTTTTCGTTTTT-TTCTAT
1 TTTTTTCTTTTTC-TTTTTATTTTAT
1699300 TTTTTTC-TTTTCTTT
1 TTTTTTCTTTTTCTTT
1699315 CTTTTTGTAA
Statistics
Matches: 55, Mismatches: 8, Indels: 9
0.76 0.11 0.12
Matches are distributed among these distances:
23 3 0.05
24 5 0.09
25 14 0.25
26 20 0.36
27 6 0.11
28 7 0.13
ACGTcount: A:0.04, C:0.14, G:0.02, T:0.79
Consensus pattern (25 bp):
TTTTTTCTTTTTCTTTTTATTTTAT
Found at i:1702256 original size:20 final size:20
Alignment explanation
Indices: 1702231--1702273 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1702221 CCATTATTCC
* * *
1702231 ATAACCATATACCATAGGCA
1 ATAACCATAAACAATAGACA
1702251 ATAACCATAAACAATAGACA
1 ATAACCATAAACAATAGACA
1702271 ATA
1 ATA
1702274 GCCCAATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.53, C:0.21, G:0.07, T:0.19
Consensus pattern (20 bp):
ATAACCATAAACAATAGACA
Found at i:1708576 original size:37 final size:37
Alignment explanation
Indices: 1708526--1708597 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
1708516 TACCCCAAAA
* * *
1708526 TCATTCTAGAAATTTTACTTTAAATCGTGGTTACTAT
1 TCATGCTAGAAATTTTACTTTAAAACATGGTTACTAT
*
1708563 TCATGCTATAAATTTTACTTTAAAACATGGTTACT
1 TCATGCTAGAAATTTTACTTTAAAACATGGTTACT
1708598 TTAAAACCTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44
Consensus pattern (37 bp):
TCATGCTAGAAATTTTACTTTAAAACATGGTTACTAT
Found at i:1709060 original size:20 final size:20
Alignment explanation
Indices: 1709035--1709077 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1709025 CCATTATTCC
* *
1709035 ATAACCATAGACCATAGACA
1 ATAACCATAAACAATAGACA
1709055 ATAACCATAAACAATAGACA
1 ATAACCATAAACAATAGACA
1709075 ATA
1 ATA
1709078 GCCCAATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.56, C:0.21, G:0.07, T:0.16
Consensus pattern (20 bp):
ATAACCATAAACAATAGACA
Found at i:1715517 original size:2 final size:2
Alignment explanation
Indices: 1715510--1715548 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1715500 GAAGGAGAAG
1715510 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1715549 CATGAGAATC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1720101 original size:10 final size:9
Alignment explanation
Indices: 1720088--1720166 Score: 54
Period size: 10 Copynumber: 8.2 Consensus size: 9
1720078 ATATACACAC
1720088 ATAACTAATA
1 ATAA-TAATA
1720098 ATAAT-ATA
1 ATAATAATA
1720106 ATATATAA-A
1 ATA-ATAATA
1720115 TATAACTAATA
1 -ATAA-TAATA
*
1720126 ATGATATATA
1 ATAATA-ATA
*
1720136 ATCATAACTA
1 ATAATAA-TA
*
1720146 ATAGTAATA
1 ATAATAATA
1720155 ATAACTAATA
1 ATAA-TAATA
1720165 AT
1 AT
1720167 TAACCCATAT
Statistics
Matches: 56, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
8 6 0.11
9 13 0.23
10 36 0.64
11 1 0.02
ACGTcount: A:0.57, C:0.06, G:0.03, T:0.34
Consensus pattern (9 bp):
ATAATAATA
Found at i:1720110 original size:51 final size:51
Alignment explanation
Indices: 1720055--1720154 Score: 123
Period size: 53 Copynumber: 1.9 Consensus size: 51
1720045 CCATATAAAC
*
1720055 ATATAAAAATAA-TATATATAT-ATATATACACACATAACTAATAATAATATAAT
1 ATATAAATATAACTA-ATA-ATGATATATA-A-ACATAACTAATAATAATATAAT
* *
1720108 ATATAAATATAACTAATAATGATATATAATCATAACTAATAGTAATA
1 ATATAAATATAACTAATAATGATATATAAACATAACTAATAATAATA
1720155 ATAACTAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
51 16 0.38
52 3 0.07
53 21 0.50
54 2 0.05
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.34
Consensus pattern (51 bp):
ATATAAATATAACTAATAATGATATATAAACATAACTAATAATAATATAAT
Found at i:1720119 original size:28 final size:31
Alignment explanation
Indices: 1720062--1720135 Score: 100
Period size: 28 Copynumber: 2.5 Consensus size: 31
1720052 AACATATAAA
1720062 AATAATATATATATATATATACACACATAACT
1 AATAATA-ATATATATATATACACACATAACT
*
1720094 AATAATAATATA-ATATATA-A-ATATAACT
1 AATAATAATATATATATATACACACATAACT
*
1720122 AATAATGATATATA
1 AATAATAATATATA
1720136 ATCATAACTA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
28 18 0.46
29 2 0.05
30 7 0.18
31 5 0.13
32 7 0.18
ACGTcount: A:0.57, C:0.07, G:0.01, T:0.35
Consensus pattern (31 bp):
AATAATAATATATATATATACACACATAACT
Found at i:1720153 original size:16 final size:16
Alignment explanation
Indices: 1720134--1720164 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1720124 TAATGATATA
*
1720134 TAATCATAACTAATAG
1 TAATAATAACTAATAG
1720150 TAATAATAACTAATA
1 TAATAATAACTAATA
1720165 ATTAACCCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.10, G:0.03, T:0.32
Consensus pattern (16 bp):
TAATAATAACTAATAG
Found at i:1720165 original size:23 final size:23
Alignment explanation
Indices: 1720088--1720165 Score: 83
Period size: 23 Copynumber: 3.5 Consensus size: 23
1720078 ATATACACAC
1720088 ATAACTAATAA-TAATATAATAT
1 ATAACTAATAACTAATATAATAT
* *
1720110 ATAAAT-ATAACTAATAATGATAT
1 ATAACTAATAACTAAT-ATAATAT
*
1720133 ATAA-TCATAACTAATAGTAATA-
1 ATAACTAATAACTAATA-TAATAT
1720155 ATAACTAATAA
1 ATAACTAATAA
1720166 TTAACCCATA
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
21 4 0.09
22 15 0.32
23 28 0.60
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.33
Consensus pattern (23 bp):
ATAACTAATAACTAATATAATAT
Found at i:1720166 original size:13 final size:13
Alignment explanation
Indices: 1720088--1720166 Score: 56
Period size: 13 Copynumber: 5.9 Consensus size: 13
1720078 ATATACACAC
1720088 ATAACTAATAATA
1 ATAACTAATAATA
*
1720101 ATATAATATATAA-A
1 ATA-ACTA-ATAATA
*
1720115 TATAACTAATAATG
1 -ATAACTAATAATA
*
1720129 ATATA-TAATCATA
1 ATA-ACTAATAATA
*
1720142 ACTAA-TAGTAATA
1 A-TAACTAATAATA
1720155 ATAACTAATAAT
1 ATAACTAATAAT
1720167 TAACCCATAT
Statistics
Matches: 51, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
12 3 0.06
13 31 0.61
14 10 0.20
15 7 0.14
ACGTcount: A:0.57, C:0.06, G:0.03, T:0.34
Consensus pattern (13 bp):
ATAACTAATAATA
Found at i:1720244 original size:2 final size:2
Alignment explanation
Indices: 1720239--1720295 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
1720229 ATTTAAAATA
1720239 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1720281 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
1720296 AATGAAACTT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1723726 original size:20 final size:20
Alignment explanation
Indices: 1723701--1723745 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
1723691 CATTTTTGTA
1723701 TTAATTTTGAAAAGTGACTT
1 TTAATTTTGAAAAGTGACTT
*
1723721 TTAATTTTTAAAAGTGACTT
1 TTAATTTTGAAAAGTGACTT
1723741 TTAAT
1 TTAAT
1723746 ACTATTATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.36, C:0.04, G:0.11, T:0.49
Consensus pattern (20 bp):
TTAATTTTGAAAAGTGACTT
Found at i:1723878 original size:23 final size:23
Alignment explanation
Indices: 1723852--1723913 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
1723842 TTATTAAGAG
*
1723852 AAAAT-ATATTATCAATACTTTTT
1 AAAATAATATTATAAAT-CTTTTT
* * *
1723875 AAAATGATATTTTAAATGTTTTT
1 AAAATAATATTATAAATCTTTTT
1723898 AAAATAATATTA-AAAT
1 AAAATAATATTATAAAT
1723914 AATATTTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
22 4 0.12
23 20 0.61
24 9 0.27
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (23 bp):
AAAATAATATTATAAATCTTTTT
Found at i:1729508 original size:20 final size:19
Alignment explanation
Indices: 1729470--1729510 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
1729460 TTACCACGAC
**
1729470 CGTCGGAGGCTTCAAACAT
1 CGTCGGAGGAGTCAAACAT
1729489 CGTCGGAGGAGTCGAAACAT
1 CGTCGGAGGAGTC-AAACAT
1729509 CG
1 CG
1729511 AAGGTAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.27, C:0.24, G:0.32, T:0.17
Consensus pattern (19 bp):
CGTCGGAGGAGTCAAACAT
Found at i:1730163 original size:24 final size:24
Alignment explanation
Indices: 1730136--1730203 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
1730126 ATTTTGAAAT
*
1730136 TATTATTATTATTTCT-TAAATTTA
1 TATT-TTATTATTTCTATAAATTAA
*
1730160 TATTTTTATTTATTTTTATAAATTAA
1 TA-TTTTA-TTATTTCTATAAATTAA
*
1730186 TATTTTATTATTTTTATA
1 TATTTTATTATTTCTATA
1730204 TTAACATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
24 16 0.41
25 14 0.36
26 9 0.23
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.66
Consensus pattern (24 bp):
TATTTTATTATTTCTATAAATTAA
Found at i:1732623 original size:21 final size:21
Alignment explanation
Indices: 1732586--1732645 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
1732576 CGTTAGACAT
* *
1732586 GGGGGAATC-GGTACCCCTGG
1 GGGGGAATCTGTTCCCCCTGG
1732606 GGGGGAATCTGTTCCCCCTGG
1 GGGGGAATCTGTTCCCCCTGG
*
1732627 GGGGGAATCTGTACCCCCT
1 GGGGGAATCTGTTCCCCCT
1732646 AGACAATCTG
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
20 9 0.25
21 27 0.75
ACGTcount: A:0.13, C:0.28, G:0.38, T:0.20
Consensus pattern (21 bp):
GGGGGAATCTGTTCCCCCTGG
Found at i:1734112 original size:19 final size:20
Alignment explanation
Indices: 1734069--1734116 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1734059 TCTAAATCCT
*
1734069 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
1734089 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
1734108 TTTTCAAAA
1 TTTTCAAAA
1734117 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:1735368 original size:19 final size:21
Alignment explanation
Indices: 1735328--1735368 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1735318 GGAGCGTGGG
*
1735328 GGGAATCGGTATGCCCTCATT
1 GGGAATCGGTATGCCCTAATT
1735349 GGGAATCGGT-T-CCCTAATT
1 GGGAATCGGTATGCCCTAATT
1735368 G
1 G
1735369 CAATCTGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 1 0.05
21 10 0.53
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (21 bp):
GGGAATCGGTATGCCCTAATT
Found at i:1735997 original size:65 final size:63
Alignment explanation
Indices: 1735924--1736083 Score: 203
Period size: 65 Copynumber: 2.5 Consensus size: 63
1735914 AATTAAATTG
* * *
1735924 AACATCGAATGCATTTCATGCATCGATGCACATACCATGCACCAATGCACTGAGGATTTTTTGAA
1 AACATCGAATGCATTTGATGCATCGATGCACA-ACCATGCACCAATGCACTCAGGATATTTTG-A
* * * * * *
1735989 AACCTCGAATGCATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCA-CAACCATGCACCAATGCACTCAGGATATTTTGA
*
1736053 AACATCGAATGCACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
1736084 TCTTAGTGCA
Statistics
Matches: 83, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
63 1 0.01
64 29 0.35
65 51 0.61
66 2 0.02
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACAACCATGCACCAATGCACTCAGGATATTTTGA
Found at i:1736083 original size:17 final size:19
Alignment explanation
Indices: 1736055--1736103 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1736045 TATTTTGAAA
1736055 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
1736073 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
1736092 CACCGATGCACT
1 CATCGATGCACT
1736104 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:1744067 original size:2 final size:2
Alignment explanation
Indices: 1744060--1744098 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1744050 CAACTTAAGC
1744060 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1744099 TTAATCAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1744700 original size:65 final size:65
Alignment explanation
Indices: 1744520--1744729 Score: 191
Period size: 65 Copynumber: 3.2 Consensus size: 65
1744510 TTTTTCAGAG
* * ** * *
1744520 TGATGCA-CTGATGCACCA-ATCCATGCATCGATGCAC-CATGAATTAAATTG-AACATAGATTG
1 TGATGCATC-GATGCACCATA-CCATGCACCGATGCACTCA-GGATTTTA-TGAAACATCGAATG
1744581 CATT
62 CATT
* *
1744585 TCATGCATCGATGCA-CATACCATGCACCGATGCACTGAGGATTTTATGAAAACATCGAATGCAT
1 TGATGCATCGATGCACCATACCATGCACCGATGCACTCAGGATTTTATG-AAACATCGAATGCAT
1744649 T
65 T
* * * * * *
1744650 TGATGCATCGATGCACCA-GCCATGCATCGATGCACTCTGGCTATTT-TGAAACATCAAATGCAC
1 TGATGCATCGATGCACCATACCATGCACCGATGCACTCAGGAT-TTTATGAAACATCGAATGCAT
1744713 T
65 T
1744714 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
1744730 TCTTAGTGCA
Statistics
Matches: 122, Mismatches: 16, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
63 2 0.02
64 52 0.43
65 62 0.51
66 6 0.05
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.27
Consensus pattern (65 bp):
TGATGCATCGATGCACCATACCATGCACCGATGCACTCAGGATTTTATGAAACATCGAATGCATT
Found at i:1744729 original size:17 final size:19
Alignment explanation
Indices: 1744707--1744749 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
1744697 GAAACATCAA
*
1744707 ATGCACT-TGA-TGCATCG
1 ATGCACTCTGAGTGCACCG
*
1744724 ATGCACTCTTAGTGCACCG
1 ATGCACTCTGAGTGCACCG
1744743 ATGCACT
1 ATGCACT
1744750 AAGGGTCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 2 0.09
19 13 0.59
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (19 bp):
ATGCACTCTGAGTGCACCG
Found at i:1744745 original size:64 final size:63
Alignment explanation
Indices: 1744587--1744749 Score: 161
Period size: 64 Copynumber: 2.5 Consensus size: 63
1744577 ATTGCATTTC
* * * * *
1744587 ATGCATCGATGCACATACCATGCACCGATGCACTGAGGATTTTATGAAAACATCGAATGCATTTG
1 ATGCATCGATGCAC-CAGC-TGCACCGATGCACTCAGGATTTTATGAAAACATCAAATGCACTTG
* * *
1744652 ATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTT-TG-AAACATCAAATGCACTT
1 ATGCATCGATGCACCAG-C-TGCACCGATGCACTCAGGAT-TTTATGAAAACATCAAATGCACTT
1744715 G
63 G
1744716 ATGCATCGATGCACTCTTAG-TGCACCGATGCACT
1 ATGCATCGATGCAC-C--AGCTGCACCGATGCACT
1744750 AAGGGTCCAA
Statistics
Matches: 84, Mismatches: 9, Indels: 11
0.81 0.09 0.11
Matches are distributed among these distances:
64 44 0.52
65 35 0.42
66 3 0.04
67 2 0.02
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (63 bp):
ATGCATCGATGCACCAGCTGCACCGATGCACTCAGGATTTTATGAAAACATCAAATGCACTTG
Found at i:1748277 original size:24 final size:24
Alignment explanation
Indices: 1748215--1748277 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 24
1748205 TATGGCAATA
1748215 CGGTGC-ATTTCTACGTGACACTT
1 CGGTGCAATTTCTACGTGACACTT
* * *
1748238 TGGTGCAAATTCTACGTGGCACTT
1 CGGTGCAATTTCTACGTGACACTT
*
1748262 CGGTGCAATTTATACG
1 CGGTGCAATTTCTACG
1748278 AGCCGTGGTG
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 5 0.15
24 28 0.85
ACGTcount: A:0.21, C:0.22, G:0.24, T:0.33
Consensus pattern (24 bp):
CGGTGCAATTTCTACGTGACACTT
Found at i:1751392 original size:32 final size:31
Alignment explanation
Indices: 1751311--1751396 Score: 102
Period size: 32 Copynumber: 2.7 Consensus size: 31
1751301 AGAGACAATG
*
1751311 GGGGCATCTTTGAAGATTCAACATCAAAAGT
1 GGGGCATCTTTGGAGATTCAACATCAAAAGT
* * *
1751342 GGGGTAT-TGTTGGAGATTCAACATCGAATATT
1 GGGGCATCT-TTGGAGATTCAACATC-AAAAGT
*
1751374 GGGGCATCTTTGGGGATTCAACA
1 GGGGCATCTTTGGAGATTCAACA
1751397 CCCTAATGCG
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
30 1 0.02
31 21 0.46
32 23 0.50
33 1 0.02
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (31 bp):
GGGGCATCTTTGGAGATTCAACATCAAAAGT
Found at i:1751674 original size:64 final size:64
Alignment explanation
Indices: 1751573--1751744 Score: 299
Period size: 64 Copynumber: 2.7 Consensus size: 64
1751563 TTTTACAGCT
*
1751573 TTTAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCTAGTTTCA
1 TTTAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCAAGTTTCA
*
1751637 TTTAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAATTTTCAAGTTTCA
1 TTTAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCAAGTTTCA
* * *
1751701 TTCAGAGTTAATTTCAACTTCACAGCGAAGGATATTGGACTCAA
1 TTTAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAA
1751745 AGCAATGCAA
Statistics
Matches: 103, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 103 1.00
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (64 bp):
TTTAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCAAGTTTCA
Found at i:1751888 original size:121 final size:121
Alignment explanation
Indices: 1751711--1752029 Score: 468
Period size: 121 Copynumber: 2.7 Consensus size: 121
1751701 TTCAGAGTTA
* ** *
1751711 ATTTCAACTTCACAGCGAAGGATAT--TGGACTCAA--AGCAATGCAACCCTTGGATTTCAACTT
1 ATTTCAACTTCACAACGAAGGATATCGTGCCCACAAGTAGCAATGCAACCCTTGGATTTCAACTT
*
1751772 CAAGACGAAGGATATCCAATTCAAAGCTCAATTTCACAACGAAGGAACCATCCACG
66 CAAGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAACCATCCACG
* *
1751828 ATTTCAACTTCACAACGAAGGATATCGTGCCCATAAGTGGCAATGCAACCCTTGGATTTCAACTT
1 ATTTCAACTTCACAACGAAGGATATCGTGCCCACAAGTAGCAATGCAACCCTTGGATTTCAACTT
* * * *
1751893 CACGATGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCACG
66 CAAGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAACCATCCACG
* *
1751949 ATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGTAGCAATGCAACCCATGGATTTCAACTT
1 ATTTCAACTTCACAACGAAGGATATCGTGCCCACAAGTAGCAATGCAACCCTTGGATTTCAACTT
*
1752014 CACA-ACGAAGTATATC
66 CA-AGACGAAGGATATC
1752030 GTGCCCACAA
Statistics
Matches: 179, Mismatches: 18, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
117 24 0.13
119 5 0.03
121 150 0.84
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.23
Consensus pattern (121 bp):
ATTTCAACTTCACAACGAAGGATATCGTGCCCACAAGTAGCAATGCAACCCTTGGATTTCAACTT
CAAGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAACCATCCACG
Found at i:1751893 original size:55 final size:55
Alignment explanation
Indices: 1751827--1752084 Score: 212
Period size: 55 Copynumber: 4.5 Consensus size: 55
1751817 AACCATCCAC
* * **
1751827 GATTTCAACTTCACAACGAAGGATATCGTGCCCATAAGTGGCAATGCAACCCTTG
1 GATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGTAACAATGCAACCCTTG
* * * * * * * *
1751882 GATTTCAACTTCACGATGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATG-AGCCATCC
1 GATTTCAACTTCACGACGAAGGATAT-C-GTGC---CCACAA-GT---AAC-AATGCAACC--CT
**
1751946 AC
54 TG
* *
1751948 GATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGTAGCAATGCAACCCATG
1 GATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGTAACAATGCAACCCTTG
* * * *
1752003 GATTTCAACTTCACAACGAAGTATATCGTGCCCACAAGTAACAATGTAACCATTG
1 GATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGTAACAATGCAACCCTTG
*
1752058 GATTTCAACTTCACGACGAATGATATC
1 GATTTCAACTTCACGACGAAGGATATC
1752085 CAATTCAAAG
Statistics
Matches: 156, Mismatches: 34, Indels: 26
0.72 0.16 0.12
Matches are distributed among these distances:
55 98 0.63
56 5 0.03
57 7 0.04
60 4 0.03
61 5 0.03
64 6 0.04
65 5 0.03
66 26 0.17
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.24
Consensus pattern (55 bp):
GATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGTAACAATGCAACCCTTG
Found at i:1752032 original size:176 final size:176
Alignment explanation
Indices: 1751827--1752157 Score: 572
Period size: 176 Copynumber: 1.9 Consensus size: 176
1751817 AACCATCCAC
* ** *
1751827 GATTTCAACTTCACAACGAAGGATATCGTGCCCATAAGTGGCAATGCAACCCTTGGATTTCAACT
1 GATTTCAACTTCACAACGAAGGATATCGTGCCCACAAGTAACAATGCAACCATTGGATTTCAACT
* *
1751892 TCACGATGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCACGATTTCAAC
66 TCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATAAGCCATCCACGATTTCAAC
*
1751957 TTCACGACGAAGGATATCGTGCCCACAAGTAGCAATGCAACCCATG
131 TTCACGACAAAGGATATCGTGCCCACAAGTAGCAATGCAACCCATG
* *
1752003 GATTTCAACTTCACAACGAAGTATATCGTGCCCACAAGTAACAATGTAACCATTGGATTTCAACT
1 GATTTCAACTTCACAACGAAGGATATCGTGCCCACAAGTAACAATGCAACCATTGGATTTCAACT
*
1752068 TCACGACGAATGATATCCAATTCAAAGCTCAACTTCACAACGAATAAGCCATCCACGATTTCAAC
66 TCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATAAGCCATCCACGATTTCAAC
1752133 TTCACGACAAAGGATATCGTGCCCA
131 TTCACGACAAAGGATATCGTGCCCA
1752158 ACAGATCGAC
Statistics
Matches: 145, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
176 145 1.00
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.23
Consensus pattern (176 bp):
GATTTCAACTTCACAACGAAGGATATCGTGCCCACAAGTAACAATGCAACCATTGGATTTCAACT
TCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATAAGCCATCCACGATTTCAAC
TTCACGACAAAGGATATCGTGCCCACAAGTAGCAATGCAACCCATG
Found at i:1752454 original size:84 final size:84
Alignment explanation
Indices: 1752266--1752939 Score: 825
Period size: 84 Copynumber: 8.0 Consensus size: 84
1752256 ATCATCAAAT
* * * * * * * * *
1752266 ACCTTCGAGTTCGATTACATTCAACTCAAAGACATATCAAATTTACAGTATAACTCGAGGCTAGA
1 ACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATC--ATTTGCAGCATAGCTCAAGGCGAGA
* ** *
1752331 AGGGTTGTAGGTCAACAAAA-
64 AGGGTTATCTGCCAACAAAAG
* * * * *
1752351 ACCTTCGAGTTCGATTACACTCTGCTCAAAGACACATCATTTGCAGCATAGCTTAGGGCAAGAAG
1 ACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCGAGAAG
*
1752416 GGCTATCTGCCAACAAAAG
66 GGTTATCTGCCAACAAAAG
* *
1752435 ACCTTCGAGTTCGATTACACTCAGCTCAATGGCAAATCATTTGCAGCATAGCTCAAGGCGAGAAG
1 ACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCGAGAAG
1752500 GGTTATCTGCCAACAAAAG
66 GGTTATCTGCCAACAAAAG
1752519 ACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCGAGAAG
1 ACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCGAGAAG
1752584 GGTTATCTGCCAACAAAAG
66 GGTTATCTGCCAACAAAAG
* * * *
1752603 ACCTTCGAGTTTGATTACACTCAGCTCAAAGGAACATCATTTGCAGCTTAGCTCAAGGCAAGAAG
1 ACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCGAGAAG
* *
1752668 GGTTATCTTCCAATAAAAG
66 GGTTATCTGCCAACAAAAG
* *
1752687 ACCTTCAAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCGATAAG
1 ACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCGAGAAG
* * *
1752752 GGTTATATGTCAATAGAAA-
66 GGTTATCTGCCAACA-AAAG
* * * *
1752771 A-CTATCGAGTTTGATTACATTCAGCTCAAAGGCATATCCTATTTACAGCATAGCTCAAGGCGAG
1 ACCT-TCGAGTTCGATTACACTCAGCTCAAAGGCACAT-C-ATTTGCAGCATAGCTCAAGGCGAG
* *
1752835 AAGGGTTATCTGTCAAC-CAAG
63 AAGGGTTATCTGCCAACAAAAG
* * * * * *
1752856 ACCTTCGAGTTCGATTACATTCAGCTTAAAGGCATATCAAATTTACAACATAGCTCAAGGTGAGA
1 ACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATC--ATTTGCAGCATAGCTCAAGGCGAGA
* * *
1752921 AGGGCTATATGTCAACAAA
64 AGGGTTATCTGCCAACAAA
1752940 CACTGTCAAG
Statistics
Matches: 522, Mismatches: 58, Indels: 17
0.87 0.10 0.03
Matches are distributed among these distances:
83 35 0.07
84 340 0.65
85 107 0.20
86 40 0.08
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.25
Consensus pattern (84 bp):
ACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCGAGAAG
GGTTATCTGCCAACAAAAG
Found at i:1754189 original size:30 final size:28
Alignment explanation
Indices: 1754149--1754218 Score: 70
Period size: 28 Copynumber: 2.4 Consensus size: 28
1754139 TTTGAAATTA
* *
1754149 TTATTATTATTATTTCCTAAATTTTATATT
1 TTATT-TTATTATTTCATAAA-TTAATATT
*
1754179 TTATATTTATT-TTTTATAAATTAATATT
1 TTAT-TTTATTATTTCATAAATTAATATT
*
1754207 TTATTTTTTTAT
1 TTATTTTATTAT
1754219 ATTAATATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
27 5 0.15
28 12 0.35
29 7 0.21
30 9 0.26
31 1 0.03
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (28 bp):
TTATTTTATTATTTCATAAATTAATATT
Found at i:1754229 original size:21 final size:21
Alignment explanation
Indices: 1754170--1754229 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 21
1754160 ATTTCCTAAA
*
1754170 TTTTATATT-TTATATTTATTT
1 TTTTATATTAATAT-TTTATTT
*
1754191 TTTATAAATTAATATTTTATTT
1 TTT-TATATTAATATTTTATTT
1754213 TTTTATATTAATATTTT
1 TTTTATATTAATATTTT
1754230 CTTAACTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 16 0.47
22 15 0.44
23 3 0.09
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTATATTAATATTTTATTT
Found at i:1754423 original size:19 final size:19
Alignment explanation
Indices: 1754401--1754439 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1754391 AAGTAATTCG
*
1754401 AATTGAATTTTTAAATTTC
1 AATTGAAATTTTAAATTTC
* *
1754420 AATTTAAATTTTAACTTTC
1 AATTGAAATTTTAAATTTC
1754439 A
1 A
1754440 CAATTAAGAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (19 bp):
AATTGAAATTTTAAATTTC
Found at i:1755367 original size:23 final size:24
Alignment explanation
Indices: 1755319--1755367 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
1755309 CAGCTTGATT
**
1755319 TTTTTCTAACTTTTAAATTATTTA
1 TTTTTCTAACTTTTAAATTAGATA
1755343 TTTTTC-AATCTTTTAAA-TAGATA
1 TTTTTCTAA-CTTTTAAATTAGATA
1755366 TT
1 TT
1755368 AAGTATTTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.31, C:0.08, G:0.02, T:0.59
Consensus pattern (24 bp):
TTTTTCTAACTTTTAAATTAGATA
Found at i:1755733 original size:3 final size:3
Alignment explanation
Indices: 1755725--1755786 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
1755715 AAGATAAAAG
1755725 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1755773 ATA ATA ATA ATA AT
1 ATA ATA ATA ATA AT
1755787 TTTAAAATTT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1763669 original size:53 final size:53
Alignment explanation
Indices: 1763567--1763881 Score: 364
Period size: 53 Copynumber: 5.9 Consensus size: 53
1763557 TCTTCAAATG
* * * ***
1763567 ACGGG-TCTGCTCCCTCTTG-TTCAAGGATTAAGGAACTCAAACAATCTTCTAAAA
1 ACGGGTTC-GCTCCCTCTTGCTTCAGGGAGT-A-GAACTCGAACAATCTTCTACCT
* * * *
1763621 ACGGGTTCGCTCCCTATTGCTTAAGGGAGTAGAACTCGAATAATCTTCTACTT
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTACCT
* * * *
1763674 ACAGGTTTGCTCCCTCTTGCTTCAGGGGGTAGAACTCGAACAATCTTCTGCCT
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTACCT
* * * *
1763727 ATGGGTTCACTCCCTCTTGTTTTAGGGAGTAGAACTCGAACAATCTTCTACCT
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTACCT
* * * **
1763780 ATGGGTTCGCTCCCTCTCGCTTCAGGGAGTAAAACTCGAACAATCTTCTGTCT
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTACCT
* *
1763833 ACGGGTTCGCTCCATCTTGCTTCAGGGAGTAGAACTCAAACAATCTTCT
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCT
1763882 GGTGTGATTC
Statistics
Matches: 222, Mismatches: 37, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
53 197 0.89
54 16 0.07
55 9 0.04
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (53 bp):
ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTACCT
Found at i:1764330 original size:42 final size:41
Alignment explanation
Indices: 1764256--1764334 Score: 122
Period size: 42 Copynumber: 1.9 Consensus size: 41
1764246 AGAAGGCTTA
* *
1764256 AAATGGCCCGAAGGAATTATCATCTTGCTCGAAAGACATAC
1 AAATGACCCGAAGGAATTATCATCATGCTCGAAAGACATAC
*
1764297 AAATGACCCGAAGGATTTCATCATCATGCTCGAAAGAC
1 AAATGACCCGAAGGAATT-ATCATCATGCTCGAAAGAC
1764335 TTGCTCATGG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
41 16 0.47
42 18 0.53
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.22
Consensus pattern (41 bp):
AAATGACCCGAAGGAATTATCATCATGCTCGAAAGACATAC
Found at i:1764432 original size:42 final size:42
Alignment explanation
Indices: 1764383--1764732 Score: 183
Period size: 42 Copynumber: 8.2 Consensus size: 42
1764373 GTACAAATTA
1764383 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
1 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
* * * * *
1764425 CTCGAAGGACTTCATCATCATGCTCAAAAAACTTACTGATGG
1 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
*** * * * * * * * ** **
1764467 ---GTTTGCTTCACT-ACTC-TTC-CGTGAAGGCTAACAAATTT
1 CCCGAAGGATTTAATCA-TCATGCTCG-AAAGACTTACTGATGG
1764505 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
1 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
* * *
1764547 CCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGA
1 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
* * ** * * * * ** **
1764589 CACTTACTGATGGGTTTGCTTCACTACTCTTCCCTG-AAGGCTTACAAATTA
1 C-C---C-GAAGGATTT-AATCA-T-C-ATGCTC-GAAAGACTTACTGATGG
* * *
1764640 CCCTAAGGATTTAATCATCATGCTCGAAAGACTAACTAATGG
1 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
* * *
1764682 CCCTAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATGG
1 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
1764724 CCCGAAGGA
1 CCCGAAGGA
1764733 CTTACTAAGT
Statistics
Matches: 220, Mismatches: 69, Indels: 38
0.67 0.21 0.12
Matches are distributed among these distances:
37 1 0.00
38 11 0.05
39 6 0.03
41 9 0.04
42 148 0.67
43 4 0.02
44 1 0.00
45 3 0.01
46 7 0.03
47 7 0.03
48 4 0.02
49 1 0.00
50 2 0.01
51 15 0.07
52 1 0.00
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (42 bp):
CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
Found at i:1764441 original size:122 final size:121
Alignment explanation
Indices: 1764237--1764715 Score: 557
Period size: 122 Copynumber: 3.8 Consensus size: 121
1764227 TTGCTCTAAC
* ** * * * *
1764237 ACTCTTCCGAGAAGGCTTA-AAATGGCCCGAAGGAATT-ATCATCTTGCTCGAAAGACATACAAA
1 ACTCTTCCGTGAAGGC-TACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTAA
* * *
1764300 TGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTGCTCATGGATTTGCTTCACT
65 TGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTGCTCATGGGTTTGCTTCACT
* *
1764357 ACTCTTCGGTGAAGGCGTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGA
1 ACTCTTCCGTGAAGGC-TACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTAA
* * * * *
1764422 TGGCTCGAAGGACTTCATCATCATGCTCAAAAAACTTACTGATGGGTTTGCTTCACT
65 TGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTGCTCATGGGTTTGCTTCACT
* *
1764479 ACTCTTCCGTGAAGGCTAACAAATTTCCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGA
1 ACTCTTCCGTGAAGGCT-ACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTAA
1764544 TGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGACACTTACTGATGGGTTTGCT
65 TGGCCCGAAGGACTTCATCATCATGCTCGAAAG----ACT--TG---C-T-C--ATGGGTTTGCT
1764609 TCACT
117 TCACT
* * *
1764614 ACTCTTCCCTGAAGGCTTACAAATTACCCTAAGGATTTAATCATCATGCTCGAAAGACTAACTAA
1 ACTCTTCCGTGAAGGC-TACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTAA
* * * *
1764679 TGGCCCTAAGGATTTAAGCATCATGCTCGAAAGACTT
65 TGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTT
1764716 ATTGATGGCC
Statistics
Matches: 308, Mismatches: 34, Indels: 25
0.84 0.09 0.07
Matches are distributed among these distances:
120 16 0.05
121 16 0.05
122 162 0.53
126 3 0.01
128 1 0.00
129 1 0.00
131 4 0.01
132 1 0.00
135 103 0.33
136 1 0.00
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (121 bp):
ACTCTTCCGTGAAGGCTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTAAT
GGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTGCTCATGGGTTTGCTTCACT
Found at i:1764579 original size:22 final size:21
Alignment explanation
Indices: 1764518--1764581 Score: 69
Period size: 20 Copynumber: 3.0 Consensus size: 21
1764508 GAAGGATTTA
1764518 ATCATCATGCTCGAAAGACTT
1 ATCATCATGCTCGAAAGACTT
* * *
1764539 A-C-TGATGGCCCGAAGGACTT
1 ATCATCAT-GCTCGAAAGACTT
1764559 CATCATCATGCTCGAAAGACTT
1 -ATCATCATGCTCGAAAGACTT
1764581 A
1 A
1764582 CTGATGACAC
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
19 3 0.09
20 12 0.36
21 3 0.09
22 12 0.36
23 3 0.09
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (21 bp):
ATCATCATGCTCGAAAGACTT
Found at i:1764701 original size:135 final size:135
Alignment explanation
Indices: 1764455--1764722 Score: 437
Period size: 135 Copynumber: 2.0 Consensus size: 135
1764445 TGCTCAAAAA
* *
1764455 ACTTACTGATGGGTTTGCTTCACTACTCTTCCGTGAAGGCTAACAAATTTCCCGAAGGATTTAAT
1 ACTTACTGATGGGTTTGCTTCACTACTCTTCCCTGAAGGCTAACAAATTACCCGAAGGATTTAAT
* * * *
1764520 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTG
66 CATCATGCTCGAAAGACTAACTAATGGCCCGAAGGACTTAAGCATCATGCTCGAAAGACTTACTG
1764585 ATGAC
131 ATGAC
* *
1764590 ACTTACTGATGGGTTTGCTTCACTACTCTTCCCTGAAGGCTTACAAATTACCCTAAGGATTTAAT
1 ACTTACTGATGGGTTTGCTTCACTACTCTTCCCTGAAGGCTAACAAATTACCCGAAGGATTTAAT
* * *
1764655 CATCATGCTCGAAAGACTAACTAATGGCCCTAAGGATTTAAGCATCATGCTCGAAAGACTTATTG
66 CATCATGCTCGAAAGACTAACTAATGGCCCGAAGGACTTAAGCATCATGCTCGAAAGACTTACTG
1764720 ATG
131 ATG
1764723 GCCCGAAGGA
Statistics
Matches: 122, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
135 122 1.00
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (135 bp):
ACTTACTGATGGGTTTGCTTCACTACTCTTCCCTGAAGGCTAACAAATTACCCGAAGGATTTAAT
CATCATGCTCGAAAGACTAACTAATGGCCCGAAGGACTTAAGCATCATGCTCGAAAGACTTACTG
ATGAC
Found at i:1773379 original size:2 final size:2
Alignment explanation
Indices: 1773374--1773402 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1773364 TAATGCGTAC
1773374 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1773403 TATGCACATC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1775516 original size:2 final size:2
Alignment explanation
Indices: 1775509--1775564 Score: 64
Period size: 2 Copynumber: 29.5 Consensus size: 2
1775499 TAATATTAAC
* * *
1775509 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT TT TT TT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1775549 -T AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
1775565 AACTTTTATG
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
1 3 0.06
2 46 0.94
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
AT
Found at i:1775579 original size:29 final size:31
Alignment explanation
Indices: 1775518--1775576 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
1775508 CATATATATA
* * * *
1775518 TATATATATATATATATATTATTTTTTTAAT
1 TATATATATATATATAAACTATTTATGTAAT
1775549 TATATATATATATATAAACT-TTTATGTA
1 TATATATATATATATAAACTATTTATGTA
1775577 TTAAATTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 6 0.25
31 18 0.75
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (31 bp):
TATATATATATATATAAACTATTTATGTAAT
Found at i:1775806 original size:31 final size:31
Alignment explanation
Indices: 1775754--1775834 Score: 98
Period size: 31 Copynumber: 2.7 Consensus size: 31
1775744 CACTAAAGTT
1775754 TCAA-AAATAAC-AA-TAGTCATTAA-TATTA
1 TCAATAAATAACAAATTAGTCATTAACT-TTA
** *
1775782 TCAATTTATAACAAATTGGTCATTAACTTTA
1 TCAATAAATAACAAATTAGTCATTAACTTTA
1775813 TCAATAAATAACAAATTAGTCA
1 TCAATAAATAACAAATTAGTCA
1775835 CTTGAGACCA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
28 4 0.09
29 5 0.12
30 2 0.05
31 31 0.72
32 1 0.02
ACGTcount: A:0.48, C:0.12, G:0.05, T:0.35
Consensus pattern (31 bp):
TCAATAAATAACAAATTAGTCATTAACTTTA
Found at i:1777761 original size:29 final size:29
Alignment explanation
Indices: 1777720--1777790 Score: 133
Period size: 29 Copynumber: 2.4 Consensus size: 29
1777710 CTGCATGGAT
*
1777720 TGCATGGCGACCTGGTAGGTCGTTGGGCG
1 TGCATGGCGACCTGGTAGGTCGCTGGGCG
1777749 TGCATGGCGACCTGGTAGGTCGCTGGGCG
1 TGCATGGCGACCTGGTAGGTCGCTGGGCG
1777778 TGCATGGCGACCT
1 TGCATGGCGACCT
1777791 ACCCCATCTA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.11, C:0.24, G:0.42, T:0.23
Consensus pattern (29 bp):
TGCATGGCGACCTGGTAGGTCGCTGGGCG
Found at i:1778376 original size:2 final size:2
Alignment explanation
Indices: 1778369--1778395 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1778359 TATTTATGAT
1778369 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 T
1778396 GAACCAAGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1782935 original size:231 final size:231
Alignment explanation
Indices: 1782532--1782979 Score: 779
Period size: 231 Copynumber: 1.9 Consensus size: 231
1782522 TTTTAGTGTG
* * ** *
1782532 TCTCAACAGAGATTTTTTGCAGACATAAGGACTCGTATTGGAGACCTTACTCAAGCAAATATCAA
1 TCTCAACAGAGATTTTCTACAGACATAAGGACTCAAACTGGAGACCTTACTCAAGCAAATATCAA
* * * *
1782597 GCACCTTACCATTTTAATCATCCCATATTTATATATTTGTTAAGTTTTTCAAATTTGGTAATTAT
66 GCACCTTACCACTTGAATCAACCCATATTTATATATTTATTAAGTTTTTCAAATTTGGTAATTAT
*
1782662 AGATTTTTTAAAAATGAGGGATGGATCAATTTAAATACATCTTGAGTTTAATTTTACATCTTGTT
131 AGATTTTTTAAAAATGAGGGATGGATCAATTTAAATACATCTTGAGTTTAATTTTACATCTTATT
1782727 CAATTAATTCATAAAATAAATTTTAGTGCGTGAATC
196 CAATTAATTCATAAAATAAATTTTAGTGCGTGAATC
1782763 TCTCAACAGAGATTTTCTACAGACATAAGGACTCAAACTGGAGACCTTACTCAAGCAAATATCAA
1 TCTCAACAGAGATTTTCTACAGACATAAGGACTCAAACTGGAGACCTTACTCAAGCAAATATCAA
* *
1782828 GCACCTTACCGCTTGAATCAACCTATATTTATATATTTATTAAGTTTTTCAAATTTGGTAATTAT
66 GCACCTTACCACTTGAATCAACCCATATTTATATATTTATTAAGTTTTTCAAATTTGGTAATTAT
*
1782893 AGATTTTTTAAAATTGAGGGATGGATCAATTTAAATACATCTTGAGTTTAATTTTACATCTTATT
131 AGATTTTTTAAAAATGAGGGATGGATCAATTTAAATACATCTTGAGTTTAATTTTACATCTTATT
1782958 CAATTAATTCATAAAATAAATT
196 CAATTAATTCATAAAATAAATT
1782980 CAAACCTTAA
Statistics
Matches: 204, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
231 204 1.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.38
Consensus pattern (231 bp):
TCTCAACAGAGATTTTCTACAGACATAAGGACTCAAACTGGAGACCTTACTCAAGCAAATATCAA
GCACCTTACCACTTGAATCAACCCATATTTATATATTTATTAAGTTTTTCAAATTTGGTAATTAT
AGATTTTTTAAAAATGAGGGATGGATCAATTTAAATACATCTTGAGTTTAATTTTACATCTTATT
CAATTAATTCATAAAATAAATTTTAGTGCGTGAATC
Done.