Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007936.1 Hibiscus syriacus cultivar Beakdansim tig00110346_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: 2869312
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 11
Found at i:1697040 original size:22 final size:23
Alignment explanation
Indices: 1697010--1697055 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
1697000 AATTTGTTTG
* *
1697010 AATTTGTTATTATAACTA-AAAT
1 AATTGGTTATGATAACTATAAAT
1697032 AATTGGTTATGATAACTATAAAT
1 AATTGGTTATGATAACTATAAAT
1697055 A
1 A
1697056 TATTTAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.46, C:0.04, G:0.09, T:0.41
Consensus pattern (23 bp):
AATTGGTTATGATAACTATAAAT
Found at i:1698795 original size:32 final size:32
Alignment explanation
Indices: 1698758--1698822 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
1698748 ATATTTAAGA
**
1698758 TAGAATATAAAAATGTGCATAAATTTATTTGG
1 TAGAATATAAAAATGTAAATAAATTTATTTGG
1698790 TAGAATATAAAAATGTAAATAAATTTATTTGG
1 TAGAATATAAAAATGTAAATAAATTTATTTGG
1698822 T
1 T
1698823 TGAAAAAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.46, C:0.02, G:0.14, T:0.38
Consensus pattern (32 bp):
TAGAATATAAAAATGTAAATAAATTTATTTGG
Found at i:1698829 original size:28 final size:30
Alignment explanation
Indices: 1698764--1698831 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 30
1698754 AAGATAGAAT
**
1698764 ATAAAAATGTGCATAAATTTATTTGGTAGAA
1 ATAAAAATGTAAATAAATTTATTTGGTAG-A
*
1698795 TATAAAAATGTAAATAAATTTATTTGGTTGA
1 -ATAAAAATGTAAATAAATTTATTTGGTAGA
1698826 A-AAAAA
1 ATAAAAA
1698832 CTTACCTTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 5 0.15
30 1 0.03
31 1 0.03
32 26 0.79
ACGTcount: A:0.50, C:0.01, G:0.13, T:0.35
Consensus pattern (30 bp):
ATAAAAATGTAAATAAATTTATTTGGTAGA
Found at i:1700644 original size:3 final size:3
Alignment explanation
Indices: 1700636--1700688 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
1700626 TCCTTTTAAG
1700636 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
1700684 ATA AT
1 ATA AT
1700689 TAAATCATAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1701258 original size:21 final size:21
Alignment explanation
Indices: 1701232--1701277 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
1701222 TTGTTAACCG
1701232 TTACGATATTAACGTGACACT
1 TTACGATATTAACGTGACACT
* *
1701253 TTACGATGTTGACGTGACACT
1 TTACGATATTAACGTGACACT
1701274 TTAC
1 TTAC
1701278 AATACACGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (21 bp):
TTACGATATTAACGTGACACT
Found at i:1701428 original size:9 final size:9
Alignment explanation
Indices: 1701414--1701438 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1701404 AATAAAATAA
1701414 AAAATATTT
1 AAAATATTT
1701423 AAAATATTT
1 AAAATATTT
1701432 AAAATAT
1 AAAATAT
1701439 AAAAATAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
AAAATATTT
Found at i:1701452 original size:25 final size:24
Alignment explanation
Indices: 1701401--1701471 Score: 65
Period size: 25 Copynumber: 2.9 Consensus size: 24
1701391 GATTTTTTTC
* *
1701401 AAAAATAAAATA-AAAAATATTTA
1 AAAAATAAAATATAAAAATAATCA
*
1701424 AAATATTTAAAATATAAAAATAATCA
1 AAA-A-ATAAAATATAAAAATAATCA
1701450 AATAAA-ATAAATATAAAAATAA
1 AA-AAATA-AAATATAAAAATAA
1701472 AGATACAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
23 3 0.08
24 2 0.05
25 21 0.54
26 12 0.31
27 1 0.03
ACGTcount: A:0.72, C:0.01, G:0.00, T:0.27
Consensus pattern (24 bp):
AAAAATAAAATATAAAAATAATCA
Found at i:1701481 original size:25 final size:25
Alignment explanation
Indices: 1701433--1701481 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
1701423 AAAATATTTA
* *
1701433 AAATATAAAAATAATCAAATAAAAT
1 AAATATAAAAATAAACAAACAAAAT
* *
1701458 AAATATAAAAATAAAGATACAAAA
1 AAATATAAAAATAAACAAACAAAA
1701482 ATACAAAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.20
Consensus pattern (25 bp):
AAATATAAAAATAAACAAACAAAAT
Found at i:1701824 original size:21 final size:21
Alignment explanation
Indices: 1701777--1701842 Score: 53
Period size: 22 Copynumber: 3.0 Consensus size: 21
1701767 TATTTTTTTA
*
1701777 ATTTTCTAGTAATTTAATTTTT
1 ATTTT-TAGTAATTTAATATTT
* * *
1701799 GTTTTTAGTATTTTTATATTT
1 ATTTTTAGTAATTTAATATTT
*
1701820 ATTTTTTA-TATATTTAAAATTT
1 A-TTTTTAGTA-ATTTAATATTT
1701842 A
1 A
1701843 AAATAATGTT
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
21 15 0.44
22 19 0.56
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.65
Consensus pattern (21 bp):
ATTTTTAGTAATTTAATATTT
Found at i:1706421 original size:47 final size:42
Alignment explanation
Indices: 1706265--1706382 Score: 211
Period size: 42 Copynumber: 2.8 Consensus size: 42
1706255 TGATGTTGAT
* *
1706265 TTTA-TTTAGACTTATTGAGACTTATTAGTGTTATGGTGTTA
1 TTTATTTTAGACTTATTGAGACTTAATGGTGTTATGGTGTTA
1706306 TTTATTTTAGACTTATTGAGACTTAATGGTGTTATGGTGTTA
1 TTTATTTTAGACTTATTGAGACTTAATGGTGTTATGGTGTTA
1706348 TTTATTTTAGACTTATTGAGACTTAATGGTGTTAT
1 TTTATTTTAGACTTATTGAGACTTAATGGTGTTAT
1706383 TTATTTACTT
Statistics
Matches: 74, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
41 4 0.05
42 70 0.95
ACGTcount: A:0.25, C:0.05, G:0.19, T:0.51
Consensus pattern (42 bp):
TTTATTTTAGACTTATTGAGACTTAATGGTGTTATGGTGTTA
Found at i:1706589 original size:9 final size:9
Alignment explanation
Indices: 1706566--1706601 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
1706556 TAATTGACTT
1706566 TTGGTGTTA
1 TTGGTGTTA
1706575 -TGGTGTTA
1 TTGGTGTTA
1706583 TTGGTGTTA
1 TTGGTGTTA
1706592 TTGGTGTTA
1 TTGGTGTTA
1706601 T
1 T
1706602 GGTTGGATCC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 8 0.31
9 18 0.69
ACGTcount: A:0.11, C:0.00, G:0.33, T:0.56
Consensus pattern (9 bp):
TTGGTGTTA
Found at i:1706604 original size:17 final size:18
Alignment explanation
Indices: 1706566--1706601 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
1706556 TAATTGACTT
1706566 TTGGTGTTA-TGGTGTTA
1 TTGGTGTTATTGGTGTTA
1706583 TTGGTGTTATTGGTGTTA
1 TTGGTGTTATTGGTGTTA
1706601 T
1 T
1706602 GGTTGGATCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.11, C:0.00, G:0.33, T:0.56
Consensus pattern (18 bp):
TTGGTGTTATTGGTGTTA
Found at i:1709654 original size:24 final size:22
Alignment explanation
Indices: 1709627--1709675 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
1709617 TCTTCTTCAT
1709627 TTTACTGATGTGCCTACTCTGAAA
1 TTTACTGATGT-CC-ACTCTGAAA
* * *
1709651 TTTATTGGTGTCCACTTTGAAA
1 TTTACTGATGTCCACTCTGAAA
1709673 TTT
1 TTT
1709676 TAGTGCATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 11 0.50
23 2 0.09
24 9 0.41
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.45
Consensus pattern (22 bp):
TTTACTGATGTCCACTCTGAAA
Found at i:1714383 original size:288 final size:285
Alignment explanation
Indices: 1713869--1714387 Score: 869
Period size: 288 Copynumber: 1.8 Consensus size: 285
1713859 TTACTTTAGG
* *
1713869 TTCGTATTGAATCATGTTTTTAAGTTGAATTTATATCTATAAATGATATATATAGTGTTTACAGT
1 TTCGTATTGAATCATGTTTTTAAGTTGAATTTATATCTAGAAATGATATATATAGTGTTTACACT
* * * *
1713934 TTTTATTGCATTAAAAACATGTTTTACTCCAAAAATTTCAAAAATTTATTTAAAAGGGGATTTCA
66 TTTTATTGCATTAAAAACATGATTTACTCAAAAAAATTCAAAAATTTATTTAAAAGAGGATTTCA
*
1713999 AAATTTTCAAAATATATGCAATATTTGATCAATATAAATAAAATTGATTGTTTTATTGGGATATT
131 AAATTTTCAAAATATATGCAATATTTGATCAATATAAATAAAATTGATTGGTTTATTGGGATATT
*
1714064 CTTTGCATGTTTTTCTTGCAGGAGATCAACCCATTCACTATGTTTAACCTAAAACATAGTGAATG
196 CTTTGCATGATTTTCTTGCAGGAGATCAACCCATTCACTATGTTTAACCTAAAACATAGTGAATG
1714129 GGTTGACCTAAAATATTGCTTTAAA
261 GGTTGACCTAAAATATTGCTTTAAA
1714154 TTCGTATTGAATCATGTTTTTAAGTTGAATTTAGT-TCTAGAAATGATATATATAGTGTTTACAC
1 TTCGTATTGAATCATGTTTTTAAGTTGAATTTA-TATCTAGAAATGATATATATAGTGTTTACAC
* *
1714218 TTTTTATTGTATTAAAAACATGATTTACTCAAAAAAAAAATTCAAAATTTTATTTAAAAGAGGAT
65 TTTTTATTGCATTAAAAACATGATTTACTC---AAAAAAATTCAAAAATTTATTTAAAAGAGGAT
* * *
1714283 TTCAAAATTTTCAAAATCTATGCAATATTTTATCAATATAAATGAAATTGATTGGTTTATTGGGA
127 TTCAAAATTTTCAAAATATATGCAATATTTGATCAATATAAATAAAATTGATTGGTTTATTGGGA
*
1714348 TATTCTTTGCATGATTTTCTTGCAGGAGGTCAACCCATTC
192 TATTCTTTGCATGATTTTCTTGCAGGAGATCAACCCATTC
1714388 TGTAACACCC
Statistics
Matches: 216, Mismatches: 14, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
285 88 0.41
286 1 0.00
288 127 0.59
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.41
Consensus pattern (285 bp):
TTCGTATTGAATCATGTTTTTAAGTTGAATTTATATCTAGAAATGATATATATAGTGTTTACACT
TTTTATTGCATTAAAAACATGATTTACTCAAAAAAATTCAAAAATTTATTTAAAAGAGGATTTCA
AAATTTTCAAAATATATGCAATATTTGATCAATATAAATAAAATTGATTGGTTTATTGGGATATT
CTTTGCATGATTTTCTTGCAGGAGATCAACCCATTCACTATGTTTAACCTAAAACATAGTGAATG
GGTTGACCTAAAATATTGCTTTAAA
Found at i:1715004 original size:54 final size:54
Alignment explanation
Indices: 1714942--1715402 Score: 712
Period size: 54 Copynumber: 8.5 Consensus size: 54
1714932 GCACACCCAA
* * *
1714942 TGCCAATACGAAAATTCATAAACTTATTGTGAATTTCTTAAGTTGTACACATAG
1 TGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAG
* *
1714996 TGCGAATAC-AGAAATTCATAAACTCATTATGAATTTCTTAGGTTGCACACATAG
1 TGCCAATACGA-AAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAG
* * *
1715050 TGCTAATACGGAAATTCATAAACTCATTATGAATTTCTTAGGTTGCACACATAG
1 TGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAG
*
1715104 TGCCAATACGAAAATTCATTAACTCATTATGAATTTCTTAAGTTGCACACATAG
1 TGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAG
*
1715158 TGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAG
1 TGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAG
* *
1715212 TGCCAATACTAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACAAATAG
1 TGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAG
* * *
1715266 TTCCAATACTAAAACTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAG
1 TGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAG
* *
1715320 TGACAATACGAAAA-TCTATAAACTCTTTATGAATTTCTTAAGTTGCACACATAG
1 TGCCAATACGAAAATTC-ATAAACTCATTATGAATTTCTTAAGTTGCACACATAG
*
1715374 TACCAATAC-AGAAATTCATAAACTCATTA
1 TGCCAATACGA-AAATTCATAAACTCATTA
1715403 AGAAACATGA
Statistics
Matches: 376, Mismatches: 26, Indels: 10
0.91 0.06 0.02
Matches are distributed among these distances:
53 4 0.01
54 370 0.98
55 2 0.01
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (54 bp):
TGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAG
Found at i:1715853 original size:94 final size:95
Alignment explanation
Indices: 1715720--1715895 Score: 248
Period size: 94 Copynumber: 1.9 Consensus size: 95
1715710 ACCATGGTAT
* * * *
1715720 CGATACTTCTATAATGTGGTATCGATACTCTCTTTCAGTATCGATACCATTTCTACATTCTGG-A
1 CGATACTTCTATAATATGATATCGATACTCTCTTACAGTATCGATACAATTTCTACATTCTGGAA
1715784 TCAATGGTATCGATACTTTTCTCCTAGTAC
66 TCAATGGTATCGATACTTTTCTCCTAGTAC
* * **
1715814 CGATACTTCTATACTATGATATCGATACTC-CATTACAGTATCGATATAATTTCTGTATTCTGGA
1 CGATACTTCTATAATATGATATCGATACTCTC-TTACAGTATCGATACAATTTCTACATTCTGGA
*
1715878 ATTAATGGTATCGATACT
65 ATCAATGGTATCGATACT
1715896 ATAACTAGTA
Statistics
Matches: 71, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
93 1 0.01
94 53 0.75
95 17 0.24
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (95 bp):
CGATACTTCTATAATATGATATCGATACTCTCTTACAGTATCGATACAATTTCTACATTCTGGAA
TCAATGGTATCGATACTTTTCTCCTAGTAC
Found at i:1722065 original size:54 final size:54
Alignment explanation
Indices: 1722007--1722523 Score: 748
Period size: 54 Copynumber: 9.6 Consensus size: 54
1721997 TTGATCACCA
* * * * *
1722007 AGTGTCAATACAGAAATTCATATACTTATTATGAATTTCTTAAGTTGAACACAT
1 AGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACAT
** * *
1722061 AGTGTGAATATGGAAATTCATAAACTCATTATGAATTTCTTAAGTTACACACAT
1 AGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACAT
* * **
1722115 AGTGCCAATACGGAAATTCATAAACTCATCATGAATTTCTTAGGTTGCACGTAT
1 AGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACAT
*** * *
1722169 AGTGCCAATACGGAAATTCATAAACTCACCCTAAATTTCTTAAGTTACACACAT
1 AGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACAT
* *
1722223 AGTGCCAATACGAAAATTCATAAACTCATCATGAATTTCTTAAGTTGCACACAT
1 AGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACAT
* *
1722277 AGTACCAATACGGAAATTCATAAACTCACTATGAATTTCTTAAGTTGCACACAT
1 AGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACAT
*
1722331 AGTGCCAATATGGAAATAT-ATAAACTCATTATGAATTTCTTAAGTTGCACACAT
1 AGTGCCAATACGGAAAT-TCATAAACTCATTATGAATTTCTTAAGTTGCACACAT
* *
1722385 AGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAGTTACACACGT
1 AGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACAT
* *
1722439 AGTGTCAATACGGAAATTCATAAACTAATTATGAATTTCTTAAGTTGCACACAT
1 AGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACAT
* **
1722493 AGTTCCAATAATGAAATTCATAAACTCATTA
1 AGTGCCAATACGGAAATTCATAAACTCATTA
1722524 AGCAACATGC
Statistics
Matches: 415, Mismatches: 46, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
53 1 0.00
54 413 1.00
55 1 0.00
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.32
Consensus pattern (54 bp):
AGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACAT
Found at i:1722933 original size:20 final size:20
Alignment explanation
Indices: 1722908--1722964 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
1722898 ATTCTAGATC
*
1722908 CCTAGTATCGATACTTTTCT
1 CCTAGTACCGATACTTTTCT
*
1722928 CCTAGTACCGATACTTTTAT
1 CCTAGTACCGATACTTTTCT
*
1722948 ACTATGGTACCGATACT
1 CCTA--GTACCGATACT
1722965 CTATTACAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
20 21 0.66
22 11 0.34
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.39
Consensus pattern (20 bp):
CCTAGTACCGATACTTTTCT
Found at i:1726404 original size:2 final size:2
Alignment explanation
Indices: 1726397--1726480 Score: 168
Period size: 2 Copynumber: 42.0 Consensus size: 2
1726387 GAGCTCAACA
1726397 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
1726439 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
1726481 TATTTGTACC
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 82 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1727817 original size:93 final size:93
Alignment explanation
Indices: 1727658--1727844 Score: 338
Period size: 93 Copynumber: 2.0 Consensus size: 93
1727648 TTAACCGAGG
*
1727658 TAATGATGTGATTTGATATAACAATAATTTTACTCCTTAAACTTTATTTGAAACTTTTTAAGTTG
1 TAATGATGTGATTTGATATAACAATAATTTTACACCTTAAACTTTATTTGAAACTTTTTAAGTTG
1727723 AATCGAGTTTATGAAATTCAAATTAAGT
66 AATCGAGTTTATGAAATTCAAATTAAGT
* *
1727751 TAATGTTGTGATTTGATATAACAATAATTTTACACCTTAAACTTTATTTGAAATTTTTTAAGTTG
1 TAATGATGTGATTTGATATAACAATAATTTTACACCTTAAACTTTATTTGAAACTTTTTAAGTTG
*
1727816 AATCGAGTTTATGAAATTCAGATTAAGT
66 AATCGAGTTTATGAAATTCAAATTAAGT
1727844 T
1 T
1727845 TATAAGTTTC
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 90 1.00
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.44
Consensus pattern (93 bp):
TAATGATGTGATTTGATATAACAATAATTTTACACCTTAAACTTTATTTGAAACTTTTTAAGTTG
AATCGAGTTTATGAAATTCAAATTAAGT
Found at i:1727922 original size:2 final size:2
Alignment explanation
Indices: 1727915--1727948 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1727905 TCCTCTAATC
1727915 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
1727949 GTTATTTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1732902 original size:6 final size:6
Alignment explanation
Indices: 1732893--1732965 Score: 83
Period size: 6 Copynumber: 12.0 Consensus size: 6
1732883 GATGGAGGAT
* * * *
1732893 GGGGGA GGGGGA GGGGGA GGGGAAA GGGAAA GGGGAA GGGGAA GGGGAA
1 GGGGAA GGGGAA GGGGAA GGGG-AA GGGGAA GGGGAA GGGGAA GGGGAA
* *
1732942 GGGGAA GGGAAA GGGAAA GGGGAA
1 GGGGAA GGGGAA GGGGAA GGGGAA
1732966 ATGGAAAGAG
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
6 57 0.93
7 4 0.07
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (6 bp):
GGGGAA
Found at i:1732965 original size:18 final size:18
Alignment explanation
Indices: 1732906--1732965 Score: 93
Period size: 18 Copynumber: 3.3 Consensus size: 18
1732896 GGAGGGGGAG
*
1732906 GGGGAGGGGAAAGGGAAA
1 GGGGAAGGGAAAGGGAAA
* *
1732924 GGGGAAGGGGAAGGGGAA
1 GGGGAAGGGAAAGGGAAA
1732942 GGGGAAGGGAAAGGGAAA
1 GGGGAAGGGAAAGGGAAA
1732960 GGGGAA
1 GGGGAA
1732966 ATGGAAAGAG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (18 bp):
GGGGAAGGGAAAGGGAAA
Found at i:1734567 original size:24 final size:23
Alignment explanation
Indices: 1734540--1734594 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
1734530 ATTATTTTTA
1734540 ATATAT-ATACTTTTAATAAAATTT
1 ATATATAAT-CTTTTAATAAAA-TT
* *
1734564 ATATATAATTTTTTTATAAAATT
1 ATATATAATCTTTTAATAAAATT
1734587 ATATATAA
1 ATATATAA
1734595 ATTGGTAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 10 0.36
24 16 0.57
25 2 0.07
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
ATATATAATCTTTTAATAAAATT
Found at i:1734588 original size:23 final size:24
Alignment explanation
Indices: 1734550--1734594 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
1734540 ATATATATAC
1734550 TTTTAATAAAATTTATATATAATT
1 TTTTAATAAAATTTATATATAATT
*
1734574 TTTTTATAAAA-TTATATATAA
1 TTTTAATAAAATTTATATATAA
1734595 ATTGGTAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
TTTTAATAAAATTTATATATAATT
Found at i:1735710 original size:15 final size:15
Alignment explanation
Indices: 1735692--1735735 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 15
1735682 GACCCGACCC
1735692 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
*
1735707 GACCAGTTGACCGTT
1 GACCCGTTGACCGTT
1735722 GACCTGCGTTGACC
1 GACC--CGTTGACC
1735736 ACTGTTGACC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 18 0.72
17 7 0.28
ACGTcount: A:0.16, C:0.32, G:0.27, T:0.25
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:1735715 original size:8 final size:7
Alignment explanation
Indices: 1735695--1735725 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
1735685 CCGACCCGAC
1735695 CCGTTGA
1 CCGTTGA
1735702 CCGTTGA
1 CCGTTGA
1735709 CCAGTTGA
1 CC-GTTGA
1735717 CCGTTGA
1 CCGTTGA
1735724 CC
1 CC
1735726 TGCGTTGACC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 16 0.70
8 7 0.30
ACGTcount: A:0.16, C:0.32, G:0.26, T:0.26
Consensus pattern (7 bp):
CCGTTGA
Found at i:1738274 original size:24 final size:24
Alignment explanation
Indices: 1738247--1738362 Score: 146
Period size: 24 Copynumber: 4.8 Consensus size: 24
1738237 TTCGATTTGA
1738247 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
1738271 ATTCTGATCTGATA-TCTGACATGG
1 ATTCTGATCTGATACT-TGACATGG
* *
1738295 ATTTTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
* * *
1738319 ATTCTGATTTGTTACTTGACCT-G
1 ATTCTGATCTGATACTTGACATGG
*
1738342 ATTTCTGATATGATACTTGAC
1 A-TTCTGATCTGATACTTGAC
1738363 CTGATTTATG
Statistics
Matches: 81, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
23 3 0.04
24 77 0.95
25 1 0.01
ACGTcount: A:0.23, C:0.16, G:0.19, T:0.42
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:1738379 original size:24 final size:24
Alignment explanation
Indices: 1738248--1738379 Score: 110
Period size: 24 Copynumber: 5.5 Consensus size: 24
1738238 TCGATTTGAA
* *
1738248 TTCTGATCTGATACTTGACATGGA-
1 TTCTGATTTGATACTTGACCT-GAT
* *
1738272 TTCTGATCTGATA-TCTGACATGGAT
1 TTCTGATTTGATACT-TGACCT-GAT
* *
1738297 TT-TGATCTGATACTTGACTTGGA-
1 TTCTGATTTGATACTTGACCT-GAT
*
1738320 TTCTGATTTGTTACTTGACCTGAT
1 TTCTGATTTGATACTTGACCTGAT
*
1738344 TTCTGATATGATACTTGACCTGAT
1 TTCTGATTTGATACTTGACCTGAT
* *
1738368 TTATGTTTTGAT
1 TTCTGATTTGAT
1738380 TTTTTGATAT
Statistics
Matches: 94, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
23 5 0.05
24 86 0.91
25 3 0.03
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.45
Consensus pattern (24 bp):
TTCTGATTTGATACTTGACCTGAT
Found at i:1738553 original size:2 final size:2
Alignment explanation
Indices: 1738546--1738595 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
1738536 GGGATGGGGG
1738546 TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1738587 TA TA TA TA T
1 TA TA TA TA T
1738596 GTTTTAAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1743415 original size:17 final size:16
Alignment explanation
Indices: 1743395--1743432 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 16
1743385 GTACTATTGT
1743395 TTTTTATTAACTATGAG
1 TTTTT-TTAACTATGAG
1743412 --TTTTTAACTATGAG
1 TTTTTTTAACTATGAG
1743426 TTTTTTT
1 TTTTTTT
1743433 CCAGTTTGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 5
0.79 0.00 0.21
Matches are distributed among these distances:
14 11 0.58
15 3 0.16
16 5 0.26
ACGTcount: A:0.24, C:0.05, G:0.11, T:0.61
Consensus pattern (16 bp):
TTTTTTTAACTATGAG
Found at i:1743420 original size:14 final size:14
Alignment explanation
Indices: 1743401--1743430 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1743391 TTGTTTTTTA
1743401 TTAACTATGAGTTT
1 TTAACTATGAGTTT
1743415 TTAACTATGAGTTT
1 TTAACTATGAGTTT
1743429 TT
1 TT
1743431 TTCCAGTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.07, G:0.13, T:0.53
Consensus pattern (14 bp):
TTAACTATGAGTTT
Found at i:1747010 original size:15 final size:15
Alignment explanation
Indices: 1746992--1747020 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1746982 TTTTATCCAT
1746992 ATCTTTCTTTTCTTC
1 ATCTTTCTTTTCTTC
1747007 ATCTTTCTTTTCTT
1 ATCTTTCTTTTCTT
1747021 GCTTTTCTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.24, G:0.00, T:0.69
Consensus pattern (15 bp):
ATCTTTCTTTTCTTC
Found at i:1754029 original size:17 final size:18
Alignment explanation
Indices: 1754007--1754049 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1753997 AGTTTGAGCA
*
1754007 TTTCAAGCCT-ATTTTTC
1 TTTCAAGACTCATTTTTC
* *
1754024 TTTCAATATTCATTTTTC
1 TTTCAAGACTCATTTTTC
1754042 TTTCAAGA
1 TTTCAAGA
1754050 ACTCTTATTG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.23, C:0.19, G:0.05, T:0.53
Consensus pattern (18 bp):
TTTCAAGACTCATTTTTC
Found at i:1755223 original size:33 final size:33
Alignment explanation
Indices: 1755186--1755249 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
1755176 AAATGAAAAT
*
1755186 GGATTTTGAA-AATCAAAATGAAATCTTGAAGAA
1 GGATTTAGAACAATCAAAATGAAAT-TTGAAGAA
**
1755219 GGATTTAGAACTCTCAAAATGAAATTTGAAG
1 GGATTTAGAACAATCAAAATGAAATTTGAAG
1755250 TATGAAAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 15 0.56
34 12 0.44
ACGTcount: A:0.45, C:0.08, G:0.19, T:0.28
Consensus pattern (33 bp):
GGATTTAGAACAATCAAAATGAAATTTGAAGAA
Found at i:1758654 original size:14 final size:14
Alignment explanation
Indices: 1758635--1758666 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
1758625 ATTCCTATCA
1758635 AGTGTGACAATACT
1 AGTGTGACAATACT
1758649 AGTGTGACAATACT
1 AGTGTGACAATACT
1758663 AGTG
1 AGTG
1758667 CTATTTGTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.28
Consensus pattern (14 bp):
AGTGTGACAATACT
Found at i:1759210 original size:21 final size:21
Alignment explanation
Indices: 1759184--1759223 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1759174 CCCCCTTTGA
*
1759184 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
1759205 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
1759224 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:1764681 original size:13 final size:14
Alignment explanation
Indices: 1764647--1764679 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1764637 AAAATTTAAT
*
1764647 AATAAAA-AAGAAA
1 AATAAAATACGAAA
1764660 AATAAAATACGAAA
1 AATAAAATACGAAA
1764674 AATAAA
1 AATAAA
1764680 TAAATAGAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.79, C:0.03, G:0.06, T:0.12
Consensus pattern (14 bp):
AATAAAATACGAAA
Found at i:1766134 original size:17 final size:17
Alignment explanation
Indices: 1766112--1766146 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1766102 ATATATTTTT
*
1766112 TCAAAATAATATATATA
1 TCAAAACAATATATATA
*
1766129 TCAAAACCATATATATA
1 TCAAAACAATATATATA
1766146 T
1 T
1766147 ATATTAAAAT
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:0.54, C:0.11, G:0.00, T:0.34
Consensus pattern (17 bp):
TCAAAACAATATATATA
Found at i:1766858 original size:33 final size:31
Alignment explanation
Indices: 1766808--1766869 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 31
1766798 GTCAAAACTA
*
1766808 TTAGGATTGATTTAATTTAAATTGAATTTGACG
1 TTAGGATTGATTGAATTT-AA-TGAATTTGACG
1766841 TTAGGA-TGATTGGAATTTAATGAATTTGA
1 TTAGGATTGATT-GAATTTAATGAATTTGA
1766870 TTCTAGGAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 9 0.33
32 7 0.26
33 11 0.41
ACGTcount: A:0.34, C:0.02, G:0.21, T:0.44
Consensus pattern (31 bp):
TTAGGATTGATTGAATTTAATGAATTTGACG
Found at i:1768535 original size:19 final size:19
Alignment explanation
Indices: 1768482--1768536 Score: 74
Period size: 19 Copynumber: 2.9 Consensus size: 19
1768472 TATACATTGG
* *
1768482 GCTATGAATTTGAAATTGA
1 GCTATGAATATGAAAATGA
1768501 GCTATGAATATGAAAATGA
1 GCTATGAATATGAAAATGA
* *
1768520 GTTATGAATCTGAAAAT
1 GCTATGAATATGAAAAT
1768537 AAAGAAATGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.42, C:0.05, G:0.20, T:0.33
Consensus pattern (19 bp):
GCTATGAATATGAAAATGA
Found at i:1781594 original size:18 final size:18
Alignment explanation
Indices: 1781568--1781603 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1781558 CGAATACATT
1781568 GATTATGACGCTTTGCTC
1 GATTATGACGCTTTGCTC
*
1781586 GATTGTGACGCTTTGCTC
1 GATTATGACGCTTTGCTC
1781604 TCCTACCCGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.22, G:0.25, T:0.39
Consensus pattern (18 bp):
GATTATGACGCTTTGCTC
Found at i:1791187 original size:90 final size:90
Alignment explanation
Indices: 1791078--1791244 Score: 298
Period size: 90 Copynumber: 1.9 Consensus size: 90
1791068 ATTTAATTTT
* *
1791078 AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGATTAGGGTAAATT
1 AATTAATTAAATATAGATTTAATTAAATTGAAATAATAAAAACCCTAATATGATTAGGGTAAATT
1791143 GGATATAAAAGGATTATTAAATTCC
66 GGATATAAAAGGATTATTAAATTCC
*
1791168 AATTAATTAAATATAGATTTAATTAAATTGAAATAATAAAAACCCTAATATGATTAGGGTAACTT
1 AATTAATTAAATATAGATTTAATTAAATTGAAATAATAAAAACCCTAATATGATTAGGGTAAATT
*
1791233 GGCTATAAAAGG
66 GGATATAAAAGG
1791245 GTGTGTTAGG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
90 73 1.00
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (90 bp):
AATTAATTAAATATAGATTTAATTAAATTGAAATAATAAAAACCCTAATATGATTAGGGTAAATT
GGATATAAAAGGATTATTAAATTCC
Found at i:1797979 original size:90 final size:90
Alignment explanation
Indices: 1797868--1798043 Score: 289
Period size: 90 Copynumber: 2.0 Consensus size: 90
1797858 TAATCCCGAA
* * * * *
1797868 TATTTAATTTCAATTAATTAAATATAGATTTAATTCATTTGAAATAATAAAATCCCTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATGTAATTAATTTGAAATAATAAAAACCCTAATATGAT
1797933 TAGGGTAACTTGGATATAAAAGGAT
66 TAGGGTAACTTGGATATAAAAGGAT
*
1797958 TATTAAATTCCAATTAATTAAATATGGATGTAATTAATTTGAAATAATAAAAACCCTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATGTAATTAATTTGAAATAATAAAAACCCTAATATGAT
*
1798023 TAGGGTAACTTGGCTATAAAA
66 TAGGGTAACTTGGATATAAAA
1798044 AGGTGTGTTA
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
90 79 1.00
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.37
Consensus pattern (90 bp):
TATTAAATTCCAATTAATTAAATATAGATGTAATTAATTTGAAATAATAAAAACCCTAATATGAT
TAGGGTAACTTGGATATAAAAGGAT
Found at i:1812313 original size:16 final size:16
Alignment explanation
Indices: 1812292--1812335 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
1812282 GAAGGAAGAA
**
1812292 TTATTTTACTTTGTAT
1 TTATTTTACTTTACAT
*
1812308 TTATTTAACTTTACAT
1 TTATTTTACTTTACAT
1812324 TTATTTTACTTT
1 TTATTTTACTTT
1812336 CACCTACCCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.66
Consensus pattern (16 bp):
TTATTTTACTTTACAT
Found at i:1818262 original size:20 final size:20
Alignment explanation
Indices: 1818220--1818269 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
1818210 ATGCAATCAA
1818220 TATCGATACCGAAAGGGAAG
1 TATCGATACCGAAAGGGAAG
* *
1818240 TATCTATACCG-AGGGGAAGG
1 TATCGATACCGAAAGGGAA-G
*
1818260 TATAGATACC
1 TATCGATACC
1818270 ATTCAAAACT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 6 0.24
20 19 0.76
ACGTcount: A:0.36, C:0.16, G:0.28, T:0.20
Consensus pattern (20 bp):
TATCGATACCGAAAGGGAAG
Found at i:1818344 original size:22 final size:22
Alignment explanation
Indices: 1818293--1818346 Score: 69
Period size: 19 Copynumber: 2.6 Consensus size: 22
1818283 TGCAAAAATG
1818293 GTATCGATACCATAATAGAGTA
1 GTATCGATACCATAATAGAGTA
* *
1818315 -T-TAG-TACCATAATATAGTA
1 GTATCGATACCATAATAGAGTA
1818334 GTATCGATACCAT
1 GTATCGATACCAT
1818347 GGTAGGGGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
19 14 0.54
20 3 0.12
21 3 0.12
22 6 0.23
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (22 bp):
GTATCGATACCATAATAGAGTA
Found at i:1819236 original size:55 final size:55
Alignment explanation
Indices: 1818702--1819219 Score: 727
Period size: 55 Copynumber: 9.4 Consensus size: 55
1818692 AAGTGTGCAA
* *
1818702 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCTATATGGGCACTTTATATGTT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCTGTATGGGCACTTTATGTG-T
* ** * *
1818758 AAA-TTAAGAAATTCATACTAAGTGGATGAATTTCCGTATAAGCACCTTGTGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCTGTATGGGCACTTTATGTGT
*
1818812 AAACTTAAGAAATTCATACTAAGTGGATAAATTTCTGTATGGGCACTTTATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCTGTATGGGCACTTTATGTGT
* * * * * * *
1818867 AAAGTTAAGAAATTTATACTAAGTGGAAGAATTTCCGTATGGGCACCTTGTGCGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCTGTATGGGCACTTTATGTGT
* *
1818922 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCTGTGTGGGCACTTAATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCTGTATGGGCACTTTATGTGT
* * * * * *
1818977 AAAATTAAGAAATTTATACTAAGTGGATGAATTTCCGTATGGACACATTCTGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCTGTATGGGCACTTTATGTGT
*
1819032 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCTGTATGAGCACTTTATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCTGTATGGGCACTTTATGTGT
* * *
1819087 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCTGTATAGGCACCTTGTGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCTGTATGGGCACTTTATGTGT
*
1819142 AAACTTAAGGAATTCATACTAAGTGGATGAATTTCTGTATGGGCACTTTATGT-T
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCTGTATGGGCACTTTATGTGT
*
1819196 CAAAAC-TAGGAAATTCATACTAAG
1 --AAACTTAAGAAATTCATACTAAG
1819220 AGTATAAATT
Statistics
Matches: 404, Mismatches: 55, Indels: 7
0.87 0.12 0.02
Matches are distributed among these distances:
54 5 0.01
55 392 0.97
56 7 0.02
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34
Consensus pattern (55 bp):
AAACTTAAGAAATTCATACTAAGTGGATGAATTTCTGTATGGGCACTTTATGTGT
Found at i:1819236 original size:110 final size:110
Alignment explanation
Indices: 1818702--1819219 Score: 815
Period size: 110 Copynumber: 4.7 Consensus size: 110
1818692 AAGTGTGCAA
* * *
1818702 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCTATATGGGCACTTTATATGTTAAATTAAGA
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCTGTATGGGCACTTTATGTGTAAAATTAAGA
*
1818767 AATTCATACTAAGTGGATGAATTTCCGTATAAGCACCTTGTGTGT
66 AATTCATACTAAGTGGATGAATTTCCGTATAGGCACCTTGTGTGT
* *
1818812 AAACTTAAGAAATTCATACTAAGTGGATAAATTTCTGTATGGGCACTTTATGTGTAAAGTTAAGA
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCTGTATGGGCACTTTATGTGTAAAATTAAGA
* * * *
1818877 AATTTATACTAAGTGGAAGAATTTCCGTATGGGCACCTTGTGCGT
66 AATTCATACTAAGTGGATGAATTTCCGTATAGGCACCTTGTGTGT
* *
1818922 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCTGTGTGGGCACTTAATGTGTAAAATTAAGA
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCTGTATGGGCACTTTATGTGTAAAATTAAGA
* * *
1818987 AATTTATACTAAGTGGATGAATTTCCGTAT-GGACACATTCTGTGT
66 AATTCATACTAAGTGGATGAATTTCCGTATAGG-CACCTTGTGTGT
* *
1819032 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCTGTATGAGCACTTTATGTGTAAACTTAAGA
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCTGTATGGGCACTTTATGTGTAAAATTAAGA
*
1819097 AATTCATACTAAGTGGATGAATTTCTGTATAGGCACCTTGTGTGT
66 AATTCATACTAAGTGGATGAATTTCCGTATAGGCACCTTGTGTGT
* * *
1819142 AAACTTAAGGAATTCATACTAAGTGGATGAATTTCTGTATGGGCACTTTATGT-TCAAAACTAGG
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCTGTATGGGCACTTTATGTGT-AAAATTAAG
1819206 AAATTCATACTAAG
65 AAATTCATACTAAG
1819220 AGTATAAATT
Statistics
Matches: 374, Mismatches: 31, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
109 3 0.01
110 369 0.99
111 2 0.01
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34
Consensus pattern (110 bp):
AAACTTAAGAAATTCATACTAAGTGGATGAATTTCTGTATGGGCACTTTATGTGTAAAATTAAGA
AATTCATACTAAGTGGATGAATTTCCGTATAGGCACCTTGTGTGT
Found at i:1820708 original size:17 final size:18
Alignment explanation
Indices: 1820681--1820720 Score: 73
Period size: 17 Copynumber: 2.3 Consensus size: 18
1820671 AGTGATAAAC
1820681 AGAGCGAAGGCTATTGAA
1 AGAGCGAAGGCTATTGAA
1820699 AGAGCG-AGGCTATTGAA
1 AGAGCGAAGGCTATTGAA
1820716 AGAGC
1 AGAGC
1820721 TCAAGAGGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 16 0.73
18 6 0.27
ACGTcount: A:0.38, C:0.12, G:0.35, T:0.15
Consensus pattern (18 bp):
AGAGCGAAGGCTATTGAA
Found at i:1825148 original size:20 final size:21
Alignment explanation
Indices: 1825123--1825173 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
1825113 ATGCAATCAA
1825123 TATCGATACCAAAAGAGAA-G
1 TATCGATACCAAAAGAGAATG
* * *
1825143 TATCGATATC-GAAGGGAATG
1 TATCGATACCAAAAGAGAATG
1825163 TATCGATACCA
1 TATCGATACCA
1825174 TTCAAAATAG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
19 6 0.24
20 19 0.76
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.22
Consensus pattern (21 bp):
TATCGATACCAAAAGAGAATG
Found at i:1825693 original size:55 final size:55
Alignment explanation
Indices: 1825604--1825780 Score: 248
Period size: 55 Copynumber: 3.2 Consensus size: 55
1825594 TAAGTGTGCA
* *
1825604 AAAACTTAAGAAATTCATACTAAGTGGATGAATTTAT-GTATGAGCACTTTATGTGT
1 AAAA-TTAAGAAATTCATACTAAGTGGATGAATTT-TCGTATGGGCACATTATGTGT
*
1825660 AAAATTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGCACCTTATGTGT
1 AAAATTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGCACATTATGTGT
* * * * *
1825715 AAACTTAAGAAATTCATACTATGTGGAAGAATTTTCGTATGGGCACATTGTGTGC
1 AAAATTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGCACATTATGTGT
*
1825770 AAACTTAAGAA
1 AAAATTAAGAA
1825781 GAAGAAGAGA
Statistics
Matches: 112, Mismatches: 8, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
54 1 0.01
55 107 0.96
56 4 0.04
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.33
Consensus pattern (55 bp):
AAAATTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGCACATTATGTGT
Found at i:1827953 original size:17 final size:17
Alignment explanation
Indices: 1827933--1827983 Score: 66
Period size: 17 Copynumber: 3.0 Consensus size: 17
1827923 AATAAAGTTT
*
1827933 GTTCACTAATCAAACTA
1 GTTCATTAATCAAACTA
*
1827950 GTTCATTTATCAAACTA
1 GTTCATTAATCAAACTA
**
1827967 GTGGATTAATCAAACTA
1 GTTCATTAATCAAACTA
1827984 AATCTTAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.33
Consensus pattern (17 bp):
GTTCATTAATCAAACTA
Found at i:1830843 original size:236 final size:237
Alignment explanation
Indices: 1830400--1830866 Score: 756
Period size: 236 Copynumber: 2.0 Consensus size: 237
1830390 ATGGAGTTGA
*
1830400 AAATGTGTATAAAGAAGAAAAAGAACGGACTTTATCTAACCAATCTTTTCTTCCTATTTTTTCTT
1 AAATGTGTATAAAGAAGAAAAAGAACGGACTTTATCTAACCAATCTTTTCTTCCTATTCTTTCTT
* * *
1830465 CTTTTATTTTATAGGATTCTCTAAAAGACATGCCATTTCAAATTGATGAAATAAGCATCATGCCT
66 ATTTTATTTTATAGGATTCTCTAAAAGACATGCCATTTAAAATTGATGAAACAAGCATCATGCCT
* *
1830530 ATTGAAGAACCAACGGGCGTCCCACAAGATGCATCATTTAAAGCACCAAAAGTTGCGTTTGTTGG
131 ATTGAAGAACCAACGGGCGCCCCACAAGATGCATCATTTAAAGCACAAAAAGTTGCGTTTGTTGG
*
1830595 CATCCTGAGTTCATTACCAATCTTGAAGGAAATTCAACAGCC
196 CATCCCGAGTTCATTACCAATCTTGAAGGAAATTCAACAGCC
* *
1830637 AAATGTGTATAAATAA-AAAAATAACGGACTTTATCTAACCAATCTTTTCTTCCTATTCTTTCTT
1 AAATGTGTATAAAGAAGAAAAAGAACGGACTTTATCTAACCAATCTTTTCTTCCTATTCTTTCTT
* * *
1830701 ATTTTGTTTTGTAGGATTCTCTAAAAGACATTCCATTTAAAATTGATGAAACAAGCATCATGCCT
66 ATTTTATTTTATAGGATTCTCTAAAAGACATGCCATTTAAAATTGATGAAACAAGCATCATGCCT
* * ** *
1830766 ATTGAAGAACCAACGGGTGCCCCACAAGATGCATCATTTTAAGTGCAAAAAGTTGTGTTTGTTGG
131 ATTGAAGAACCAACGGGCGCCCCACAAGATGCATCATTTAAAGCACAAAAAGTTGCGTTTGTTGG
* *
1830831 CTTCCCGAGTTCATTGCCAATCTTGAAGGAAATTCA
196 CATCCCGAGTTCATTACCAATCTTGAAGGAAATTCA
1830867 GCAACCAACG
Statistics
Matches: 211, Mismatches: 19, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
236 196 0.93
237 15 0.07
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (237 bp):
AAATGTGTATAAAGAAGAAAAAGAACGGACTTTATCTAACCAATCTTTTCTTCCTATTCTTTCTT
ATTTTATTTTATAGGATTCTCTAAAAGACATGCCATTTAAAATTGATGAAACAAGCATCATGCCT
ATTGAAGAACCAACGGGCGCCCCACAAGATGCATCATTTAAAGCACAAAAAGTTGCGTTTGTTGG
CATCCCGAGTTCATTACCAATCTTGAAGGAAATTCAACAGCC
Found at i:1832247 original size:16 final size:17
Alignment explanation
Indices: 1832209--1832247 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
1832199 AAGTATGTTG
1832209 TTCATTAAAGCATGCAT
1 TTCATTAAAGCATGCAT
* *
1832226 TGCATT-AAGCATGTAT
1 TTCATTAAAGCATGCAT
1832242 TTCATT
1 TTCATT
1832248 TAGGGAAGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (17 bp):
TTCATTAAAGCATGCAT
Found at i:1832343 original size:17 final size:17
Alignment explanation
Indices: 1832323--1832375 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
1832313 TTAATAAAGT
*
1832323 TAGTTCACTAATCAAAC
1 TAGTTCATTAATCAAAC
* *
1832340 TAGTTCATTTATTAAAC
1 TAGTTCATTAATCAAAC
*
1832357 TAGTGCATTAATCAAAC
1 TAGTTCATTAATCAAAC
1832374 TA
1 TA
1832376 ACTCTTAATT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.36
Consensus pattern (17 bp):
TAGTTCATTAATCAAAC
Found at i:1835211 original size:15 final size:15
Alignment explanation
Indices: 1835180--1835221 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
1835170 ATGAAAAATA
*
1835180 AAGAAAA-AAAGATT
1 AAGAAAATAAAGAAT
1835194 AAGAAAATAAAGAAT
1 AAGAAAATAAAGAAT
*
1835209 AAGATAATAAAGA
1 AAGAAAATAAAGA
1835222 TAAAAAAGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 7 0.28
15 18 0.72
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (15 bp):
AAGAAAATAAAGAAT
Found at i:1841077 original size:22 final size:22
Alignment explanation
Indices: 1841050--1841138 Score: 124
Period size: 22 Copynumber: 4.0 Consensus size: 22
1841040 TGTCAAGGGT
* * *
1841050 TACATAGGTCCTCCGGGAAATA
1 TACAAAGGTCCTTCGGGATATA
* *
1841072 TGCATAGGTCCTTCGGGATATA
1 TACAAAGGTCCTTCGGGATATA
1841094 TACAAAGGTCCTTCGGGATATA
1 TACAAAGGTCCTTCGGGATATA
*
1841116 TACAAAGGTCCTTCGGGACATA
1 TACAAAGGTCCTTCGGGATATA
1841138 T
1 T
1841139 TTTACATGTC
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 61 1.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (22 bp):
TACAAAGGTCCTTCGGGATATA
Found at i:1847256 original size:20 final size:20
Alignment explanation
Indices: 1847233--1847281 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
1847223 GGTTTAGGGG
1847233 TATCGATACTGGTTGAACAA
1 TATCGATACTGGTTGAACAA
*
1847253 TATCGATACTGGTTGAACAG
1 TATCGATACTGGTTGAACAA
1847273 TATCGATAC
1 TATCGATAC
1847282 CTGGGAGGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (20 bp):
TATCGATACTGGTTGAACAA
Found at i:1851531 original size:5 final size:5
Alignment explanation
Indices: 1851521--1851624 Score: 54
Period size: 5 Copynumber: 20.6 Consensus size: 5
1851511 TATTTAGAGA
* * * * *
1851521 AAAAT AAAAT ACAAT TAATT AAAAT AAAAT -AAAT ATAAT AAAAAT AAAGT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT AAAAT
** * *
1851571 TCACT GAAAAT AAAAT -AAA- AAAAT AAAAGT AAAA- ACGTAAT AAAAT
1 AAAAT -AAAAT AAAAT AAAAT AAAAT AAAA-T AAAAT A--AAAT AAAAT
1851617 AAAAT AAA
1 AAAAT AAA
1851625 CAAAAATAGA
Statistics
Matches: 73, Mismatches: 17, Indels: 18
0.68 0.16 0.17
Matches are distributed among these distances:
4 11 0.15
5 48 0.66
6 13 0.18
7 1 0.01
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.22
Consensus pattern (5 bp):
AAAAT
Found at i:1851546 original size:20 final size:20
Alignment explanation
Indices: 1851520--1851568 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1851510 CTATTTAGAG
1851520 AAAAATAAAATACAAT-TAAT
1 AAAAATAAAATA-AATATAAT
*
1851540 TAAAATAAAATAAATATAAT
1 AAAAATAAAATAAATATAAT
1851560 AAAAATAAA
1 AAAAATAAA
1851569 GTTCACTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 3 0.12
20 23 0.88
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (20 bp):
AAAAATAAAATAAATATAAT
Found at i:1851605 original size:14 final size:13
Alignment explanation
Indices: 1851577--1851620 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 13
1851567 AAGTTCACTG
1851577 AAAATAAAATAAA
1 AAAATAAAATAAA
1851590 AAAATAAAAGTAAA
1 AAAATAAAA-TAAA
1851604 AACGTAATAAAATAAA
1 AA---AATAAAATAAA
1851620 A
1 A
1851621 TAAACAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 9 0.33
14 6 0.22
16 5 0.19
17 7 0.26
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.16
Consensus pattern (13 bp):
AAAATAAAATAAA
Found at i:1861238 original size:15 final size:15
Alignment explanation
Indices: 1861218--1861247 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1861208 GTCTTAAACA
1861218 TATATATATATATAT
1 TATATATATATATAT
1861233 TATATATATATATAT
1 TATATATATATATAT
1861248 ATACTCCACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATATATATATATAT
Found at i:1861239 original size:17 final size:17
Alignment explanation
Indices: 1861217--1861249 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1861207 TGTCTTAAAC
1861217 ATATATATATATATATT
1 ATATATATATATATATT
1861234 ATATATATATATATAT
1 ATATATATATATATAT
1861250 ACTCCACCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATATATATATATATATT
Found at i:1861270 original size:2 final size:2
Alignment explanation
Indices: 1861217--1861250 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1861207 TGTCTTAAAC
1861217 AT AT AT AT AT AT AT AT -T 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 A
1861251 CTCCACCTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1874742 original size:3 final size:3
Alignment explanation
Indices: 1874729--1874823 Score: 75
Period size: 3 Copynumber: 31.3 Consensus size: 3
1874719 TTTTACGTAA
* * ** *
1874729 ATT ACT ATT ATT ATT ATT TTT AAAA ATT ACT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT
* * * * *
1874775 ATT ATT -TA AAT ATT AAT ATT AAT ATT AAT ATT ATT ATT ATT ATAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T
1874820 ATT A
1 ATT A
1874824 AATAAATAAA
Statistics
Matches: 69, Mismatches: 20, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
2 1 0.01
3 65 0.94
4 3 0.04
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:1875903 original size:2 final size:2
Alignment explanation
Indices: 1875896--1875948 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
1875886 CTTATATGCT
1875896 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1875938 TA TA TA TA TA T
1 TA TA TA TA TA T
1875949 TAGGTAAATA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1877979 original size:16 final size:18
Alignment explanation
Indices: 1877948--1877980 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
1877938 TACCTTTACT
1877948 CATATAACTGAAACCCTG
1 CATATAACTGAAACCCTG
1877966 CATATAA-T-AAACCCT
1 CATATAACTGAAACCCT
1877981 AGAAATGCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 1 0.07
18 7 0.47
ACGTcount: A:0.42, C:0.27, G:0.06, T:0.24
Consensus pattern (18 bp):
CATATAACTGAAACCCTG
Found at i:1882407 original size:32 final size:32
Alignment explanation
Indices: 1882351--1882412 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
1882341 TCTGGAAACA
* *
1882351 AGAAGTATCTCTACGGAATGAGCATAACAACG
1 AGAAGTATCTCTACAGAATAAGCATAACAACG
1882383 AGAAGTATCTCTACCAG-ATAAGCATAACAA
1 AGAAGTATCTCTA-CAGAATAAGCATAACAA
1882413 TCATTTCTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 25 0.93
33 2 0.07
ACGTcount: A:0.44, C:0.19, G:0.18, T:0.19
Consensus pattern (32 bp):
AGAAGTATCTCTACAGAATAAGCATAACAACG
Found at i:1886331 original size:54 final size:54
Alignment explanation
Indices: 1886258--1886410 Score: 184
Period size: 54 Copynumber: 2.8 Consensus size: 54
1886248 AATCTGTGCC
* *
1886258 GAAACCAC-AGAAAATGATGAATGTGTTGTCAAATGCTTTACGAACATCT-GGCCA
1 GAAACCACAAG-AAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTAGG-CA
* * * *
1886312 GAAGCCATAAGAAAGGATGAATGTGTTATCAAATGTTTTACGAACATCTATGCA
1 GAAACCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTAGGCA
* * * *
1886366 GAAACCACGAGAAATGATGAATGTATTGTCACATGTTTTACGAAC
1 GAAACCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
1886411 CAGTGATTAT
Statistics
Matches: 84, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
54 81 0.96
55 3 0.04
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (54 bp):
GAAACCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTAGGCA
Found at i:1886803 original size:22 final size:22
Alignment explanation
Indices: 1886778--1886832 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
1886768 ACATCTACAT
1886778 TCTTCAAAGATGACAGATTTTC
1 TCTTCAAAGATGACAGATTTTC
*
1886800 TCTTCAAAGATGATAGATTTTC
1 TCTTCAAAGATGACAGATTTTC
*
1886822 TTTTCAAAGAT
1 TCTTCAAAGAT
1886833 AGGATCTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.40
Consensus pattern (22 bp):
TCTTCAAAGATGACAGATTTTC
Found at i:1887551 original size:45 final size:45
Alignment explanation
Indices: 1887487--1887935 Score: 745
Period size: 45 Copynumber: 10.0 Consensus size: 45
1887477 CTATTTCCCA
* * *
1887487 CATCTGTAATCCCTTCAGTGCATGATGTTTTCAAAACCTTTGGAT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
1887532 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTAGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
1887577 CATCTGTAAGCCCTTCAGTGCATGATGTTTTTAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1887622 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * *
1887667 CATCTGTAAGTCCTTTAGTGCATGATGTTTTCAAAACCTTTGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
1887712 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAATCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
1887757 CATCTGTAAGCCCTTTAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
1887802 CATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAACCTTTGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * *
1887847 CATCTGTATGCCCTTCAATGCATGATGTTATCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
1887892 CATCTGTAAGCCCTACAGTGCATGATGTTTTCAAAACCTCCGGG
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGG
1887936 ATATTCATAA
Statistics
Matches: 378, Mismatches: 26, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 378 1.00
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (45 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
Found at i:1888133 original size:3 final size:3
Alignment explanation
Indices: 1888122--1888188 Score: 64
Period size: 3 Copynumber: 22.3 Consensus size: 3
1888112 ATTTTTAAAA
* * * * * *
1888122 ATT ACT ATT ATT ATT ATT ATT ATT -TA AAT ATT AAT AAT ATT ATT ATA
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1888169 ATT ATTT ATT ATT ATT ATT A
1 ATT A-TT ATT ATT ATT ATT A
1888189 AATAAATACA
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
2 1 0.02
3 48 0.92
4 3 0.06
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:1888154 original size:29 final size:29
Alignment explanation
Indices: 1888106--1888176 Score: 99
Period size: 29 Copynumber: 2.5 Consensus size: 29
1888096 AATTACCTAA
* *
1888106 ATTATTATT-TTTAAAAATTACTATTATT
1 ATTATTATTATTTAAAAATTAATAATATT
*
1888134 ATTATTATTATTTAAATATTAATAATATT
1 ATTATTATTATTTAAAAATTAATAATATT
*
1888163 ATTATAATTATTTA
1 ATTATTATTATTTA
1888177 TTATTATTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
28 9 0.24
29 29 0.76
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.56
Consensus pattern (29 bp):
ATTATTATTATTTAAAAATTAATAATATT
Found at i:1889536 original size:2 final size:2
Alignment explanation
Indices: 1889529--1889567 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1889519 TTTAATTTAG
1889529 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
1889568 TTTAAGATAA
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:1890074 original size:14 final size:13
Alignment explanation
Indices: 1890055--1890109 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 13
1890045 ATATATATTT
1890055 ATTATTTTATTTAA
1 ATTATTTT-TTTAA
*
1890069 ATTATTTTCTTAA
1 ATTATTTTTTTAA
1890082 ATTATTATTTTTAA
1 ATTATT-TTTTTAA
1890096 TATTTATTTATTTT
1 -A-TTATTT-TTTT
1890110 TCAAATATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
13 10 0.29
14 14 0.40
15 2 0.06
16 9 0.26
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (13 bp):
ATTATTTTTTTAA
Found at i:1890083 original size:13 final size:14
Alignment explanation
Indices: 1890055--1890087 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1890045 ATATATATTT
*
1890055 ATTATTTTATTTAA
1 ATTATTTTACTTAA
1890069 ATTATTTT-CTTAA
1 ATTATTTTACTTAA
1890082 ATTATT
1 ATTATT
1890088 ATTTTTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (14 bp):
ATTATTTTACTTAA
Found at i:1890210 original size:151 final size:146
Alignment explanation
Indices: 1889929--1890322 Score: 405
Period size: 151 Copynumber: 2.7 Consensus size: 146
1889919 TTCATAGGAA
*
1889929 AAATTATTATTTTTAATATTTATTTATTTTAAAAATATTAAGAAATGG-CAGTCTTAAAGCAACT
1 AAATTATTATTTTTAATATTTATTTATTTT-TAAATATTAAGAAA-GGACAGTCTTAAAGCAACT
* * * *
1889993 AGATGTCATATTATTG-TATTTTAAAAATAAATAAATATAAAAACCAAAATATATATATATTTAT
64 AGATGTCTTATT-CTGATATTTTAAAAATAAATGAATATAAAAACCAAAATATATATATATTCAT
** *
1890057 TA-TTTTATTTAAATTATTTTCTT
128 TATTTTTA-GGAAA--A--TTATT
1890080 AAATTATTATTTTTAATATTTATTTATTTTTCAAATATTAAGAAAGGACAGTCTTAAAGCAACTA
1 AAATTATTATTTTTAATATTTATTTATTTTT-AAATATTAAGAAAGGACAGTCTTAAAGCAACTA
**** *
1890145 GATGTCTTATTCTGATATTTTAAAAATAAATGAATAT-CCTGCTTATAAA-A-ATATATACTTCA
65 GATGTCTTATTCTGATATTTTAAAAATAAATGAATATAAAAAC-CA-AAATATATATATA-TTCA
1890207 TTATTTTTAGGAAAATTATT
127 TTATTTTTAGGAAAATTATT
* * * *
1890227 --A-TATTCTTATTAATATTTATTTATTTATT-AATATTAAAGAAAAGACAGTCTTAAAGCAGCT
1 AAATTATTATTTTTAATATTTATTTATTT-TTAAATATT-AAGAAAGGACAGTCTTAAAGCAACT
1890288 AGATGTTCTT-TTCTGATATTTTAAATAAATAAATG
64 AGATG-TCTTATTCTGATATTTT-AA-AAATAAATG
1890323 TCCTATTTAC
Statistics
Matches: 214, Mismatches: 17, Indels: 29
0.82 0.07 0.11
Matches are distributed among these distances:
143 6 0.03
144 63 0.29
145 9 0.04
146 9 0.04
147 4 0.02
149 1 0.00
150 12 0.06
151 102 0.48
152 8 0.04
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (146 bp):
AAATTATTATTTTTAATATTTATTTATTTTTAAATATTAAGAAAGGACAGTCTTAAAGCAACTAG
ATGTCTTATTCTGATATTTTAAAAATAAATGAATATAAAAACCAAAATATATATATATTCATTAT
TTTTAGGAAAATTATT
Found at i:1893672 original size:2 final size:2
Alignment explanation
Indices: 1893665--1893719 Score: 51
Period size: 2 Copynumber: 28.0 Consensus size: 2
1893655 GTCATAAACG
* * **
1893665 TA TA TA TA TA TA TA TA T- TA TA TA TA CTC CA CC TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
1893706 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
1893720 ACATAAAACG
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
1 2 0.05
2 41 0.93
3 1 0.02
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:1896365 original size:55 final size:54
Alignment explanation
Indices: 1896295--1896429 Score: 180
Period size: 55 Copynumber: 2.5 Consensus size: 54
1896285 TTGTTACATT
* *
1896295 TTTCGTATTGACACTATGTGTGCAACCTCACGAAATTCATAATAAGTTTATGAA
1 TTTCGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATAAGTTTATGAA
* * *
1896349 TTTCTGTATTGGCACTATGTGTGCAACCCCACGTAATTCATAATCAGTTTGTGAA
1 TTTC-GTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATAAGTTTATGAA
* * *
1896404 TTACCGTATCGGCACTACGTGTGCAA
1 TT-TCGTATTGGCACTATGTGTGCAA
1896430 AACCATGGAA
Statistics
Matches: 71, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
54 4 0.06
55 66 0.93
56 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (54 bp):
TTTCGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATAAGTTTATGAA
Found at i:1902605 original size:20 final size:21
Alignment explanation
Indices: 1902561--1902605 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
1902551 GGAGGATTGG
* *
1902561 TACCATAGTATAGAAGTATCGA
1 TACCATAGAATAG-AGTACCGA
1902583 TACCATAGAATAG-GTACCGA
1 TACCATAGAATAGAGTACCGA
1902603 TAC
1 TAC
1902606 TAATCTGCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 9 0.43
22 12 0.57
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.24
Consensus pattern (21 bp):
TACCATAGAATAGAGTACCGA
Found at i:1902985 original size:55 final size:55
Alignment explanation
Indices: 1902912--1903128 Score: 330
Period size: 55 Copynumber: 3.9 Consensus size: 55
1902902 TATATGTTGA
* *
1902912 AATTTTCATATTGTCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTAT-
1 AATTTTCGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATG
1902966 AACTTTTCGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATG
1 AA-TTTTCGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATG
1903022 AA-TTTCTGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATG
1 AATTTTC-GTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATG
* * * * * *
1903077 TATTTTTGTATTGGCACTAAGTGTGCAACCCCACGTAATTCATAACGAGTTT
1 AATTTTCGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTT
1903129 TTAAATTACC
Statistics
Matches: 151, Mismatches: 8, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
54 6 0.04
55 140 0.93
56 5 0.03
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.37
Consensus pattern (55 bp):
AATTTTCGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATG
Found at i:1903156 original size:55 final size:55
Alignment explanation
Indices: 1902911--1903156 Score: 312
Period size: 55 Copynumber: 4.5 Consensus size: 55
1902901 GTATATGTTG
* * *
1902911 AAATTTTCATATTGTCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTAT
1 AAATTTCCGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTAT
* *
1902966 AACTTTTCGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTAT
1 AAATTTCCGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTAT
* *
1903021 GAATTTCTGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTAT
1 AAATTTCCGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTAT
** ** * * * * *
1903076 GTATTTTTGTATTGGCACTAAGTGTGCAACCCCACGTAATTCATAACGAGTTTTT
1 AAATTTCCGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTAT
* * * *
1903131 AAATTACCGTATAGGCAATACGTGTG
1 AAATTTCCGTATTGGCACTATGTGTG
1903157 AAAAACCGAA
Statistics
Matches: 169, Mismatches: 22, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 169 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (55 bp):
AAATTTCCGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTAT
Found at i:1905688 original size:19 final size:19
Alignment explanation
Indices: 1905620--1905691 Score: 63
Period size: 21 Copynumber: 3.6 Consensus size: 19
1905610 CAAAACAACG
*
1905620 AAGGGATTGATCCTTTCTTGA
1 AAGGGATCGATCC-TT-TTGA
* *
1905641 AAGGGATCGATCATTTTTCA
1 AAGGGATCGATC-CTTTTGA
**
1905661 TGGGGGATCGATCCTTTTGA
1 -AAGGGATCGATCCTTTTGA
1905681 AAGGGATCGAT
1 AAGGGATCGAT
1905692 TCATTGCAAA
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
19 9 0.22
20 8 0.20
21 23 0.57
ACGTcount: A:0.25, C:0.14, G:0.28, T:0.33
Consensus pattern (19 bp):
AAGGGATCGATCCTTTTGA
Found at i:1906188 original size:21 final size:21
Alignment explanation
Indices: 1906162--1906217 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
1906152 CATCAAATCC
1906162 CAAACCAAAATCCACTTATTA
1 CAAACCAAAATCCACTTATTA
1906183 CAAACCAAAATCCACTTATTA
1 CAAACCAAAATCCACTTATTA
*
1906204 CAAACAAAAATCCA
1 CAAACCAAAATCCA
1906218 ACATTATAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.52, C:0.29, G:0.00, T:0.20
Consensus pattern (21 bp):
CAAACCAAAATCCACTTATTA
Found at i:1913566 original size:19 final size:20
Alignment explanation
Indices: 1913542--1913584 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1913532 AGCATTTATC
*
1913542 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
1913561 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
1913581 TTCA
1 TTCA
1913585 AAGGGGTTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:1914334 original size:6 final size:6
Alignment explanation
Indices: 1914323--1914365 Score: 61
Period size: 6 Copynumber: 7.2 Consensus size: 6
1914313 GTGTTGCAAC
*
1914323 AAAAAG AAAAAG AAAGAAG AAAAAC AAAAAG -AAAAG AAAAAG A
1 AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG A
1914366 CTCCTACATC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 5 0.15
6 22 0.67
7 6 0.18
ACGTcount: A:0.81, C:0.02, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:1914345 original size:19 final size:17
Alignment explanation
Indices: 1914323--1914365 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 17
1914313 GTGTTGCAAC
1914323 AAAAAGAAAAAGAAAGAAG
1 AAAAAGAAAAAG-AA-AAG
*
1914342 AAAAACAAAAAGAAAAG
1 AAAAAGAAAAAGAAAAG
1914359 AAAAAGA
1 AAAAAGA
1914366 CTCCTACATC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 9 0.41
18 2 0.09
19 11 0.50
ACGTcount: A:0.81, C:0.02, G:0.16, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAAGAAAAG
Found at i:1914348 original size:25 final size:23
Alignment explanation
Indices: 1914320--1914365 Score: 74
Period size: 25 Copynumber: 1.9 Consensus size: 23
1914310 AAAGTGTTGC
1914320 AACAAAAAGAAAAAGAAAGAAGAAA
1 AACAAAAAG-AAAAGAAA-AAGAAA
1914345 AACAAAAAGAAAAGAAAAAGA
1 AACAAAAAGAAAAGAAAAAGA
1914366 CTCCTACATC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 4 0.19
24 8 0.38
25 9 0.43
ACGTcount: A:0.80, C:0.04, G:0.15, T:0.00
Consensus pattern (23 bp):
AACAAAAAGAAAAGAAAAAGAAA
Found at i:1914637 original size:17 final size:17
Alignment explanation
Indices: 1914617--1914652 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1914607 TCCTACCTTT
*
1914617 TACCATATCCATTTCTA
1 TACCATAACCATTTCTA
*
1914634 TACCCTAACCATTTCTA
1 TACCATAACCATTTCTA
1914651 TA
1 TA
1914653 GCCAACACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.39
Consensus pattern (17 bp):
TACCATAACCATTTCTA
Found at i:1917660 original size:19 final size:20
Alignment explanation
Indices: 1917636--1917678 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1917626 AGCATTTATC
*
1917636 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
1917655 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
1917675 TTCA
1 TTCA
1917679 AAGGGTTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:1921062 original size:153 final size:153
Alignment explanation
Indices: 1920784--1921089 Score: 585
Period size: 153 Copynumber: 2.0 Consensus size: 153
1920774 TGCAAAAGAT
1920784 GGGTTACCACTTTCTCATCTATTCTTTGCGAATGATCTCATCCTTTATGCCAAGACCACTCTCCA
1 GGGTTACCACTTTCTCATCTATTCTTTGCGAATGATCTCATCCTTTATGCCAAGACCACTCTCCA
* *
1920849 ACAATGTTCAACCATTAATTCCATCTTACCAACCTTTGGAACTTTCCCATCGGGTAAGCCATCAA
66 ACAATGTTCAACCATTAATTCCATCATACCAACCTTTGGAACTTTCCCATCGGGTAAGCCATAAA
1920914 AAAATCTCAGATTCGGTTCTCTC
131 AAAATCTCAGATTCGGTTCTCTC
1920937 GGGTTACCACTTTCTCATCTATTCTTTGCGAATGATCTCATCCTTTATGCCAAGACCACTCTCCA
1 GGGTTACCACTTTCTCATCTATTCTTTGCGAATGATCTCATCCTTTATGCCAAGACCACTCTCCA
*
1921002 ACAATGTTCAACCATTAATTCCATCATATCAACCTTTGGAACTTTCCCATCGGGTAAGCCATAAA
66 ACAATGTTCAACCATTAATTCCATCATACCAACCTTTGGAACTTTCCCATCGGGTAAGCCATAAA
1921067 AAAATCTCAGATTCGGTTCTCTC
131 AAAATCTCAGATTCGGTTCTCTC
1921090 CTAACACTGA
Statistics
Matches: 150, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
153 150 1.00
ACGTcount: A:0.27, C:0.29, G:0.12, T:0.33
Consensus pattern (153 bp):
GGGTTACCACTTTCTCATCTATTCTTTGCGAATGATCTCATCCTTTATGCCAAGACCACTCTCCA
ACAATGTTCAACCATTAATTCCATCATACCAACCTTTGGAACTTTCCCATCGGGTAAGCCATAAA
AAAATCTCAGATTCGGTTCTCTC
Found at i:1924726 original size:15 final size:15
Alignment explanation
Indices: 1924703--1924756 Score: 65
Period size: 16 Copynumber: 3.5 Consensus size: 15
1924693 TTTTTCTTCT
1924703 TTAATTTTATTTTGTT-
1 TTAA-TTTATTTT-TTC
1924719 TTAATTTATTTTTTAC
1 TTAATTTATTTTTT-C
*
1924735 ATAATTTATTTTTTC
1 TTAATTTATTTTTTC
1924750 TTAATTT
1 TTAATTT
1924757 CAGTTGTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
14 2 0.06
15 15 0.44
16 17 0.50
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.70
Consensus pattern (15 bp):
TTAATTTATTTTTTC
Found at i:1931874 original size:117 final size:117
Alignment explanation
Indices: 1931734--1931957 Score: 403
Period size: 117 Copynumber: 1.9 Consensus size: 117
1931724 ACAAAGAAAA
*
1931734 GCTCGGTGCCAATGCGAGTGGCGAAGCAACTAAGCCGAGGATAAAGAAGCGAGAGCCATTGAAGT
1 GCTCGGTGACAATGCGAGTGGCGAAGCAACTAAGCCGAGGATAAAGAAGCGAGAGCCATTGAAGT
* *
1931799 GTTTCCAATGTGATGGAGAACACAAGGTGCGAGATTGCACCAATGAAGCAGG
66 GTTTCCAATGCGATGGACAACACAAGGTGCGAGATTGCACCAATGAAGCAGG
*
1931851 GCTCGGTGACAATGCGAGTGGCGAAGCAACTAAGCCGAGGGTAAAGAAGCGAGAGCCATTGAAGT
1 GCTCGGTGACAATGCGAGTGGCGAAGCAACTAAGCCGAGGATAAAGAAGCGAGAGCCATTGAAGT
*
1931916 GTTTCCAATGCGGTGGACAACACAAGGTGCGAGATTGCACCA
66 GTTTCCAATGCGATGGACAACACAAGGTGCGAGATTGCACCA
1931958 CCAAAGTAAA
Statistics
Matches: 102, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
117 102 1.00
ACGTcount: A:0.32, C:0.20, G:0.33, T:0.16
Consensus pattern (117 bp):
GCTCGGTGACAATGCGAGTGGCGAAGCAACTAAGCCGAGGATAAAGAAGCGAGAGCCATTGAAGT
GTTTCCAATGCGATGGACAACACAAGGTGCGAGATTGCACCAATGAAGCAGG
Found at i:1931972 original size:117 final size:117
Alignment explanation
Indices: 1931723--1931975 Score: 398
Period size: 117 Copynumber: 2.2 Consensus size: 117
1931713 GAGTTGCCCA
*
1931723 AACAAAGAAAAGCTCGGTGCCAATGCGAGTGGCGAAGCAACTAAGCCGAGGATAAAGAAGCGAGA
1 AACAAAGAAAAGCTCGGTGACAATGCGAGTGGCGAAGCAACTAAGCCGAGGATAAAGAAGCGAGA
* *
1931788 GCCATTGAAGTGTTTCCAATGTGATGGAGAACACAAGGTGCGAGATTGCACC
66 GCCATTGAAGTGTTTCCAATGCGATGGACAACACAAGGTGCGAGATTGCACC
** * ** *
1931840 AATGAAGCAGGGCTCGGTGACAATGCGAGTGGCGAAGCAACTAAGCCGAGGGTAAAGAAGCGAGA
1 AACAAAGAAAAGCTCGGTGACAATGCGAGTGGCGAAGCAACTAAGCCGAGGATAAAGAAGCGAGA
*
1931905 GCCATTGAAGTGTTTCCAATGCGGTGGACAACACAAGGTGCGAGATTGCACC
66 GCCATTGAAGTGTTTCCAATGCGATGGACAACACAAGGTGCGAGATTGCACC
* *
1931957 ACCAAAGTAAAGCTCGGTG
1 AACAAAGAAAAGCTCGGTG
1931976 CGAAAGCCAA
Statistics
Matches: 120, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
117 120 1.00
ACGTcount: A:0.34, C:0.19, G:0.31, T:0.15
Consensus pattern (117 bp):
AACAAAGAAAAGCTCGGTGACAATGCGAGTGGCGAAGCAACTAAGCCGAGGATAAAGAAGCGAGA
GCCATTGAAGTGTTTCCAATGCGATGGACAACACAAGGTGCGAGATTGCACC
Found at i:1932004 original size:117 final size:116
Alignment explanation
Indices: 1931723--1932038 Score: 350
Period size: 117 Copynumber: 2.7 Consensus size: 116
1931713 GAGTTGCCCA
* * * * * *
1931723 AACAAAGAAAAGCTCGGTGCCAATGCGAGTGGCGAAGCAACTAAGCCGAGGATAAAGAAGCGAGA
1 AACAAAGCAAAGCTCGGTGACAAAGCAAGTGGCCAAGCAAC-AAGCCGAGGGTAAAGAAGCGAGA
* *
1931788 GCCATTGAAGTGTTTCCAATGTGATGGAGAACACAAGGTGCGAGATTGCACC
65 GCCATTGAAGTGTTTCCAATGCGATGGACAACACAAGGTGCGAGATTGCACC
** ** * * *
1931840 AATGAAGCAGGGCTCGGTGACAATGCGAGTGGCGAAGCAACTAAGCCGAGGGTAAAGAAGCGAGA
1 AACAAAGCAAAGCTCGGTGACAAAGCAAGTGGCCAAGCAAC-AAGCCGAGGGTAAAGAAGCGAGA
*
1931905 GCCATTGAAGTGTTTCCAATGCGGTGGACAACACAAGGTGCGAGATTGCACC
65 GCCATTGAAGTGTTTCCAATGCGATGGACAACACAAGGTGCGAGATTGCACC
* * * *
1931957 ACCAAAGTAAAGCTCGGTG-CGAAAGCCAAG-GGCCAAGCTGAA-GAGCCGAGGGTAAATAAGCG
1 AACAAAGCAAAGCTCGGTGAC-AAAG-CAAGTGGCCAAGC--AACAAGCCGAGGGTAAAGAAGCG
* * *
1932019 AGAGCAACTGGAGTGTTTCC
62 AGAGCCATTGAAGTGTTTCC
1932039 GGTGCAAAGG
Statistics
Matches: 171, Mismatches: 24, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
116 1 0.01
117 165 0.96
118 3 0.02
119 2 0.01
ACGTcount: A:0.34, C:0.20, G:0.32, T:0.15
Consensus pattern (116 bp):
AACAAAGCAAAGCTCGGTGACAAAGCAAGTGGCCAAGCAACAAGCCGAGGGTAAAGAAGCGAGAG
CCATTGAAGTGTTTCCAATGCGATGGACAACACAAGGTGCGAGATTGCACC
Found at i:1932498 original size:159 final size:160
Alignment explanation
Indices: 1932279--1932598 Score: 592
Period size: 162 Copynumber: 2.0 Consensus size: 160
1932269 GGACTAAAAG
1932279 AGTCCGAGACCTTTCAGAGCAATCGAGCTCAGTGCATGCCGAGAGTAAGGCATGGTCTAAGTTGG
1 AGTCCGAGACCTTTCAGAGCAATCGAGCTCAGTGCATGCCGAGAGTAAGGCATGGTCTAAGTTGG
1932344 TGAATCTT-GACA-GATGGGACGTTGAAGGAGTA-TGAGAGTTCGAGGAACTCATGCTCCAAGTC
66 TGAATCTTAGACATGATGGG-CGTTGAAGGAGTAGTGAGAGTTCGAGGAACTCATGCTCCAAGTC
1932406 CCAGAGTTGACTGAAGAAGATGCATTCTTCA
130 CCAGAGTTGACTGAAGAAGATGCATTCTTCA
1932437 AGTCCGAGACCTTTCAAGAGCAATCGAGCTCAGTGCATGCCGAGAGTAAGGCATGGTCTAAGTTG
1 AGTCCGAGACCTTTC-AGAGCAATCGAGCTCAGTGCATGCCGAGAGTAAGGCATGGTCTAAGTTG
1932502 GTGAATCTTAGACATGATGGGCGTTGAAGGAGTATGTGAGAGTTCGAGGAACTCATGCTCCAAGT
65 GTGAATCTTAGACATGATGGGCGTTGAAGGAGTA-GTGAGAGTTCGAGGAACTCATGCTCCAAGT
1932567 CCCAGAGTTGACTGAAGAAGATGCATTCTTCA
129 CCCAGAGTTGACTGAAGAAGATGCATTCTTCA
1932599 CCTTCACAGA
Statistics
Matches: 157, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
158 15 0.10
159 58 0.37
160 17 0.11
161 6 0.04
162 61 0.39
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (160 bp):
AGTCCGAGACCTTTCAGAGCAATCGAGCTCAGTGCATGCCGAGAGTAAGGCATGGTCTAAGTTGG
TGAATCTTAGACATGATGGGCGTTGAAGGAGTAGTGAGAGTTCGAGGAACTCATGCTCCAAGTCC
CAGAGTTGACTGAAGAAGATGCATTCTTCA
Found at i:1932832 original size:14 final size:15
Alignment explanation
Indices: 1932801--1932834 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1932791 AGCAAGGCTC
1932801 TTCGAGTGAAGCTTG
1 TTCGAGTGAAGCTTG
*
1932816 TTCGAGTG-AGTTTG
1 TTCGAGTGAAGCTTG
1932830 TTCGA
1 TTCGA
1932835 ATGGTGAGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.18, C:0.12, G:0.32, T:0.38
Consensus pattern (15 bp):
TTCGAGTGAAGCTTG
Found at i:1934887 original size:19 final size:21
Alignment explanation
Indices: 1934865--1934908 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 21
1934855 CATCCTTGAA
*
1934865 TGAATTAATCTTC-CTTGGT-
1 TGAATTAATATTCTCTTGGTG
*
1934884 TGAATTCATATTCTCTTGGTG
1 TGAATTAATATTCTCTTGGTG
1934905 TGAA
1 TGAA
1934909 CATGGCGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 11 0.52
20 6 0.29
21 4 0.19
ACGTcount: A:0.23, C:0.14, G:0.18, T:0.45
Consensus pattern (21 bp):
TGAATTAATATTCTCTTGGTG
Found at i:1937462 original size:2 final size:2
Alignment explanation
Indices: 1937391--1937443 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
1937381 ATAAACCTTC
1937391 AT AT AT AT AT AT AT AT AT AT AT A- 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
1937432 AT AT AT AT AT AT
1 AT AT AT AT AT AT
1937444 CATGATAAAC
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1939909 original size:29 final size:30
Alignment explanation
Indices: 1939867--1939931 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
1939857 TCAAACACCT
*
1939867 AACTTTTAAAAATTA-CATTTTTGTCCCTG
1 AACTTTTAAAAATTACCATTTTTGTCCCTA
*
1939896 AACTTTTAAAAATTACCCTTTTTGTCCCTA
1 AACTTTTAAAAATTACCATTTTTGTCCCTA
1939926 AACTTT
1 AACTTT
1939932 ATACTTTATC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
29 15 0.45
30 18 0.55
ACGTcount: A:0.31, C:0.20, G:0.05, T:0.45
Consensus pattern (30 bp):
AACTTTTAAAAATTACCATTTTTGTCCCTA
Found at i:1944073 original size:40 final size:40
Alignment explanation
Indices: 1944029--1944137 Score: 191
Period size: 40 Copynumber: 2.7 Consensus size: 40
1944019 GGACACTAAG
*
1944029 TGTATATGGTGGGCACGACCTTATGTGTAATACATTTCGA
1 TGTATATGGTGGGCACGACCTTATGTGTAATACACTTCGA
* *
1944069 TGTATATGGTAGGCACGACCTTATGTGTAATACACTTCGG
1 TGTATATGGTGGGCACGACCTTATGTGTAATACACTTCGA
1944109 TGTATATGGTGGGCACGACCTTATGTGTA
1 TGTATATGGTGGGCACGACCTTATGTGTA
1944138 GCACTACGGT
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 65 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.34
Consensus pattern (40 bp):
TGTATATGGTGGGCACGACCTTATGTGTAATACACTTCGA
Found at i:1945340 original size:24 final size:24
Alignment explanation
Indices: 1945313--1945419 Score: 106
Period size: 24 Copynumber: 4.5 Consensus size: 24
1945303 AAACGGAGAT
*
1945313 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
1945337 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
1945361 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** *
1945385 ATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
1945409 ATCAGAAATCA
1 ATCAGAAATCA
1945420 GATAAAATAT
Statistics
Matches: 63, Mismatches: 20, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 63 1.00
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:1945419 original size:48 final size:48
Alignment explanation
Indices: 1945313--1945421 Score: 128
Period size: 48 Copynumber: 2.3 Consensus size: 48
1945303 AAACGGAGAT
* * * *
1945313 ATCAGAAATCAAAACATAATTCAGATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
1945361 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
1945409 ATCAGAAATCAGA
1 ATCAGAAATCAGA
1945422 TAAAATATTC
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.48, C:0.17, G:0.16, T:0.20
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:1947926 original size:13 final size:13
Alignment explanation
Indices: 1947910--1947946 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
1947900 GTCAACGGGT
1947910 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
1947923 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
1947936 CGGGTCGGGTC
1 CGGGTCGGGTC
1947947 GGGTTGTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.11, C:0.24, G:0.49, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:1947950 original size:18 final size:18
Alignment explanation
Indices: 1947899--1947933 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1947889 ACGGGGCAAT
1947899 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
1947917 GGTCAACGGGTCGGGTC
1 GGTCAACGGGTCGGGTC
1947934 AACGGGTCGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.23, G:0.49, T:0.17
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:1950099 original size:24 final size:24
Alignment explanation
Indices: 1950072--1950178 Score: 99
Period size: 24 Copynumber: 4.5 Consensus size: 24
1950062 AAACGGAGAT
*
1950072 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* *
1950096 ATCAGATATCAGAACAGAA-TCTAG
1 ATCAGAAATCAAAACAGAATTC-AG
* * * * *
1950120 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** *
1950144 ATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
1950168 ATCAGAAATCA
1 ATCAGAAATCA
1950179 GATAAAATAT
Statistics
Matches: 63, Mismatches: 18, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
23 2 0.03
24 59 0.94
25 2 0.03
ACGTcount: A:0.48, C:0.16, G:0.15, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:1950178 original size:48 final size:48
Alignment explanation
Indices: 1950072--1950180 Score: 121
Period size: 48 Copynumber: 2.3 Consensus size: 48
1950062 AAACGGAGAT
* * * *
1950072 ATCAGAAATCAAAACATAATTCAGATCAGATATCAGAACAGAATCTAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCTAA
* * * * *
1950120 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAAT-TCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCT-AA
1950168 ATCAGAAATCAGA
1 ATCAGAAATCAGA
1950181 TAAAATATTC
Statistics
Matches: 48, Mismatches: 12, Indels: 2
0.77 0.19 0.03
Matches are distributed among these distances:
47 1 0.02
48 47 0.98
ACGTcount: A:0.48, C:0.16, G:0.16, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCTAA
Found at i:1952662 original size:15 final size:15
Alignment explanation
Indices: 1952642--1952687 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
1952632 GGTCAACTCC
1952642 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
*
1952657 GGTCAATGGTCAACG
1 GGTCAACGGTCAACG
*
1952672 GGTC--GGGTCAACG
1 GGTCAACGGTCAACG
1952685 GGT
1 GGT
1952688 GGGGTCGGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 11 0.38
15 18 0.62
ACGTcount: A:0.22, C:0.22, G:0.39, T:0.17
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:1952694 original size:18 final size:18
Alignment explanation
Indices: 1952670--1952715 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
1952660 CAATGGTCAA
1952670 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
*
1952688 GGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
1952706 CGGGTCGGGT
1 CGGGTCGGGT
1952716 TGTGACCGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.09, C:0.20, G:0.54, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:1952711 original size:13 final size:13
Alignment explanation
Indices: 1952649--1952693 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
1952639 TCCGGTCAAC
*
1952649 GGTCAACGGGTCAAT
1 GGTCAACGGGTC--G
1952664 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
1952677 GGTCAACGGGTGG
1 GGTCAACGGGTCG
1952690 GGTC
1 GGTC
1952694 GGGTCAACGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 16 0.57
15 12 0.43
ACGTcount: A:0.18, C:0.20, G:0.44, T:0.18
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:1960441 original size:40 final size:40
Alignment explanation
Indices: 1960397--1960505 Score: 191
Period size: 40 Copynumber: 2.7 Consensus size: 40
1960387 GGACTCTAAG
*
1960397 TGTATATGGTGGGCACAACCTTATGTGTAATACATTTCGA
1 TGTATATGGTGGGCACAACCTTATGTGTAATACACTTCGA
*
1960437 TGTATATGGTGGGCACAACCTTATGTGTAATACACTTCGG
1 TGTATATGGTGGGCACAACCTTATGTGTAATACACTTCGA
*
1960477 TGTATATGGTGGGCACGACCTTATGTGTA
1 TGTATATGGTGGGCACAACCTTATGTGTA
1960506 GCACTACGGT
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 66 1.00
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.34
Consensus pattern (40 bp):
TGTATATGGTGGGCACAACCTTATGTGTAATACACTTCGA
Found at i:1963011 original size:19 final size:21
Alignment explanation
Indices: 1962968--1963019 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
1962958 GAAACCCCTT
1962968 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
1962989 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
1963008 TGAAGATACATG
1 TGAAAATACATG
1963020 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:1967549 original size:17 final size:18
Alignment explanation
Indices: 1967527--1967560 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1967517 TGATATACTG
1967527 ATGTTGT-GACATTGTTA
1 ATGTTGTAGACATTGTTA
*
1967544 ATGTTGTAGCCATTGTT
1 ATGTTGTAGACATTGTT
1967561 GTGTGATGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.21, C:0.09, G:0.24, T:0.47
Consensus pattern (18 bp):
ATGTTGTAGACATTGTTA
Found at i:1970901 original size:50 final size:50
Alignment explanation
Indices: 1970837--1970941 Score: 183
Period size: 50 Copynumber: 2.1 Consensus size: 50
1970827 TTTTCTTTAG
1970837 TTTTGAAATCAATAGCGTATAGGATAAATATGTTGTTTTATTAAATTACT
1 TTTTGAAATCAATAGCGTATAGGATAAATATGTTGTTTTATTAAATTACT
* * *
1970887 TTTTTAAATCAATAGTGTATAGGATAAATCTGTTGTTTTATTAAATTACT
1 TTTTGAAATCAATAGCGTATAGGATAAATATGTTGTTTTATTAAATTACT
1970937 TTTTG
1 TTTTG
1970942 CTAATTTTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.33, C:0.06, G:0.13, T:0.48
Consensus pattern (50 bp):
TTTTGAAATCAATAGCGTATAGGATAAATATGTTGTTTTATTAAATTACT
Found at i:1988050 original size:2 final size:2
Alignment explanation
Indices: 1988043--1988070 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1988033 TGTAATTCTG
1988043 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
1988071 TGGGCTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1999501 original size:38 final size:37
Alignment explanation
Indices: 1999396--1999517 Score: 110
Period size: 38 Copynumber: 3.3 Consensus size: 37
1999386 ACAGAGTCAG
1999396 TTCCCTTTGAAACATCAAATTTGTATC-TT-TTGAGAT-T
1 TTCCC-TTGAAACATCAAATTT-T-TCTTTCTTGAGATGT
* **
1999433 GTTCCCTT-AAACATC-AATTTATCTCCCTTGAGATAGT
1 -TTCCCTTGAAACATCAAATTTTTCTTTCTTGAGAT-GT
* *
1999470 TTCCCTTGAAACACCAAATTTTTCTTTCTTGAGACTTT
1 TTCCCTTGAAACATCAAATTTTTCTTTCTTGAGA-TGT
1999508 TTCCCTTGAA
1 TTCCCTTGAA
1999518 GCAATAGTTT
Statistics
Matches: 69, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
33 2 0.03
35 12 0.17
36 14 0.20
37 9 0.13
38 31 0.45
39 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.10, T:0.43
Consensus pattern (37 bp):
TTCCCTTGAAACATCAAATTTTTCTTTCTTGAGATGT
Found at i:2000383 original size:117 final size:116
Alignment explanation
Indices: 2000149--2000416 Score: 292
Period size: 117 Copynumber: 2.3 Consensus size: 116
2000139 GTGATCAAGA
* * * * * *
2000149 AAGAATAAGTTCATATATGAGAGCTTCTTCGACCTCAACATGACCTTTATGGGAGAATATGTGGT
1 AAGAAGAAATTCATATATGAGAGCTTGTTCTACCTCAACATGACCTTTATGGGAAAATATGTGGC
* * ** *
2000214 TTATATAGGAGAGCTCATTACTCTTTCCAAAGATAGGAGGAAATGATCAGG
66 TTATATAGGAGAGCTCATTACTCTTTCCAAAGACAAGAGGAAACAACCAGG
*
2000265 AAAGAAGAGAATT-ATATATGAGAGCTTGTTCTACCTCAATATGACCTTTATGGGAAAATATG-G
1 -AAGAAGA-AATTCATATATGAGAGCTTGTTCTACCTCAACATGACCTTTATGGGAAAATATGTG
** * * *
2000328 AGCTTATATAGGAGAGCTTGTCTACTCTTT-C-GAGACAAGATGATACAACCAAGG
64 -GCTTATATAGGAGAGCTCAT-TACTCTTTCCAAAGACAAGAGGAAACAACC-AGG
* *
2000382 AAGAAGAAGTTCATATATGAGAGTTTGTTCTACCT
1 AAGAAGAAATTCATATATGAGAGCTTGTTCTACCT
2000417 TATCAAAACC
Statistics
Matches: 127, Mismatches: 19, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
115 3 0.02
116 41 0.32
117 72 0.57
118 11 0.09
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (116 bp):
AAGAAGAAATTCATATATGAGAGCTTGTTCTACCTCAACATGACCTTTATGGGAAAATATGTGGC
TTATATAGGAGAGCTCATTACTCTTTCCAAAGACAAGAGGAAACAACCAGG
Found at i:2000742 original size:43 final size:46
Alignment explanation
Indices: 2000671--2000755 Score: 131
Period size: 43 Copynumber: 1.9 Consensus size: 46
2000661 GAAAAATGAA
2000671 AAAAATGAAATATTTAAAAAATAAAGAGAAAAT-AAGAAATATGGG
1 AAAAATGAAATATTTAAAAAATAAAGAGAAAATGAAGAAATATGGG
* *
2000716 AAAAA-GAAA-ATTTTAAAAATAGAGAGAAAATGAAGAAATA
1 AAAAATGAAATATTTAAAAAATAAAGAGAAAATGAAGAAATA
2000756 AGAAAAAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
43 20 0.54
44 12 0.32
45 5 0.14
ACGTcount: A:0.66, C:0.00, G:0.15, T:0.19
Consensus pattern (46 bp):
AAAAATGAAATATTTAAAAAATAAAGAGAAAATGAAGAAATATGGG
Found at i:2000763 original size:43 final size:45
Alignment explanation
Indices: 2000670--2000769 Score: 127
Period size: 43 Copynumber: 2.3 Consensus size: 45
2000660 TGAAAAATGA
*
2000670 AAAAAATGAAATATTTAAAAAATAAAGAGAAAATAAGAAATATGG
1 AAAAAATGAAATATTTAAAAAATAAAGAGAAAATAAGAAATATAG
* * *
2000715 GAAAAA-GAAA-ATTTTAAAAATAGAGAGAAAATGAAGAAATA-AG
1 AAAAAATGAAATATTTAAAAAATAAAGAGAAAAT-AAGAAATATAG
2000758 AAAAAAT-AAATA
1 AAAAAATGAAATA
2000770 ATGGAAATAA
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
43 29 0.62
44 13 0.28
45 5 0.11
ACGTcount: A:0.68, C:0.00, G:0.14, T:0.18
Consensus pattern (45 bp):
AAAAAATGAAATATTTAAAAAATAAAGAGAAAATAAGAAATATAG
Done.