Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A06
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: 115140250
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2234201 characters in sequence are not A, C, G, or T
File 89 of 345
Found at i:29370678 original size:18 final size:19
Alignment explanation
Indices: 29370641--29370679 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
29370631 ATTACAAAAC
*
29370641 AATTCAAAATAATTTTTAA
1 AATTCAAAATAATTTATAA
*
29370660 AATTCAAAGT-ATTTATAA
1 AATTCAAAATAATTTATAA
29370678 AA
1 AA
29370680 ATGATAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (19 bp):
AATTCAAAATAATTTATAA
Found at i:29373037 original size:5 final size:5
Alignment explanation
Indices: 29373027--29373064 Score: 58
Period size: 5 Copynumber: 7.4 Consensus size: 5
29373017 AATTTGTGTG
*
29373027 TTATT TTATT TTTTCT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTAT-T TTATT TTATT TTATT TTATT TT
29373065 TTTCACAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 26 0.87
6 4 0.13
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.82
Consensus pattern (5 bp):
TTATT
Found at i:29377477 original size:5 final size:5
Alignment explanation
Indices: 29377467--29377505 Score: 51
Period size: 5 Copynumber: 7.4 Consensus size: 5
29377457 AATTTGTGTG
*
29377467 TTATT TTATT TTTTCT TTATT TTATT TTATT TTAATT TT
1 TTATT TTATT TTAT-T TTATT TTATT TTATT TT-ATT TT
29377506 TTCACAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
5 21 0.70
6 9 0.30
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (5 bp):
TTATT
Found at i:29378324 original size:25 final size:25
Alignment explanation
Indices: 29378290--29378340 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
29378280 GTAGGGTGAT
29378290 AGGTTTGAAGTTTAGAAAGATATGA
1 AGGTTTGAAGTTTAGAAAGATATGA
29378315 AGGTTTGAAGTTTAGAAAGATATGA
1 AGGTTTGAAGTTTAGAAAGATATGA
29378340 A
1 A
29378341 AAAAAATGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.41, C:0.00, G:0.27, T:0.31
Consensus pattern (25 bp):
AGGTTTGAAGTTTAGAAAGATATGA
Found at i:29379661 original size:17 final size:19
Alignment explanation
Indices: 29379641--29379688 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 19
29379631 AGACATTAGA
29379641 TTAAAATTATATT-AAT-G
1 TTAAAATTATATTAAATAG
*
29379658 TT-AAATGATAGTTAAATAG
1 TTAAAATTATA-TTAAATAG
29379677 TTAAAA-TATATT
1 TTAAAATTATATT
29379689 TTTATTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
16 7 0.28
17 4 0.16
18 5 0.20
19 6 0.24
20 3 0.12
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (19 bp):
TTAAAATTATATTAAATAG
Found at i:29379724 original size:28 final size:24
Alignment explanation
Indices: 29379668--29379729 Score: 70
Period size: 28 Copynumber: 2.4 Consensus size: 24
29379658 TTAAATGATA
*
29379668 GTTAAATAGTTAAAATATATTTTT
1 GTTAAATAATTAAAATATATTTTT
*
29379692 ATTAAATAATTAAATATAATTATTTTTT
1 GTTAAATAATTAAA-AT-A-TA-TTTTT
29379720 GTTAAATAAT
1 GTTAAATAAT
29379730 AATTTAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
24 12 0.39
25 2 0.06
26 1 0.03
27 2 0.06
28 14 0.45
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (24 bp):
GTTAAATAATTAAAATATATTTTT
Found at i:29380320 original size:26 final size:25
Alignment explanation
Indices: 29380291--29380400 Score: 148
Period size: 26 Copynumber: 4.2 Consensus size: 25
29380281 TGGTACAAAT
29380291 TGATAATAGGTTAGGTAAATGTTCAA
1 TGATAATAGGTTAGGTAAATGTTC-A
29380317 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTT-CA
* *
29380343 TGATAATGGGTTAGGTAAATATTTCA
1 TGATAATAGGTTAGGTAAAT-GTTCA
**
29380369 TGATAAGGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATG-TTCA
29380395 TGATAA
1 TGATAA
29380401 GAATTTCATG
Statistics
Matches: 77, Mismatches: 4, Indels: 6
0.89 0.05 0.07
Matches are distributed among these distances:
26 74 0.96
27 3 0.04
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (25 bp):
TGATAATAGGTTAGGTAAATGTTCA
Found at i:29382050 original size:27 final size:27
Alignment explanation
Indices: 29382020--29382140 Score: 170
Period size: 27 Copynumber: 4.4 Consensus size: 27
29382010 GAGGAAGCGT
* *
29382020 TCTGATGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
29382047 TCTGGTGGCTCTGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
29382074 TCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
29382101 TCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
*
29382129 TCTGGTGACTCT
1 TCTGGTGGCTCT
29382141 ATCACATTAT
Statistics
Matches: 84, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
27 73 0.87
28 11 0.13
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:29382097 original size:54 final size:55
Alignment explanation
Indices: 29382020--29382159 Score: 185
Period size: 54 Copynumber: 2.6 Consensus size: 55
29382010 GAGGAAGCGT
* * * *
29382020 TCTGATGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACAAATATCTG-A
1 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACAAATATCTGTA
* *
29382074 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACAAATATCTGTA
* **
29382129 TCTGGTGACTCTATCACAT-TATCTGTTCTGG
1 TCTGGTGGCTCTGCCACATATATCTGTTCTGG
29382160 CAGCCATGCT
Statistics
Matches: 76, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
54 59 0.78
55 17 0.22
ACGTcount: A:0.19, C:0.24, G:0.21, T:0.35
Consensus pattern (55 bp):
TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACAAATATCTGTA
Found at i:29382149 original size:27 final size:28
Alignment explanation
Indices: 29382020--29382159 Score: 157
Period size: 27 Copynumber: 5.2 Consensus size: 28
29382010 GAGGAAGCGT
* * *
29382020 TCTGATGGCTATGCCACAAATATCTG-A
1 TCTGGTGGCTCTGCCACAATTATCTGTA
*
29382047 TCTGGTGGCTCTGCCACAAATATCTG-A
1 TCTGGTGGCTCTGCCACAATTATCTGTA
29382074 TCTGGTGGCTCTGCCAC-ATATATCTGT-
1 TCTGGTGGCTCTGCCACAAT-TATCTGTA
*
29382101 TCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAATTATCTGTA
* **
29382129 TCTGGTGACTCTATCAC-ATTATCTGT-
1 TCTGGTGGCTCTGCCACAATTATCTGTA
29382155 TCTGG
1 TCTGG
29382160 CAGCCATGCT
Statistics
Matches: 103, Mismatches: 6, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
26 6 0.06
27 81 0.79
28 16 0.16
ACGTcount: A:0.19, C:0.24, G:0.21, T:0.35
Consensus pattern (28 bp):
TCTGGTGGCTCTGCCACAATTATCTGTA
Found at i:29395648 original size:173 final size:173
Alignment explanation
Indices: 29395359--29395683 Score: 506
Period size: 173 Copynumber: 1.9 Consensus size: 173
29395349 GTTTTAAGGA
* * *
29395359 AGTTCTTGAAGAGAAGTATGTATCTAAATGCTAAGAAAGGTATCCTTCATGTTAATCTATTGGTG
1 AGTTCTTGAAGAGAAATATGTATCTAAATGCTAAGAAAGGTATCATTCATGTTAATCTATTAGTG
* * **
29395424 TTGAATATGGGCGTACTCGCAGTTGAGAAACATAAAAAATTGTTTATTTGAATTCGTCTGTGTTG
66 TTGAATATGGGCGTACTCACAGTTAAGAAACATAAAAAATTGTTTATTTGAAACCGTCTGTGTTG
29395489 TATAGTGCTGAAATCTAATTATAATTAGATTGTAAAGTAATTG
131 TATAGTGCTGAAATCTAATTATAATTAGATTGTAAAGTAATTG
* * * *
29395532 AGTTCTTGAAGAGAAATATGTGTCTAAATGCTAGGAAGGGTATCATTCATGTTAATCTGTTAGTG
1 AGTTCTTGAAGAGAAATATGTATCTAAATGCTAAGAAAGGTATCATTCATGTTAATCTATTAGTG
* * *
29395597 TTGAATATGGGCGTACTCACAGTTAAGAAACATAAGAAATTTTTTATTTGAAACCGTTTGTGTTG
66 TTGAATATGGGCGTACTCACAGTTAAGAAACATAAAAAATTGTTTATTTGAAACCGTCTGTGTTG
* *
29395662 TATAGTGTTGAAATCTGATTAT
131 TATAGTGCTGAAATCTAATTAT
29395684 CTGGTATATG
Statistics
Matches: 136, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
173 136 1.00
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.37
Consensus pattern (173 bp):
AGTTCTTGAAGAGAAATATGTATCTAAATGCTAAGAAAGGTATCATTCATGTTAATCTATTAGTG
TTGAATATGGGCGTACTCACAGTTAAGAAACATAAAAAATTGTTTATTTGAAACCGTCTGTGTTG
TATAGTGCTGAAATCTAATTATAATTAGATTGTAAAGTAATTG
Found at i:29399142 original size:106 final size:106
Alignment explanation
Indices: 29398957--29399169 Score: 426
Period size: 106 Copynumber: 2.0 Consensus size: 106
29398947 GGGTTGTATT
29398957 TACTTAGATTTTTAGTGAGATTTTAGTATGAATGATAACCCAGTCCAGTTGTGGCTCCTGCACTT
1 TACTTAGATTTTTAGTGAGATTTTAGTATGAATGATAACCCAGTCCAGTTGTGGCTCCTGCACTT
29399022 AGAACCGACGAACGGGTCAGGCTAGTTTGTTGCACTATTAA
66 AGAACCGACGAACGGGTCAGGCTAGTTTGTTGCACTATTAA
29399063 TACTTAGATTTTTAGTGAGATTTTAGTATGAATGATAACCCAGTCCAGTTGTGGCTCCTGCACTT
1 TACTTAGATTTTTAGTGAGATTTTAGTATGAATGATAACCCAGTCCAGTTGTGGCTCCTGCACTT
29399128 AGAACCGACGAACGGGTCAGGCTAGTTTGTTGCACTATTAA
66 AGAACCGACGAACGGGTCAGGCTAGTTTGTTGCACTATTAA
29399169 T
1 T
29399170 CTATTGTATT
Statistics
Matches: 107, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
106 107 1.00
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (106 bp):
TACTTAGATTTTTAGTGAGATTTTAGTATGAATGATAACCCAGTCCAGTTGTGGCTCCTGCACTT
AGAACCGACGAACGGGTCAGGCTAGTTTGTTGCACTATTAA
Found at i:29401567 original size:53 final size:55
Alignment explanation
Indices: 29401504--29401618 Score: 153
Period size: 60 Copynumber: 2.0 Consensus size: 55
29401494 CAACAAGGAG
29401504 CCCAAAA-C-TCAATTATATATATTAAAGTTCAAGTTGACCTTAAGTATGACCTC
1 CCCAAAACCATCAATTATATATATTAAAGTTCAAGTTGACCTTAAGTATGACCTC
**
29401557 CCCAAAACTCAATTATCAATTATATATATTAAAGTTCAAGTTGATGTTAAGTATGACCTC
1 CCCAAAAC-C----ATCAATTATATATATTAAAGTTCAAGTTGACCTTAAGTATGACCTC
29401617 CC
1 CC
29401619 ATTTGTTTTG
Statistics
Matches: 53, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
53 7 0.13
55 1 0.02
60 45 0.85
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.33
Consensus pattern (55 bp):
CCCAAAACCATCAATTATATATATTAAAGTTCAAGTTGACCTTAAGTATGACCTC
Found at i:29409568 original size:12 final size:11
Alignment explanation
Indices: 29409541--29409615 Score: 52
Period size: 12 Copynumber: 6.8 Consensus size: 11
29409531 TATTAAATAC
29409541 AATTTAATAA-
1 AATTTAATAAT
29409551 AA--TAATATAT
1 AATTTAATA-AT
*
29409561 AATTTAATAAC
1 AATTTAATAAT
*
29409572 ATTCTTAAT-AT
1 AAT-TTAATAAT
29409583 AATTATTAATAAT
1 AA-T-TTAATAAT
29409596 -ATTTAATAAT
1 AATTTAATAAT
29409606 AATTTTAATA
1 AA-TTTAATA
29409616 TAAAATTATT
Statistics
Matches: 51, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
8 5 0.10
9 1 0.02
10 12 0.24
11 7 0.14
12 24 0.47
13 2 0.04
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (11 bp):
AATTTAATAAT
Found at i:29409607 original size:13 final size:12
Alignment explanation
Indices: 29409553--29409615 Score: 55
Period size: 12 Copynumber: 5.4 Consensus size: 12
29409543 TTTAATAAAA
29409553 TAATATATAA-TT
1 TAATA-ATAATTT
*
29409565 TAATAA-CATTCT
1 TAATAATAATT-T
29409577 TAAT-ATAATTAT
1 TAATAATAATT-T
29409589 TAATAAT-A-TT
1 TAATAATAATTT
29409599 TAATAATAATTT
1 TAATAATAATTT
29409611 TAATA
1 TAATA
29409616 TAAAATTATT
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
10 9 0.21
11 5 0.12
12 26 0.62
13 2 0.05
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (12 bp):
TAATAATAATTT
Found at i:29410044 original size:27 final size:27
Alignment explanation
Indices: 29409962--29410050 Score: 94
Period size: 27 Copynumber: 3.2 Consensus size: 27
29409952 AATAAAAAAT
*
29409962 AAAAACTCATAG-TCCTT-TGTTATTC
1 AAAAACTCATAGTTCTTTATGTTATTC
*
29409987 AAAAAC-CATAGTCCTTAATTTTATGTTATTC
1 AAAAACTCATAG---TT--CTTTATGTTATTC
29410018 AAAAACTCATAGTTCTTTATGTTATTC
1 AAAAACTCATAGTTCTTTATGTTATTC
29410045 AAAAAC
1 AAAAAC
29410051 ATGAAGAAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
24 5 0.09
25 6 0.11
27 18 0.34
28 1 0.02
29 2 0.04
30 2 0.04
31 14 0.26
32 5 0.09
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.39
Consensus pattern (27 bp):
AAAAACTCATAGTTCTTTATGTTATTC
Found at i:29413451 original size:23 final size:23
Alignment explanation
Indices: 29413421--29413472 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
29413411 ATGGAATGGG
29413421 GGAGGAATGGGAATTCATTGAAT
1 GGAGGAATGGGAATTCATTGAAT
*
29413444 GGAGGAATGGGAATTCGTTGAAT
1 GGAGGAATGGGAATTCATTGAAT
29413467 GGAGGA
1 GGAGGA
29413473 TTCAGTGAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.33, C:0.04, G:0.40, T:0.23
Consensus pattern (23 bp):
GGAGGAATGGGAATTCATTGAAT
Found at i:29415340 original size:70 final size:72
Alignment explanation
Indices: 29415226--29415376 Score: 243
Period size: 71 Copynumber: 2.1 Consensus size: 72
29415216 GGGGAATCAT
* *
29415226 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTT-TCATTTCAAATATACAATG
1 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATG
29415290 GATATCG
66 GATATCG
***
29415297 CACTTAGCAACCCCTC-GGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
1 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATG
29415361 GATATCG
66 GATATCG
29415368 CACTTAGCA
1 CACTTAGCA
29415377 CCACCAATGA
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
70 28 0.38
71 46 0.62
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (72 bp):
CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATG
GATATCG
Found at i:29415480 original size:104 final size:103
Alignment explanation
Indices: 29415296--29415518 Score: 367
Period size: 104 Copynumber: 2.2 Consensus size: 103
29415286 AATGGATATC
29415296 GCACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
1 GCACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
* *
29415361 GATATCGCACTTAGCACCACCAATGAACCGGGGAATCA
66 GATATCGCACATAGCACCACCAATAAACCGGGGAATCA
29415399 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTC-GGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
29415464 GGATCA-CGCACATAGCACCACCCATAAATCGGGGAATCA
65 GGAT-ATCGCACATAGCACCACCAATAAACCGGGGAATCA
**
29415503 GCACACAGCAACCCCT
1 GCACTTAGCAACCCCT
29415519 TTTATATACA
Statistics
Matches: 112, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
103 17 0.15
104 94 0.84
105 1 0.01
ACGTcount: A:0.31, C:0.32, G:0.19, T:0.18
Consensus pattern (103 bp):
GCACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
GATATCGCACATAGCACCACCAATAAACCGGGGAATCA
Found at i:29415879 original size:29 final size:29
Alignment explanation
Indices: 29415846--29415909 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
29415836 TAATCCACCA
29415846 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
29415875 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
29415905 CCCAA
1 CCCAA
29415910 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:29415883 original size:30 final size:30
Alignment explanation
Indices: 29415853--29415909 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
29415843 CCACCCAACT
29415853 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
29415882 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
29415910 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:29424150 original size:104 final size:104
Alignment explanation
Indices: 29424028--29424251 Score: 378
Period size: 104 Copynumber: 2.2 Consensus size: 104
29424018 AATGGATATC
29424028 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
29424093 GGAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCA
66 GGATCA-CGCACATAGCACCACCAATAAACCGGGGAATCA
29424132 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
29424197 GGATCACGCACATAGCACCACCCATAAATCGGGGAATCA
66 GGATCACGCACATAGCACCACCAATAAACCGGGGAATCA
**
29424236 GCACACAGCAACCCCT
1 GCACTTAGCAACCCCT
29424252 TTTATATACA
Statistics
Matches: 113, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
104 112 0.99
105 1 0.01
ACGTcount: A:0.31, C:0.32, G:0.19, T:0.18
Consensus pattern (104 bp):
GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
GGATCACGCACATAGCACCACCAATAAACCGGGGAATCA
Found at i:29424618 original size:31 final size:31
Alignment explanation
Indices: 29424587--29424644 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
29424577 CCACCCAACT
29424587 TTTTG-AAAATTACAATTTTGCCCCCAAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAAC
* * *
29424617 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
29424645 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 5 0.21
31 19 0.79
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (31 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAAC
Found at i:29427206 original size:20 final size:21
Alignment explanation
Indices: 29427163--29427208 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
29427153 ATTATTTTAT
29427163 TATGGG-CCAACTGTATTGAA
1 TATGGGCCCAACTGTATTGAA
*
29427183 -ATGGGCCCAACTGTGTT-AA
1 TATGGGCCCAACTGTATTGAA
29427202 TATGGGC
1 TATGGGC
29427209 AAGGCCCAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGGGCCCAACTGTATTGAA
Found at i:29431276 original size:20 final size:20
Alignment explanation
Indices: 29431233--29431277 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
29431223 ATTGTTTTGT
*
29431233 TATGGGCCAACTGTATTTAA
1 TATGGGCCAACTGTAGTTAA
29431253 -ATGGGCCCAACTGT-GTTAA
1 TATGGG-CCAACTGTAGTTAA
29431272 TATGGG
1 TATGGG
29431278 TAAGGCCCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.31
Consensus pattern (20 bp):
TATGGGCCAACTGTAGTTAA
Found at i:29432411 original size:27 final size:26
Alignment explanation
Indices: 29432378--29432431 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 26
29432368 GAAGGTTTTA
*
29432378 TAAATAAATATTATATT-TAAATATAAT
1 TAAATAAAAATTA-ATTATAAATA-AAT
29432405 TAAATAAAAATTAATTATAAATAAAT
1 TAAATAAAAATTAATTATAAATAAAT
29432431 T
1 T
29432432 CCGAAAACCC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 7 0.28
27 18 0.72
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
TAAATAAAAATTAATTATAAATAAAT
Found at i:29434534 original size:30 final size:30
Alignment explanation
Indices: 29434508--29434585 Score: 88
Period size: 30 Copynumber: 2.6 Consensus size: 30
29434498 TCTAAAATTG
29434508 GTAATACATATTTTTTAAAT-T-ATAAAAAT
1 GTAATACATA-TTTTTAAATGTAATAAAAAT
* * *
29434537 GTGATACGTATTTTTAATTGTAATAAAAAT
1 GTAATACATATTTTTAAATGTAATAAAAAT
*
29434567 GTAACACATAATTTTTAAA
1 GTAATACAT-ATTTTTAAA
29434586 CCTTAAATAA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
28 8 0.21
29 9 0.23
30 14 0.36
31 8 0.21
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (30 bp):
GTAATACATATTTTTAAATGTAATAAAAAT
Found at i:29436425 original size:26 final size:26
Alignment explanation
Indices: 29436379--29436433 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 26
29436369 TTGAAATACT
*
29436379 AAGGGATGTTTTAATGGAGTAA-TTA
1 AAGGGATGTTTTAATGAAGTAATTTA
29436404 AAGGGATGTTTTTGAAT-AAGTAATTTA
1 AAGGGATG-TTTT-AATGAAGTAATTTA
29436431 AAG
1 AAG
29436434 TATGTTATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 8 0.31
26 9 0.35
27 9 0.35
ACGTcount: A:0.38, C:0.00, G:0.25, T:0.36
Consensus pattern (26 bp):
AAGGGATGTTTTAATGAAGTAATTTA
Found at i:29446103 original size:21 final size:22
Alignment explanation
Indices: 29446070--29446113 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
29446060 ATAAGATAAT
*
29446070 AAACATATTTAA-TAATACATGA
1 AAACATATGTAATTAATA-ATGA
29446092 AAACATA-GTAATTAATAATGA
1 AAACATATGTAATTAATAATGA
29446113 A
1 A
29446114 TTTTGAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.30
Consensus pattern (22 bp):
AAACATATGTAATTAATAATGA
Found at i:29448232 original size:37 final size:37
Alignment explanation
Indices: 29448182--29448255 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
29448172 AACAACTTCT
29448182 CAAATTCAAGAAACACTAGGTATTAAATCTCTTTACA
1 CAAATTCAAGAAACACTAGGTATTAAATCTCTTTACA
29448219 CAAATTCAAGAAACACTAGGTATTAAATCTCTTTACA
1 CAAATTCAAGAAACACTAGGTATTAAATCTCTTTACA
29448256 AAAGAACAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.43, C:0.19, G:0.08, T:0.30
Consensus pattern (37 bp):
CAAATTCAAGAAACACTAGGTATTAAATCTCTTTACA
Found at i:29458065 original size:25 final size:25
Alignment explanation
Indices: 29458031--29458089 Score: 91
Period size: 25 Copynumber: 2.4 Consensus size: 25
29458021 CATCTCGACG
*
29458031 AGAAGAAAATGGCACATCGACAACA
1 AGAAGAAAATGGCACACCGACAACA
* *
29458056 AGAAGAAAATGGTACCCCGACAACA
1 AGAAGAAAATGGCACACCGACAACA
29458081 AGAAGAAAA
1 AGAAGAAAA
29458090 CGACGTCCCG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.54, C:0.19, G:0.20, T:0.07
Consensus pattern (25 bp):
AGAAGAAAATGGCACACCGACAACA
Found at i:29462174 original size:59 final size:59
Alignment explanation
Indices: 29462046--29462176 Score: 174
Period size: 59 Copynumber: 2.2 Consensus size: 59
29462036 ATGTTAAAAA
* * * * *
29462046 ATAAATATATAATATATGCATGCTTTGATTGGTTTAATGTATGTTGTATTTTTGTATGT
1 ATAAATATATAATATATACATGCTTTGATTGGTTTAATGCATGTTGAATTTTGGAATGT
*
29462105 ATAAATATATAATATATACATGCTTTGATTGGTTTAATGCATGTT-AATTTTGGGAAATTAT
1 ATAAATATATAATATATACATGCTTTGATTGGTTTAATGCATGTTGAATTTT-GG-AA-TGT
29462166 ATAAATATATA
1 ATAAATATATA
29462177 TGATTATCTT
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
58 5 0.08
59 44 0.70
60 1 0.02
61 13 0.21
ACGTcount: A:0.35, C:0.04, G:0.15, T:0.47
Consensus pattern (59 bp):
ATAAATATATAATATATACATGCTTTGATTGGTTTAATGCATGTTGAATTTTGGAATGT
Found at i:29462484 original size:88 final size:88
Alignment explanation
Indices: 29462335--29462513 Score: 358
Period size: 88 Copynumber: 2.0 Consensus size: 88
29462325 GAAATATTAA
29462335 GATGATTATATGTTTTTGTGATTCACGCGTTTATTAATTGACCCAAAGGTAAGTTAATATTTGGC
1 GATGATTATATGTTTTTGTGATTCACGCGTTTATTAATTGACCCAAAGGTAAGTTAATATTTGGC
29462400 AGAATTTCAACGACATCTATGGT
66 AGAATTTCAACGACATCTATGGT
29462423 GATGATTATATGTTTTTGTGATTCACGCGTTTATTAATTGACCCAAAGGTAAGTTAATATTTGGC
1 GATGATTATATGTTTTTGTGATTCACGCGTTTATTAATTGACCCAAAGGTAAGTTAATATTTGGC
29462488 AGAATTTCAACGACATCTATGGT
66 AGAATTTCAACGACATCTATGGT
29462511 GAT
1 GAT
29462514 AAATGTGTGA
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 91 1.00
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.39
Consensus pattern (88 bp):
GATGATTATATGTTTTTGTGATTCACGCGTTTATTAATTGACCCAAAGGTAAGTTAATATTTGGC
AGAATTTCAACGACATCTATGGT
Found at i:29468146 original size:29 final size:29
Alignment explanation
Indices: 29468113--29468169 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
29468103 GGAATCAAGA
29468113 CTTGCTTACATATTATATCAATTACAATT
1 CTTGCTTACATATTATATCAATTACAATT
29468142 CTTGCTTACATATTATATCAATTACAAT
1 CTTGCTTACATATTATATCAATTACAAT
29468170 CAATATTCCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.35, C:0.18, G:0.04, T:0.44
Consensus pattern (29 bp):
CTTGCTTACATATTATATCAATTACAATT
Found at i:29470867 original size:16 final size:15
Alignment explanation
Indices: 29470828--29470866 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
29470818 CAATTACAAT
*
29470828 ATTTAATGTT-CATA
1 ATTTAATTTTACATA
*
29470842 TTTTAATTTTACATA
1 ATTTAATTTTACATA
29470857 ATTTAATTTT
1 ATTTAATTTT
29470867 TTAATACTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (15 bp):
ATTTAATTTTACATA
Found at i:29471558 original size:6 final size:6
Alignment explanation
Indices: 29471547--29471571 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
29471537 TGTTGATCCC
29471547 CTACTG CTACTG CTACTG CTACTG C
1 CTACTG CTACTG CTACTG CTACTG C
29471572 AGTTGGAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.36, G:0.16, T:0.32
Consensus pattern (6 bp):
CTACTG
Found at i:29475844 original size:265 final size:264
Alignment explanation
Indices: 29475592--29476097 Score: 594
Period size: 265 Copynumber: 1.9 Consensus size: 264
29475582 TTTTTTAGAG
**
29475592 TTTTTAAGAA-ACATGAGG-GAAATTCCAAAGGGGATGTTCGATTA-TTTGGAAGC-AAC-AGGA
1 TTTTTAA-AAGACAT-AGGTGAAATTCCAAA-GGGACCTTCGATTACTTT-G-AGCAAACGA-GA
* * * ** * *
29475652 AATTGCAACCCAGCACGATAGGGCACGATTCCTTGAATTGCCAAACATCGAACATTACCTTCGTT
60 AATTGCAACCCAACACGATAGGGCACAATCCCGCGAATTGCCAAACATCGAACATCACCTCCGTT
* *
29475717 TT-GGAGAGTTTTTAGAAA-ACATAAGTGAAATTCAAAAGGGACCTTCGATTATTTTGAACAAAC
125 TTAGGAGAGTTTTTA-AAAGACATAAGTGAAATTCAAAAGGGACATTCGATCATTTTGAACAAAC
* * *
29475780 GAGAAATTGCAACCCAGCACGATAGGGCACGATTCCGTGAATTGCCGAATATCGAACATTGCCTT
189 GAGAAATTGCAACCCAACACGATAGGGCACGATTCCGCGAATTGCCAAATATCGAACATTGCCTT
29475845 TGTTTAAAGGA
254 TGTTTAAAGGA
* *
29475856 TTTTTAAAAGACGTAGGTGAAATTCTAAAGGGACCTTCGATTACTTTGAGCAAACGAGAAATTGC
1 TTTTTAAAAGACATAGGTGAAATTCCAAAGGGACCTTCGATTACTTTGAGCAAACGAGAAATTGC
* * * * *
29475921 CACCCAACACGTTAGGGCACAATCCCGCGAATTGCCAAATATCGAATATCGCCTCCGTTTTAAGG
66 AACCCAACACGATAGGGCACAATCCCGCGAATTGCCAAACATCGAACATCACCTCCGTTTT-AGG
* ** ** * * * * *
29475986 GGTTTTTTTAAAAGACATGGGTGAAATTCTAAAGGGATATTCGATCATTTTGAGCAAATGCGAAA
130 AGAGTTTTTAAAAGACATAAGTGAAATTCAAAAGGGACATTCGATCATTTTGAACAAACGAGAAA
* *
29476051 TTGCAACCCAACACGTTAGGGCACGATTTCGCGAATTGCCAAATATC
195 TTGCAACCCAACACGATAGGGCACGATTCCGCGAATTGCCAAATATC
29476098 AAATCTCGTC
Statistics
Matches: 201, Mismatches: 33, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
262 3 0.01
263 78 0.39
264 27 0.13
265 93 0.46
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (264 bp):
TTTTTAAAAGACATAGGTGAAATTCCAAAGGGACCTTCGATTACTTTGAGCAAACGAGAAATTGC
AACCCAACACGATAGGGCACAATCCCGCGAATTGCCAAACATCGAACATCACCTCCGTTTTAGGA
GAGTTTTTAAAAGACATAAGTGAAATTCAAAAGGGACATTCGATCATTTTGAACAAACGAGAAAT
TGCAACCCAACACGATAGGGCACGATTCCGCGAATTGCCAAATATCGAACATTGCCTTTGTTTAA
AGGA
Found at i:29475926 original size:131 final size:131
Alignment explanation
Indices: 29475592--29476097 Score: 547
Period size: 131 Copynumber: 3.8 Consensus size: 131
29475582 TTTTTTAGAG
* ** *
29475592 TTTTTAAGAA-ACATGAGG-GAAATTCCAAAGGGGATGTTCGATTATTTGGAAGC-AAC-AGGAA
1 TTTTTAA-AAGACAT-AGGTGAAATTCTAAA-GGGACCTTCGATTATTTTG-AGCAAACGA-GAA
* ** * *
29475653 ATTGCAACCCAGCACGATAGGGCACGATTCCTTGAATTGCCAAACATCGAACATTACCTTCGTTT
61 ATTGCAACCCAACACGATAGGGCACGATTCCGCGAATTGCCAAATATCGAACATTGCCTTCGTTT
*
29475718 -TGGAGA
126 AAGG-GA
* * *
29475724 GTTTTTAGAAA-ACATAAGTGAAATTCAAAAGGGACCTTCGATTATTTTGAACAAACGAGAAATT
1 -TTTTTA-AAAGACATAGGTGAAATTCTAAAGGGACCTTCGATTATTTTGAGCAAACGAGAAATT
* * * * *
29475788 GCAACCCAGCACGATAGGGCACGATTCCGTGAATTGCCGAATATCGAACATTGCCTTTGTTTAAA
64 GCAACCCAACACGATAGGGCACGATTCCGCGAATTGCCAAATATCGAACATTGCCTTCGTTTAAG
29475853 GGA
129 GGA
* *
29475856 TTTTTAAAAGACGTAGGTGAAATTCTAAAGGGACCTTCGATTACTTTGAGCAAACGAGAAATTGC
1 TTTTTAAAAGACATAGGTGAAATTCTAAAGGGACCTTCGATTATTTTGAGCAAACGAGAAATTGC
* * * * * * *
29475921 CACCCAACACGTTAGGGCACAATCCCGCGAATTGCCAAATATCGAATATCGCCTCCGTTTTAAGG
66 AACCCAACACGATAGGGCACGATTCCGCGAATTGCCAAATATCGAACATTGCCTTCG-TTTAA-G
*
29475986 GGTT
129 GG-A
* ** * * *
29475990 TTTTTAAAAGACATGGGTGAAATTCTAAAGGGATATTCGATCATTTTGAGCAAATGCGAAATTGC
1 TTTTTAAAAGACATAGGTGAAATTCTAAAGGGACCTTCGATTATTTTGAGCAAACGAGAAATTGC
* *
29476055 AACCCAACACGTTAGGGCACGATTTCGCGAATTGCCAAATATC
66 AACCCAACACGATAGGGCACGATTCCGCGAATTGCCAAATATC
29476098 AAATCTCGTC
Statistics
Matches: 321, Mismatches: 43, Indels: 17
0.84 0.11 0.04
Matches are distributed among these distances:
130 3 0.01
131 104 0.32
132 91 0.28
133 26 0.08
134 97 0.30
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (131 bp):
TTTTTAAAAGACATAGGTGAAATTCTAAAGGGACCTTCGATTATTTTGAGCAAACGAGAAATTGC
AACCCAACACGATAGGGCACGATTCCGCGAATTGCCAAATATCGAACATTGCCTTCGTTTAAGGG
A
Found at i:29476126 original size:134 final size:133
Alignment explanation
Indices: 29475592--29476126 Score: 552
Period size: 134 Copynumber: 4.0 Consensus size: 133
29475582 TTTTTTAGAG
* ** *
29475592 TTTTTAAGAAACATGAGG-GAAATTCCAAAGGGGATGTTCGATTATTTGGAAGC-AAC-AGGAAA
1 TTTTTAA-AAACAT-AGGTGAAATTCTAAA-GGGACCTTCGATTATTTTG-AGCAAACGA-GAAA
* ** * *
29475654 TTGCAACCCAGCACGATAGGGCACGATTCCTTGAATTGCCAAACATCGAACATT-ACCTTCGTTT
61 TTGCAACCCAACACGATAGGGCACGATTCCGCGAATTGCCAAATATCGAACATTCGCCTTCGTTT
** *
29475718 TGGA-GAG
126 TAAAGGAT
* * *
29475725 TTTTTAGAAAACATAAGTGAAATTCAAAAGGGACCTTCGATTATTTTGAACAAACGAGAAATTGC
1 TTTTTA-AAAACATAGGTGAAATTCTAAAGGGACCTTCGATTATTTTGAGCAAACGAGAAATTGC
* * * *
29475790 AACCCAGCACGATAGGGCACGATTCCGTGAATTGCCGAATATCGAACATT-GCCTTTG-TTTAAA
65 AACCCAACACGATAGGGCACGATTCCGCGAATTGCCAAATATCGAACATTCGCCTTCGTTTTAAA
29475853 GGA-
130 GGAT
* *
29475856 TTTTTAAAAGACGTAGGTGAAATTCTAAAGGGACCTTCGATTACTTTGAGCAAACGAGAAATTGC
1 TTTTTAAAA-ACATAGGTGAAATTCTAAAGGGACCTTCGATTATTTTGAGCAAACGAGAAATTGC
* * * * * *
29475921 CACCCAACACGTTAGGGCACAATCCCGCGAATTGCCAAATATCGAATA-TCGCCTCCGTTTTAAG
65 AACCCAACACGATAGGGCACGATTCCGCGAATTGCCAAATATCGAACATTCGCCTTCGTTTTAA-
* *
29475985 GGGTT
129 AGGAT
* ** * * *
29475990 TTTTTAAAAGACATGGGTGAAATTCTAAAGGGATATTCGATCATTTTGAGCAAATGCGAAATTGC
1 TTTTTAAAA-ACATAGGTGAAATTCTAAAGGGACCTTCGATTATTTTGAGCAAACGAGAAATTGC
* * *
29476055 AACCCAACACGTTAGGGCACGATTTCGCGAATTGCCAAATATC-AA-ATCTCGTCTTCGTTTTAA
65 AACCCAACACGATAGGGCACGATTCCGCGAATTGCCAAATATCGAACAT-TCGCCTTCGTTTTAA
*
29476118 AGAAT
129 AGGAT
29476123 TTTT
1 TTTT
29476127 AACTGAATAA
Statistics
Matches: 343, Mismatches: 47, Indels: 24
0.83 0.11 0.06
Matches are distributed among these distances:
130 4 0.01
131 107 0.31
132 89 0.26
133 33 0.10
134 110 0.32
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (133 bp):
TTTTTAAAAACATAGGTGAAATTCTAAAGGGACCTTCGATTATTTTGAGCAAACGAGAAATTGCA
ACCCAACACGATAGGGCACGATTCCGCGAATTGCCAAATATCGAACATTCGCCTTCGTTTTAAAG
GAT
Found at i:29479787 original size:48 final size:48
Alignment explanation
Indices: 29479716--29479812 Score: 160
Period size: 48 Copynumber: 2.0 Consensus size: 48
29479706 TAACCATTTT
29479716 AATTGGTGGGTCTTATTAAATTGGTTATAATTAGAGCACCTCA-ATTAG
1 AATTGGTGGGTCTTATTAAATTGGTTATAATTAGAGCACCT-AGATTAG
* *
29479764 AATTGGTGGGTCTTATTGAATTGGTTATAATTGGAGCACCTAGATTAG
1 AATTGGTGGGTCTTATTAAATTGGTTATAATTAGAGCACCTAGATTAG
29479812 A
1 A
29479813 CTTTTCAACT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
47 1 0.02
48 45 0.98
ACGTcount: A:0.30, C:0.09, G:0.24, T:0.37
Consensus pattern (48 bp):
AATTGGTGGGTCTTATTAAATTGGTTATAATTAGAGCACCTAGATTAG
Found at i:29489199 original size:5 final size:5
Alignment explanation
Indices: 29489189--29489213 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
29489179 TCCTGCTGAG
29489189 CAAAA CAAAA CAAAA CAAAA CAAAA
1 CAAAA CAAAA CAAAA CAAAA CAAAA
29489214 ATGAATTGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.20, G:0.00, T:0.00
Consensus pattern (5 bp):
CAAAA
Found at i:29489670 original size:21 final size:18
Alignment explanation
Indices: 29489646--29489688 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 18
29489636 AAGGTAAAAA
29489646 TATTATTATAATAATATTTAT
1 TATTATTAT-ATAAT-TTT-T
*
29489667 TATTTTTATATAATTTTT
1 TATTATTATATAATTTTT
29489685 TATT
1 TATT
29489689 GAATTAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 5 0.24
19 3 0.14
20 5 0.24
21 8 0.38
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TATTATTATATAATTTTT
Found at i:29490711 original size:8 final size:8
Alignment explanation
Indices: 29490700--29490728 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
29490690 ACTAAAATTT
29490700 AAAAAATA
1 AAAAAATA
29490708 AAAAAATA
1 AAAAAATA
29490716 AAAAAATA
1 AAAAAATA
29490724 AAAAA
1 AAAAA
29490729 GGTAATGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (8 bp):
AAAAAATA
Found at i:29499781 original size:23 final size:24
Alignment explanation
Indices: 29499755--29499806 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
29499745 CATGTACACA
*
29499755 TTATTTTCA-TGATTATTA-TGTGT
1 TTATTTTCACT-ATTATTATTGTAT
*
29499778 TTATTTTTACTATTATTATTGTAT
1 TTATTTTCACTATTATTATTGTAT
29499802 TTATT
1 TTATT
29499807 ATTAGTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 15 0.60
24 10 0.40
ACGTcount: A:0.23, C:0.04, G:0.08, T:0.65
Consensus pattern (24 bp):
TTATTTTCACTATTATTATTGTAT
Found at i:29499804 original size:24 final size:24
Alignment explanation
Indices: 29499766--29499821 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
29499756 TATTTTCATG
* *
29499766 ATTATTA-TGTGTTTATTTTTACT
1 ATTATTATTGTATTTATTATTACT
*
29499789 ATTATTATTGTATTTATTATTAGT
1 ATTATTATTGTATTTATTATTACT
*
29499813 ATTAGTATT
1 ATTATTATT
29499822 ATAATTACTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 7 0.25
24 21 0.75
ACGTcount: A:0.27, C:0.02, G:0.09, T:0.62
Consensus pattern (24 bp):
ATTATTATTGTATTTATTATTACT
Found at i:29499805 original size:12 final size:13
Alignment explanation
Indices: 29499766--29499815 Score: 50
Period size: 12 Copynumber: 3.9 Consensus size: 13
29499756 TATTTTCATG
*
29499766 ATTATTATGTGTTT
1 ATTATTA-GTATTT
* *
29499780 ATTTTTACTA-TT
1 ATTATTAGTATTT
29499792 ATTATT-GTATTT
1 ATTATTAGTATTT
29499804 ATTATTAGTATT
1 ATTATTAGTATT
29499816 AGTATTATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
11 2 0.07
12 15 0.52
13 6 0.21
14 6 0.21
ACGTcount: A:0.26, C:0.02, G:0.08, T:0.64
Consensus pattern (13 bp):
ATTATTAGTATTT
Found at i:29500036 original size:14 final size:14
Alignment explanation
Indices: 29500013--29500074 Score: 65
Period size: 14 Copynumber: 4.4 Consensus size: 14
29500003 GTGTATGTAT
29500013 TATATATATTTTTA
1 TATATATATTTTTA
*
29500027 -ATACTATATTATGTA
1 TATA-TATATT-TTTA
29500042 TATATTATATTTTTA
1 TATA-TATATTTTTA
*
29500057 TGTATATATTTTTA
1 TATATATATTTTTA
29500071 -ATAT
1 TATAT
29500075 CACATTATTC
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
13 6 0.15
14 16 0.40
15 9 0.22
16 9 0.22
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.60
Consensus pattern (14 bp):
TATATATATTTTTA
Found at i:29500293 original size:26 final size:26
Alignment explanation
Indices: 29500241--29500293 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
29500231 TTTAAATTCA
*
29500241 TATATTATTATCATTATTTTCTACAT
1 TATATTATTATCATTATTTTATACAT
*
29500267 TATATTATTATTATTATTATTAT-CAT
1 TATATTATTATCATTATT-TTATACAT
29500293 T
1 T
29500294 GTCATTGCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 21 0.88
27 3 0.12
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (26 bp):
TATATTATTATCATTATTTTATACAT
Found at i:29512677 original size:44 final size:44
Alignment explanation
Indices: 29512627--29513030 Score: 595
Period size: 44 Copynumber: 9.3 Consensus size: 44
29512617 TTCCTTGAAA
** * *
29512627 AAGATAACAGATTTACCATCTCTGTAGCCGCGGAGAGCAGATCG
1 AAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCG
* *
29512671 AAGATAACAGATTTGACGTCTCTGTAGTGGCGGAGAGCAGATCG
1 AAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCG
* * *
29512715 AAGAT----GATTTGGCATCTCTATAGCGGCGGAGAGTAGATCG
1 AAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCG
29512755 AAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCG
1 AAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCG
* *
29512799 AAGATAGCAGATTTGGCGTCTCTGTAGCGACGGAGAGCAGATCG
1 AAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCG
* *
29512843 AAGATAGCAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCC
1 AAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCG
*
29512887 AAGATAACAGATTTGGCGTCTCTGTAGTGGCGGAGAGCAGATCG
1 AAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCG
* * *
29512931 AAGATAACAGATTTGGCGTCTCTGTAGCAGCAGAGAGCAGATGG
1 AAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCG
29512975 AAGATAACAGATTTGGCGTCTCTGTAGCGGCAGG-GAGCAGATCGG
1 AAGATAACAGATTTGGCGTCTCTGTAGCGGC-GGAGAGCAGATC-G
29513020 AA-ATAACAGAT
1 AAGATAACAGAT
29513031 CGGTGTTCCT
Statistics
Matches: 327, Mismatches: 27, Indels: 12
0.89 0.07 0.03
Matches are distributed among these distances:
40 35 0.11
44 288 0.88
45 4 0.01
ACGTcount: A:0.29, C:0.18, G:0.32, T:0.21
Consensus pattern (44 bp):
AAGATAACAGATTTGGCGTCTCTGTAGCGGCGGAGAGCAGATCG
Found at i:29514798 original size:29 final size:29
Alignment explanation
Indices: 29514766--29514826 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
29514756 TTCTAATGTG
*
29514766 TATGTAT-TATATATATTTTA-ATACTATAT
1 TATGTATATAT-TATATTATATATA-TATAT
29514795 TATGTATATATTATATTATATATATATAT
1 TATGTATATATTATATTATATATATATAT
29514824 TAT
1 TAT
29514827 ATTTTTATGT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 23 0.79
30 6 0.21
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (29 bp):
TATGTATATATTATATTATATATATATAT
Found at i:29514845 original size:13 final size:12
Alignment explanation
Indices: 29514775--29514845 Score: 58
Period size: 13 Copynumber: 5.8 Consensus size: 12
29514765 GTATGTATTA
29514775 TATATATTTTA-
1 TATATATTTTAT
*
29514786 -ATACTATATTAT
1 TATA-TATTTTAT
*
29514798 GTATATATTATAT
1 -TATATATTTTAT
*
29514811 TATATATATATAT
1 TATATAT-TTTAT
29514824 TATAT-TTTTAT
1 TATATATTTTAT
29514835 GTATATATTTT
1 -TATATATTTT
29514846 TAATATCACA
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
10 3 0.06
11 10 0.20
12 13 0.27
13 20 0.41
14 3 0.06
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (12 bp):
TATATATTTTAT
Found at i:29515026 original size:3 final size:3
Alignment explanation
Indices: 29515018--29515067 Score: 52
Period size: 3 Copynumber: 17.0 Consensus size: 3
29515008 TAAATTCATA
*
29515018 TAT TAT TAT CAT TAT T-T T-T TACGT TA- TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TA--T TAT TAT TAT TAT TAT TAT TAT
29515062 TAT TAT
1 TAT TAT
29515068 CATTGTCATT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
2 6 0.15
3 32 0.78
5 3 0.07
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:29520321 original size:44 final size:45
Alignment explanation
Indices: 29520219--29520331 Score: 122
Period size: 45 Copynumber: 2.5 Consensus size: 45
29520209 AAGCTACAAT
* * * *
29520219 TCTTATCTCCCTGAAGTTATAGCGAAGCAGACTGAAAGTAGCGGA
1 TCTTATCTCCCTGAAGTTACAGTGAAGCAGACTGAAAGCAGCAGA
* * * *
29520264 TCTTATCTTCCTGAAGTTACAGTGAAGTAGATTG-AAGCCATCAG-
1 TCTTATCTCCCTGAAGTTACAGTGAAGCAGACTGAAAG-CAGCAGA
*
29520308 TCTTATCTCCCTGAAGTTGCAGTG
1 TCTTATCTCCCTGAAGTTACAGTG
29520332 GAGGAGGTTG
Statistics
Matches: 57, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
44 25 0.44
45 32 0.56
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.30
Consensus pattern (45 bp):
TCTTATCTCCCTGAAGTTACAGTGAAGCAGACTGAAAGCAGCAGA
Found at i:29520601 original size:44 final size:44
Alignment explanation
Indices: 29520551--29520636 Score: 127
Period size: 44 Copynumber: 2.0 Consensus size: 44
29520541 TAAGTTCCAA
* * *
29520551 TGGAGTAGATTGAAGCTACAAATCTCTTCTCCCTGAAATTACAT
1 TGGAGTAAATCGAAGCTACAAATCTCATCTCCCTGAAATTACAT
* *
29520595 TGGAGTAAATCGAAGCTACAAGTCTCATCTCCCTGAAGTTAC
1 TGGAGTAAATCGAAGCTACAAATCTCATCTCCCTGAAATTAC
29520637 GGTGGGTGAG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.29
Consensus pattern (44 bp):
TGGAGTAAATCGAAGCTACAAATCTCATCTCCCTGAAATTACAT
Found at i:29520634 original size:176 final size:176
Alignment explanation
Indices: 29520310--29520634 Score: 438
Period size: 176 Copynumber: 1.8 Consensus size: 176
29520300 GCCATCAGTC
* * * * *
29520310 TTATCTCCCTGAAGTTGCAGTGGAGGAGGTTGAAATTACCAATTCTTATCTCCTTGAAATTACAG
1 TTATCTCCCTGAAGTTGCAGCGGAGCAAGTTGAAATTACCAATTCTTACCTCCTTGAAATTACAA
* *
29520375 CGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTAAAATTATATTGAAACAAATCTAAGTCACAA
66 CGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTAAAATTACATTGAAACAAATCGAAGTCACAA
* *
29520440 TCCTTATCTCCTTGAAGTTGCAGTGGAGCAGGAAAATACACAAACT
131 TCCTCATCTCCCTGAAGTTGCAGTGGAGCAGGAAAATACACAAACT
* * * * *
29520486 TTATCTCTCTGAAGTTGCAGCGGAGCAAGTTGAAATTACCAATTCTTACCTCTTTTAAGTTCCAA
1 TTATCTCCCTGAAGTTGCAGCGGAGCAAGTTGAAATTACCAATTCTTACCTCCTTGAAATTACAA
* * * * **
29520551 TGGAGTAGATTGAAGCTACAAATCTCTTCTCCCTGAAATTACATTGGAGTAAATCGAAG-CTACA
66 CGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTAAAATTACATTGAAACAAATCGAAGTC-ACA
29520615 AGT-CTCATCTCCCTGAAGTT
130 A-TCCTCATCTCCCTGAAGTT
29520635 ACGGTGGGTG
Statistics
Matches: 127, Mismatches: 20, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
175 1 0.01
176 125 0.98
177 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (176 bp):
TTATCTCCCTGAAGTTGCAGCGGAGCAAGTTGAAATTACCAATTCTTACCTCCTTGAAATTACAA
CGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTAAAATTACATTGAAACAAATCGAAGTCACAA
TCCTCATCTCCCTGAAGTTGCAGTGGAGCAGGAAAATACACAAACT
Found at i:29526280 original size:28 final size:27
Alignment explanation
Indices: 29526212--29526296 Score: 66
Period size: 28 Copynumber: 3.1 Consensus size: 27
29526202 CAATAAACAA
* ***
29526212 ATTAAAAATATAATAAAAAGTGGTTAT
1 ATTAAAAATAAAATAAAAAGTAAATAT
* *
29526239 ATTAAAATTGAAAATAAAATGTAAATAT
1 ATTAAAAAT-AAAATAAAAAGTAAATAT
29526267 GATTAAAAATAAAAAATAAAAA--AAATAT
1 -ATTAAAAAT--AAAATAAAAAGTAAATAT
29526295 AT
1 AT
29526297 ATTTAGTATA
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
27 10 0.22
28 19 0.41
29 8 0.17
30 9 0.20
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (27 bp):
ATTAAAAATAAAATAAAAAGTAAATAT
Found at i:29530092 original size:21 final size:23
Alignment explanation
Indices: 29530067--29530114 Score: 73
Period size: 21 Copynumber: 2.2 Consensus size: 23
29530057 TCAGGAATAT
*
29530067 TTTATGTATATT-TTTTCCTT-A
1 TTTATGCATATTATTTTCCTTGA
29530088 TTTATGCATATTATTTTCCTTGA
1 TTTATGCATATTATTTTCCTTGA
29530111 TTTA
1 TTTA
29530115 CTAGCTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 11 0.46
22 8 0.33
23 5 0.21
ACGTcount: A:0.21, C:0.10, G:0.06, T:0.62
Consensus pattern (23 bp):
TTTATGCATATTATTTTCCTTGA
Found at i:29532321 original size:16 final size:16
Alignment explanation
Indices: 29532300--29532332 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
29532290 AAGTTACATC
*
29532300 CCTACTCCTCTTTTAT
1 CCTACTCCTCTATTAT
29532316 CCTACTCCTCTATTAT
1 CCTACTCCTCTATTAT
29532332 C
1 C
29532333 TAGACGCAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.15, C:0.39, G:0.00, T:0.45
Consensus pattern (16 bp):
CCTACTCCTCTATTAT
Found at i:29532597 original size:53 final size:53
Alignment explanation
Indices: 29532534--29532644 Score: 222
Period size: 53 Copynumber: 2.1 Consensus size: 53
29532524 ACAAAATTTT
29532534 CACCTCTAGAGATACAGTTTTCTATGAAAACATTTTTCCTTTTTGTGATATTC
1 CACCTCTAGAGATACAGTTTTCTATGAAAACATTTTTCCTTTTTGTGATATTC
29532587 CACCTCTAGAGATACAGTTTTCTATGAAAACATTTTTCCTTTTTGTGATATTC
1 CACCTCTAGAGATACAGTTTTCTATGAAAACATTTTTCCTTTTTGTGATATTC
29532640 CACCT
1 CACCT
29532645 TTAACTCAAC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 58 1.00
ACGTcount: A:0.26, C:0.21, G:0.11, T:0.42
Consensus pattern (53 bp):
CACCTCTAGAGATACAGTTTTCTATGAAAACATTTTTCCTTTTTGTGATATTC
Found at i:29537803 original size:11 final size:11
Alignment explanation
Indices: 29537747--29537809 Score: 51
Period size: 11 Copynumber: 5.8 Consensus size: 11
29537737 AGATAAATAT
29537747 TATTTTATTAA
1 TATTTTATTAA
* *
29537758 TACTTTAATAAGA
1 TA-TTTTATTA-A
29537771 TATTTTATTAA
1 TATTTTATTAA
* *
29537782 TA---AAATAA
1 TATTTTATTAA
29537790 TATTTTATTAA
1 TATTTTATTAA
29537801 TATTTTATT
1 TATTTTATT
29537810 TTATTAGTAT
Statistics
Matches: 39, Mismatches: 8, Indels: 10
0.68 0.14 0.18
Matches are distributed among these distances:
8 6 0.15
11 18 0.46
12 12 0.31
13 3 0.08
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:29539138 original size:26 final size:24
Alignment explanation
Indices: 29539108--29539157 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
29539098 AAATAAAAAA
*
29539108 ATTTAAAAATATAATAAATCAAATAT
1 ATTTAAAAACATAA-AAA-CAAATAT
29539134 ATTTAAAAACATAAAAACAAATAT
1 ATTTAAAAACATAAAAACAAATAT
29539158 TAAAACAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (24 bp):
ATTTAAAAACATAAAAACAAATAT
Found at i:29539177 original size:21 final size:21
Alignment explanation
Indices: 29539128--29539186 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
29539118 ATAATAAATC
*
29539128 AAAT-ATATTTAAAA-ACATAA
1 AAATAATA-TTAAAACAAATAA
*
29539148 AAACAAATATTAAAACAAATAA
1 AAA-TAATATTAAAACAAATAA
*
29539170 AAATAATACTAAAACAA
1 AAATAATATTAAAACAA
29539187 TTCTTAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
20 3 0.09
21 18 0.56
22 11 0.34
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.22
Consensus pattern (21 bp):
AAATAATATTAAAACAAATAA
Found at i:29539264 original size:15 final size:16
Alignment explanation
Indices: 29539234--29539266 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
29539224 AAATATTTAT
29539234 ATTAAAAATTTAAAATA
1 ATTAAAAA-TTAAAATA
29539251 ATTAAAAA-TAAAATA
1 ATTAAAAATTAAAATA
29539266 A
1 A
29539267 AATAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
17 8 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
ATTAAAAATTAAAATA
Found at i:29540589 original size:38 final size:39
Alignment explanation
Indices: 29540539--29540704 Score: 190
Period size: 46 Copynumber: 3.9 Consensus size: 39
29540529 TCTGATTGAA
29540539 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
1 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
29540578 -TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG
1 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC-----TG
29540621 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
1 --ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
*
29540662 ACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 --ATG---TG--TAAGACCATGGTTGAAAGATACCATGGCAAC
29540705 ATGACAGAAA
Statistics
Matches: 112, Mismatches: 2, Indels: 19
0.84 0.02 0.14
Matches are distributed among these distances:
38 36 0.32
41 6 0.05
43 2 0.02
44 1 0.01
46 67 0.60
ACGTcount: A:0.37, C:0.17, G:0.24, T:0.22
Consensus pattern (39 bp):
ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
Found at i:29540645 original size:46 final size:46
Alignment explanation
Indices: 29540581--29540748 Score: 248
Period size: 46 Copynumber: 3.7 Consensus size: 46
29540571 CAACCTGTGT
* *
29540581 GTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGT
1 GTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAATGA
*
29540627 GTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAAAGA
1 GTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAATGA
* *
29540673 ATAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAATGA
1 GTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATG-AAATGA
* * *
29540719 GTAAGACCATAGTTGAAAGACACTATGGCA
1 GTAAGACCATGGTTGAAAGATACCATGGCA
29540749 TCACGTCAAA
Statistics
Matches: 111, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
45 1 0.01
46 110 0.99
ACGTcount: A:0.41, C:0.16, G:0.23, T:0.20
Consensus pattern (46 bp):
GTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAATGA
Found at i:29541054 original size:23 final size:25
Alignment explanation
Indices: 29541009--29541055 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
29540999 AATAAATATA
*
29541009 CATAAAATATATGGAAATGATGAAG
1 CATAAAATATATGGAAATAATGAAG
*
29541034 CATAAAATAT-T-GATATAATGAA
1 CATAAAATATATGGAAATAATGAA
29541056 ATGAATGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 1 0.05
25 10 0.50
ACGTcount: A:0.53, C:0.04, G:0.15, T:0.28
Consensus pattern (25 bp):
CATAAAATATATGGAAATAATGAAG
Found at i:29543050 original size:26 final size:26
Alignment explanation
Indices: 29543012--29543119 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
29543002 ATGGTACAAT
*
29543012 TGATAATGTGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
29543038 TGATAATGGGTTAGGTAGATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
29543064 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
29543090 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
29543116 TGAT
1 TGAT
29543120 GGGCATTTCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.30, C:0.06, G:0.26, T:0.38
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:29550116 original size:26 final size:26
Alignment explanation
Indices: 29550087--29550168 Score: 137
Period size: 26 Copynumber: 3.2 Consensus size: 26
29550077 TGGTACAAAT
*
29550087 TGATAATGTGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
29550113 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
29550139 TGATAATGGGCTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
29550165 TGAT
1 TGAT
29550169 GGGCATTTCA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 52 1.00
ACGTcount: A:0.30, C:0.07, G:0.26, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:29555024 original size:22 final size:20
Alignment explanation
Indices: 29554999--29555039 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
29554989 TTTCTGTTCC
29554999 TTTTATTAGAAATATTCTTTTT
1 TTTTATTAG-AATATT-TTTTT
*
29555021 TTTTTTTAGAATATTTTTT
1 TTTTATTAGAATATTTTTT
29555040 CAGTTGCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 6 0.33
22 8 0.44
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.68
Consensus pattern (20 bp):
TTTTATTAGAATATTTTTTT
Found at i:29559455 original size:45 final size:44
Alignment explanation
Indices: 29559374--29559460 Score: 111
Period size: 45 Copynumber: 2.0 Consensus size: 44
29559364 GCTATATGCC
* * * *
29559374 TAAAATGAGTAAGACCATAGTTGAAAAATGATATGGCATCATAA
1 TAAAATGAGTAAAACCATAGCTGAAAAATCACATGGCATCATAA
* *
29559418 TAAAAGTGAGTAAAACCATAGCTGAAAGATCCCATGGCATCAT
1 TAAAA-TGAGTAAAACCATAGCTGAAAAATCACATGGCATCAT
29559461 GGGAATAATG
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
44 5 0.14
45 31 0.86
ACGTcount: A:0.45, C:0.14, G:0.18, T:0.23
Consensus pattern (44 bp):
TAAAATGAGTAAAACCATAGCTGAAAAATCACATGGCATCATAA
Found at i:29563703 original size:63 final size:63
Alignment explanation
Indices: 29563626--29563751 Score: 234
Period size: 63 Copynumber: 2.0 Consensus size: 63
29563616 CTATTTATGT
*
29563626 GTTGTGGGATTAAATTCAATAAAATTGTGTTTAAATGAGGTTAATTTGGAATTATATAGATCA
1 GTTGTGGGATTAAATTCAATAAAATTGTGTTTAAATGAAGTTAATTTGGAATTATATAGATCA
*
29563689 GTTGTGGGATTAAATTCAATAAAATTGTGTTTAAATGAAGTTATTTTGGAATTATATAGATCA
1 GTTGTGGGATTAAATTCAATAAAATTGTGTTTAAATGAAGTTAATTTGGAATTATATAGATCA
29563752 AGAACAAAAG
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.37, C:0.03, G:0.20, T:0.40
Consensus pattern (63 bp):
GTTGTGGGATTAAATTCAATAAAATTGTGTTTAAATGAAGTTAATTTGGAATTATATAGATCA
Found at i:29564254 original size:35 final size:35
Alignment explanation
Indices: 29564215--29564331 Score: 162
Period size: 35 Copynumber: 3.3 Consensus size: 35
29564205 TATATGAGCC
* *
29564215 TTGTATAATAGGCCATATGTGATGATATATGGAAT
1 TTGTATATTCGGCCATATGTGATGATATATGGAAT
**
29564250 TTGTATATTCGGCCATATGTGATGATATATTTAAT
1 TTGTATATTCGGCCATATGTGATGATATATGGAAT
* * *
29564285 TTGTATATTCGGCCATATGTAATGATATATTGAACC
1 TTGTATATTCGGCCATATGTGATGATATATGGAA-T
29564321 TTGTATATTCG
1 TTGTATATTCG
29564332 ATCTTATAGG
Statistics
Matches: 74, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 63 0.85
36 11 0.15
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.42
Consensus pattern (35 bp):
TTGTATATTCGGCCATATGTGATGATATATGGAAT
Found at i:29565830 original size:38 final size:38
Alignment explanation
Indices: 29565749--29565871 Score: 131
Period size: 38 Copynumber: 3.2 Consensus size: 38
29565739 CCAAACTAAC
* * *** *
29565749 ACCAGCACGAAGCCTACGGGACTTTAAACTTAGATATAAT
1 ACCAGCACGAAGCCTGCGAGA-TTT-AACCCGGATATATT
* *
29565789 ACCAGCACTAGGCCTGCGAGATTTAACCCGGATATATT
1 ACCAGCACGAAGCCTGCGAGATTTAACCCGGATATATT
*
29565827 ACCAGCACGAAGCCTGCGGGATTTAACCCGGATATAATT
1 ACCAGCACGAAGCCTGCGAGATTTAACCCGGATAT-ATT
29565866 -CCAGCA
1 ACCAGCA
29565872 TATAGCCTGC
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
38 48 0.68
39 6 0.08
40 17 0.24
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (38 bp):
ACCAGCACGAAGCCTGCGAGATTTAACCCGGATATATT
Found at i:29565879 original size:38 final size:38
Alignment explanation
Indices: 29565781--29565900 Score: 145
Period size: 38 Copynumber: 3.1 Consensus size: 38
29565771 TTTAAACTTA
* * *
29565781 GATATAATACCAGCACTAGGCCTGCGAGATTTAACCCG
1 GATATAATTCCAGCACTAAGCCTGCGGGATTTAACCCG
*
29565819 GATAT-ATTACCAGCACGAAGCCTGCGGGATTTAACCCG
1 GATATAATT-CCAGCACTAAGCCTGCGGGATTTAACCCG
*
29565857 GATATAATTCCAGCA-TATAGCCTGCGGGTCTTTAAGCCCG
1 GATATAATTCCAGCACTA-AGCCTGCGGG-ATTTAA-CCCG
29565897 GATA
1 GATA
29565901 CACATCAATA
Statistics
Matches: 71, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
37 3 0.04
38 52 0.73
39 8 0.11
40 8 0.11
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (38 bp):
GATATAATTCCAGCACTAAGCCTGCGGGATTTAACCCG
Found at i:29565897 original size:78 final size:78
Alignment explanation
Indices: 29565749--29565900 Score: 184
Period size: 78 Copynumber: 1.9 Consensus size: 78
29565739 CCAAACTAAC
** *
29565749 ACCAGCACGAAGCCTACGGGACTTTAAACTTAGATATAATACCAGCACTAGGCCTGCGAGATTTA
1 ACCAGCACGAAGCCTACGGGACTTTAAACCCAGATATAATACCAGCACTAAGCCTGCGAGATTTA
29565814 ACCCGGATATATT
66 ACCCGGATATATT
* * * * *
29565827 ACCAGCACGAAGCCTGCGGGA-TTT-AACCCGGATATAATTCCAGCA-TATAGCCTGCGGGTCTT
1 ACCAGCACGAAGCCTACGGGACTTTAAACCCAGATATAATACCAGCACTA-AGCCTGCGAG-ATT
29565889 TAAGCCCGGATA
64 TAA-CCCGGATA
29565901 CACATCAATA
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
75 2 0.03
76 25 0.40
77 8 0.13
78 28 0.44
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (78 bp):
ACCAGCACGAAGCCTACGGGACTTTAAACCCAGATATAATACCAGCACTAAGCCTGCGAGATTTA
ACCCGGATATATT
Found at i:29570381 original size:43 final size:43
Alignment explanation
Indices: 29570315--29570493 Score: 295
Period size: 43 Copynumber: 4.2 Consensus size: 43
29570305 CCTTGCTCGA
** *
29570315 ATCACCGGCATTAAGCCTGCTAGGCACGAAGACCCGAATACAC
1 ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
* *
29570358 ATCACTGGCACGAAGCCTACTAGGCACGAAGGCCCGAATACAC
1 ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
*
29570401 ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACTC
1 ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
*
29570444 ATCACCGGCACGAAGCCTGCTAGGCACAAAGGCCCGAATACAC
1 ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
29570487 ATCACCG
1 ATCACCG
29570494 AGTTTCATGC
Statistics
Matches: 126, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 126 1.00
ACGTcount: A:0.31, C:0.34, G:0.23, T:0.12
Consensus pattern (43 bp):
ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
Found at i:29572132 original size:35 final size:37
Alignment explanation
Indices: 29572055--29572186 Score: 121
Period size: 38 Copynumber: 3.5 Consensus size: 37
29572045 CAAACATAAC
* * *
29572055 ACCAGCACGAAGCCTAC-GGACTTTAAACTCAGATATAAT
1 ACCAGCACGAAGCCTGCGGGA-TTT-AAC-CGGATATATT
* *
29572094 ACCAGCACTAGGCCTGC-GGATTTAA-CGGATATATT
1 ACCAGCACGAAGCCTGCGGGATTTAACCGGATATATT
29572129 ACCAGCACGAAGCCTGCGGGATTTAACCCGGATATAATT
1 ACCAGCACGAAGCCTGCGGGATTTAA-CCGGATAT-ATT
*
29572168 -CCAGCA-TATAGCCTGCGGG
1 ACCAGCACGA-AGCCTGCGGG
29572187 TCTTTAAGCC
Statistics
Matches: 80, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
35 23 0.29
36 8 0.10
37 3 0.04
38 26 0.32
39 20 0.25
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.21
Consensus pattern (37 bp):
ACCAGCACGAAGCCTGCGGGATTTAACCGGATATATT
Found at i:29572172 original size:38 final size:37
Alignment explanation
Indices: 29572056--29572173 Score: 125
Period size: 35 Copynumber: 3.2 Consensus size: 37
29572046 AAACATAACA
* * * *
29572056 CCAGCACGAAGCCTACGGACTTTAAACTCAGATATAATA
1 CCAGCACGAAGCCTGCGGA-TTT-AACCCGGATATAATT
* *
29572095 CCAGCACTAGGCCTGCGGATTTAA--CGGATAT-ATT
1 CCAGCACGAAGCCTGCGGATTTAACCCGGATATAATT
29572129 ACCAGCACGAAGCCTGCGGGATTTAACCCGGATATAATT
1 -CCAGCACGAAGCCTGC-GGATTTAACCCGGATATAATT
29572168 CCAGCA
1 CCAGCA
29572174 TATAGCCTGC
Statistics
Matches: 67, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
34 2 0.03
35 20 0.30
36 8 0.12
37 2 0.03
38 16 0.24
39 19 0.28
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.21
Consensus pattern (37 bp):
CCAGCACGAAGCCTGCGGATTTAACCCGGATATAATT
Found at i:29572181 original size:38 final size:38
Alignment explanation
Indices: 29572086--29572202 Score: 127
Period size: 38 Copynumber: 3.1 Consensus size: 38
29572076 TTTAAACTCA
* *
29572086 GATATAATACCAGCACTAGGCCTGC-GGATTTAA--CG
1 GATATAATTCCAGCACTAAGCCTGCGGGATTTAACCCG
*
29572121 GATAT-ATTACCAGCACGAAGCCTGCGGGATTTAACCCG
1 GATATAATT-CCAGCACTAAGCCTGCGGGATTTAACCCG
*
29572159 GATATAATTCCAGCA-TATAGCCTGCGGGTCTTTAAGCCCG
1 GATATAATTCCAGCACTA-AGCCTGCGGG-ATTTAA-CCCG
29572199 GATA
1 GATA
29572203 CACATCAATA
Statistics
Matches: 69, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
34 2 0.03
35 19 0.28
36 8 0.12
37 1 0.01
38 23 0.33
39 8 0.12
40 8 0.12
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.24
Consensus pattern (38 bp):
GATATAATTCCAGCACTAAGCCTGCGGGATTTAACCCG
Found at i:29577966 original size:43 final size:43
Alignment explanation
Indices: 29577865--29577980 Score: 144
Period size: 43 Copynumber: 2.7 Consensus size: 43
29577855 ATAAACCGAG
* *
29577865 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTT
1 ATGTGATTACATGTAAGACCATGTCTGGGACAGTGGCATCGAT
* * * *
29577908 AT-TCAATTTCCTGTAAGACCCTGTCTGGGACAGTGGCATCGAT
1 ATGT-GATTACATGTAAGACCATGTCTGGGACAGTGGCATCGAT
* *
29577951 ATGTGATAACATGTAAGACCATATCTGGGA
1 ATGTGATTACATGTAAGACCATGTCTGGGA
29577981 TATGGAATTG
Statistics
Matches: 59, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
42 1 0.02
43 57 0.97
44 1 0.02
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (43 bp):
ATGTGATTACATGTAAGACCATGTCTGGGACAGTGGCATCGAT
Found at i:29593321 original size:3 final size:3
Alignment explanation
Indices: 29593313--29593369 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
29593303 TTGACATTTT
29593313 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
29593361 ATA ATA ATA
1 ATA ATA ATA
29593370 TATTTTTATT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:29593668 original size:3 final size:3
Alignment explanation
Indices: 29593660--29593701 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
29593650 AGAAAAGGGA
29593660 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
29593702 TGTTATGAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:29595769 original size:27 final size:27
Alignment explanation
Indices: 29595721--29595879 Score: 164
Period size: 27 Copynumber: 5.9 Consensus size: 27
29595711 GCGAGGCTGC
* * * *
29595721 CAGAGATTGTGACAAAGTCACCAGATA
1 CAGATATTGTGGCAGAGCCACCAGATA
*
29595748 CAGGTATTGTGGCAGAGCCACCAGA-A
1 CAGATATTGTGGCAGAGCCACCAGATA
29595774 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* * *
29595801 CCGATAATCGTGGCATAGCCACCAGA-A
1 CAGAT-ATTGTGGCAGAGCCACCAGATA
*
29595828 CAGATATATGTGGCAGAACCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
*
29595855 CAGATAATTGTGGCATAGCCACCAG
1 CAGAT-ATTGTGGCAGAGCCACCAG
29595880 GACGCTTCCT
Statistics
Matches: 110, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
26 9 0.08
27 97 0.88
28 4 0.04
ACGTcount: A:0.35, C:0.23, G:0.25, T:0.18
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:29595821 original size:54 final size:54
Alignment explanation
Indices: 29595739--29595879 Score: 212
Period size: 54 Copynumber: 2.6 Consensus size: 54
29595729 GTGACAAAGT
* * * *
29595739 CACCAGATACAGGT-ATTGTGGCAGAGCCACCAGAACAGATATATGTGGCAGAGC
1 CACCAGAT-CAGATAATCGTGGCATAGCCACCAGAACAGATATATGTGGCAGAAC
*
29595793 CACCAGATCCGATAATCGTGGCATAGCCACCAGAACAGATATATGTGGCAGAAC
1 CACCAGATCAGATAATCGTGGCATAGCCACCAGAACAGATATATGTGGCAGAAC
*
29595847 CACCAGATCAGATAATTGTGGCATAGCCACCAG
1 CACCAGATCAGATAATCGTGGCATAGCCACCAG
29595880 GACGCTTCCT
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
53 3 0.04
54 76 0.96
ACGTcount: A:0.34, C:0.25, G:0.24, T:0.17
Consensus pattern (54 bp):
CACCAGATCAGATAATCGTGGCATAGCCACCAGAACAGATATATGTGGCAGAAC
Found at i:29597501 original size:26 final size:26
Alignment explanation
Indices: 29597465--29597548 Score: 141
Period size: 26 Copynumber: 3.2 Consensus size: 26
29597455 CATGAAATTC
29597465 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
29597491 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* * *
29597517 TTATCGTGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
29597543 TTATCA
1 TTATCA
29597549 ATTTGTATCA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 54 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:29607744 original size:14 final size:14
Alignment explanation
Indices: 29607727--29607758 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
29607717 AATTTACAAT
29607727 ATTTTAAAATCCTA
1 ATTTTAAAATCCTA
29607741 ATTTTAAAATCCTA
1 ATTTTAAAATCCTA
29607755 ATTT
1 ATTT
29607759 CCAAACGATA
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:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (14 bp):
ATTTTAAAATCCTA
Found at i:29613579 original size:3 final size:3
Alignment explanation
Indices: 29613571--29613611 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
29613561 GGAAAGGAGT
29613571 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
29613612 TCCCAACTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:29613913 original size:18 final size:18
Alignment explanation
Indices: 29613876--29613913 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
29613866 GAGAATATTA
*
29613876 TTAAATTGTTAATATAAT
1 TTAAATTGTTAACATAAT
29613894 TTAAATT-TTAACATAGAT
1 TTAAATTGTTAACATA-AT
29613912 TT
1 TT
29613914 CAACTAATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (18 bp):
TTAAATTGTTAACATAAT
Found at i:29614011 original size:20 final size:20
Alignment explanation
Indices: 29613985--29614035 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
29613975 ACATGTATAA
29613985 TAAAATATAAATATAATAGTG
1 TAAAATATAAATATAA-AGTG
* *
29614006 -AAAATATTAATTTAAAGTG
1 TAAAATATAAATATAAAGTG
*
29614025 TAAACTATAAA
1 TAAAATATAAA
29614036 AATAGTCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.57, C:0.02, G:0.08, T:0.33
Consensus pattern (20 bp):
TAAAATATAAATATAAAGTG
Found at i:29616910 original size:62 final size:62
Alignment explanation
Indices: 29616813--29616935 Score: 149
Period size: 62 Copynumber: 2.0 Consensus size: 62
29616803 TGCGCAATGA
* * *
29616813 ACCATTAATCACAAATCTTCAAAACTTAATTCAAATACAGTAGCATCCTAAGTACCATCACT
1 ACCATTAATCACAAATCTTCAAAACTCAATTCAAATACAATAGCATCCTAAGAACCATCACT
* * * * * *
29616875 ACCATTAAT-ATCAAATCTTCATAGCTCAGTTCAAATGCAATAGCCTCGTAAGAACCATCAC
1 ACCATTAATCA-CAAATCTTCAAAACTCAATTCAAATACAATAGCATCCTAAGAACCATCAC
29616936 GCAATGAACC
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
61 1 0.02
62 50 0.98
ACGTcount: A:0.40, C:0.26, G:0.07, T:0.27
Consensus pattern (62 bp):
ACCATTAATCACAAATCTTCAAAACTCAATTCAAATACAATAGCATCCTAAGAACCATCACT
Found at i:29618548 original size:47 final size:47
Alignment explanation
Indices: 29618479--29618572 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
29618469 CATAATGCCT
29618479 TAGTTTTTTCCCGAATCGTCTCATTGTCGAGTCATCCCTTCCTTCAG
1 TAGTTTTTTCCCGAATCGTCTCATTGTCGAGTCATCCCTTCCTTCAG
29618526 TAGTTTTTTCCCGAATCGTCTCATTGTCGAGTCATCCCTTCCTTCAG
1 TAGTTTTTTCCCGAATCGTCTCATTGTCGAGTCATCCCTTCCTTCAG
29618573 AACTTTGGCT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.15, C:0.30, G:0.15, T:0.40
Consensus pattern (47 bp):
TAGTTTTTTCCCGAATCGTCTCATTGTCGAGTCATCCCTTCCTTCAG
Found at i:29623388 original size:15 final size:14
Alignment explanation
Indices: 29623348--29623391 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
29623338 CAATAACACA
29623348 AGTAATTAAAATAT
1 AGTAATTAAAATAT
* * *
29623362 AATATTTTAAATAT
1 AGTAATTAAAATAT
29623376 AGGTAATTAAAATAT
1 A-GTAATTAAAATAT
29623391 A
1 A
29623392 ATAAAAAAAT
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.39
Consensus pattern (14 bp):
AGTAATTAAAATAT
Found at i:29623558 original size:18 final size:18
Alignment explanation
Indices: 29623530--29623588 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
29623520 TCCTCACCTC
* *
29623530 CATGCCCATGTCCATGA-
1 CATGACCATGTCCATCAT
29623547 CTATGACCATGTCCATCAT
1 C-ATGACCATGTCCATCAT
*
29623566 CATGACCATGAT-CATGAT
1 CATGACCATG-TCCATCAT
29623584 CATGA
1 CATGA
29623589 TGATGTGCAC
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
17 1 0.03
18 33 0.92
19 2 0.06
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (18 bp):
CATGACCATGTCCATCAT
Found at i:29623587 original size:12 final size:12
Alignment explanation
Indices: 29623542--29623589 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
29623532 TGCCCATGTC
* *
29623542 CATGACTATGAC
1 CATGACCATGAT
* *
29623554 CATGTCCATCAT
1 CATGACCATGAT
29623566 CATGACCATGAT
1 CATGACCATGAT
*
29623578 CATGATCATGAT
1 CATGACCATGAT
29623590 GATGTGCACG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (12 bp):
CATGACCATGAT
Found at i:29629098 original size:24 final size:23
Alignment explanation
Indices: 29629058--29629102 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
29629048 TCACATAAAC
29629058 TCATAATTCAACTCAATTCAATTT
1 TCATAATTCAACTCAA-TCAATTT
*
29629082 TCATATTTCAA-TACAATCAAT
1 TCATAATTCAACT-CAATCAAT
29629103 ATCCAATATC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (23 bp):
TCATAATTCAACTCAATCAATTT
Found at i:29629871 original size:17 final size:17
Alignment explanation
Indices: 29629851--29629887 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
29629841 TCTTCTGTTC
29629851 TTTCTTTTATTGT-TTTA
1 TTTCTTTTATT-TATTTA
29629868 TTTCTTTTATTTATTTA
1 TTTCTTTTATTTATTTA
29629885 TTT
1 TTT
29629888 TACTTTATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 1 0.05
17 18 0.95
ACGTcount: A:0.14, C:0.05, G:0.03, T:0.78
Consensus pattern (17 bp):
TTTCTTTTATTTATTTA
Found at i:29630043 original size:5 final size:5
Alignment explanation
Indices: 29630032--29630071 Score: 71
Period size: 5 Copynumber: 8.0 Consensus size: 5
29630022 TTTATTTATT
*
29630032 TAATA TAGTA TAATA TAATA TAATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
29630072 ATATTTTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (5 bp):
TAATA
Found at i:29631108 original size:23 final size:23
Alignment explanation
Indices: 29631078--29631122 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
29631068 CTTGAAATGA
29631078 AATTTCTATAAATTTAGATTTTT
1 AATTTCTATAAATTTAGATTTTT
29631101 AATTTCTATAAATTTAGATTTT
1 AATTTCTATAAATTTAGATTTT
29631123 AGAGGGTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.56
Consensus pattern (23 bp):
AATTTCTATAAATTTAGATTTTT
Found at i:29635318 original size:146 final size:146
Alignment explanation
Indices: 29635112--29635381 Score: 522
Period size: 146 Copynumber: 1.8 Consensus size: 146
29635102 TTATTATGCC
29635112 ATCATCAATCATCCATGATCATATCCACAATTCACCCATGCCAAATGAGTTTAACCACAACATGA
1 ATCATCAATCATCCATGATCATATCCACAATTCACCCATGCCAAATGAGTTTAACCACAACATGA
*
29635177 GTGAACATAGCACATGCATGCATATATGAATAGGATTACATTCCCATAATTAATATGAAACATTA
66 GTGAACATAGCACATGCATGCATATATGAATAGGATTACATCCCCATAATTAATATGAAACATTA
29635242 ATTTACTCATATTTCT
131 ATTTACTCATATTTCT
*
29635258 ATCATCAATCATCTATGATCATATCCACAATTCACCCATGCCAAATGAGTTTAACCACAACATGA
1 ATCATCAATCATCCATGATCATATCCACAATTCACCCATGCCAAATGAGTTTAACCACAACATGA
29635323 GTGAACATAGCACATGCATGCATATATGAATAGGATTACATCCCCATAATTAATATGAA
66 GTGAACATAGCACATGCATGCATATATGAATAGGATTACATCCCCATAATTAATATGAA
29635382 CCATATCTCA
Statistics
Matches: 122, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
146 122 1.00
ACGTcount: A:0.39, C:0.22, G:0.10, T:0.29
Consensus pattern (146 bp):
ATCATCAATCATCCATGATCATATCCACAATTCACCCATGCCAAATGAGTTTAACCACAACATGA
GTGAACATAGCACATGCATGCATATATGAATAGGATTACATCCCCATAATTAATATGAAACATTA
ATTTACTCATATTTCT
Found at i:29636113 original size:48 final size:48
Alignment explanation
Indices: 29635961--29636114 Score: 155
Period size: 48 Copynumber: 3.2 Consensus size: 48
29635951 GCATGGTAGG
* * * * * *
29635961 ATGCCAATGCCATTTCCCGAATATGGTCTAACGTGGGATCAAATATTA
1 ATGCCAATGCCATGTCCCAAACATGGTCTTACATGGGATCAAATATCA
* * * ** **
29636009 CTACCAATGCCATGTCCCAGACATGGTCTTACATGGGATCGTAGGTCA
1 ATGCCAATGCCATGTCCCAAACATGGTCTTACATGGGATCAAATATCA
* * *
29636057 ATGTCAATGCCATGTCCCAAACATGGTCTTACATGGGATCACATATCG
1 ATGCCAATGCCATGTCCCAAACATGGTCTTACATGGGATCAAATATCA
*
29636105 TTGCCAATGC
1 ATGCCAATGC
29636115 TGTAACGCCC
Statistics
Matches: 82, Mismatches: 24, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
48 82 1.00
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (48 bp):
ATGCCAATGCCATGTCCCAAACATGGTCTTACATGGGATCAAATATCA
Found at i:29637334 original size:36 final size:36
Alignment explanation
Indices: 29637287--29637359 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
29637277 TATTTGTGTG
29637287 AATAATGGTTAATAGGATTCGGTTAGAATGCAAGTA
1 AATAATGGTTAATAGGATTCGGTTAGAATGCAAGTA
* *
29637323 AATAATGGTTAATAGGATTCGGTTGGAATGCAGGTA
1 AATAATGGTTAATAGGATTCGGTTAGAATGCAAGTA
29637359 A
1 A
29637360 TCACTAAGGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.37, C:0.05, G:0.27, T:0.30
Consensus pattern (36 bp):
AATAATGGTTAATAGGATTCGGTTAGAATGCAAGTA
Found at i:29665710 original size:12 final size:13
Alignment explanation
Indices: 29665693--29665724 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
29665683 GCAAATGTTA
29665693 AGTTTTG-TGCAT
1 AGTTTTGATGCAT
29665705 AGTTTTGATGCAT
1 AGTTTTGATGCAT
29665718 -GTTTTGA
1 AGTTTTGA
29665725 ATTGTGCTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.19, C:0.06, G:0.25, T:0.50
Consensus pattern (13 bp):
AGTTTTGATGCAT
Found at i:29684645 original size:21 final size:21
Alignment explanation
Indices: 29684608--29684647 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
29684598 AATCATTAAA
*
29684608 TTGATGTTATGATATGTGTCT
1 TTGATGTTATGAAATGTGTCT
29684629 TTGATGTGTAT-AAATGTGT
1 TTGATGT-TATGAAATGTGT
29684648 AAGGGATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.23, C:0.03, G:0.25, T:0.50
Consensus pattern (21 bp):
TTGATGTTATGAAATGTGTCT
Found at i:29687950 original size:46 final size:44
Alignment explanation
Indices: 29687861--29688077 Score: 141
Period size: 46 Copynumber: 4.7 Consensus size: 44
29687851 ACGTAACCGT
* *
29687861 GCCGATGCCATGTCCCGGACATGGTCTTACATTGACACATCTCGTA-
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGACACATCTCG-AG
* * *
29687907 GCCGATGCATGTCCCAGACATGTCTTATACTGGCTTACCTCTCGAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTGAC--ACATCTCGAG
** * * * *
29687953 GTTGATGCATGTCCTAGACATGTCTTACACTAGTACTCATCTCAAT
1 GCCGATGCATGTCCCAGACATGTCTTACACT-G-ACACATCTCGAG
* * * * * *
29687999 GTCGATGCCATGTCCTAGACATGGTCTTACACTGGCTC-TCATAATGTG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGACACATC-T--CGAG
**
29688047 GATGATGCATGTCCCAGACATGTCTTACACT
1 GCCGATGCATGTCCCAGACATGTCTTACACT
29688078 AGCTCACACA
Statistics
Matches: 138, Mismatches: 23, Indels: 20
0.76 0.13 0.11
Matches are distributed among these distances:
44 10 0.07
45 16 0.12
46 67 0.49
47 29 0.21
48 16 0.12
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30
Consensus pattern (44 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGACACATCTCGAG
Found at i:29688058 original size:47 final size:48
Alignment explanation
Indices: 29687955--29688082 Score: 158
Period size: 47 Copynumber: 2.7 Consensus size: 48
29687945 CTCTCGAGGT
29687955 TGATGCATGTCCTAGACATGTCTTACACTAG-TACTCATCTCAATGTCGA
1 TGATGCATGTCCTAGACATGTCTTACACTAGCT-CTCA-CTCAATGTCGA
* * *
29688004 TG--CCATGTCCTAGACATGGTCTTACACTGGCTCTCA-T-AATGTGGA
1 TGATGCATGTCCTAGACAT-GTCTTACACTAGCTCTCACTCAATGTCGA
*
29688049 TGATGCATGTCCCAGACATGTCTTACACTAGCTC
1 TGATGCATGTCCTAGACATGTCTTACACTAGCTC
29688083 ACACAAATGC
Statistics
Matches: 69, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
45 9 0.13
46 15 0.22
47 27 0.39
48 15 0.22
49 3 0.04
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (48 bp):
TGATGCATGTCCTAGACATGTCTTACACTAGCTCTCACTCAATGTCGA
Found at i:29688457 original size:30 final size:30
Alignment explanation
Indices: 29688421--29688477 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
29688411 AATTCACATT
* *
29688421 TTTGGTAAAATGACCGTTTTGCCCCTAGAC
1 TTTGGTAAAATGACCATTTTACCCCTAGAC
29688451 TTTGGTAAAATGACCATTTTACCCCTA
1 TTTGGTAAAATGACCATTTTACCCCTA
29688478 TTCCCGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (30 bp):
TTTGGTAAAATGACCATTTTACCCCTAGAC
Found at i:29697828 original size:5 final size:5
Alignment explanation
Indices: 29697815--29697861 Score: 85
Period size: 5 Copynumber: 9.2 Consensus size: 5
29697805 TTCTTTAGTT
29697815 TATATA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA T
1 TATA-A TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA T
29697862 TAAAACATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 37 0.90
6 4 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
TATAA
Found at i:29706084 original size:17 final size:17
Alignment explanation
Indices: 29706062--29706096 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
29706052 GGGATCTTAA
29706062 GGTTCAAACTTCAATCG
1 GGTTCAAACTTCAATCG
29706079 GGTTCAAACTTCAATCG
1 GGTTCAAACTTCAATCG
29706096 G
1 G
29706097 TTAGTCAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.29
Consensus pattern (17 bp):
GGTTCAAACTTCAATCG
Found at i:29731886 original size:21 final size:21
Alignment explanation
Indices: 29731857--29731906 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
29731847 GATTATTTGA
* *
29731857 ATTGGATTGA-TTATTGATTAT
1 ATTGAATTGATTTA-TGAATAT
29731878 ATTGAATTGATTTATGAATAT
1 ATTGAATTGATTTATGAATAT
29731899 ATGTGAAT
1 AT-TGAAT
29731907 GTTTGAATCG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.34, C:0.00, G:0.18, T:0.48
Consensus pattern (21 bp):
ATTGAATTGATTTATGAATAT
Found at i:29732306 original size:45 final size:45
Alignment explanation
Indices: 29732236--29732344 Score: 130
Period size: 45 Copynumber: 2.4 Consensus size: 45
29732226 CTAATACTGT
* *** *
29732236 TACTGTTACCGTTACTATTACCGATTCGGCACTTTGTGTGTCAAA
1 TACTGTTACTGTTACTATTACCGATTCAAAACTGTGTGTGTCAAA
* **
29732281 TACTGTTACTGTTAC-AGTTATCGATTCAAAACTGTGTGTGTTGAA
1 TACTGTTACTGTTACTA-TTACCGATTCAAAACTGTGTGTGTCAAA
29732326 TACTGTTACTGTTACTATT
1 TACTGTTACTGTTACTATT
29732345 CAGGATTTGT
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
44 1 0.02
45 52 0.96
46 1 0.02
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.41
Consensus pattern (45 bp):
TACTGTTACTGTTACTATTACCGATTCAAAACTGTGTGTGTCAAA
Found at i:29732531 original size:18 final size:18
Alignment explanation
Indices: 29732508--29732772 Score: 151
Period size: 18 Copynumber: 14.3 Consensus size: 18
29732498 AAAGGTATAA
*
29732508 AATAATTGATTATTACTG
1 AATAATTGATTGTTACTG
* *
29732526 AATAATTGACTGTTACCG
1 AATAATTGATTGTTACTG
* * *
29732544 GAT-ATTAGACTGTTATTG
1 AATAATT-GATTGTTACTG
* * * *
29732562 AATAACTAAATATTACTG
1 AATAATTGATTGTTACTG
**
29732580 AATAATTGATCATTACTG
1 AATAATTGATTGTTACTG
* **
29732598 AATAACTGATTGTCGCTG
1 AATAATTGATTGTTACTG
*
29732616 AATGAA-TGACTGTTACTG
1 AAT-AATTGATTGTTACTG
*
29732634 AATAACTTAATTGTTACTG
1 AATAA-TTGATTGTTACTG
29732653 AAT-ATCTGATT-TTACTG
1 AATAAT-TGATTGTTACTG
*
29732670 AATAATTGACTGTTACTGG
1 AATAATTGATTGTTACT-G
* * *
29732689 ATAACCGATCAATTGATCGATACTA
1 ---A---AT-AATTGATTGTTACTG
* * * *
29732714 AATAACTGGTTATTATTG
1 AATAATTGATTGTTACTG
29732732 AATAATTGATTGTTACTG
1 AATAATTGATTGTTACTG
* *
29732750 AATAACTGACTGTTACTG
1 AATAATTGATTGTTACTG
29732768 AATAA
1 AATAA
29732773 ATAACTGTTC
Statistics
Matches: 186, Mismatches: 45, Indels: 32
0.71 0.17 0.12
Matches are distributed among these distances:
17 19 0.10
18 132 0.71
19 20 0.11
22 2 0.01
25 2 0.01
26 11 0.06
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (18 bp):
AATAATTGATTGTTACTG
Found at i:29732770 original size:36 final size:36
Alignment explanation
Indices: 29732508--29732772 Score: 169
Period size: 36 Copynumber: 7.1 Consensus size: 36
29732498 AAAGGTATAA
* * *
29732508 AATAATTGATTATTACTGAATAATTGACTGTTACCG
1 AATAATTGATTGTTACTGAATAACTGACTGTTACTG
* * * * * *
29732544 GAT-ATTAGACTGTTATTGAATAACTAAATATTACTG
1 AATAATT-GATTGTTACTGAATAACTGACTGTTACTG
** * **
29732580 AATAATTGATCATTACTGAATAACTGATTGTCGCTG
1 AATAATTGATTGTTACTGAATAACTGACTGTTACTG
* * *
29732616 AATGAA-TGACTGTTACTGAATAACTTAATTGTTACTG
1 AAT-AATTGATTGTTACTGAATAAC-TGACTGTTACTG
*
29732653 AAT-ATCTGATT-TTACTGAATAATTGACTGTTACTGG
1 AATAAT-TGATTGTTACTGAATAACTGACTGTTACT-G
* * * ** * *
29732689 ATAACCGATCAATTGATCGATACTAAATAACTGGTTATTATTG
1 ---A---AT-AATTGATTGTTACTGAATAACTGACTGTTACTG
29732732 AATAATTGATTGTTACTGAATAACTGACTGTTACTG
1 AATAATTGATTGTTACTGAATAACTGACTGTTACTG
29732768 AATAA
1 AATAA
29732773 ATAACTGTTC
Statistics
Matches: 169, Mismatches: 44, Indels: 32
0.69 0.18 0.13
Matches are distributed among these distances:
35 13 0.08
36 106 0.63
37 23 0.14
39 1 0.01
40 1 0.01
42 2 0.01
43 5 0.03
44 18 0.11
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (36 bp):
AATAATTGATTGTTACTGAATAACTGACTGTTACTG
Found at i:29732779 original size:18 final size:18
Alignment explanation
Indices: 29732742--29732785 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
29732732 AATAATTGAT
* *
29732742 TGTTACTGAATAACTGAC
1 TGTTACTGAATAAATAAC
29732760 TGTTACTGAATAAATAAC
1 TGTTACTGAATAAATAAC
29732778 TGTT-CTGA
1 TGTTACTGA
29732786 GTGTTAATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 4 0.17
18 20 0.83
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (18 bp):
TGTTACTGAATAAATAAC
Found at i:29741468 original size:13 final size:13
Alignment explanation
Indices: 29741450--29741474 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29741440 TGTGGGTGCA
29741450 CACGGCCGTGTCG
1 CACGGCCGTGTCG
29741463 CACGGCCGTGTC
1 CACGGCCGTGTC
29741475 TAACTTCATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.40, G:0.36, T:0.16
Consensus pattern (13 bp):
CACGGCCGTGTCG
Found at i:29749780 original size:66 final size:66
Alignment explanation
Indices: 29749674--29749842 Score: 248
Period size: 66 Copynumber: 2.6 Consensus size: 66
29749664 GTCAGTAGCC
* * * * *
29749674 TCACATGGCCTAGCACTCGGGCGTGTGGCTTGGTTGTGTGTCACAAGTCAGTATACTCATCATTT
1 TCACACGGCCTAGCACACAGGCGTGTGGCTTGGCTGTGTGTCACAAGTCAGTATACTCACCATTT
29749739 T
66 T
* * *
29749740 TCACACGTCCTAGTACACAGGCGTGTGGCTTGGCTGTGTGTCACAAGTCAGTATGCTCACCATTT
1 TCACACGGCCTAGCACACAGGCGTGTGGCTTGGCTGTGTGTCACAAGTCAGTATACTCACCATTT
29749805 T
66 T
**
29749806 TCACACGGCCTAGCACATGGGCGTGTGGCTTGGCTGT
1 TCACACGGCCTAGCACACAGGCGTGTGGCTTGGCTGT
29749843 ATGGATTGGT
Statistics
Matches: 91, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
66 91 1.00
ACGTcount: A:0.18, C:0.25, G:0.27, T:0.30
Consensus pattern (66 bp):
TCACACGGCCTAGCACACAGGCGTGTGGCTTGGCTGTGTGTCACAAGTCAGTATACTCACCATTT
T
Found at i:29752684 original size:23 final size:21
Alignment explanation
Indices: 29752658--29752702 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
29752648 ACCAGAGAGA
29752658 CCCTTCAGTGGTATCGCGACATC
1 CCCTT-AG-GGTATCGCGACATC
* *
29752681 CCCTTTGGGTATCGCGATATC
1 CCCTTAGGGTATCGCGACATC
29752702 C
1 C
29752703 ACATGTTAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 14 0.70
22 1 0.05
23 5 0.25
ACGTcount: A:0.16, C:0.33, G:0.22, T:0.29
Consensus pattern (21 bp):
CCCTTAGGGTATCGCGACATC
Found at i:29754245 original size:95 final size:95
Alignment explanation
Indices: 29754083--29754320 Score: 281
Period size: 95 Copynumber: 2.5 Consensus size: 95
29754073 GACGTTTGAG
* *
29754083 TGATATGTGTGCTAGTGTAAGACATGTCTGGGACAT-GCATCGG--CCACATTATGAGAGCCAGT
1 TGATATGTGT-C-AGTGTAAGACAAGTCTGGGACATGGCATCGGCACCACATGATGAGAGCCAGT
29754145 GTAAGACCATGTCTGGGACATGGC-TTCGG-CT
64 GTAAGACCATGTCTGGGACATGGCATT-GGTCT
*
29754176 TGATATGTGTCAGTGTAAGACCAAATCTGGGACATGGCATCGGCACCA-ATAGATGAGAGCCAGT
1 TGATATGTGTCAGTGTAAGA-CAAGTCTGGGACATGGCATCGGCACCACAT-GATGAGAGCCAGT
*
29754240 GTAAGACCATGTTTGGGACATGGCATTGGTCT
64 GTAAGACCATGTCTGGGACATGGCATTGGTCT
* * *
29754272 CGATATATGAGAGTCAGTGTAAGACAATGTCTGGGACATGGCGTCGGCA
1 TG--ATAT--GTGTCAGTGTAAGACAA-GTCTGGGACATGGCATCGGCA
29754321 TCTTACCCTA
Statistics
Matches: 125, Mismatches: 8, Indels: 17
0.83 0.05 0.11
Matches are distributed among these distances:
91 9 0.07
92 13 0.10
93 17 0.14
94 2 0.02
95 40 0.32
96 5 0.04
98 4 0.03
99 3 0.02
100 32 0.26
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.25
Consensus pattern (95 bp):
TGATATGTGTCAGTGTAAGACAAGTCTGGGACATGGCATCGGCACCACATGATGAGAGCCAGTGT
AAGACCATGTCTGGGACATGGCATTGGTCT
Found at i:29754257 original size:50 final size:49
Alignment explanation
Indices: 29754096--29754319 Score: 214
Period size: 50 Copynumber: 4.7 Consensus size: 49
29754086 TATGTGTGCT
*
29754096 AGTGTAAGA-CATGTCTGGGACAT-GCATCGG-CCACAT-TATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCCA-ATAGATGAGAGCC
* * * *
29754142 AGTGTAAGACCATGTCTGGGACATGGCTTCGG--C--TTGAT-ATGTGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCCAATAGATGA-GAGCC
**
29754187 AGTGTAAGACCAAATCTGGGACATGGCATCGGCACCAATAGATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC-CCAATAGATGAGAGCC
* * * * * *
29754237 AGTGTAAGACCATGTTTGGGACATGGCATTGGTCTCGATATATGAGAGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGG-CCCAATAGATGAGAGCC
* *
29754287 AGTGTAAGACAATGTCTGGGACATGGCGTCGGC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC
29754320 ATCTTACCCT
Statistics
Matches: 145, Mismatches: 22, Indels: 19
0.78 0.12 0.10
Matches are distributed among these distances:
44 2 0.01
45 34 0.23
46 9 0.06
47 15 0.10
48 7 0.05
49 1 0.01
50 75 0.52
51 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (49 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCCCAATAGATGAGAGCC
Found at i:29760805 original size:15 final size:15
Alignment explanation
Indices: 29760785--29760841 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
29760775 CGATGAATTT
*
29760785 ATTGAATTTATATTG
1 ATTGAAATTATATTG
*
29760800 ATTGAAATTATTTTG
1 ATTGAAATTATATTG
29760815 ATTGAAATTATATTG
1 ATTGAAATTATATTG
29760830 ATTG-AATTATAT
1 ATTGAAATTATAT
29760842 AATATATATG
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
14 8 0.21
15 31 0.79
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (15 bp):
ATTGAAATTATATTG
Found at i:29761261 original size:21 final size:21
Alignment explanation
Indices: 29761237--29761342 Score: 149
Period size: 21 Copynumber: 5.0 Consensus size: 21
29761227 GTGTCATATT
29761237 TCAGGCACCTCGTGTGTCGTA
1 TCAGGCACCTCGTGTGTCGTA
29761258 TCAGGCACCTCGTGTGTCGTA
1 TCAGGCACCTCGTGTGTCGTA
*
29761279 TCAGGCACCTCGTGTGTCTTA
1 TCAGGCACCTCGTGTGTCGTA
* *
29761300 TCAGGCATCTCGTGTGTCGTT
1 TCAGGCACCTCGTGTGTCGTA
* * **
29761321 TTAGGCACTTTATGTGTCGTA
1 TCAGGCACCTCGTGTGTCGTA
29761342 T
1 T
29761343 ACTGATCAGG
Statistics
Matches: 75, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 75 1.00
ACGTcount: A:0.14, C:0.25, G:0.26, T:0.35
Consensus pattern (21 bp):
TCAGGCACCTCGTGTGTCGTA
Done.