Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold908

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: 16211
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30


Found at i:5495 original size:1 final size:1

Alignment explanation

Indices: 5489--5550 Score: 61 Period size: 1 Copynumber: 62.0 Consensus size: 1 5479 CCTTCTCTTT * * * * * * * 5489 AAAAAAAGAAAAAAAACAAAAACAAAAAAACAAAAAAAAACAAAACAAAAAAAAAAGAAAAA 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 5551 TCTGCTTAAG Statistics Matches: 47, Mismatches: 14, Indels: 0 0.77 0.23 0.00 Matches are distributed among these distances: 1 47 1.00 ACGTcount: A:0.89, C:0.08, G:0.03, T:0.00 Consensus pattern (1 bp): A Found at i:5515 original size:14 final size:13 Alignment explanation

Indices: 5492--5544 Score: 70 Period size: 14 Copynumber: 3.8 Consensus size: 13 5482 TCTCTTTAAA 5492 AAAAGAAAAAAAAC 1 AAAA-AAAAAAAAC 5506 AAAAACAAAAAAAC 1 AAAAA-AAAAAAAC 5520 AAAAAAAAACAAAAC 1 -AAAAAAAA-AAAAC 5535 AAAAAAAAAA 1 AAAAAAAAAA 5545 GAAAAATCTG Statistics Matches: 36, Mismatches: 0, Indels: 7 0.84 0.00 0.16 Matches are distributed among these distances: 13 3 0.08 14 23 0.64 15 10 0.28 ACGTcount: A:0.89, C:0.09, G:0.02, T:0.00 Consensus pattern (13 bp): AAAAAAAAAAAAC Found at i:5515 original size:15 final size:14 Alignment explanation

Indices: 5491--5544 Score: 81 Period size: 15 Copynumber: 3.7 Consensus size: 14 5481 TTCTCTTTAA 5491 AAAAAGAAAAAAAAC 1 AAAAA-AAAAAAAAC * 5506 AAAAACAAAAAAAC 1 AAAAAAAAAAAAAC 5520 AAAAAAAAACAAAAC 1 AAAAAAAAA-AAAAC 5535 AAAAAAAAAA 1 AAAAAAAAAA 5545 GAAAAATCTG Statistics Matches: 36, Mismatches: 2, Indels: 3 0.88 0.05 0.07 Matches are distributed among these distances: 14 17 0.47 15 19 0.53 ACGTcount: A:0.89, C:0.09, G:0.02, T:0.00 Consensus pattern (14 bp): AAAAAAAAAAAAAC Found at i:5524 original size:24 final size:22 Alignment explanation

Indices: 5489--5550 Score: 88 Period size: 23 Copynumber: 2.7 Consensus size: 22 5479 CCTTCTCTTT * 5489 AAAAAAAGAAAAAAAACAAAAAC 1 AAAAAAAAAAAAAAAAC-AAAAC 5512 AAAAAAACAAAAAAAAACAAAAC 1 AAAAAAA-AAAAAAAAACAAAAC * 5535 AAAAAAAAAAGAAAAA 1 AAAAAAAAAAAAAAAA 5551 TCTGCTTAAG Statistics Matches: 36, Mismatches: 2, Indels: 3 0.88 0.05 0.07 Matches are distributed among these distances: 22 8 0.22 23 19 0.53 24 9 0.25 ACGTcount: A:0.89, C:0.08, G:0.03, T:0.00 Consensus pattern (22 bp): AAAAAAAAAAAAAAAACAAAAC Found at i:6732 original size:175 final size:174 Alignment explanation

Indices: 6512--7047 Score: 617 Period size: 175 Copynumber: 3.1 Consensus size: 174 6502 TCCTTCCACT * * * 6512 TTTCAGTCCTCAAAGAGCAGGATACCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCCAGTCC 1 TTTCCGTCCTCAAAGAGCAGGA-CCCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-TCAGTCC * * 6576 TCAAAGAGCAGGATGCCTTCTCCTTTTAAAACCCACACAAGTTGGTGGCATTTTCCAGTCCTCAA 64 TCAAAGAGCAGGA-GCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAA * * * 6641 AGAGCGGGACGTCTTTTCTTTCAAAGCCCACATAAGTTGGTGGCACC 128 AGAGCAGGACGCCTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACC * * 6688 TTTCCGTCCCCAAAGAGCAGGACCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTC-GTCCC 1 TTTCCGTCCTCAAAGAGCAGGACCCTTTTAAAGCCCACACAAGTTGGTGGCACC-TTTCAGTCCT * 6752 CAAAGAGCAGGA--C--C-CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAG 65 CAAAGAGCAGGAGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAG * 6812 AGCAGGACGCCTTCTTCTTTTAAAGCCCACACAAGTTGGTGGCACC 130 AGCAGGACGCCTT-TTCTTTCAAAGCCCACACAAGTTGGTGGCACC * 6858 --TCCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC 1 TTTCC-GTCCTCAAAGAGCAGGAC-CC---T-TTT-AAAGCCCACACAAGTTGGTGGCACCTTTC * 6921 AGTCCTCAAAGAGCAGGACGCCTT-T-C----AAAGCCCACATAAGTTGGTGGCACCTTTCCAGT 59 AGTCCTCAAAGAGCAGGA-GCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTTCCAGT * * * * * 6980 CCTCAAAAAGCAGGACG-C----CTTTCAAACCCCACACGAGTTGGTGGTACT 122 CCTCAAAGAGCAGGACGCCTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACC ** 7028 TTTTAGTCCTCAAAGAGCAG 1 TTTCCGTCCTCAAAGAGCAG 7048 AATACACTTT Statistics Matches: 314, Mismatches: 26, Indels: 45 0.82 0.07 0.12 Matches are distributed among these distances: 168 3 0.01 169 70 0.22 170 58 0.18 171 14 0.04 172 2 0.01 173 1 0.00 174 7 0.02 175 109 0.35 176 46 0.15 177 2 0.01 178 1 0.00 179 1 0.00 ACGTcount: A:0.26, C:0.30, G:0.20, T:0.24 Consensus pattern (174 bp): TTTCCGTCCTCAAAGAGCAGGACCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTC AAAGAGCAGGAGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGA GCAGGACGCCTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACC Found at i:6794 original size:55 final size:56 Alignment explanation

Indices: 6510--7047 Score: 565 Period size: 55 Copynumber: 9.4 Consensus size: 56 6500 TCTCCTTCCA * ** 6510 CTTTTCAGTCCTCAAAGAGCAGGATACCTTTTAAAGCCCACACAAGTTGGTGGCA- 1 CTTTCCAGTCCTCAAAGAGCAGGACCCCTTTTAAAGCCCACACAAGTTGGTGGCAC * * 6565 CTTCCCAGTCCTCAAAGAGCAGGATGCCTTCTCCTTTTAAAACCCACACAAGTTGGTGGCA- 1 CTTTCCAGTCCTCAAAGAGCAGGA---C--C-CCTTTTAAAGCCCACACAAGTTGGTGGCAC * * * * * 6626 TTTTCCAGTCCTCAAAGAGCGGGACGTCTTTTCTTTCAAAGCCCACATAAGTTGGTGGCAC 1 CTTTCCAGTCCTCAAAGAGCAGGAC--C---CCTTTTAAAGCCCACACAAGTTGGTGGCAC * 6687 CTTTCC-GTCCCCAAAGAGCAGGA-CCCTTTTAAAGCCCACACAAGTTGGTGGCAC 1 CTTTCCAGTCCTCAAAGAGCAGGACCCCTTTTAAAGCCCACACAAGTTGGTGGCAC * * 6741 CTTTTC-GTCCCCAAAGAGCAGGACCCCTTTTAAAGCCCACACAAGTTGGTGGCA- 1 CTTTCCAGTCCTCAAAGAGCAGGACCCCTTTTAAAGCCCACACAAGTTGGTGGCAC * 6795 CTTCCCAGTCCTCAAAGAGCAGGACGCCTTCTTCTTTTAAAGCCCACACAAGTTGGTGGCAC 1 CTTTCCAGTCCTCAAAGAGCAGGA--CC--C--CTTTTAAAGCCCACACAAGTTGGTGGCAC * * 6857 C--TCCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTCAAAGCCCACACAAGTTGGTGGCAC 1 CTTTCCAGTCCTCAAAGAGCAGGAC-CC----CTTTTAAAGCCCACACAAGTTGGTGGCAC * * * 6916 CTTT-CAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACATAAGTTGGTGGCAC 1 CTTTCCAGTCCTCAAAGAGCAGGACCCCTTTTAAAGCCCACACAAGTTGGTGGCAC * * * * * * 6971 CTTTCCAGTCCTCAAAAAGCAGGACGCCTTTCAAACCCCACACGAGTTGGTGGTA- 1 CTTTCCAGTCCTCAAAGAGCAGGACCCCTTTTAAAGCCCACACAAGTTGGTGGCAC ** 7026 CTTTTTAGTCCTCAAAGAGCAG 1 CTTTCCAGTCCTCAAAGAGCAG 7048 AATACACTTT Statistics Matches: 422, Mismatches: 37, Indels: 48 0.83 0.07 0.09 Matches are distributed among these distances: 54 53 0.13 55 119 0.28 56 45 0.11 57 4 0.01 58 4 0.01 59 34 0.08 60 79 0.19 61 83 0.20 62 1 0.00 ACGTcount: A:0.26, C:0.30, G:0.20, T:0.24 Consensus pattern (56 bp): CTTTCCAGTCCTCAAAGAGCAGGACCCCTTTTAAAGCCCACACAAGTTGGTGGCAC Found at i:6953 original size:230 final size:231 Alignment explanation

Indices: 6510--7047 Score: 837 Period size: 230 Copynumber: 2.3 Consensus size: 231 6500 TCTCCTTCCA * 6510 CTTTTCAGTCCTCAAAGAGCAGGATACCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTC 1 CTTTTCAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTC * ** 6575 CTCAAAGAGCAGGATGCCTTCTCCTTTTAAAACCCACACAAGTTGGTGGCATTTTCCAGTCCTCA 66 CTCAAAGAGCAGGACGCCTTCTCCTTTTAAAACCCACACAAGTTGGTGGCATCCTCCAGTCCTCA * * * 6640 AAGAGCGGGACGTCTTTTCTTTCAAAGCCCACATAAGTTGGTGGCACCTTTCCGTCCCCAAAGAG 131 AAGAGCGGGACGCCTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAG * 6705 CAGGACCCTTTTAAAGCCCACACAAGTTGGTGGCAC 196 CAGGACCCTTTCAAAGCCCACACAAGTTGGTGGCAC * * 6741 CTTTTC-GTCCCCAAAGAGCAGGACCCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTC 1 CTTTTCAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTC * * 6805 CTCAAAGAGCAGGACGCCTTCTTCTTTTAAAGCCCACACAAGTTGGTGGCA-CCTCCAGTCCTCA 66 CTCAAAGAGCAGGACGCCTTCTCCTTTTAAAACCCACACAAGTTGGTGGCATCCTCCAGTCCTCA * 6869 AAGAGCGGGACGCCTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAG 131 AAGAGCGGGACGCCTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAG * 6934 CAGGACGCCTTTCAAAGCCCACATAAGTTGGTGGCAC 196 CAGGAC-CCTTTCAAAGCCCACACAAGTTGGTGGCAC * * * * * * * *** 6971 CTTTCCAGTCCTCAAAAAGCAGGACGCCTTTCAAACCCCACACGAGTTGGTGGTACTTTTTAGTC 1 CTTTTCAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTC 7036 CTCAAAGAGCAG 66 CTCAAAGAGCAG 7048 AATACACTTT Statistics Matches: 280, Mismatches: 25, Indels: 4 0.91 0.08 0.01 Matches are distributed among these distances: 229 78 0.28 230 136 0.49 231 66 0.24 ACGTcount: A:0.26, C:0.30, G:0.20, T:0.24 Consensus pattern (231 bp): CTTTTCAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTC CTCAAAGAGCAGGACGCCTTCTCCTTTTAAAACCCACACAAGTTGGTGGCATCCTCCAGTCCTCA AAGAGCGGGACGCCTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAG CAGGACCCTTTCAAAGCCCACACAAGTTGGTGGCAC Found at i:7809 original size:21 final size:21 Alignment explanation

Indices: 7785--7861 Score: 104 Period size: 21 Copynumber: 3.7 Consensus size: 21 7775 AATTTATCCA 7785 AATGTATCGATACATTTGAAG 1 AATGTATCGATACATTTGAAG ** 7806 AATGTATCGATACATTTGTGG 1 AATGTATCGATACATTTGAAG 7827 AATGTATCGATACATTCT-ACA- 1 AATGTATCGATACATT-TGA-AG 7848 AATGTATCGATACA 1 AATGTATCGATACA 7862 GGGTCCCAAC Statistics Matches: 50, Mismatches: 4, Indels: 4 0.86 0.07 0.07 Matches are distributed among these distances: 21 49 0.98 22 1 0.02 ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34 Consensus pattern (21 bp): AATGTATCGATACATTTGAAG Found at i:7921 original size:19 final size:19 Alignment explanation

Indices: 7897--7964 Score: 85 Period size: 19 Copynumber: 3.9 Consensus size: 19 7887 AATTCAACAA 7897 TTTGTATCGATACATAAGT 1 TTTGTATCGATACATAAGT 7916 TTTGTATCGATAC--AA-- 1 TTTGTATCGATACATAAGT 7931 --TGTATCGATACATAAGT 1 TTTGTATCGATACATAAGT * 7948 ATTGTATCGATACATAA 1 TTTGTATCGATACATAA 7965 TTAGCTACTG Statistics Matches: 43, Mismatches: 0, Indels: 12 0.78 0.00 0.22 Matches are distributed among these distances: 13 11 0.26 15 2 0.05 17 2 0.05 19 28 0.65 ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38 Consensus pattern (19 bp): TTTGTATCGATACATAAGT Found at i:7936 original size:13 final size:13 Alignment explanation

Indices: 7918--7942 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 7908 ACATAAGTTT 7918 TGTATCGATACAA 1 TGTATCGATACAA 7931 TGTATCGATACA 1 TGTATCGATACA 7943 TAAGTATTGT 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:0.36, C:0.16, G:0.16, T:0.32 Consensus pattern (13 bp): TGTATCGATACAA Found at i:7940 original size:32 final size:32 Alignment explanation

Indices: 7899--7961 Score: 117 Period size: 32 Copynumber: 2.0 Consensus size: 32 7889 TTCAACAATT * 7899 TGTATCGATACATAAGTTTTGTATCGATACAA 1 TGTATCGATACATAAGTATTGTATCGATACAA 7931 TGTATCGATACATAAGTATTGTATCGATACA 1 TGTATCGATACATAAGTATTGTATCGATACA 7962 TAATTAGCTA Statistics Matches: 30, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 32 30 1.00 ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37 Consensus pattern (32 bp): TGTATCGATACATAAGTATTGTATCGATACAA Found at i:10201 original size:54 final size:51 Alignment explanation

Indices: 10074--10209 Score: 148 Period size: 52 Copynumber: 2.6 Consensus size: 51 10064 TTGAGTTTCT * * * 10074 CAATTCTCCACAATACGGGGATATTCCAACTCCGATTTTATTTTCAAAACAC 1 CAATTCTTCACAAT-CGGGGATACTCCAACTCCGATTTTATTTCCAAAACAC * * * * 10126 TAATT-TTCTATAATCGGGGGATACTCTAACTCTGATTTTATTTCCAAAAAACAC 1 CAATTCTTC-ACAATC-GGGGATACTCCAACTCCGATTTTATTTCC--AAAACAC 10180 CAATTTCTTCACAATCGGGGATACTCCAAC 1 CAA-TTCTTCACAATCGGGGATACTCCAAC 10210 CCCGTTAATC Statistics Matches: 68, Mismatches: 10, Indels: 10 0.77 0.11 0.11 Matches are distributed among these distances: 51 3 0.04 52 33 0.49 54 22 0.32 55 7 0.10 56 3 0.04 ACGTcount: A:0.32, C:0.24, G:0.11, T:0.32 Consensus pattern (51 bp): CAATTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACAC Found at i:10223 original size:27 final size:28 Alignment explanation

Indices: 10193--10265 Score: 105 Period size: 27 Copynumber: 2.6 Consensus size: 28 10183 TTTCTTCACA 10193 ATCGGGGATACTCCAACCCCGTTA-ATC 1 ATCGGGGATACTCCAACCCCGTTATATC * 10220 ATCGGGGATACTCCAACCCCGTTATTTC 1 ATCGGGGATACTCCAACCCCGTTATATC * 10248 -TGAGGGGATACTCCAACC 1 AT-CGGGGATACTCCAACC 10266 TCGGTTTTTA Statistics Matches: 42, Mismatches: 2, Indels: 3 0.89 0.04 0.06 Matches are distributed among these distances: 27 25 0.60 28 17 0.40 ACGTcount: A:0.25, C:0.32, G:0.21, T:0.23 Consensus pattern (28 bp): ATCGGGGATACTCCAACCCCGTTATATC Found at i:10357 original size:53 final size:52 Alignment explanation

Indices: 10251--10422 Score: 174 Period size: 53 Copynumber: 3.3 Consensus size: 52 10241 TTATTTCTGA * 10251 GGGGATACTCCAACCTCGGTTTT-TATCGCTAAAACACTAATTTTTCCACAATC 1 GGGGATACTCCAACC-CGGTTTTAT-TTGCTAAAACACTAATTTTTCCACAATC * * ** 10304 GGGGATACTCCAATCCCGGTTTTATTTTC-AAAACGCTAATTTTTCCGTTAATC 1 GGGGATACTCCAA-CCCGGTTTTATTTGCTAAAACACTAATTTTTCC-ACAATC * * * 10357 GGGGATACTCCAACTCCGATTTTATTT-CTAAAAATACCAATTTTT-CACAATC 1 GGGGATACTCCAAC-CCGGTTTTATTTGCT-AAAACACTAATTTTTCCACAATC * 10409 GAGGATACT-CAACC 1 GGGGATACTCCAACC 10423 TCGTTATTTC Statistics Matches: 101, Mismatches: 12, Indels: 15 0.79 0.09 0.12 Matches are distributed among these distances: 50 1 0.01 51 4 0.04 52 30 0.30 53 51 0.50 54 15 0.15 ACGTcount: A:0.29, C:0.24, G:0.13, T:0.33 Consensus pattern (52 bp): GGGGATACTCCAACCCGGTTTTATTTGCTAAAACACTAATTTTTCCACAATC Found at i:10456 original size:213 final size:217 Alignment explanation

Indices: 10080--10480 Score: 568 Period size: 214 Copynumber: 1.9 Consensus size: 217 10070 TTCTCAATTC * 10080 TCCACAATACGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGG 1 TCCACAATACGGGGATACTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGG * * * 10145 GATACTCTAACTCTGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAAC 66 GATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAAC * 10210 CCCGTTAATCATCGGGGATACTCCAACCCCGTTA-T-TTCTGAGGGGATACTCCAACCTCGGTTT 131 CCCGTTAATCATCGGGGATACTCCAACCCCGTTACTATTCCGAGGGGATACTCCAACCTCGGTTT 10273 TTATCGCTAAAACACTAATTTT 196 TTATCGCTAAAACACTAATTTT * * 10295 TCCACAAT-CGGGGATACTCCAA-TCCCGGTTTTATTTTCAAAACGCTAATTTTTCCGT-TAATC 1 TCCACAATACGGGGATACTCCAACT-CCGATTTTATTTTCAAAACACTAA-TTTT-C-TATAATC * * 10357 -GGGGATACTCCAACTCCGATTTTATTT-CTAAAAATACCAATTT-TTCACAATCGAGGATACT- 62 GGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTC * * * 10418 CAACCTCGTTATTTCATTGGGGATACTCCAACCCCGTTACTTACTTCCGAGGGGATACTCCAA 127 CAACCCCGTTA-ATCATCGGGGATACTCCAACCCCGTTAC-TA-TTCCGAGGGGATACTCCAA 10481 TCCCGATTTT Statistics Matches: 165, Mismatches: 12, Indels: 16 0.85 0.06 0.08 Matches are distributed among these distances: 212 10 0.06 213 43 0.26 214 49 0.30 215 38 0.23 216 6 0.04 217 19 0.12 ACGTcount: A:0.28, C:0.25, G:0.14, T:0.32 Consensus pattern (217 bp): TCCACAATACGGGGATACTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGG GATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAAC CCCGTTAATCATCGGGGATACTCCAACCCCGTTACTATTCCGAGGGGATACTCCAACCTCGGTTT TTATCGCTAAAACACTAATTTT Done.